#### 1700123I01Rik_ID1492_4 --> 2 - 1 Original Alignment atAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCC------g agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagacAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGGTTAATcgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from CESAR atAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCC------g agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagacAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGGTTAATcgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from Spaln_aa2Genome ATAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCC------G agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagACAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGGTTAATCgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from Spaln_nt2Genome ATAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCCG agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagACAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTT-CGgttaatcgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from Pairagon ATAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCCG------ agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagACAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGGTTAATCgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from Exonerate_protein2genome ATAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCCG agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagACAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGGttaatcgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from Exonerate_coding2genome ATAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCCGGGAAAC agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagACAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGGTTAATCgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa Alignment from GeneWise ATAAAAGCAAGTGGGAGAGAGTTTCCCACCTGAAGTTTAAACATGGGGAAAGCATCCTGACGCCCTACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCC agcctgtaccttgggtgcctactacaagctctttcctcctcctcccacagACAAAAGTAAATGGGAGAGAGTTTCCCATCTGAGGTTTAAATATGGGGAAAGCATTTTGACACCCTACCCATTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGAAGACTTGCCTTCGgttaatcgtgagtaaccaaggtgggttgtgaaaaaactaagcactcaggatgactaa #### 1700123I01Rik_ID1493_5 --> 2 - 0 Original Alignment ggAAACCAGCAGATGATATTCCTCTTGAGTTG aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacaggtAAGCCTGCCGATGACATTCCACTTGAG---gtatgaaaatctaacacctctctttatgttttcatagcaaataaaattgt Alignment from CESAR ggAAACCAGCAGATGATATTCCTCTTGAGTTG aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacaggtAAGCCTGCCGATGACATTCCACTTGAG---gtatgaaaatctaacacctctctttatgttttcatagcaaataaaat Alignment from Spaln_aa2Genome GGAAACCAGCAGATGATATTCCTCTTGAG aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacagGTAAGCCTGCCGATGACATTCCACTTGAGgtatgaaaatctaacacctctctttatgttttcatagcaaataaaattgt Alignment from Spaln_nt2Genome GGAAACCAGCAGATGATATTCCTCTTGAG aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacagGTAAGCCTGCCGATGACATTCCACTTGAGgtatgaaaatctaacacctctctttatgttttcatagcaaataaaattgt Alignment from Pairagon GGAAACCAGCAGATGATATTCCTCTTGAGTT------------------------------------------------ aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacagGTAAGCCTGCCGATGACATTCCACTTGAGGTATGAAAATCTAACACCTCTCTTTATGTTTTCATAGCAAATAAAATTGT Alignment from Exonerate_protein2genome GGAAACCAGCAGATGATATTCCTCTTGAG aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacagGTAAGCCTGCCGATGACATTCCACTTGAGgtatgaaaatctaacacctctctttatgttttcatagcaaataaaattgt Alignment from Exonerate_coding2genome aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacaggtaagcctgccgatgacattccacttgaggtatgaaaatctaacacctctctttatgttttcatagcaaataaaattgt Alignment from GeneWise GGAAACCAGCAGATGATATTCCTCTTGAG aaaccagtcttcctaacttgctggagctttcttttcatctcatttcacagGTAAGCCTGCCGATGACATTCCACTTGAGgtatgaaaatctaacacctctctttatgttttcatagcaaataaaattgt #### 1810009A15Rik_ID2454_3 --> 1 - 1 Original Alignment gTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAGCCATGGAAg tattccaaatggctgcgtgagccttatctcacagttcattcatttcatagg---TGCTCCCGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCA---------ggtgagaagacgaactagtgagtagtggatttttttcaacattctacctat Alignment from CESAR gTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAGCCATGGAAg tattccaaatggctgcgtgagccttatctcacagttcattcatttcataggTGC---TCCCGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCA---------ggtgagaagacgaactagtgagtagtggatttttttcaacatgttcctgac Alignment from Spaln_aa2Genome GTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCA- tattccaaatggctgcgtgagccttatctcacagttcattcatttcatagGTGCTCC---CGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCAGgtgagaagacgaactagtgagtagtggatttttttcaacattctacctat Alignment from Spaln_nt2Genome GTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAG tattccaaatggctgcgtgagccttatctcacagttcattcatttcatagGT---GCTCCCGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCAGgtgagaagacgaactagtgagtagtggatttttttcaacattctacctat Alignment from Pairagon GGGCGTCCAGTGCT--CGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAG tattccaaatggctgcgtgagccttatctcacagttcattcatttcatag---------GTGCTCCCGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCAGgtgagaagacgaactagtgagtagtggatttttttcaacattctacctat Alignment from Exonerate_protein2genome GTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAG tattccaaatggctgcgtgagccttatctcacagttcattcatttcatagGTGCTCC---CGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCAGgtgagaagacgaactagtgagtagtggatttttttcaacattctacctat Alignment from Exonerate_coding2genome GTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAG tattccaaatggctgcgtgagccttatctcacagttcattcatttcatagGTGCTCC---CGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCAGgtgagaagacgaactagtgagtagtggatttttttcaacattctacctat Alignment from GeneWise GTCCAGTGCTCGTGCCAACATCACGCTGTCTGGGAAGAAGCGCAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAG tattccaaatggctgcgtgagccttatctcacagttcattcatttcatagGTGCTCC---CGTGCAAACATCACACTGTCTGGGAAGAAGCGTAGAAGACTATTACAGCAGATCCGACTTGCACAGAAACAAGAAGCAGgtgagaagacgaactagtgagtagtggatttttttcaacattctacctat #### 2010012O05Rik_ID10003_2 --> 0 - 0 Original Alignment CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGC---------gtaagttaggtggcctctctattatttcatcatatgtgtcaagattttca Alignment from CESAR CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGC---------gtaagttaggtggcctctctattatttcatcatatgtgtca Alignment from Spaln_aa2Genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACAC ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCgtaagttaggtggcctctctattatttcatcatatgtgtcaagattttca Alignment from Spaln_nt2Genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACAC -TCGGAA ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCgtaagttaggtggcctctctattatttcatcatatgtgtcaagATTTTCA Alignment from Pairagon CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACAC ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCgtaagttaggtggcctctctattatttcatcatatgtgtcaagattttca Alignment from Exonerate_protein2genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCGTAAGTTAGgtggcctctctattatttcatcatatgtgtcaagattttca Alignment from Exonerate_coding2genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCGTAAGTTAGgtggcctctctattatttcatcatatgtgtcaagattttca Alignment from GeneWise CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTA ctgtactatgtagaggtgggatcataacacatctttgcctctctccatagCTGCTGGGTCAGGCTGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGcgcgtaagttaggtggcctctctattatttcatcatatgtgtcaagattttca #### 2010012O05Rik_ID10004_3 --> 0 - 2 Original Alignment AGTTTAAGGAAGATGGCAATAATAACAACACACCTTCAGTACca gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACAC---------cagtgagtatggtatgccgccatggctaggtgggcagaggatgaaaggcaca Alignment from CESAR AGTTTAAGGAAGATGGCAATAATAACAACACACCTTCAGTACca gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACAC---------cagtgagtatggtatgccgccatggctaggtgggcagaggatgaaaggcaca Alignment from Spaln_aa2Genome AGTTTAAGGAAGATGGCAATAATAACAACACACCT gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACACCAgtgagtatggtatgccgccatggctaggtgggcagaggatgaaaggcaca Alignment from Spaln_nt2Genome AGTTTAAGGAAGATGGCAATAATAACAACACACCT-TCAGTACC gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACACCAGTGAGTATGgtatgccgccatggctaggtgggcagaggatgaaaggcaca Alignment from Pairagon AGTTTAAGGAAGATGGCAATAATAACAACACACCTTCAGTACCA gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACACC---------Agtgagtatggtatgccgccatggctaggtgggcagaggatgaaaggcaca Alignment from Exonerate_protein2genome AGTTTAAGGAAGATGGCAATAATAACAACACACCTTCAGTACCAGCAAGAAGCTATTCAGAA gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACACCAGTGAGTATGGTATGCCGCCATGGCTAGgtgggcagaggatgaaaggcaca Alignment from Exonerate_coding2genome AGTTTAAGGAAGATGGCAATAATAACAACACACCTTCAGTACCAGCAAGAAGCTATTCAGAA gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagAGCTTGAGGAAGATGGCAATAATAACAACACACCAGTGAGTATGGTATGCCGCCATGGCTAGgtgggcagaggatgaaaggcaca Alignment from GeneWise gagcaagaactcagatcacaggagtatgcttggttgcccatctctcacagagcttgaggaagatggcaataataacaacacaccagtgagtatggtatgccgccatggctaggtgggcagaggatgaaaggcaca #### AI846148_ID2142_4 --> 2 - 1 Original Alignment ttACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTGACCCAg aaacaattggagagaattctgtgggagcgtcataatcctctattttccagttACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCC------ggtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from CESAR ttACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTGACCCAg aaacaattggagagaattctgtgggagcgtcataatcctctattttccagttACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCC------ggtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from Spaln_aa2Genome TTACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCT- aaacaattggagagaattctgtgggagcgtcataatcctctattttccagTTACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCCGgtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from Spaln_nt2Genome TTACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTG aaacaattggagagaattctgtgggagcgtcataatcctctattttccagTTACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCCGgtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from Pairagon TTACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTG aaacaattggagagaattctgtgggagcgtcataatcctctattttccagTTACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCCGgtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from Exonerate_protein2genome TTACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTG aaacaattggagagaattctgtgggagcgtcataatcctctattttccagTTACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCCGgtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from Exonerate_coding2genome TTACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTG aaacaattggagagaattctgtgggagcgtcataatcctctattttccagTTACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGACCCCGgtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac Alignment from GeneWise TTACCCCTGTCATAGAGCAAGGGAATAAAAAGCCCCGTGGTCAGAGATGGAAAGAGTCCCCTGAGAATGAACCTGCTAGAAAGAAGAGAAGCAGGCATATGACCAAAATCTTGGACCCTGACCCAG aaacaattggagagaattctgtgggagcgtcataatcctctattttccagTTACTCCAGTTATAGAGCAAGGGAACAAAAAGCCCCGTGGCCAAAGATGGAAAGAGTCCCTTGAGAATAAACCAGCTAGAAAGAAGAGAAGCAGGCACATGACTAAGATCTTGGAC------CCCGgtgagtatctataagcactaggggtaagagctgcagaaatcacttaacac #### Acsl5_ID11602_7 --> 0 - 0 Original Alignment AATATAGGCAAAGAGAACTTCAAAAAACCAGTG cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAAG---------gtgagtcttccccaatgcatatgtttgctagttatgcgctgcttttcacc Alignment from CESAR AATATAGGCAAAGAGAACTTCAAAAAACCAGTG cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAAG---------gtgagtcttccccaatgcatatgtttgctagttatgcgctg Alignment from Spaln_aa2Genome AATATAGGCAAAGAGAACTTCAAA cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAAGgtgagtcttccccaatgcatatgtttgctagttatgcgctgcttttcacc Alignment from Spaln_nt2Genome AATATAGGCAAAGAGAACTTCAAAAAACCAGTG cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAA---------Ggtgagtcttccccaatgcatatgtttgctagttatgcgctgcttttcacc Alignment from Pairagon AATATAGGCAAAGAGAACTTCAAAAAACCAGTG cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAA---------Ggtgagtcttccccaatgcatatgtttgctagttatgcgctgcttttcacc Alignment from Exonerate_protein2genome AATATAGGCAAAGAGAACTTCAAAAAACCAGTG cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAAG---------gtgagtcttccccaatgcatatgtttgctagttatgcgctg Alignment from Exonerate_coding2genome AATATAGGCAAAGAGAACTTCAAAAAACCAGTG cattcaaatgataatgattctttttggttaacttcttgttctccaaccagAATATAGGCAAAGAGAACTTCAAG---------gtgagtcttccccaatgcatatgtttgctagttatgcgctg Alignment from GeneWise cattcaaatgataatgattctttttggttaacttcttgttctccaaccagaatataggcaaagagaacttcaaggtgagtcttccccaatgcatatgtttgctagttatgcgctgcttttcacc #### Acsl5_ID11603_8 --> 0 - 1 Original Alignment CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAg tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACT---agtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from CESAR CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAg tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACT---agtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from Spaln_aa2Genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTA tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTAgtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from Spaln_nt2Genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTA tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTAgtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from Pairagon CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTA tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTAgtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from Exonerate_protein2genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTA tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTAgtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from Exonerate_coding2genome tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagccaccaaagccagaagatcttggcctgatttgctttgctagtgggactagtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag Alignment from GeneWise CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAG tcacctctgtaacttttattgttggcttcacccgctctccatcccaccagCCACCAAAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGG---ACTAgtaaggagtctctgaaatcccacagtactacagaaaagaccactctccag #### Acsl5_ID11610_15 --> 2 - 0 Original Alignment gtCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG--------- gatacaaatggggttactcagcagttatcaagcctaaccttctgttttaggcCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGGTGAAGGGAAGCAGgtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from CESAR gtCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG--------- gatacaaatggggttactcagcagttatcaagcctaaccttctgttttaggcCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGGTGAAGGGAAGCAGgtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from Spaln_aa2Genome GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG--------- gatacaaatggggttactcagcagttatcaagcctaaccttctgttttagGCCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGGTGAAGGGAAGCAGgtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from Spaln_nt2Genome GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAG gatacaaatggggttactcagcagttatcaagcctaaccttctgttttagGCCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGgtgaagggaagcaggtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from Pairagon GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAG gatacaaatggggttactcagcagttatcaagcctaaccttctgttttagGCCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGgtgaagggaagcaggtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from Exonerate_protein2genome GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatggggttactcagcagttatcaagcctaaccttctgttttagGCCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGGTGAAgggaagcaggtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from Exonerate_coding2genome GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatggggttactcagcagttatcaagcctaaccttctgttttagGCCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGGTGAAgggaagcaggtatccgagatatactttatcaactcagggtggatggaagaactgtctaa Alignment from GeneWise GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG--------- gatacaaatggggttactcagcagttatcaagcctaaccttctgttttagGCCATGTTGGCACTCCAGTCGCTTCAAATTTTGTAAAGCTTGAAGATGTAGCAGAGATGAACTACTTTTCAGTGAACAATAAAGGTGAAGGGAAGCAGgtatccgagatatactttatcaactcagggtggatggaagaactgtctaa #### Acsl5_ID11614_19 --> 0 - 0 Original Alignment TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgcag---GTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag Alignment from CESAR TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG aggcccctagactgcatgccctgcgtctcagtcttctctgtgcactgcag---GTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag Alignment from Spaln_aa2Genome TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgcag---GTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag Alignment from Spaln_nt2Genome TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgcag---GTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag Alignment from Pairagon TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgcag---GTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag Alignment from Exonerate_protein2genome TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgCAGGTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag Alignment from Exonerate_coding2genome TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAGGTCAAAAGTATCTTTGTGCATCCA cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgCAGGTGAAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGGTAAGAATGTGGTATGTTTTCCCTacttgatgcagtaaatcaatcaacag Alignment from GeneWise TGTGTAAAGGAAGCCATTTTAGAAGACTTGCAGAAAATTGGGAAAGAGGGTGGCCTGAAATCCTTTGAGCAG cccctagactgcatgccctgcgtattctcagtcttctctgtgcactgcagGTG---AAAGAGGCCATTCTGGAGGACTTACAGAAAATAGGGAAAGAGGGTGGTTTGAAATCCCTTGAACAGgtaagaatgtggtatgttttccctacttgatgcagtaaatcaatcaacag #### Actn3_ID691_19 --> 0 - 0 Original Alignment GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from CESAR GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from Spaln_aa2Genome GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from Spaln_nt2Genome GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from Pairagon GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from Exonerate_protein2genome GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from Exonerate_coding2genome gaccgggtaagtggcttgacaggattatcatgcctggcttctgttcctagaagcggaacaggatgatggagcccgatgactttcgagcttgtctcatctccatgggttatgatctatactacgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc Alignment from GeneWise GACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG------ GACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTATACTACgtaagaagattagagtcctatgacaccattagcctatttatgtcgttgtc #### Actn3_ID692_18 --> 0 - 0 Original Alignment CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG tccacaatagatatgttttcttgtattccccatcccctccctttcctcag---------GTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatgatctctgtgttctgttttcagAAGCGG Alignment from CESAR CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG cacaaccattccacaatagatatgtttccccatcccctccctttcctcag---------GTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatcatgcctggcttctgttcctagAAGCGG Alignment from Spaln_aa2Genome CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG tccacaatagatatgttttcttgtattccccatcccctccctttcctcag---------GTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatgatctctgtgttctgttttcagAAGCGG Alignment from Spaln_nt2Genome GTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG tccacaatagatatgttttcttgtattccccatcccctccctttcctcagGTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatgatctctgtgttctgttttcagAAGCGG Alignment from Pairagon CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG tccacaatagatatgttttcttgtattccccatcccctccctttcctcag---------GTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatgatctctgtgttctgttttcagAAGCGG Alignment from Exonerate_protein2genome CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG tccacaatagatatgttttcttgtattccccatcccctcccTTTCCTCAGGTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatgatctctgtgttctgttttcagAAGCGG Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGG tccacaatagatatgttttcttgtattccccatcccctccctttcctcagGTGGGCTGGGAGCAACTACTGACCACCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCCAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACTTTGACCGGgtaagtggcttgacaggattatgatctctgtgttctgttttcagAAGCGG #### Actn3_ID694_16 --> 0 - 0 Original Alignment GTCAGA---AAGCTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGAAAAGTGGAG tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCTCATGAGCAGACATTCCAAGAGAAGCTC---TGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAGGCA---------gtgagtatttagaagtgtgggagactgtgttcagggagatcagtccaggg Alignment from CESAR GTCAGAAAG---CTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGAAAAGTGGAG tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCTCATGAGCAGACATTCCAAGAGAAGCTC---TGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAGGCA---------gtgagtatttagaagtgtgggagactgtgttcagggagatc Alignment from Spaln_aa2Genome GTCAGAAAG---CTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGA tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCTCATGAGCAGACATTCCAAGAGAAGCTC---TGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAGGCAgtgagtatttagaagtgtgggagactgtgttcagggagatcagtccaggg Alignment from Spaln_nt2Genome GTCAGAAA---GCTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGA tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCTCATGAGCAGACATTCCAAGAGAAGCT---CTGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAGGCAgtgagtatttagaagtgtgggagactgtgttcagggagatcagtccaggg Alignment from Pairagon GTCAGAAA-------------GCTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGA tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCT----------CATGAGCAGACATTCCAAGAGAAGCT---CTGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAGGCAgtgagtatttagaagtgtgggagactgtgttcagggagatcagtccaggg Alignment from Exonerate_protein2genome GTCAGAAAG---CTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGA-----AAAGTGGAG tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCTCATGAGCAGACATTCCAAGAGAAGCTC---TGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAGGCAGTGAGTATTTAGAAgtgtgggagactgtgttcagggagatcagtccaggg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTCAGAAAG---CTGGTACCCAGCCGTGACCAGACACTGCAGGAGGAGCTGGCCCGGCAGCAGGTGAACGAGAGGCTCCGGCGACAGTTTGCAGCCCAGGCTAATGCCATAGGACCCTGGATCCAGGGAAAAGTGGAG tgatacctaagaacaccttgctgtgggtacaccccttccctgactcccagGTTAGAAAAAGGCTTGCCCCTGCTCATGAGCAGACATTCCAAGAGAAGCTC---TGGCAGCAAGTTAATGAGAGATCACGGTGGCAGTTCACAGCTCCAGCTAATGCTATAGGGCCTTGGATCCAG---------GCAgtgagtatttagaagtgtgggagactgtgttcagggagatcagtccaggg #### Actn3_ID695_15 --> 0 - 0 Original Alignment AGCCTGCTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA acccacaggcaaatatggataatgctttttttgtttgttgcttatcacag---CTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta Alignment from CESAR AGCCTGCTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA catacccacaggcaaatatggataatttttttgtttgttgcttatcacag---CTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta Alignment from Spaln_aa2Genome CTGCTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA acccacaggcaaatatggataatgctttttttgtttgttgcttatcacagCTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta Alignment from Spaln_nt2Genome CTGCTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA acccacaggcaaatatggataatgctttttttgtttgttgcttatcacagCTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta Alignment from Pairagon CAGAGCCTGCTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA acccacaggcaaatatggataatgctttttttgtttgttgcttatcacag------CTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta Alignment from Exonerate_protein2genome GCCTGCTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA acccacaggcaaatatggataatgctttttttgtttgttgcttatcacAGCTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---CTAACAGCACACGAACAGTTCAAGGCAACGTTGCCCGAGGCTGATCGAGAGCGAGGCGCCATCCTGGGCATCCAAGGAGAGATCCAGAAGATTTGCCAAACATACGGACTACGGCCAAAGTCCGGCAACCCCTACATCACCCTCAGTTCGCAGGACATCAACAATAAGTGGGATACA acccacaggcaaatatggataatgctttttttgtttgttgcttatcacagCTACTAACAGCACATGAACAATTCAAAGCTACTTTACCTGAAGCTGATCGAGAGCCAGGCGCTGTCCCAGGCATCCAAGGAAAGATTTCAAAGATCTGCCAAACATATGGGTCACGCCCAAAATTTGGAAACCCCTACATTACCCTCAGTATGAGGGATATCAATAATAAGTGGGACACTgtaagttacctctttttgtgttaagtgagagatctattgtagcaatacta #### Actn3_ID696_14 --> 0 - 0 Original Alignment ---AGGATGGAGAAGCTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTC---GTGCACTCTGTGGAGGAGACCCAG taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAA---AAAgtaatgtcaaatgtgcttggggcctgaacagatgacacaatgacttacct Alignment from CESAR ---AGGATGGAGAAGCTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTCGTG---CACTCTGTGGAGGAGACCCAG taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAA---AAAgtaatgtcaaatgtgcttggggcctgaacagatgacacaatgacttacct Alignment from Spaln_aa2Genome AGGATGGAGAAG---CTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTC---GTGCACTCTGTGGAGGAGACCCAG taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAA---AAAgtaatgtcaaatgtgcttggggcctgaacagatgacacaatgacttacct Alignment from Spaln_nt2Genome AG---GATGGAGAAGCTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTCGTG---CACTCTGTGGAGGAGACCCAG taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAAA---AAgtaatgtcaaatgtgcttggggcctgaacagatgacacaatgacttacct Alignment from Pairagon AG---GATGGAGAAGCTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTCGTG---CACTCTGTGGAGGA------------------------------------------------------ taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAAAAAGTAATGTCAAATGTGCTTGGGGCCTGAACAGATGACACAATGACTTACCT Alignment from Exonerate_protein2genome ---AGGATGGAGAAGCTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTCGTGCACTCTGTGGAGGAGACCCAG taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAAAAAgtaatgtcaaatgtgcttggggcctgaacagatgacacaatgacttacct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---AGGATGGAGAAGCTCCTGGAGACCATTGACCAGCTGCAGCTGGAGTTTGCTCGGCGGGCAGCCCCCTTCAATAACTGGCTGGATGGGGCTATTGAGGACCTGCAGGATGTGTGGCTC---GTGCACTCTGTGGAGGAGACCCAGAG taatatttgtcctttgcctggattctgagagacctctgtcttggctccagAGCAAGATGGAGAAATTCCTGGAGACAATTGACCAGCTTCAGCTAGAACTTGCTCGCAGGGCAGCTTCCTTCAATAATTGGTTTGATGGAGCTGTTAAGGATCTGCATGACGTGTGGCTAGTGGTACACTCTGTGGAAGAAAAAGTAATgtcaaatgtgcttggggcctgaacagatgacacaatgacttacct #### Actn3_ID706_4 --> 2 - 1 Original Alignment aaATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAg cataacaagggggaaaaaataactctcaaaacatccttttccattcccagaaATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATC---------ggttaggtgattcctggtctgctggataccaagccaaatttcttcgtttat Alignment from CESAR aaATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAg cataacaagggggaaaaaataactctcaaaacatccttttccattcccagaaATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATC---------ggttaggtgattcctggtctgctggataccaagctcactgtggttctctcc Alignment from Spaln_aa2Genome AAATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATC- cataacaagggggaaaaaataactctcaaaacatccttttccattcccagAAATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCGgttaggtgattcctggtctgctggataccaagccaaatttcttcgtttat Alignment from Spaln_nt2Genome AAATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAG cataacaagggggaaaaaataactctcaaaacatccttttccattcccagAAATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCGGT-TAGgtgattcctggtctgctggataccaagccaaatttcttcgttta Alignment from Pairagon AAATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAGAGACCTCAG-------------------------------------------------- cataacaagggggaaaaaataactctcaaaacatccttttccattcccagAAATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATC------------------GGTTAGGTGATTCCTGGTCTGCTGGATACCAAGCCAAATTTCTTCGTTTAT Alignment from Exonerate_protein2genome AAATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTC cataacaagggggaaaaaataactctcaaaacatccttttccattcccagAAATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCGGttaggtgattcctggtctgctggataccaagccaaatttcttcgtttat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AAATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCT cataacaagggggaaaaaataactctcaaaacatccttttccattcccagAAATAGTCGATGGAAACCTGAAGATGACCCTTGGTATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCGgttaggtgattcctggtctgctggataccaagccaaatttcttcgtttat #### Actn3_ID707_3 --> 2 - 1 Original Alignment gaGAGAGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATCGGTGCTGAAg cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcaggtGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATT---------ggtaaccgagctatcgcttggtaattgaagaataatagtagttagatgttt Alignment from CESAR gaGAGAGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATCGGTGCTGAAg cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcaggtGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATT---------ggtaaccgagctatcgcttggtaattgaagaataatagtagttagatgttt Alignment from Spaln_aa2Genome GAGAGAGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATC- cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcagGTGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATTGgtaaccgagctatcgcttggtaattgaagaataatagtagttagatgttt Alignment from Spaln_nt2Genome GAGAGAGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATCG cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcagGTGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATTGgtaaccgagctatcgcttggtaattgaagaataatagtagttagatgttt Alignment from Pairagon GAGAGAGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATCG cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcagGTGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATTGgtaaccgagctatcgcttggtaattgaagaataatagtagttagatgttt Alignment from Exonerate_protein2genome GAGAGAGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATCGGTGCTGAAG cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcagGTGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATTGGTAACCGAGctatcgcttggtaattgaagaataatagtagttagatgttt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise -----AGGCTGCCTAGGCCCGACAAAGGCAAGATGCGCTTCCACAAAATCGCCAATGTCAATAAAGCCCTAGACTTCATTGCCAGCAAAGGAGTTAAGCTAGTGTCCATCG cccttagcatgtgccatgggctttgttactgttttttgtcatttttgcagGTGCTAGGCTGCCCAGGCCGGATAAAGGCAAGATGTGCTTTCATAAAATTGCCAATGTAAATAACACACTAGACTTCATAGCTACTAAAGGAGTGAAGCTAGTCTCAATTGgtaaccgagctatcgcttggtaattgaagaataatagtagttagatgttt #### Actr1a_ID9874_6 --> 1 - 0 Original Alignment tTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcagt---GCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from CESAR tTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA cacgtgatctcaaggaactctctaacatattctactttcgctactttcagt---GCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from Spaln_aa2Genome TTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcagT---GCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from Spaln_nt2Genome TGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcagTGCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from Pairagon TTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcag---TGCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from Exonerate_protein2genome TTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcagT---GCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from Exonerate_coding2genome TTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcagT---GCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa Alignment from GeneWise TTATGCCACGGGCAGAACCACAGGCGTGGTGTTGGATTCTGGGGATGGTGTCACCCATGCAGTCCCGATTTATGAAGGCTTCGCCATGCCTCACTCCATCATGCGCATCGACATCGCTGGCCGGGATGTCTCACGCTTCCTCCGCCTCTACCTACGGAAGGAGGGCTATGATTTCCACTCCTCCTCTGAGTTTGAGATTGTCAAGGCCATAAAGGAA gtgatctcaaggaactctctaagagcatattctactttcgctactttcagT---GCCACCAGCAAGACCACAGGTGTAGTGTTGGATTCTGGGGATGGTATCACTCATGTAGTTCCAATTTATGAAGGCTTCACCATTCCTCACTCCATCATGCGCATTGACATTGCTGGACGGGATGTGTCACACCTCCTGCGTCTCTATCTACGGCAGGAGGGATATGATTTTCATGCCTCCTCTGAGTTTGAGATTGTTAAAGCTATAAAAGAAgtaactgttgtaaacacccagcttcatcatgaggtcttaagaataaaaaa #### Add3_ID11215_7 --> 0 - 0 Original Alignment ---GTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from CESAR ---GTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from Spaln_aa2Genome AAGGTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from Spaln_nt2Genome ---GTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from Pairagon ---GTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from Exonerate_protein2genome AAGGTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from Exonerate_coding2genome AAGGTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga Alignment from GeneWise ---GTGCTCGTCCTCAGGAACCATGGCATGGTGGCTCTTGGCGAGACCCTCGAGGAGGCTTTCCATTACATCTTTAATGTACAGATGGCCTGTGAGATCCAG ttgggggagtattcagagcaaactttttgactatttacttttcaccatagCGAGTGCTTGTTCTTAGGAACCATGGCATAGTGGGTCTTGGTGAAACTCTTGAGGAGGCATACCATTACATTTTTAATGTAAAGATGGCCTGTGAAATCCAGgtgagtccctaccctctctatgactgtactgagtggcagacatactagga #### Adrbk1_ID483_12 --> 1 - 2 Original Alignment GTgt gGGCACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGgg GGgtgtaggattcagattcacttcacaacccacatgcttcattttcacagg---ACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAgggtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from CESAR GTgt gGGCACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGgg GGgtgtaaggaccttcagattcactcaacccacatgcttcattttcacagg---ACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAgggtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from Spaln_aa2Genome GTGT GGGCACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGGG GGGTgtaggattcagattcacttcacaacccacatgcttcattttcacagG---ACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAGGgtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from Spaln_nt2Genome TGGG CACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGGG GGGTgtaggattcagattcacttcacaacccacatgcttcattttcacagGACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAGGgtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from Pairagon GG CACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGGG GGgtgtaggattcagattcacttcacaacccacatgcttcattttcacagGACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAGGgtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from Exonerate_protein2genome GTGTGGG CACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGGG GGGTGTAggattcagattcacttcacaacccacatgcttcattttcacagGACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAGGgtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from Exonerate_coding2genome ACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGGG gggtgtaggattcagattcacttcacaacccacatgcttcattttcacaggACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAGGgtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta Alignment from GeneWise GTGTG-GGC------------------------------------------ACACACGGGTACATGGCCCCCGAAGTCCTACAGAAGGGCGTGGCCTATGACAGCAGTGCAGACTGGTTCTCCCTGGGCTGCATGCTCTTCAAGTTGTTGCGGGG GGGTGTAGGATTCAGATTCACTTCACAACCCACATGCTTCATTTTCACAGGACACATGGGTACATAGCTCCCAAGGTACTTCAAAAAGGTATAGCCTATGATAGCAGCGCTGACTGGTTTTCCCTGAGCTGCATGCTCTTTAAATTGTTGCGAGGgtgagtccaggtgggcaccctctttaaattgtgttgcaagggtgagccta #### Adrbk1_ID485_10 --> 2 - 0 Original Alignment CATGAACg gtGGGGACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAG--- TATGAATggtgagtgagtttcataactgtgatttgggaattgctttgcagggGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGATGgtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from CESAR CATGAACg gtGGGGACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAG--- TATGAATggtaagtgagtttcataactgtgatttgggaattgctttgcagggGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGATGgtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from Spaln_aa2Genome CATGAACG GTGGGGACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAG--- TATGAATGgtgagtgagtttcataactgtgatttgggaattgctttgcagGGGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGATGgtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from Spaln_nt2Genome CATGAACG GTGGGGACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAG--- TATGAATGgtgagtgagtttcataactgtgatttgggaattgctttgcagGGGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGATGgtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from Pairagon CATGAACGGTGGG------------------------------------------GACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAG--- TATGAATGGTGAGTGAGTTTCATAACTGTGATTTGGGAATTGCTTTGCAGGGGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGATGgtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from Exonerate_protein2genome CATGAACG GTGGGGACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAG TATGAATGgtgagtgagtttcataactgtgatttgggaattgctttgcagGGGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGatggtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from Exonerate_coding2genome tatgaatggtgagtgagtttcataactgtgatttgggaattgctttgcaggggtagagttgcattatcacctctcgcagcatggggtcttctcagaagctgatatgtgcctctatgctgctgatatcattcacatgcacaatcattttgtagttttcagggatttaaagatggtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg Alignment from GeneWise CATGAACG GTGGGGACCTGCACTACCACCTGTCTCAGCATGGAGTCTTCTCTGAAGCCGACATGCGCTTCTACGCCGCTGAGATCATCCTGGGCCTTGAACACATGCACAATCGCTTTGTAGTCTACAGGGACCTGAAGCCA TATGAATGgtgagtgagtttcataactgtgatttgggaattgctttgcagGGGTAGAGTTGCATTATCACCTCTCGCAGCATGGGGTCTTCTCAGAAGCTGATATGTGCCTCTATGCTGCTGATATCATT------------CACATGCACAATCATTTTGTAGTTTTCAGGGATTTAAAGATGgtgcgttcataatgccagttgcctcatggggataggccaaaaaggatctg #### Adrbk1_ID486_9 --> 0 - 1 Original Alignment ---------GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACg gtGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagACCGTGGAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATggtaagtgagtttcataactgtttacctatctttgtactacagggGTAGAG Alignment from CESAR ---------GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACg gtGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagACCGTGGAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATggtaagtgagtttcataactgtgatttgggaattgctttgcagggGTAGAG Alignment from Spaln_aa2Genome ---------GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACG GTGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagACCGTGGAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATGgtaagtgagtttcataactgtttacctatctttgtactacagGGGTAGAG Alignment from Spaln_nt2Genome --CGGGGA---CTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACG GTGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagACCGTGGAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATGgtaagtgagtttcataactgtttacctatctttgtactacagGGGTAGAG Alignment from Pairagon ---------GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACG GTGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagACCGTGGAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATGgtaagtgagtttcataactgtttacctatctttgtactacagGGGTAGAG Alignment from Exonerate_protein2genome GGGACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACG GTGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagaccgtggAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATGgtaagtgagtttcataactgtttacctatctttgtactacagGGGTAGAG Alignment from Exonerate_coding2genome cccctctcagttcaccttctataagacaactgcttgacttttttcttcagaccgtggaagactgctccttcactgtgtgcatgtcatatgcattccacacaccggacaagctaggctttatcctggatcttatgaatggtaagtgagtttcataactgtttacctatctttgtactacaggggtagag Alignment from GeneWise ---------GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACG GTGGGGAC cccctctcagttcaccttctataagacaactgcttgacttttttcttcagACCGTGGAAGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCGGACAAGCTAGGCTTTATCCTGGATCTTATGAATGgtaagtgagtttcataactgtttacctatctttgtactacagGGGTAGAG #### Adrbk1_ID487_8 --> 1 - 0 Original Alignment g---------TACGCCATGAAGTGTCTG---GACAAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacaggTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from CESAR g------TAC---GCCATGAAGTGTCTGGAC---AAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacaggTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from Spaln_aa2Genome G---------TACGCCATGAAGTGTCTGGAC---AAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacagGTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from Spaln_nt2Genome GT---------ACGCCATGAAGTGTCTGGA---CAAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacagGTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from Pairagon GT---------ACGCCATGAAGTGTCTGG---ACAAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacagGTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from Exonerate_protein2genome G---------TACGCCATGAAGTGTCTGGAC---AAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacagGTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from Exonerate_coding2genome acccaccccatcaattgagctgtgctacagtgccatgctccatcccacaggttatggtaccatgctaagagatgtttggaaaacaagaaacacattaagatgaaacaaggagagacactggccctgaataggcggattatgctatcacttgtgagcactggtgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca Alignment from GeneWise -------ATGTACGCCATGAAGTGTCTGGAC---AAGAAACGCATCAAGATGAAGCAGGGAGAGACCCTGGCTCTGAACGAGCGGATCATGCTTTCCCTCGTCAGCACCGGG acccaccccatcaattgagctgtgctacagtgccatgctccatcccacagGTTATGGTACCATGCTAAGAGATGTTTGGAAAACAAGAAACACATTAAGATGAAACAAGGAGAGACACTGGCCCTGAATAGGCGGATTATGCTATCACTTGTGAGCACTGGTgtgagtcaagtggttaggtaaccccctctcagttcaccttctataagaca #### Adrbk1_ID488_7 --> 0 - 2 Original Alignment CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAG------at agcaactctatatagcgactctacatagtacttcatttatttaaaatcag---CCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGatgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from CESAR CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAG------at agcaactctatatagcgactctacatagtacttcatttatttaaaatcag---CCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGatgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from Spaln_aa2Genome CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGATG----- agcaactctatatagcgactctacatagtacttcatttatttaaaatcagCCCATGAATGATTTT---AGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGATgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from Spaln_nt2Genome CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAG------AT agcaactctatatagcgactctacatagtacttcatttatttaaaatcagC---CCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGATgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from Pairagon -CCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAA------GAT agcaactctatatagcgactctacatagtacttcatttatttaaaatcagCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGATgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from Exonerate_protein2genome CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAG------AT agcaactctatatagcgactctacatagtacttcatttatttaaaatCAGCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGATgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from Exonerate_coding2genome agcaactctatatagcgactctacatagtacttcatttatttaaaatcagcccatgaatgattttagtgtacgtcagatcattggacatggtggctttgatgaggtatatggttgccgccaggctgatgtaggcaagcaccggatgtatgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt Alignment from GeneWise CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGATGTACGCCATG agcaactctatatagcgactctacatagtacttcatttatttaaaatcagCCC---ATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGATGAGGTATATGGTTGCCGCCAGGCTGATGTAGGCAAGCACCGGATGTATgttgtagacaagtaaaggtgggtggtctacaaacaaagggcatctt #### Adrbk1_ID489_6 --> 1 - 0 Original Alignment tGACAAGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCAC cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagt------TTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from CESAR tGACAAGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCAC aatcaacagcttggcatgcctagtatcctaaaggcctcctgcccttgcagt------TTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from Spaln_aa2Genome TGACAAGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCAC cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagT------TTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from Spaln_nt2Genome GTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCAC cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagTTTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from Pairagon TGACAAGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCAC cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagT------TTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from Exonerate_protein2genome TGACAAGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCACCTG cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagT------TTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATGTAatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from Exonerate_coding2genome cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagtttcacacatttctgtcaatggaagaacattgaaataaacattcatgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt Alignment from GeneWise TGACAAGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCAC cagcttggcatgcctagtagtgatttcctaaaggcctcctgcccttgcagT------TTCACACATTTCTGTCAATGGAAGAACATTGAAATAAACATTCATgtaatcaggggtacttcatgaatgcggctctacatgtagtatgggtgggt #### Adrbk1_ID492_3 --> 0 - 0 Original Alignment ATCAAGAAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgcag---AAAAAATATGCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from CESAR ATCAAGAAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT ccccacacaaccagcctcaaacagtaatgatgtttccttttctcttgcag---AAAAAATATGCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from Spaln_aa2Genome ATCAAGAAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgcagAAAAAATAT---GCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from Spaln_nt2Genome ATCAAGAAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgcag---AAAAAATATGCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from Pairagon ATCAAGAAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgcag---AAAAAATATGCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from Exonerate_protein2genome ATCAAGAAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgCAGAAAAAATATGCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from Exonerate_coding2genome cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgcagaaaaaatatgcaaagctggagacagaggaggagtgtgttgtccgcagccgagagatctttgagtcctacattatgaaagagctacttgcatgctcacatgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa Alignment from GeneWise ---AAATATGAGAAGCTGGAGACAGAGGAGGAACGTGTGGTCCGCAGCCGAGAGATCTTTGACTCCTATATTATGAAAGAACTGCTGGCCTGCTCACAT cacacaaccagcctcaaacagtgataatgatgtttccttttctcttgcagAAAAAATATGCAAAGCTGGAGACAGAGGAGGAGTGTGTTGTCCGCAGCCGAGAGATCTTTGAGTCCTACATTATGAAAGAGCTACTTGCATGCTCACATgtaagggcagaatttatctctcataagaagacatttatccagccaaaaaa #### Afap1l2_ID12253_10 --> 0 - 1 Original Alignment CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGAT---------------------------------------------------g ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGATCCTGTGACCCCCCGACCACTGCTCGACATATACCCCAATGTCAATGTGCACggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from CESAR CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGAT--g ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGATCCtgtgaccccccgaccactgctcgacatataccccaatgtcaatgtgcacggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from Spaln_aa2Genome CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGATGTC ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGATCCTgtgaccccccgaccactgctcgacatataccccaatgtcaatgtgcacggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from Spaln_nt2Genome CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGATG-- ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGATCCTgtgaccccccgaccactgctcgacatataccccaatgtcaatgtgcacggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from Pairagon CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGAT---------------------------------------------------G ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGATCCTGTGACCCCCCGACCACTGCTCGACATATACCCCAATGTCAATGTGCACGgtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from Exonerate_protein2genome CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGATG ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGATCctgtgaccccccgaccactgctcgacatataccccaatgtcaatgtgcacggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from Exonerate_coding2genome ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagtctgatattgctgcaaaatacctctcagcagcagagtacggaattaccatcaatggtcaccctgagattccagaaactaaagatcctgtgaccccccgaccactgctcgacatataccccaatgtcaatgtgcacggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc Alignment from GeneWise CCAGACATAGCTGAGAAGTACCTGTCAGCAGCGGAGTACGGGATCACCATCAACGGCCACCCTGAGATCCCAGAGACCAAAGATGTCAAG ttgtctttgcagtatcataaaccatttaagatcatggctcactcttgcagTCTGATATTGCTGCAAAATACCTCTCAGCAGCAGAGTACGGAATTACCATCAATGGTCACCCTGAGATTCCAGAAACTAAAGAT---CCTgtgaccccccgaccactgctcgacatataccccaatgtcaatgtgcacggtaaggcagtaaggatccccaaagggcttttttaagcgtgtaggccagcc #### Aip_ID330_5 --> 0 - 1 Original Alignment ---------GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATg ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagCTTGGGCACGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTggtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from CESAR ---------GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATg ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagCTTGGGCACGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTggtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from Spaln_aa2Genome ---------GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagCTTGGGCACGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from Spaln_nt2Genome AGGAGCAGCCTGG-------CTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagCTTGGGCACGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from Pairagon -----------------------------------------------------------GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG CTATCATCACTGCAGCTGGGGACTGACCAGTCGTCTCTTTCCTATACCAGCTTGGGCACGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from Exonerate_protein2genome GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagcttgggcacGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from Exonerate_coding2genome GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagcttgggcacGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc Alignment from GeneWise ---------GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTAT ctatcatcactgcagctggggactgaccagtcgtctctttcctataccagCTTGGGCACGAGCAGGCTGGCTCTTCAGACTGGGTCCAGTTAGACCTGCAGATCACACCATTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATgttggtaagcgtcattgcccagtactgcccaatacaactcaactcagacttccc #### Aip_ID331_4 --> 0 - 0 Original Alignment GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG------ taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAAAAATCgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat Alignment from CESAR GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG------ taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAAAAATCgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat Alignment from Spaln_aa2Genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAGGAGCAG taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAAAAATCgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat Alignment from Spaln_nt2Genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG------ taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAAAAATCgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat Alignment from Pairagon GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGA---------------------------------------------------------- taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAAAAATCGTACCGCTCATAAATACAGTAATAGGCAATAATGTACACATGGCTATCAT Alignment from Exonerate_protein2genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAaaaatcgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat Alignment from Exonerate_coding2genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAaaaatcgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat Alignment from GeneWise GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAGGAGCAG taggaactatccatgggacatagcagaggttttttgtatgtgtcatttagATAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGATTGTACCGTGAAAGCCAGGTGAGAGAAGCTGCTCCGAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTACAAATGAAAAAAATCgtaccgctcataaatacagtaataggcaataatgtacacatggctatcat #### Aldh3b2_ID239_5 --> 2 - 0 Original Alignment ga------------------------------------------AACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTGCCCCAGTATCTGGACCAG AGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacaggaTTTCCCTACGAGAACGCTCGACAGAGGCGGTATGAACTAAGTACTTGTGTGGTATTGAGGCCATCTGATATTAGTAAGAACACAGAA---ATGCAGGCAGAGCTGCTG---CGGCATCTTGATCAAgtaaggttgattgtgcaggtttttttcctctctctcttttcagAGTTGTT Alignment from CESAR caattgcacatggaagtaataatagtaattgtacatgaggtgagatagtaa Alignment from Spaln_aa2Genome GCA------------GGAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTGCCCCAGTATCTGGACCAG AGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacaggatttccctacgagaacgctcgacagAGGCGGTATGAACTAAGTACTTGTGTGGTATTGAGGCCATCTGATATTAGTAAGAACACAGAA---ATGCAGGCAGAGCTGCTG---CGGCATCTTGATCAAgtaaggttgattgtgcaggtttttttcctctctctcttttcagAGTTGTT Alignment from Spaln_nt2Genome AAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTGCCCCAGTATCTGGACCAG AGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacaggatttccctacgagaacgctcgacagaggcggtatgaactaagTACTTGTGTGGTATTGAGGCCATCTGATATTAGTAAGAACACAGAAA---TGCAGGCAGAGCTGCTG---CGGCATCTTGATCAAgtaaggttgattgtgcaggtttttttcctctctctcttttcagAGTTGTT Alignment from Pairagon GA------------------------------------------AACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTGCCCCAGTATCTGGACCAG AGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacagGATTTCCCTACGAGAACGCTCGACAGAGGCGGTATGAACTAAGTACTTGTGTGGTATTGAGGCCATCTGATATTAGTAAGAACACAGAAA---TGCAGGCAGAGCTGCTG---CGGCATCTTGATCAAgtaaggttgattgtgcaggtttttttcctctctctcttttcagAGTTGTT Alignment from Exonerate_protein2genome GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTGCCCCAGTATCTGGACCAG AGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacaggatttccctacgagaacgctcgacagaggcggtatgaactaaGTACTTGTGTGGTATTGAGGCCATCTGATATTAGTAAGAACACAGAA---ATGCAGGCAGAGCTGCTG---CGGCATCTTGATCAAgtaaggttgattgtgcaggtttttttcctctctctcttttcagAGTTGTT Alignment from Exonerate_coding2genome GCTGCTGCCCCAGTATCTGGACCAGAGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacaggatttccctacgagaacgctcgacagaggcggtatgaactaagtacttgtgtggtattgaggccatctgatattagtaagaacacagaaatgcaggcagagctgctgcggcatcttgatcaagtaaggttgattgtgcagGTTTTTTTCCTCTCTCTCTTTTCAGAGTTGTT Alignment from GeneWise AGCTGCT cagaggagcacccagctattgtcctgggacatgtaccctcttctccacaggatttccctacgagaacgctcgacagaggcggtatgaactaagtacttgtgtggtattgaggccatctgatattagtaagaacacagaaatgcaggcagagctgctgcggcatcttgatcaagtaaggttgattgtgcaggtttttttcctctctctcttttcagAGTTGTT #### Aldh3b2_ID243_9 --> 0 - 1 Original Alignment ------GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTg ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagTGGCTGGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTggtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from CESAR ------GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTg ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagTGGCTGGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTggtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from Spaln_aa2Genome GTGGTGAATCAGATG------TTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTG ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagTGGCTGGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTGgtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from Spaln_nt2Genome ------GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTG ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagTGGCTGGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTGgtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from Pairagon ------GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTG ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagTGGCTGGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTGgtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from Exonerate_protein2genome GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTG ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagtggctgGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTGgtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from Exonerate_coding2genome GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTG ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagtggctgGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTGgtaagatcttacatgctattgccattggagagttatgttccctcggtata Alignment from GeneWise ------GTGGTGAATCAGATGTTGGAACGCACCAGCAGCGGTGGCTTTGGAGGCAACGATGGCTTCCTCTACCTGACCCTACCAGCTCTGCCTTTGGGGGGAGTTG ggcaggcctggtcctgtgtatgcctgtaggcattacactgttcaacacagTGGCTGGTGGTGAATCAGATGTTGGAGCGTACAAGCAGTGGGGGGTTTGGAGGCAATGAGGGATTCCTATACCTAACACTGCCTGCATTGCCTTTGGCTGGGGTTGgtaagatcttacatgctattgccattggagagttatgttccctcggtata #### Ankrd13d_ID461_12 --> 2 - 1 Original Alignment agATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAg atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagaa------------CATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTCTGTCCCCAACTCCAGTCTGGCAATTTCTGCTTTGggtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from CESAR agATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAg ggcctaaattacatgttaatgggtatgcgagtgctaccttatctttccagaa------------CATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTCTGTCCCCAACTCCAGTCTGGCAATTTCTGCTTTGggtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from Spaln_aa2Genome AGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAG atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagAA------------CATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTCTGTCCCCAACTCCAGTCTGGCAATTTCTGCTTTGGgtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from Spaln_nt2Genome TCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAG atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagAACATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTCTGTCCCCAACTCCAGTCTGGCAATTTCTGCTTTGGgtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from Pairagon AGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAG atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagAA------------CATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTCTGTCCCCAACTCCAGTCTGGCAATTTCTGCTTTGGgtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from Exonerate_protein2genome atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagaacatgttcacaatgcccacaccacctttagtaacctatgcagctgtgatgaacctgtgtcagtgtctgtccccaactccagtctggcaatttctgctttgggtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from Exonerate_coding2genome atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagaacatgttcacaatgcccacaccacctttagtaacctatgcagctgtgatgaacctgtgtcagtgtctgtccccaactccagtctggcaatttctgctttgggtgagtctatagccatactgacctgtctgtagccataacagccagctaga Alignment from GeneWise AGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCA- atgttaatgggtacttcacaaatgttgcgagtgctaccttatctttccagAA------------CATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTGTCA---GTGTCTGTCCCCAACTCCAGTCTGGCAATTTCTGCTTTGGgtgagtctatagccatactgacctgtctgtagccataacagccagctaga #### Ankrd13d_ID464_9 --> 2 - 0 Original Alignment gg---GGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacagataaacaagtcaaatgactttgtcttaaataaaggaGAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---ACATTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg Alignment from CESAR gg---GGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacagataaacaagtcaaatgactttgtcttaaataaaggaGAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---ACATTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg Alignment from Spaln_aa2Genome GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacagataaacaagtcaaatgactttgtcttaaataaaggagAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---ACATTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg Alignment from Spaln_nt2Genome GGGGGAAGACTCCAT---TCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacagataaacaagtcaaatgactttgtcttaaataaagGAGAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACA-TTCACCCACA--TTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg Alignment from Pairagon ------------------------------------------------------GGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG GCCTGCCTACTTACAGATAAACAAGTCAAATGACTTTGTCTTAAATAAAGGAGAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACC---CACATTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg Alignment from Exonerate_protein2genome GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacagataaacaagtcaaatgactttgtcttaaataaaggagAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---ACATTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --GGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacagataaacaagtcaaatgactttgtcttaaataaaggagAAGGAAAGACACCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---ACATTGgtgagattggttaaaccacagaccgcaaaggctgggtgagtgttgagagg #### Ankrd13d_ID469_4 --> 0 - 1 Original Alignment GCCCCTGATTTCTACGTGGAAATGAAATGGGAGTTCACTAGCTGGg atggcttataataggcatttgcttttgtcctgtgggaccgtctcttctag------------TATGTAGAAATGAAATGGGAATTCACCAGCTGGggtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg Alignment from CESAR GCCCCTGATTTCTACGTGGAAATGAAATGGGAGTTCACTAGCTGGg gtgagattcgacatggcttataatatgtcctgtgggaccgtctcttctag------------TATGTAGAAATGAAATGGGAATTCACCAGCTGGggtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg Alignment from Spaln_aa2Genome TACGTGGAAATGAAATGGGAGTTCACTAGCTGGG atggcttataataggcatttgcttttgtcctgtgggaccgtctcttctagTATGTAGAAATGAAATGGGAATTCACCAGCTGGGgtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg Alignment from Spaln_nt2Genome TACGTGGAAATGAAATGGGAGTTCACTAGCTGGG atggcttataataggcatttgcttttgtcctgtgggaccgtctcttctagTATGTAGAAATGAAATGGGAATTCACCAGCTGGGgtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg Alignment from Pairagon GCCCCTGATTTCTACGTGGAAATGAAATGGGAGTTCACTAGCTGGG atggcttataataggcatttgcttttgtcctgtgggaccgtctcttctag------------TATGTAGAAATGAAATGGGAATTCACCAGCTGGGgtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg Alignment from Exonerate_protein2genome GCCCCTGATTTC---TACGTGGAAATGAAATGGGAGTTCACTAGCTGGG atggcttataataggcatttgcttttgtcctgtggGACCGTCTCTTCTAGTATGTAGAAATGAAATGGGAATTCACCAGCTGGGgtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TACGTGGAAATGAAATGGGAGTTCACTAGCTGGG atggcttataataggcatttgcttttgtcctgtgggaccgtctcttctagTATGTAGAAATGAAATGGGAATTCACCAGCTGGGgtatgcgagccactgcagtgcagagccttggttactggagtgctgagatg #### Ankrd13d_ID471_2 --> 0 - 1 Original Alignment CACGACATTGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAg gtactccatataagaccatccctcttccttgtgacctctgattcccaaag---------GAGCAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTggtgagttattgctctattatacgtgaagggcacctagaggtttaatacta Alignment from CESAR CACGACATTGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAg cttggatgggtactccatataagactccttgtgacctctgattcccaaag---------GAGCAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTggtgagttattgctctattatacgtgaagggcacctagaggtttaatacta Alignment from Spaln_aa2Genome CACGACATTGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAG gtactccatataagaccatccctcttccttgtgacctctgattcccaaag---------GAGCAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTGgtgagttattgctctattatacgtgaagggcacctagaggtttaatacta Alignment from Spaln_nt2Genome TGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAG gtactccatataagaccatccctcttccttgtgacctctgattcccaaag-GAGCAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTGgtgagttattgctctattatacgtgaagggcacctagaggtttaatacta Alignment from Pairagon CACGACATTGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAG gtactccatataagaccatccctcttccttgtgacctctgattcccaaag---------GAGCAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTGgtgagttattgctctattatacgtgaagggcacctagaggtttaatacta Alignment from Exonerate_protein2genome CACGACATTGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAG gtactccatataagaccatccctcttccttgtgacctctgaTTCCCAAAGGAGCAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTGgtgagttattgctctattatacgtgaagggcacctagaggtttaatacta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CACGACATTGAGCAGGAGGACCCCCAAGGGCGAACCCCCCTGGAGCTTGCTGTGACCTTGGGGAACTTGGAGTCTGTGAGAGTCCTCCTCCGACATAATGCCAACGTGGGCAAAGAGAGCCACCAGGGCTGGGCAG gtactccatataagaccatccctcttccttgtgacctctgattcccaaagGAG---------CAGGAGGACCCACAGGGGCAGACCCCTTTAGAACTAGCTGTGACTTTGGGGAATTTAGAGTCTGTACGAGTCCTCCTTAAACATAATGCCAATTTAGGCAAGGAAAGCCACCAGGGCTGGGCTGgtgagttattgctctattatacgtgaagggcacctagaggtttaatacta #### Ankrd1_ID7096_7 --> 0 - 0 Original Alignment CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAG---GACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAAC---gtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt Alignment from CESAR CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAGGACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAACgtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt Alignment from Spaln_aa2Genome CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAGGACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAACgtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt Alignment from Spaln_nt2Genome CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAGGACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAACgtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt Alignment from Pairagon CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAGGACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAACgtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt Alignment from Exonerate_protein2genome CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAGGACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAACgtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTTCTCAGCACAGCGCTGCATGTGGCGGTGAGGACTGGTCATTACGAGTGCGCTGAGCACCTCATCGCCTGCGAGGCTGATCTCAATGCCAAGGACAGA gatatctatggttgtttgactccacccagccactgttccttccctcacagCTGCTCAGCTCAACACTATATGTGGCAGTCAGGACTGACCATTATAAGTGCACTGAGCATCTCTTCACCAGCAAGACTGATCTCAATGCAAGGGACAACgtgggctgtacgagtgttacctggcttgaattaggagcttatagatgatt #### Ankrd2_ID8374_8 --> 0 - 0 Original Alignment ---GAAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATGGCT---AAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from CESAR ---GAAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATG---GCTAAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from Spaln_aa2Genome GAAGGGGAC---AGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATG---GCTAAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from Spaln_nt2Genome G---AAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATGGCT---AAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from Pairagon --------------------GAAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATG---GCTAAGAACCTG tgtgggatcctttaaaatcaggacttactacagTTTCTAATGACCAACAGGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from Exonerate_protein2genome ---GAAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATG---GCTAAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from Exonerate_coding2genome ---GAAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATG---GCTAAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg Alignment from GeneWise ---GAAGGGGACAGTGCCCTACATGATGCCGTGAGACTCAACCGCTACAAAATCATCAAACTGCTGCTCTTGCATGGGGCGGACATGATGGCT---AAGAACCTG tgtgggatcctttaaaatcaggacttactacagtttctaatgaccaacagGGTGAAGGAGACAGCGCCCTACATGATGCTGTGAAAATCAACTACTACAAAAACATCAAGTTGTTGCTCTTACATGGGACAGACATGATGGCAGCCAAGAACTTAgtgagtttgcacctgtcttggtggttttcatgctagccttaacggtttgg #### Anxa1_ID4766_4 --> 0 - 0 Original Alignment CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGTGCCATGAAG GGACT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTT---GCTGATGAACTACACGGT---------gtaagcactaacaatggtggttagttcattccccttccactgtagGGACT Alignment from CESAR CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGTGCCATGAAG cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTT---GCTGATGAACTACACGGT---------gtaagcactaacaatggtggcttaaaacaccccctccaact Alignment from Spaln_aa2Genome CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGT GCCAT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTT---GCTGATGAACTACACGGTgtaagcactaacaatggtggttagttcattccccttccactgtag----- Alignment from Spaln_nt2Genome CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGT GCCAT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATT---TGCTGATGAACTACACGGTgtaagcactaacaatggtggttagttcattccccttccactgtag----- Alignment from Pairagon CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGTGCCA------------------------------------TGAAGGGACT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTTGCT---GATGAACTACACGGTGTAAGCACTAACAATGGTGGTTAGTTCATTCCCCTTCCACTGTAGGGACT Alignment from Exonerate_protein2genome CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGTGCCA TGAAGGGACT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTT---GCTGATGAACTACACGGTGTAAgcactaacaatggtggttagttcattccccttccacTGTAGGGACT Alignment from Exonerate_coding2genome CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGTGCCA TGAAGGGACT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTT---GCTGATGAACTACACGGTGTAAgcactaacaatggtggttagttcattccccttccacTGTAGGGACT Alignment from GeneWise CCCTTGGATGAAGTCTTGAGAAAAGCCCTTACAGGCCACCTGGAGGAGGTTGTTTTGGCTATGCTAAAAACTCCAGCTCAGTTTGATGCAGATGAACTCCGTGGTGCCATGAAGGGA ---CT cactgggctccttatagtaagacaaactataatcattggctcttttacagCCCCTAGATGATGTACTGAGCAAAGCTCTTACAGGACATCTTGAGGAGGTTGTTTTGGCAATGCTCAAAACTCCCGCACAATTT---GCTGATGAACTACAC------------GGTgtaagcactaacaatggtggttagttcattccccttccactgtagGGACT #### Apba1_ID5242_11 --> 0 - 0 Original Alignment ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG--- gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from CESAR ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG--- gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from Spaln_aa2Genome ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG--- gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from Spaln_nt2Genome ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAGA-- gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from Pairagon ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG--- gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from Exonerate_protein2genome ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG--- gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from Exonerate_coding2genome gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagatctgcagccttacaagagggggaatagctgaaagaggagatgtccgcgttggacatcgaatcattgagattaatggtcaaagtattgtagctataccacatgaagagattgtccacatcctgtccaatgccgtgggggagcatgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga Alignment from GeneWise ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAGATC gcatactaaaaaaatgcagtaggacaggttggacttggtttcatttgtagATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGCGTTGGACATCGAATCATTGAGATTAATGGTCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCCGTGGGGGAGCATgtaggattcaatcaattggtcaggctttatagtggtgtgtccttctcaga #### Asah2_ID6669_5 --> 0 - 2 Original Alignment ---AGCATTGATATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAag aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagTGGAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGC---GCATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAaggtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from CESAR ---AGCATTGATATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAag aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagTGGAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGC---GCATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAaggtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from Spaln_aa2Genome AGCATTGATATAGCT---CACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAAG aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagTGGAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGC---GCATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAAGgtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from Spaln_nt2Genome GAGCATTGAT--ATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAAG aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagTGGAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGCGCA---TCTTACCTGCTAAATCCACAAGCAAAGAGAGCAAGgtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from Pairagon ---AGCATTGATATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAAG aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagTGGAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGCG---CATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAAGgtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from Exonerate_protein2genome AGCATTGATATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAAG aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagtggAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGC---GCATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAAGgtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from Exonerate_coding2genome AGCATTGATATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAAG aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagtggAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGC---GCATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAAGgtatggcattccttatagtattagaggtatatacctcaggttacaaaaca Alignment from GeneWise ---AGCATTGATATAGCTCACACAAATCTTAAACCAGGCAAAATCTTTATCAACAAAGGAAATGTTGCTAATGTGCAGATCAACCGAAGCCCCTCCTCTTACCTTCTGAATCCACAGTCAGAGAGAGCAAG aaaacctcttagcatgctgaatgcatgccttcccatgtcctcctccacagTGGAGCATTGATGTTGCCCACACAAATCTCCAACCTGGCAAAATCTTTATCAATAAGGAAAATGTAGCCAATCTGCAGATCAATCGAAGC---GCATCTTACCTGCTAAATCCACAAGCAAAGAGAGCAAGgtatggcattccttatagtattagaggtatatacctcaggttacaaaaca #### Atg2a_ID1515_4 --> 2 - 2 Original Alignment tg---CTCCGGAGGATCAAGGTGACCTTCCTGAACACTGTTGTGAGGGTGGAGCATTCACTGGGTGATGAGGATCGAAGTGTGGCTGTG------------------GAGGTCCGAGTGCAGag gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagtcATTCTCAGAAGAACCAAGGTGACCCCCTTAAACATTGTTGTGAGCGTAGAACAGTCATTGAGTGATGAA---GAAAGTATTGCTGTCGAAATCAGGGCACAGAGAGAAATCCGGGAACAAaggtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from CESAR tg---CTCCGGAGGATCAAGGTGACCTTCCTGAACACTGTTGTGAGGGTGGAGCATTCACTGGGTGATGAGGATCGAAGTGTGGCTGTGGAGGTCCGAGTGCAG------------------ag gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagtcATTCTCAGAAGAACCAAGGTGACCCCCTTAAACATTGTTGTGAGCGTAGAACAGTCATTGAGTGATGAAGAA---AGTATTGCTGTCGAAATCAGGGCACAGAGAGAAATCCGGGAACAAaggtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from Spaln_aa2Genome TGCTCCGGAGG---ATCAAGGTGACCTTCCTGAACACTGTTGTGAGGGTGGAGCATTCACTGGGTGATGAGGATCGAAGTGTGGCTGTGGAGGTCCGAGTGCAGAGA----------------- gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagTCATTCTCAGAAGAACCAAGGTGACCCCCTTAAACATTGTTGTGAGCGTAGAACAGTCATTGAGTGATGAAGAA---AGTATTGCTGTCGAAATCAGGGCACAGAGAGAAATCCGGGAACAAAGgtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from Spaln_nt2Genome TG---CTCCGGAGGATCAAGGTGACCTTCCTGAACACTGTTGTGAGGGTGGAGCATTCACTGGGTGATGAGGA-----------TCGAAGTGTGG---CTGTG-GAGGTCCGAGTGCAGAG gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagTCATTCTCAGAAGAACCAAGGTGACCCCCTTAAACATTGTTGTGAGCGTAGAACAGTCATTGAGTGATGAAGAAAGTATTGCTGTCGAAATCAGGGCACAGAGAGAAATCCGGGAACAAAGgtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from Pairagon ---TGCTCCGGAGGATCAAGGTGACCTTCCTGAACACTGTTGTGAGGGTGGAGCATTCACTGGGTGATGAGGATCGAAGTGTGGCTGTGGAGGTCCGAGTGCAGAG------------------ gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagTCATTCTCAGAAGAACCAAGGTGACCCCCTTAAACATTGTTGTGAGCGTAGAACAGTCATTGAGTGATGAAGA---AAGTATTGCTGTCGAAATCAGGGCACAGAGAGAAATCCGGGAACAAAGgtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from Exonerate_protein2genome gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagtcattctcagaagaaccaaggtgacccccttaaacattgttgtgagcgtagaacagtcattgagtgatgaagaaagtattgctgtcgaaatcagggcacagagagaaatccgggaacaaaggtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from Exonerate_coding2genome gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagtcattctcagaagaaccaaggtgacccccttaaacattgttgtgagcgtagaacagtcattgagtgatgaagaaagtattgctgtcgaaatcagggcacagagagaaatccgggaacaaaggtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg Alignment from GeneWise --GTGCTCCGGAGGATCAAGGTGACCTTCCTGAACACTGTTGTGAGGGTGGAGCATTCACTGGGTGATGAGGATCGAAGTGTGGCTGTGGAGGTCCGAGTGCAGAGA----------------- gatcaccaggatagaaccctctaaggtactcccttgtccccaccctccagTCATTCTCAGAAGAACCAAGGTGACCCCCTTAAACATTGTTGTGAGCGTAGAACAGTCATTGAGTGATGAAGAA---AGTATTGCTGTCGAAATCAGGGCACAGAGAGAAATCCGGGAACAAAGgtgcgtctgagagactcaaaaattgcttaagggcgccaagacaagatggg #### Atg2a_ID1517_6 --> 0 - 1 Original Alignment TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTCAGTGCCGTCAACCTTGCAg ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACGGCAC---CATCAACTTCAGAGTCTTCTGAGT---------------ggtattttggttattaatttactgatctcctctcatggaaagactttactc Alignment from CESAR TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTCAGTGCCGTCAACCTTGCAg ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACGGCAC---CATCAACTTCAGAGTCTTCTGAGT---------------ggtattttggttattaatttactgatctcctctcatggaaaaggtgtgagc Alignment from Spaln_aa2Genome TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTC- ------AGT ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACGGCAC---CATCAACTTCAGAGTCTTCTGAgtggtattttggttattaatttactgatctcctctcatggaaagACTTTACTC Alignment from Spaln_nt2Genome TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTCAGTGCCGTCAACCTTG ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACG---GCACCATCAACTTCAGAGTCTTCTGAGTG--GT--ATTTTGgttattaatttactgatctcctctcatggaaagacttt Alignment from Pairagon TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTCAGTG ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACGGCA---CCATCAACTTCAGAGTCTTCTGAGTGgtattttggttattaatttactgatctcctctcatggaaagactttactc Alignment from Exonerate_protein2genome TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTCAGTGCCGTCAACC ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACGGCAC---CATCAACTTCAGAGTCTTCTGAGTGGTATTTTGGttattaatttactgatctcctctcatggaaagactttactc Alignment from Exonerate_coding2genome ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagctggaagtatcaggaaagctgggatcactccatctgcttctgtccccacggcaccatcaacttcagagtcttctgagtggtattttggttattaatttactgatctcctctcatggaaagactttactc Alignment from GeneWise TTGGAGGTATCAGGACAACTGGGATCCCTGCACCTGCTTTTGACCCCGCGTCAGCTCCAGCAGCTCCAGAGGCTGCTCAGT- --------G ggatggccacaagatcgtgcaaccactcatttttctaaaacctaccctagCTGGAAGTATCAGGAAAGCTGGGATCACTCCATCTGCTTCTGTCCCCACGGCAC---CATCAACTTCAGAGTCTTCTGAGTGgtattttggttattaatttactgatctcctctcatggaaagACTTTACTC #### Atg2a_ID1518_7 --> 2 - 1 Original Alignment acCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGg ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagatCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAACTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCC------------------------------ggtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg Alignment from CESAR acCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGg ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagatCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAACTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCC------------------------------ggtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg Alignment from Spaln_aa2Genome ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCA ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAACTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCGgtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg Alignment from Spaln_nt2Genome ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGG ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAACTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCGGTAAGTGTTGACT---GTTGGTTTGCAGTGgccccaatgaagagacagca Alignment from Pairagon ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGG ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAACTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCC------------------------------Ggtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg Alignment from Exonerate_protein2genome ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagatcctgctggactggctgacaagctgaacaagagctgccaactggggccagaagatctgtggctcattgagcaagacctgaatcagcaactgcaagcaggtgctgtggcagagtctctcagcttgtaccccggtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg Alignment from Exonerate_coding2genome ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagatcctgctggactggctgacaagctgaacaagagctgccaactggggccagaagatctgtggctcattgagcaagacctgaatcagcaactgcaagcaggtgctgtggcagagtctctcagcttgtaccccggtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg Alignment from GeneWise ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCA ctcatggaaagacagacattcgagcaggtgtgagcccttcccgtccacagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAACTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCGgtaagtgttgactgttggtttgcagtggccccaatgaagagacagcaacg #### Atg2a_ID1525_14 --> 2 - 2 Original Alignment gaATCTACGAAGATGGAGAGAAGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTca tcaaggtcacgtaggtccgtggcataaaacacttccttctgtctctctagga---------------------CCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTcagtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from CESAR gaATCTACGAAGATGGAGAGAAGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTca cagtcaggaggtgtgactatatcaaaaaacacttccttctgtctctctagga---------------------CCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTcagtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from Spaln_aa2Genome GATGGAGAGA AGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTCA TCAAGGTCACgtaggtccgtggcataaaacacttccttctgtctctctagGACCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTCAgtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from Spaln_nt2Genome --CCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTCA tcaaggtcacgtaggtccgtggcataaaacacttccttctgtctctctagGACCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTCAgtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from Pairagon GAATCTACGAAGATGGAGAGAAGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTCA tcaaggtcacgtaggtccgtggcataaaacacttccttctgtctctctagGA---------------------CCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTCAgtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from Exonerate_protein2genome AGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTCA tcaaggtcacgtaggtccgtggcataaaacacttccttctgtctctctagGACCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTCAgtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from Exonerate_coding2genome AGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTCA tcaaggtcacgtaggtccgtggcataaaacacttccttctgtctctctagGACCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTCAgtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg Alignment from GeneWise GAATCTACGAAGATGGAGAGAAGCCACCAGTCCCCTGCCTGCGGGTCTCCAAAGCTCTGAATCCCAGGAGCACTGAGGCCAAGTACTTTCTACCTCA tcaaggtcacgtaggtccgtggcataaaacacttccttctgtctctctagGA---------------------CCACTTATACCCTGCCTGAGAATCTCCAAAGCTCTGAACTCACGGAGTACTGAAGCTAAGTACTTTCTCCCTCAgtaagtggcttgttagaaaaagtgagtgcagaatactaaatctttcaggg #### Atg2a_ID1526_15 --> 1 - 0 Original Alignment gGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagggtgccagttctttccttctatgtacagg---GTGGTGACCTTGAACCCC---CCAAGTAGTACCCAGCGGCAGACAGCTCAG---AAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from CESAR gGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA gagtgcagaatactaaatctttcaggccagttctttccttctatgtacagg---GTGGTGACCTTGAACCCC---CCAAGTAGTACCCAGCGGCAGACAGCT---CAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from Spaln_aa2Genome GGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagggtgccagttctttccttctatgtacagG---GTGGTGACCTTGAACCCCCCAAGTAGT---ACCCAGCGGCAGACAGCT---CAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from Spaln_nt2Genome GGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagggtgccagttctttccttctatgtacagG---GTGGTGACCTTGAACCCCC---CAAGTAGTACCCAGCGGCAGACAGC---TCAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from Pairagon GGT-------------------------AGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagGGTGCCAGTTCTTTCCTTCTATGTACAGGGTGGTGACCTTGAACCCCC---CAAGTAGTACCCAGCGGCAGACAGC---TCAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from Exonerate_protein2genome GGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagggtgccagttctttccttctatgtacagG---GTGGTGACCTTGAACCCCCCAAGTAGT---ACCCAGCGGCAGACAGCT---CAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from Exonerate_coding2genome GGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagggtgccagttctttccttctatgtacagG---GTGGTGACCTTGAACCCCCCAAGTAGT---ACCCAGCGGCAGACAGCT---CAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt Alignment from GeneWise GGTAGTGGTGACCCTGAACCCCCAGTCCAGTGGCACACAGTGGGAGACAGCCTATGAGAAAGGCCGGGATCTAGAGCTGTCCACCGAGAGTCCGTGTGAGCTACAGCAACCTGAGCCCTCGCCCTTCTCCTCCAAGCGGACCATGTACGAGACTGAGGAA tgcagaatactaaatctttcagggtgccagttctttccttctatgtacagG---GTGGTGACCTTGAACCCCCCAAGTAGT---ACCCAGCGGCAGACAGCT---CAGAAAGGCCGGGACTTAGAACTTTCTGCGGAGAGCCCATGTGAGCTACAGCAACCGGAACCCTCATCCTTTTCTTCAAAGAAGTCTATGTATGAGTCTGAGGAGgtaagttgatcttcccatgccatgacctgtctatccttcacccaatagtt #### Atg2a_ID1528_17 --> 1 - 1 Original Alignment gATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAg tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacaga---AATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAggtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from CESAR gATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAg ctttcaagtttcattaagaaacctttgtgaaggtcttgtgatttccacaga---AATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAggtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from Spaln_aa2Genome GATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAG tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacagA---AATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAGgtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from Spaln_nt2Genome GATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAG tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacag---AAATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAGgtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from Pairagon GATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAG tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacag---AAATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAGgtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from Exonerate_protein2genome GATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAG tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacagA---AATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAGgtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from Exonerate_coding2genome GATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAG tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacagA---AATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAGgtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc Alignment from GeneWise GATCAATAACGACCTGCTCATGTGGGAGCCTGCAGACCTGCTTCCCACATCCAGCGCTGCTGCTCGGCCGCCTGGCTCTTCGGGGTTCAAGATGTGCAAGTCAGCCTTCAAGCTAG tcaagtttcattaagaaaccttgggtgtgaaggtcttgtgatttccacagA---AATAATGACTTACTAATGTGGGAGCCAGCAGATCCACTTCCCTCACCAAGTACTGCCGCCAGGCCCCCTGGCGCATCCGGATTCAAAATGTGCAAGTCAGCTTTCAAGCTAGgtaggagaggtccaccctgggcagtaggtgaccataccaaatctctattc #### Atg2a_ID1529_18 --> 2 - 0 Original Alignment acTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAGGCTAAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagacTCAGAAGCAGAGGCAGAAAAAGCCCAGTTT---TCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGTAAG------gtgagtgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from CESAR acTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAGGCTAAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagacTCAGAAGCAGAGGCAGAAAAAGCCCAG---TTTTCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGT------AAGgtgagtgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from Spaln_aa2Genome ACTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAGGCTAAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagACTCAGAAGCAGAGGCAGAAAAAGCCCAG---TTTTCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGTAAGGTGAGTgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from Spaln_nt2Genome ACTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagACTCAGAAGCAGAGGCAGAAAAAGCCCAG---TTTTCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGTAAGgtgagtgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from Pairagon ACTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAGGCTAAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagACTCAGAAGCAGAGGCAGAAAAAGCCCAG---TTTTCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCG------TAAGgtgagtgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from Exonerate_protein2genome ACTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagACTCAGAAGCAGAGGCAGAAAAAGCCCAG---TTTTCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGTAAGgtgagtgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from Exonerate_coding2genome ACTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagACTCAGAAGCAGAGGCAGAAAAAGCCCAG---TTTTCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGTAAGgtgagtgttacttggcctgtagccattaggcactgatgggggaacctaat Alignment from GeneWise ACTCGGATTCAGATGAAGAAGACGCCCAGTTCTTCTCGATGGCATCAGGTGTCCCCCAGACACCTGCCCCAGAACCTTCCCGTCGTCAGTCCCAGAGTACCTTCTCCACACTGGTGACAGTGCTGAAGGGTCGGATCACTGCGCTCTGTGAGGCTAAG gtcagacagacattcctggtcagcagtgtagtatttgattttatttacagACTCAGAAGCAGAGGCAGAAAAAGCCCAGTTT---TCAATGGCAGCAGGTGTGCCCCACACTCCTGCCCCAGAGCCTCCCCATTGCCAATCCCAGAGCACCTTCTCTACACTTGTGACAGTACTCAAAGGACGGATCACTGCACTTCGTAAGGTGAGTgttacttggcctgtagccattaggcactgatgggggaacctaat #### Atg2a_ID1532_21 --> 0 - 0 Original Alignment ------GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataagGAATCTGAGTTTCTAGTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAACAT---------TCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from CESAR GAA------TTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataagGAATCTGAGTTTCTAGTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from Spaln_aa2Genome GTCAAGGAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataagGAATCTGAGTTTCTAGTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from Spaln_nt2Genome TGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataaggaatctgagtttctagTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from Pairagon GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataaggaatctgagtttctag----------TGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from Exonerate_protein2genome GTCAAGGAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataagGAATCTGAGTTTCTAGTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from Exonerate_coding2genome GTCAAGGAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataagGAATCTGAGTTTCTAGTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc Alignment from GeneWise GTCAAGGAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctcttttgtgccagcttgcccttctctggtttgtattataagGAATCTGAGTTTCTAGTGACAGTCAGATCACACACATCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCTAAGgtatactaagaccacgaagtcatgcccttacatgacaattatatccttgc #### Atg2a_ID1534_23 --> 1 - 2 Original Alignment gCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTCag ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagaCCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACA---------aagtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from CESAR gCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTCag ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagaCCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACA---------aagtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from Spaln_aa2Genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTT ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagACCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACAAAgtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from Spaln_nt2Genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTT ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagACCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACAAAgtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from Pairagon GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCAT ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagACCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATgtactcacctacaaagtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from Exonerate_protein2genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTT ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagACCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACAAAgtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from Exonerate_coding2genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACC ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagACCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACAaagtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt Alignment from GeneWise GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATT ggattacatgaaggttaggcaagtccctacatgtgctcaaccctgtccagACCTCTCTACCTCCCTGTGCAGGTCCTGGTTACTGCAGAGACTTTCACTCTCTCCAGCAACATTgttatgtactcacctacaaagtaagttgtctgctcgtatccattgtggtcgattaaatacctgtataatt #### Atg2a_ID1539_28 --> 2 - 0 Original Alignment gtGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATTGCG taagaaactgaaagttggactttatagtgtttccctggcctggttttcaggtGGCAGACTGACTCAGGCCTCCCCTAATTCGTCTTAT---TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGGT---AAGGCAAGGGAGCATGAA------GAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATA---------gtatagtggaattcgttggaatgctggttagaactgcagcttccactaga Alignment from CESAR gtGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATTGCG taagaaactgaaagttggactttatagtgtttccctggcctggttttcaggtGGCAGACTGACTCAGGCCTCCCCTAATTCGTCTTAT---TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATA---------gtatagtggaattcgttggaatgctggttagaactgcagct Alignment from Spaln_aa2Genome GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTA taagaaactgaaagttggactttatagtgtttccctggcctggttttcagGTGGCAGACTGACTCAGGCCTCCCCTAATTCGTCTTAT---TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAgtatagtggaattcgttggaatgctggttagaactgcagcttccactaga Alignment from Spaln_nt2Genome GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATT taagaaactgaaagttggactttatagtgtttccctggcctggttttcagGTGGCAGACTGACTCAGGCCTC-CCCTAATTCGTCT-TAT-TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGG---TAAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATA-GTATAgtggaattcgttggaatgctggttagaactgcagcttccactag Alignment from Pairagon GTGGCCCACTTCCTCAGGCCTCTCC-----CGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTA taagaaactgaaagttggactttatagtgtttccctggcctggttttcagGTGGCAGACTGACTCAGGCCTCCCCTAATTCGTCT-----TAT---TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGG---TAAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAgtatagtggaattcgttggaatgctggttagaactgcagcttccactaga Alignment from Exonerate_protein2genome GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTA taagaaactgaaagttggactttatagtgtttccctggcctggttttcagGTGGCAGACTGACTCAGGCCTCCCCTAATTCGTCTTAT---TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAgtatagtggaattcgttggaatgctggttagaactgcagcttccactaga Alignment from Exonerate_coding2genome taagaaactgaaagttggactttatagtgtttccctggcctggttttcaggtggcagactgactcaggcctcccctaattcgtcttatttccctggtggtcagagtggagtgcaggcaccttcacatcctccaggagcctcctcacacaccttgggtaaggcaagggagcatgaagaggaaggtgatggggacagtctggatagtgatgaattctgcatcctcgatgcccctggcatagtatagtggaattcgttggaatgctggttagaactgcagcttccactaga Alignment from GeneWise GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATTGCG taagaaactgaaagttggactttatagtgtttccctggcctggttttcagGTGGCAGACTGACTCAGGCCTCCCCTAATTCGTCTTAT---TTCCCTGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCAGGAGCCTCCTCACACACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGC---------ATAgtatagtggaattcgttggaatgctggttagaactgcagcttccactaga #### Atg2a_ID1540_29 --> 0 - 2 Original Alignment ---CCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACag atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATaggtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from CESAR ---CCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACag atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATaggtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from Spaln_aa2Genome GCGCCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACAG atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATAGgtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from Spaln_nt2Genome ---CCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACAG atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATAGgtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from Pairagon GCGCCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACAG atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATAGgtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from Exonerate_protein2genome GCGCCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACAG atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATAGgtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from Exonerate_coding2genome atgcatataggacaaccacactgttgaatgtgttactcttttctccacaggtccctcgagatggggaaccaattgtaacacaactccaccccggacctattattgtgcatgacagttacttctcccagcccctggggagctctgacctattgcatgcagctgctcatttccctgtgcccagcagccgtgtggtactatgggaagtttccttcatttggcacctatgtggtggcagagacttcggcctgcaccccacttataggtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac Alignment from GeneWise ---CCTCGAGACGGGGAGCCCATCGTGACACAGCTGCATCCAGGCCCCATCATCGTGCACGACGGTCACTTCTCCCAGCCCCTGGGAAGCACTGACCTGCTGCGCGCTCCTGCCCACTTCCCAGTGCCCAGCAGCCGTGTGGTACTACGGGAGGTCTCCTTCATCTGGCACCTCTATGGGGGTAGAGACTTTGGCCTTCACCCCACTTACAG atgcatataggacaaccacactgttgaatgtgttactcttttctccacagGTCCCTCGAGATGGGGAACCAATTGTAACACAACTCCACCCCGGACCTATTATTGTGCATGACAGTTACTTCTCCCAGCCCCTGGGGAGCTCTGACCTATTGCATGCAGCTGCTCATTTCCCTGTGCCCAGCAGCCGTGTGGTACTATGGGAAGTTTCCTTCATTTGGCACCTATGTGGTGGCAGAGACTTCGGCCTGCACCCCACTTATAGgtgagtacaactattcaactagcatcactacaaggaccagtgtgcctaac #### Atg2a_ID1546_35 --> 1 - 0 Original Alignment gGAGTTCCGCTTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG gtcagggtgacacaaacctcttctattaatcttgcacatgttttttgtagt---------TTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from CESAR gGAGTTCCGCTTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG gggcatccagacagggtgacacaaattaatcttgcacatgttttttgtagt---------TTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from Spaln_aa2Genome GGAGTTCCGCTTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG gtcagggtgacacaaacctcttctattaatcttgcacatgttttttgtagT---------TTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from Spaln_nt2Genome CTTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG gtcagggtgacacaaacctcttctattaatcttgcacatgttttttgtagTTTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from Pairagon GGAGTTCCGCTTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG gtcagggtgacacaaacctcttctattaatcttgcacatgttttttgtag---------TTTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from Exonerate_protein2genome CCGCTTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG gtcagggtgacacaaacctcttctattaatcttgcacatgttttttgTAGTTTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from Exonerate_coding2genome gtcagggtgacacaaacctcttctattaatcttgcacatgttttttgtagtttcacgtctgaggttcccatttgcttggcctaccatggtaagcatgtcactgtggatcaggtggtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa Alignment from GeneWise TTCCGC---------------------------------------------TTCACATCTGAGGTGCCCATCTGCCTGGATTACCATGGCAAGCATGTCACTGTGGACCAGGTG GTCAGGGTGACACAAACCTCTTCTATTAATCTTGCACATGTTTTTTGTAGTTTCACGTCTGAGGTTCCCATTTGCTTGGCCTACCATGGTAAGCATGTCACTGTGGATCAGGTGgtgagtcccactgggcaggatttggaggatgtgacaatctttaagtataa #### Atg2a_ID1548_37 --> 1 - 1 Original Alignment g---CTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACATC---CGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTCt ggtctggacttctgtagccctgcaggatccactccctctttctgttctagtTGGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTggtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from CESAR g---CTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACATC---CGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTCt ggtctggacttctgtagccctgcaggatccactccctctttctgttctagtTGGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTggtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from Spaln_aa2Genome G---CTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACATC---CGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTC ggtctggacttctgtagccctgcaggatccactccctctttctgttctagTTGGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTGgtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from Spaln_nt2Genome ---GCTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACATC---CGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTCT ggtctggacttctgtagccctgcaggatccactccctctttctgttctagTTGGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTGgtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from Pairagon ---GCTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACAT---CCGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTCT ggtctggacttctgtagccctgcaggatccactccctctttctgttctagTTGGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTGgtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from Exonerate_protein2genome GCTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACATC---CGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTCT ggtctggacttctgtagccctgcaggatccactccctctttctgttctagttgGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTGgtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from Exonerate_coding2genome ggtctggacttctgtagccctgcaggatccactccctctttctgttctagttggctcctgcgtgtggataaggcacgttgctatgctatcaatgaatggttgcaggacatttatcataagaagcagctgccaagtttactggccagtgtgggacccatacactcagtcctgcagtttggtaagtcatagggatcatatcccacactgattaggcacatgggttacaca Alignment from GeneWise -GGGCTCCTGGGTGTGGACAAGGTGCTGTGCTATGCCCTCAATGAATGGCTGCAGGACATC---CGTAAGAACCAGCTGCCCGGCCTGCTGGGAGGCGTGGGCCCCATGCACTCGGTTGTGCAGCTCT ggtctggacttctgtagccctgcaggatccactccctctttctgttctagTTGGCTCCTGCGTGTGGATAAGGCACGTTGCTATGCTATCAATGAATGGTTGCAGGACATTTATCATAAGAAGCAGCTGCCAAGTTTACTGGCCAGTGTGGGACCCATACACTCAGTCCTGCAGTTTGgtaagtcatagggatcatatcccacactgattaggcacatgggttacaca #### Atg2a_ID1550_39 --> 0 - 0 Original Alignment ---GCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGAG agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc Alignment from CESAR ---GCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGAG agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttaaccccttgac Alignment from Spaln_aa2Genome ---GCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGA agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc Alignment from Spaln_nt2Genome --GGCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGAG agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc Alignment from Pairagon ---GCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGAG agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc Alignment from Exonerate_protein2genome ---GCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGAG agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc Alignment from Exonerate_coding2genome agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagatggccatagctgaaactgtctatgacatcctctctccagcttctcctgtctcccggtctctgcaagaaaggcgctcttcgcaaaaggtgcgtaggggtcatcaacctgctgacctacaggaagtcatggctaaagcctaccatgcagtgcgggaggtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc Alignment from GeneWise ---GCTACAGCTGAGACAGTGTATGACATCCTGTCCCCGGCTTCTCCTGTCTCCCGATCCCTACAAGACAAGCGCTCTTCGCGGAAGCTACGCAGAGGTCAACAACCTGCTGACCTCCGGGAAGGCATGGCTAAGGCTTATGATGCTGTTCGAGAG agcggcgtgttgaaatgaaaaatatctgtcagctgctttttctccgacagATGGCCATAGCTGAAACTGTCTATGACATCCTCTCTCCAGCTTCTCCTGTCTCCCGGTCTCTGCAAGAAAGGCGCTCTTCGCAAAAGGTGCGTAGGGGTCATCAACCTGCTGACCTACAGGAAGTCATGGCTAAAGCCTACCATGCAGTGCGGGAGgtaagccactgcagaaataagctcatacccccttcatttatgatgcctcc #### B3gat3_ID2492_4 --> 0 - 0 Original Alignment ---ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAG agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGgttggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa Alignment from CESAR ---ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAG agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGgttggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa Alignment from Spaln_aa2Genome ATGCGTTGG---ACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAG agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGgttggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa Alignment from Spaln_nt2Genome ---ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAG agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGgttggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa Alignment from Pairagon --------------------------------------ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAGGTACTGGTATGGCACACCCGGACAGAGAAACCTAAGATGAAGCAGGAGGA agtcagtcttttcagACTAACCTCCCCTTACATTCATCTCTTTTATATAGTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGGT------------------------------------------------ Alignment from Exonerate_protein2genome ---ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAG agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGgttggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa Alignment from Exonerate_coding2genome ---ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAGGTA agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGGTTggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa Alignment from GeneWise ---ATGCGTTGGACTCGCGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGATTTGAAGGTCCTCAGGTACAGGATGGCCGCGTTGTGGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGACATGGCGGGATTTGCGGTTGCCCTGCCCTTGCTATTGGCTAAGCCCAATGCCCAGTTTGATGCTACTGCACCCCGGGGCCACCTGGAAAGTAGTCTCCTGAGCCACCTTGTAGATCCCAAGGACCTGGAGCCACGGGCTGCCAATTGTACTCAG agtcagtcttttcagactaacctccccttacattcatctcttttatatagTGTATGCGCTGGACACGTGGTGTCTCTGTGTGGCCTGTTGGCTTGGTGGGTGGCCTACGATTTGAAAGTCCCCAAGTACAGGATGGTCGTGTTGTTGGTTTCCACACAGCATGGGAACCCAACAGGCCCTTTCCCTTGGATATGGCAGGATTTGCGATCGCCCTGCCCTTACTATTAGCTAAACCCAATGCCCAATTTGATGCTACTGCACCCCGGGGACACCTGGAAAGTAGCCTCCTAAGCCACCTTGTAGATCCAACAGATTTGGAATCGCGGGCTGCCAATTGTACTCAGgttggcggtcagttagcaggtcaggaacatggaggatggtgggctaagaa #### BC048609_ID1423_2 --> 0 - 1 Original Alignment TTCTCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGa aatgattgtgcacccatctggtatcagttgactgtttttaatatttgcag---TCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGagtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from CESAR TTCTCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGa tgcaatgattgtgcacccatctggtagttgactgtttttaatatttgcag---TCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGagtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from Spaln_aa2Genome TTCTCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGA aatgattgtgcacccatctggtatcagttgactgtttttaatatttgcag---TCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGAgtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from Spaln_nt2Genome TCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGA aatgattgtgcacccatctggtatcagttgactgtttttaatatttgcagTCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGAgtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from Pairagon TCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGA aatgattgtgcacccatctggtatcagttgactgtttttaatatttgcagTCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGAgtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from Exonerate_protein2genome TTCTCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGA aatgattgtgcacccatctggtatcagttgactgtttttaatatttgCAGTCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGAgtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from Exonerate_coding2genome TTCTCCCAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGA aatgattgtgcacccatctggtatcagttgactgtttttaatatttgCAGTCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGAgtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct Alignment from GeneWise ---CAGGTGATCAGCATCGGCTGGGCTGCCATGGGGTCACTCTACGCAGAGATGACCGGTGACAAGTTTCTTAGATGCTTTGCTTTGACCATTCTGA aatgattgtgcacccatctggtatcagttgactgtttttaatatttgcagTCTCAAGTAATCAGTATTGGTTGGGCTACCATAGGACCACTGTACCATGAGATGACTGGTGACAAGTTTCTTAGATGCTTTGCACTGACCATCTTGAgtaagagggggcaggagcatgaagggtgggctaactacgacatcagttct #### Bbs1_ID721_13 --> 2 - 1 Original Alignment gtGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGGAAGCTGGCACAg aagaatcatgaacagggatccagaagtatctctctctctctctctccaaggcAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGGT---------cgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from CESAR gtGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGGAAGCTGGCACAg aagaatcatgaacagggatccagaagtatctctctctctctctctccaaggcAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGGT---------cgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from Spaln_aa2Genome GTGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGGAA- aagaatcatgaacagggatccagaagtatctctctctctctctctccaagGCAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGGTCgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from Spaln_nt2Genome GTGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGGAAGCTGGC aagaatcatgaacagggatccagaagtatctctctctctctctctccaagGCAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGG-----GTCgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from Pairagon GTGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCA-------------------- aagaatcatgaacagggatccagaagtatctctctctctctctctccaagGCAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGGTCgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from Exonerate_protein2genome GTGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGGAAG aagaatcatgaacagggatccagaagtatctctctctctctctctccaagGCAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGGTCgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from Exonerate_coding2genome GTGGCGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGGAAG aagaatcatgaacagggatccagaagtatctctctctctctctctccaagGCAGTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGGTCgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag Alignment from GeneWise CGGCCTGATCATCAAGATCCTGAAGCGCACAGCAGTGTTTGTGGAAGGGACGGGTGAGGTGGGCCCACCGCTAGCACAGACCACAAAACTCAGTGTGCCCCGAAAGACCCGGCTGTATGTGGATCAGACCCTGCGGGAGCGGG aagaatcatgaacagggatccagaagtatctctctctctctctctccaaggcagTGGCCTGATCACCAAGCTCCTGAAGCGAACAGCTGTGTTCACAGAAGGTACAGGTGAAGTGGGCCCACTGCTAGCACAGACTACAAAGCTCAGTGTTCCTCGAAAAGGCCGGCTATATGTGGATCAAGCATTATGGGAGAGGGgtcgtatgtaatcaatgttaaaagcacggtttaaaatataggttactctcaag #### Best1_ID2631_8 --> 0 - 2 Original Alignment GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCag cctttgatcaaatcatttaaccatttattattttgactgttgattcctag------TTGTCATTTGTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCA---GCTCATCCT------ACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCaggtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg Alignment from CESAR GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCag cctctgcctttgatcaaatcatttatattattttgactgttgattcctagTTGTCATTT------GTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCAGCT---CATCCT------ACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCaggtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg Alignment from Spaln_aa2Genome GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctttgatcaaatcatttaaccatttattattttgactgttgattcctagTTGTCATTT------GTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCAGCTCATCCT---------ACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCAGgtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg Alignment from Spaln_nt2Genome CCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctttgatcaaatcatttaaccatttattattttgactgttgattcctag-TTGTCATTTGTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCAG---CTCATCC------TACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCAGgtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg Alignment from Pairagon GTGTCCCTGTTGTC---CGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctttgatcaaatcatttaaccatttattattttgactgttgattcctag---------TTGTCATTTGTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCAGCTCATC---------CTACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCAGgtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg Alignment from Exonerate_protein2genome CTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctttgatcaaatcatttaaccatttattattttgactgttgattcctagTTGTCATTTGTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCAGCT---CATCCT------ACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCAGgtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctttgatcaaatcatttaaccatttattattttgactgttgattcctagTTGTCATTT------GTTGACCGAATGTACCAGAACCTGCCACCCATGGAGCGTGAAATGTACTGGAATGAATCAGCT---CATCCT------ACAGCTGCCTCAGCCAAATCCCGATGGCGCTCATTCATGGGAACAACCTTTAACCCCAGgtaaggtatcccgcaatgcatccaggagaacatttcatatgctcaaactg #### Best1_ID2637_2 --> 1 - 1 Original Alignment aATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGg aagcttagagagtgtagcttgtgcgagtcctactctggctctccctgcaga---------------GACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAggtgggggcttgattcttcatacaatgtctacctgacttccatacatacat Alignment from CESAR aATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGg tcacagtgcaagtaaaagcttagagagtcctactctggctctccctgcaga---------------GACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAggtgggggcttgattcttcatacaatgtctacctgacttccatacatacat Alignment from Spaln_aa2Genome AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGG aagcttagagagtgtagcttgtgcgagtcctactctggctctccctgcagA---------------GACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAGgtgggggcttgattcttcatacaatgtctacctgacttccatacatacat Alignment from Spaln_nt2Genome TGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGG aagcttagagagtgtagcttgtgcgagtcctactctggctctccctgcagAGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAGgtgggggcttgattcttcatacaatgtctacctgacttccatacatacat Alignment from Pairagon AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGG aagcttagagagtgtagcttgtgcgagtcctactctggctctccctgcagA---------------GACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAGgtgggggcttgattcttcatacaatgtctacctgacttccatacatacat Alignment from Exonerate_protein2genome AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGG aagcttagagagtgtagcttgtgcgagtcctactcTGGCTCTCCCTGCAGAGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAGgtgggggcttgattcttcatacaatgtctacctgacttccatacatacat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGG aagcttagagagtgtagcttgtgcgagtcctactctggctctccctgcagA---------------GACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAACTCATCCCAATAGCATTTGTCCTAGgtgggggcttgattcttcatacaatgtctacctgacttccatacatacat #### Bscl2_ID2422_5 --> 0 - 0 Original Alignment GTGATGCTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAA---------------GTAGAACTCTACTCTGACTATAGGGAGAATTCG tcacgacacccttctgcacctaaagttgtctctccattcctcccacacag------CTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTAT---GACAACTCAgcaagtgggcaagttgtaatatatttctcaatgggccagaattgcatctg Alignment from CESAR GTGATGCTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAA---------------GTAGAACTCTACTCTGACTATAGGGAGAATTCG cagtgatcacgacacccttctgcacttgtctctccattcctcccacacag------CTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTAT---GACAACTCAgcaagtgggcaagttgtaatatatttctcaatgggccagaattgcatatc Alignment from Spaln_aa2Genome GTGATGCTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAA---------------GTAGAACTCTACTCTGACTATAGGGAGAATTCG tcacgacacccttctgcacctaaagttgtctctccattcctcccacacag------CTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTAT---GACAACTCAgcaagtgggcaagttgtaatatatttctcaatgggccagaattgcatctg Alignment from Spaln_nt2Genome GCTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAAG---------------TAGAACTCTACTCTGACTATAGGGAGAATTCG tcacgacacccttctgcacctaaagttgtctctccattcctcccacacag-CTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTAT---GACAACTCAgcaagtgggcaagttgtaatatatttctcaatgggccagaattgcatctg Alignment from Pairagon T------------------------------------------------GCTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAAG---------------TAGAACTCTACTCTGACTATAGGGAGAATTCG TCACGACACCCTTCTGCACCTAAAGTTGTCTCTCCATTCCTCCCACACAGCTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTAT---GACAACTCAgcaagtgggcaagttgtaatatatttctcaatgggccagaattgcatctg Alignment from Exonerate_protein2genome CTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAAGTAGAACTCTACTCTGACTATAGGGAGAATTCGTATGTGCCAACAACTG tcacgacacccttctgcacctaaagttgtctctccattcctcccacacagCTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTATGACAACTCAGCAAgtgggcaagttgtaatatatttctcaatgggccagaattgcatctg Alignment from Exonerate_coding2genome CTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAAGTAGAACTCTACTCTGACTATAGGGAGAATTCGTATGTGCCAACAACTG tcacgacacccttctgcacctaaagttgtctctccattcctcccacacagCTGCAATATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTATGACAACTCAGCAAgtgggcaagttgtaatatatttctcaatgggccagaattgcatctg Alignment from GeneWise GTGATGCTGCATTACCGCTCGCAGCTGCTCCAGGTGCTCGACACGCTGCTGTTCTCCAGCCTCCTGCTGTTTGGCTTCGCTGAACAGAAGCAGCTCCTGGAA---------------GTAGAACTCTACTCTGACTATAGGGAGAATTCG--------- tcacgacacccttctgcacctaaagttgtctctccattcctcccacacagCTGCAA------TATTGCTTACAATTGCTTCAAGTTCTTGACAAAGTGCTATTCTCCAGCCTCTTGCTCTTCGGCTTTGCAAATCAAAAGCAGCTATTGGAAGGCATGAGACCACCATTAGAAATCTATAGTGACTATGACAACTCAGCAAGTGGGCAAgttgtaatatatttctcaatgggccagaattgcatctg #### Bscl2_ID2423_6 --> 0 - 2 Original Alignment TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTC---ag tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCaggtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from CESAR TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTC---ag tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCaggtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from Spaln_aa2Genome TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCAGG-- tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCAGgtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from Spaln_nt2Genome TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTC---AG tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCAGgtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from Pairagon TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCT---CAG tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCAGgtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from Exonerate_protein2genome TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTC---AG tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCAGgtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from Exonerate_coding2genome TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTC---AG tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCAGgtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt Alignment from GeneWise TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCAGG-- tatatttctcaatgggccagaattgcatatcttttgcttttttcttctagTATGTTCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGGGCCTACCTCTGGATCCATGCCCACTTCACAGGGCTCTCCAGgtaagcaaagtgtagaagggacaactgttctacaatatggcccaaatagt #### Bscl2_ID2424_7 --> 1 - 0 Original Alignment g---TACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcaggAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from CESAR g---TACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcaggAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from Spaln_aa2Genome GTACCTGCTGTACAACTTC---CCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcagGAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from Spaln_nt2Genome GTACCTGCTGTACA---ACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcagGAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from Pairagon ---GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcagGAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from Exonerate_protein2genome G---TACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcagGAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from Exonerate_coding2genome G---TACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcagGAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGgtaagtgttcttgagccattttctcccaccagacaaacgaacctatactg Alignment from GeneWise -AGGTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAGGTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGAT ccaacttaactctagcagccatatatttttcatctgtgcttcctctgcagGAAGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTACTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGGTAAGTGTTCTTGAGCCA------------TTTTCTCCCACCAGACAAAC #### Bscl2_ID2425_8 --> 0 - 1 Original Alignment GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAg gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtag---------TGTCAAAGGGACAACTCACAG------------GACCATATTTCACACCACCAACCAggtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from CESAR GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAg ccagtagaggatcacaactcattggctcctgttttcttcttacaccgtag---------TGTCAAAGGGACAACTCACAGGAC------------CATATTTCACACCACCAACCAggtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from Spaln_aa2Genome CGTCGGATCTCGCGCCATCAGCCAG gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtagtgtcaaagggacaactcacagGACCATATTTCACACCACCAACCAGgtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from Spaln_nt2Genome GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAG gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtag---------TGTCAAAGGGACAACTCACAGGAC------------CATATTTCACACCACCAACCAGgtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from Pairagon gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtagtgtcaaagggacaactcacaggaccatatttcacaccaccaaccaggtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from Exonerate_protein2genome gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtagtgtcaaagggacaactcacaggaccatatttcacaccaccaaccaggtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from Exonerate_coding2genome gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtagtgtcaaagggacaactcacaggaccatatttcacaccaccaaccaggtaccagaattaggcattaggaacttggaaatagaccagggattcctcca Alignment from GeneWise gatcacaactcattggttgcatgttctcctgttttcttcttacaccgtagtgtcaaagggacaactcacaggaccatatttcacaccaccaaccaggtaccagaattaggcattaggaacttggaaatagaccagggattcctcca #### Bscl2_ID2426_9 --> 2 - 1 Original Alignment gtCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCAGGAACAg agtgttaggtcctcatgttgggggtaaatctccctcgcctcctctcttaggtCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTCAAGA---ggtaagtgggtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from CESAR gtCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCAGGAACAg agtgttaggtcctcatgttgggggtaaatctccctcgcctcctctcttaggtCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTCAAGA---ggtaagtgggtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from Spaln_aa2Genome GTCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCAGGAACAGAGGGC agtgttaggtcctcatgttgggggtaaatctccctcgcctcctctcttagGTCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTCAAGAGGTAAGTGGgtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from Spaln_nt2Genome GTCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCAGGAACAG agtgttaggtcctcatgttgggggtaaatctccctcgcctcctctcttagGTCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTC---AAGAGgtaagtgggtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from Pairagon GTCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCAGGAACAGAGGGCCAGCTGTCTGAGGAAGAG agtgttaggtcctcatgttgggggtaaatctccctcgcctcctctcttagGTCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTC--------------------------AAGAGgtaagtgggtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from Exonerate_protein2genome GGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAGGTCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCA AGTGTTAGGTCCTCATGTTGGGGGTAAATCTCCCTCGCCTCCTCTCTTAGGTCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTCAagaggtaagtgggtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from Exonerate_coding2genome GGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAGGTCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCA AGTGTTAGGTCCTCATGTTGGGGGTAAATCTCCCTCGCCTCCTCTCTTAGGTCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTCAagaggtaagtgggtcagtctccctaagatctttattgagatagatcttcaggtc Alignment from GeneWise GGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAGGTCAGGAATCTACCCAGCAGTCGGATGTGACGGAGGATGGTGAGAGCCCTGAAGATCCCTCAGGAACAGAGGGC TGTTGGGGGTAAATCTCCCTCGCCTCCTCTCTTA---------------GGTCAGAAATCCACCCAGCAGTCAGATGTTATGGAAGATGGTGAGAGCCCTGAAGATCCTTCAAGAGGTAAGTGGgtcagtctccctaagatctttattgagatagatcttcaggtc #### Btaf1_ID7248_27 --> 0 - 2 Original Alignment GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGag gGCCCAGGAATATGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCA---------------aggtatgggccttgctttaatttgtttcttccttaggGCCCAGGAATATGCA Alignment from CESAR GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGag gGCCCAGGAATATGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCA---------------aggtatgggccttggcttcacgctcttcattcacaggGCCCAGGAATATGCA Alignment from Spaln_aa2Genome GGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAG GAGATCACTGTCAGAGG acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAAGgtatgggccttgctttaatttgtttcttccttagG--------------- Alignment from Spaln_nt2Genome GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGAG GGCCCAGGAATATGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCA---------------AGgtatgggccttgctttaatttgtttcttccttagGGCCCAGGAATATGCA Alignment from Pairagon GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGAG GGCCCAGGAATATGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCA---------------AGgtatgggccttgctttaatttgtttcttccttagGGCCCAGGAATATGCA Alignment from Exonerate_protein2genome GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAaggtatgggccttgctttaatttgtttcttccttagggcccaggaatatgca Alignment from Exonerate_coding2genome GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAaggtatgggccttgctttaatttgtttcttccttagggcccaggaatatgca Alignment from GeneWise GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTA-GCAGGAGATCACTGTCAG------------------AGGGCCCAGGAATATGCA acattcgtctcaatttcattgccttcccttgttttgttttccttaattagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGATATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAAGGTATGGGCCTTGCTTTAATTTGTTTCTTCCTTAGGGCCCAGGAATATGCA #### Btaf1_ID7249_28 --> 1 - 2 Original Alignment GAGATCACTGTCAGag gGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATA---ag GAGATCACTGTCAGaggtaagtgccttggcttcacgctcttcattcacaggGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCaggttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from CESAR GAGATCACTGTCAGag gGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATA---ag GAGATCACTGTCAGaggtaatcgccttggcttcacgctcttcattcacaggGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCaggttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from Spaln_aa2Genome GAGATCACTGTCAGA GGGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATAAGG- GAGATCACTGTCAGAGgtaagtgccttggcttcacgctcttcattcacagGGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCAGgttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from Spaln_nt2Genome GAGATCACTG----------------------------------TCAGAGGGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATA---AG GAGATCACTGTCAGAGGTAAGTGCCTTGGCTTCACGCTCTTCATTCACAGGGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCAGgttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from Pairagon GAGATCACTGTCAGAG GGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATA---AG GAGATCACTGTCAGAGgtaagtgccttggcttcacgctcttcattcacagGGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCAGgttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from Exonerate_protein2genome GAGATCACTGTCAGAG GGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATA---AG GAGATCACTGTCAGAGgtaagtgccttggcttcacgctcttcattcacagGGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCAGgttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from Exonerate_coding2genome GAGATCACTGTCAGAG GGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATA---AG GAGATCACTGTCAGAGgtaagtgccttggcttcacgctcttcattcacagGGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCAGgttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg Alignment from GeneWise GAGATCACTGTCAGAG GGCCCAGGAATATGCAAGATCGAAATTGGCAGAATGTATGCCACTTCCTTCCTTGGTGGTTTGTCCACCAACATTAACAGGTCATTGGGTAGATGAAGTAGGTAAATTTTGTTCCAGAGAATATCTCAATCCGTTGCATTATACTGGCCCTCCCACTGAAAGGATAAGG-- GAGATCACTGTCAGAGgtaagtgccttggcttcacgctcttcattcacagGGCCCAGGAATATGCAAGATCAAGATTAGTAGAGTGTATGTCACTCCCTTCCCTAGTGGTTTGTCCTCCATCATTGACAGGTCACTGGGTAGACGAAGTAGGGAAATTTTGTTCTAGAGAATATCTGAATCCACTTCATTATACCGGCCCTTCTACTGAAAGGATACGCAGgttaaagggtggattatctaacaatccgtagctaaagacaaggtcctttg #### Btaf1_ID7254_33 --> 0 - 0 Original Alignment ------GTTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAGgtaaagatgagatttactttcaccattattgtaacactaatgtctagtgc Alignment from CESAR ------GTTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAGgtaaagatgagatttactttcaccattattgtaacactaatgtctagtgc Alignment from Spaln_aa2Genome GGTTCAGCTTTAT------GAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCA cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAGgtaaagatgagatttactttcaccattattgtaacactaatgtctagtgc Alignment from Spaln_nt2Genome G------TTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAGgtaaagatgagatttactttcaccattattgtaacactaatgtctagtgc Alignment from Pairagon ------GTTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAGgtaaagatgagatttactttcaccattattgtaacactaatgtctagtgc Alignment from Exonerate_protein2genome ------GTTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAGGCG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAG---gtaaagatgagatttactttcaccattattgtaacactaatgtctag Alignment from Exonerate_coding2genome ------GTTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAGGCG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAG---gtaaagatgagatttactttcaccattattgtaacactaatgtctag Alignment from GeneWise ------GTTCAGCTTTATGAAGATTTTGCTAAGTCGCGTGCCAAGTGTGATGTTGATGAGACCGTGTCTTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTTAAAGCGACAGGTCATGTATTCCAG cctagttcctgtccatttaaagtttgcataaaaaatttttttcttattagGGAAGTGTACAGCTTTATGAAGATTTTGCTAAGTCTCGTGCCAAGTGTGATGTTGATGAGACTGTGTCCTCAGCTGCACTTTCAGAAGAAACTGAAAAACCAAAACTCAAAGCCACAGGGCATGTTTTCCAGgtaaagatgagatttactttcaccattattgtaacactaatgtctagtgc #### Btaf1_ID7258_37 --> 0 - 0 Original Alignment AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG aggccccttgagtctgacaagaccatggtgtctccaccttcttctggcag---CGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from CESAR AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG gttaggccccttgagtctgacaagatggtgtctccaccttcttctggcag---CGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from Spaln_aa2Genome GAAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAA aggccccttgagtctgacaagaccatggtgtctccaccttcttctggcag---CGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from Spaln_nt2Genome AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG aggccccttgagtctgacaagaccatggtgtctccaccttcttctggcag---CGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from Pairagon AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG aggccccttgagtctgacaagaccatggtgtctccaccttcttctggcag---CGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from Exonerate_protein2genome AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG aggccccttgagtctgacaagaccatggtgtctccaccttcttctggCAGCGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from Exonerate_coding2genome AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG aggccccttgagtctgacaagaccatggtgtctccaccttcttctggCAGCGTGTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc Alignment from GeneWise AAACGTGTGGTTAATGTCTACCGGTTGATAACCAGAGGAACACTAGAAGAAAAGATAATGGGCTTGCAGAAATTCAAGATGAACATCGCAAATACTGTTATTAGCCAAGAAAACTCTAGCTTACAGAGTATGGGCACTGATCAACTTCTTGACCTGTTCACTCTAGATAAG aggccccttgagtctgacaagaccatggtgtctccaccttcttctggcagCGT---GTAGTCAATGTCTACCGATTGATAACTCGAGGAACACTAGAAGACAAGATAATGGGTTTGCAGAAGTTCAAGATGAACATTGCAAATACTGTTATTAGCCAAGAGAACTCTAGCTTACAGAGCATGGGCACTGATCAACTCCTTGACCTGTTTACCCTGGATAAGgtaagtatataatgagtgatactaccacacattaacttactgcaatgatc #### Btrc_ID9463_12 --> 1 - 2 Original Alignment gCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGAT------------------gg gcctagttattgagaagcaacctactttctctgtctcctggcttctacaggCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACATTCGTGTGGGCTGGgggtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from CESAR gCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGAT------------------gg gcctagttattgagaagcaacctactttctctgtctcctggcttctacaggCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACATTCGTGTGGGCTGGgggtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from Spaln_aa2Genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGGG----------------- gcctagttattgagaagcaacctactttctctgtctcctggcttctacagGCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACATTCGTGTGGGCTGGGGgtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from Spaln_nt2Genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGAT-------GG gcctagttattgagaagcaacctactttctctgtctcctggcttctacagGCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACATTCGTgtgggctgggggtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from Pairagon GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGAT------------------GG gcctagttattgagaagcaacctactttctctgtctcctggcttctacagGCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACATTCGTGTGGGCTGGGGgtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from Exonerate_protein2genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGGG gcctagttattgagaagcaacctactttctctgtctcctggcttctacagGCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACattcgtgtgggctgggggtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from Exonerate_coding2genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGGG gcctagttattgagaagcaacctactttctctgtctcctggcttctacagGCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACattcgtgtgggctgggggtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca Alignment from GeneWise GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGAT------------------GG gcctagttattgagaagcaacctactttctctgtctcctggcttctacagGCTCTGGGACATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCAAGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATCACATTCGTGTGGGCTGGGGgtgagtttgctggtaatatcttatgggcagagaaagaggttgaagacaca #### Cabp2_ID287_2 --> 0 - 0 Original Alignment ---------GAACGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTC gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagGGCAGGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAGCT------CAGCTTgtaattacattggccttatccacgattcatgttggactggcactggacat Alignment from CESAR GAA---------CGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTC gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagGGCAGGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAGCT------CAGCTTgtaattacattggccttatccacgattcatgttggactggcactggacat Alignment from Spaln_aa2Genome GAA---------CGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTCGATCGAGAGCTGAGACCAGAAGAGATCGAAGAG gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagGGCAGGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAGCTCAGCTTGTAATTACATTGGCCTTATCCACGATTCATGTTGGACTGgcactggacat Alignment from Spaln_nt2Genome GAACG----CTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTC gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagggcagGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAG------CTCAGCTTgtaattacattggccttatccacgattcatgttggactggcactggacat Alignment from Pairagon ---------GAACGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTC gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagGGCAGGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAG------CTCAGCTTgtaattacattggccttatccacgattcatgttggactggcactggacat Alignment from Exonerate_protein2genome TAAGGAACGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTCGATCGAGAGCTGAGACCAGAAGAGATCG gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagggcagGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAGCTCAGCTTGTAATTACATTGGCCTTATCCACGATTCATGTTGgactggcactggacat Alignment from Exonerate_coding2genome TAAGGAACGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTCGATCGAGAGCTGAGACCAGAAGAGATCG gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagggcagGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAGCTCAGCTTGTAATTACATTGGCCTTATCCACGATTCATGTTGgactggcactggacat Alignment from GeneWise ---------GAACGCTGGCAGTGGCCTGGATCCCCCCTAGGGGGCTCCCGCCCCAGCCCTGGTCCCAGAACTGAGGAGCAGGAGGGGACACAGGGCTACTCAGTGCTCGGCAGCCTGGTGGGGCCAGCATGCATCTTCCTTCGACCCAGCATCGCGGCTACCCAGCTCGATCGAGAGCTGAGACCAGAAGAGATCGAAGAG gccatattgacacctatatgtggaggtgcttgctgtaatttttatatcagGGCAGGCTCGTCCGCTGGCAATGGCCTGGATCTCCATTAGGAGGCTCACTTCCCAGCCCAGGTCCAAGAACTGAGGAGCAGGAAGGTTCACAGGGCTACTCAGTCCTTAGTAGTATTGTAGGTCCCACATGTATATTCCTACGACCTACTATAGCT------CAGCTTGTAATTACATTGGCCTTATCCACGATT---CATgttggactggcactgga #### Cabp2_ID289_4 --> 2 - 1 Original Alignment agCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCa ccttataacagctatggtgctctcatcccccctcctgtacctttccccagag---------GGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTagtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from CESAR agCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCa tgttaacccccttataacagctatgtcccccctcctgtacctttccccagag---------GGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTagtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from Spaln_aa2Genome TCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctatggtgctctcatcccccctcctgtacctttccccagAGGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from Spaln_nt2Genome --GCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAG ccttataacagctatggtgctctcatcccccctcctgtacctttccccagAGGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGgttagtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from Pairagon CGCGGCTACCCAGCTCGATCGAGAGCTGAGACCAGAAGAGATCGAAGAGCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctatggtgctctcatcccccctcctgtacctttccccagag----------------------------------------------------------GGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from Exonerate_protein2genome ATCGAAGAGCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctatggtgctctcatcccccctcCTGTACCTTTCCCCAGAGGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from Exonerate_coding2genome ATCGAAGAGCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctatggtgctctcatcccccctcCTGTACCTTTCCCCAGAGGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc Alignment from GeneWise GAGCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctatggtgctctcatcccccctcctgtacctttccccagagGGC------------TTCCAGGAGTTTGACCGAGACAGGGACGGCTACATTGGGTACCGGGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaagggtgacttttgtggtcagtgcatgtagccccctggcacatggtgc #### Cabp2_ID291_6 --> 0 - 1 Original Alignment TTCGACACCAACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAAg gtagacaccatgactaaacactttttttgccttcctttgtccctgaatag---------AATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAggtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from CESAR TTCGACACCAACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAAg gactgaactgtagacaccatgactatttgccttcctttgtccctgaatag---------AATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAggtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from Spaln_aa2Genome AACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAAG gtagacaccatgactaaacactttttttgccttcctttgtccctgaatagAATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAGgtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from Spaln_nt2Genome AACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAAG gtagacaccatgactaaacactttttttgccttcctttgtccctgaatagAATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAGgtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from Pairagon TTCGACACCAACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAAG gtagacaccatgactaaacactttttttgccttcctttgtccctgaatag---------AATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAGgtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from Exonerate_protein2genome TTCGACACCAACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAAG gtagacaccatgactaaacactttttttgccttcctttgtcCCTGAATAGAATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAGgtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from Exonerate_coding2genome TTCGACACCAACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAA gtagacaccatgactaaacactttttttgccttcctttgtcCCTGAATAGAATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAggtaagtctctacctgctctgtccctttaccttgtaagccttctcacacac Alignment from GeneWise AACGGTGATGGCTGCATCAGCGTAGGGGAGCTCCGGGCAGCCCTCAAAGCTCTGCTGGGGGAACGCCTCAGCCAACGGGAAGTAGATGAGATACTCCAAGACATTGACCTCAATGGAGATGGCCTGGTTGACTTTGAA---GAATTTGTTCGGATGATGTCTCGG gtagacaccatgactaaacactttttttgccttcctttgtccctgaatagAATGGTGATGGCTGCATCAGTGTTGGAGAACTCCAAGCCGCACTTAAAGCCCTGCTGGGTGTACATCTCAGTCAACAAGAAGTAGATGAAATACTCCAAGACATTGACCTAAATGGGGATGGCCTGGTTGACTTTGAAGGTAAGTCTCTACCTGCTCTGTCCCTTtaccttgtaagccttctcacacac #### Capn1_ID1356_20 --> 2 - 0 Original Alignment ggTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTTAAG gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagggTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTT---gtaagtaggatataagaatgaattctaacccatctgatcattaagatgta Alignment from CESAR ggTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTTAAG gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagggTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTT---gtaagtaggatataagaatgaattctaacccatctgatcattaagat Alignment from Spaln_aa2Genome GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTT gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagGGTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTTgtaagtaggatataagaatgaattctaacccatctgatcattaagatgta Alignment from Spaln_nt2Genome GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTT gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagGGTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTTgtaagtaggatataagaatgaattctaacccatctgatcattaagatgta Alignment from Pairagon GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTT gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagGGTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTTgtaagtaggatataagaatgaattctaacccatctgatcattaagatgta Alignment from Exonerate_protein2genome GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTT gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagGGTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTTgtaagtaggatataagaatgaattctaacccatctgatcattaagatgta Alignment from Exonerate_coding2genome GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTT gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagGGTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTTgtaagtaggatataagaatgaattctaacccatctgatcattaagatgta Alignment from GeneWise GGTTTTTCAAACTTCTGGACACAGACCTGGATGGTGTTGTGACCTTTGATCTATTT gcaaggagaaccaggggaagccagccagatgttcggtgttttgtacatagGGTTTTCCAAACTACTAGACCGAGGCCTGGATGGTGTTGTTACCTTTGATCTTTTTgtaagtaggatataagaatgaattctaacccatctgatcattaagatgta #### Capn1_ID1363_13 --> 1 - 0 Original Alignment g------GAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctaggCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from CESAR g------GAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctaggCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from Spaln_aa2Genome GGAACTAGATGAC------CAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctagGCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from Spaln_nt2Genome GGAACTAGAT------GACCAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctagGCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from Pairagon ---------------------------------------------------------GAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG CTTCCATATGCGGGTTTGAACCCCTTTAACATGTTTTATTTTTATCCTAGGCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from Exonerate_protein2genome G------GAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctagGCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from Exonerate_coding2genome G------GAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctagGCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc Alignment from GeneWise ----CAGGAACTAGATGACCAGATCCAGGCCAACCTCCCTGATGAG cttccatatgcgggtttgaacccctttaacatgttttatttttatcctagGCTCTTCGAACTAGATGACCAGATTCAGGTTAACCTCCCTGATGAAgtgggctcccatgtgactctggtagcctctcagttttcattccaactagc #### Carns1_ID388_4 --> 2 - 0 Original Alignment gaAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAG--------------------- tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccaggaAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGGGGCCGTTTTTCACTGATGCTGgtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from CESAR gaAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAG tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccaggaAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGGggccgtttttcactgatgctggtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from Spaln_aa2Genome AACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAGGTGGCTG tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccagGAAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGG---GGCCgtttttcactgatgctggtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from Spaln_nt2Genome GAAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAG- tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccagGAAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGGGgccgtttttcactgatgctggtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from Pairagon GAAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCA---------------------CAG tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccagGAAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGGGGCCGTTTTTCACTGATGCTGgtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from Exonerate_protein2genome GAAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAG tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccagGAAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGGggccgtttttcactgatgctggtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from Exonerate_coding2genome GAAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAG tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccagGAAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGGggccgtttttcactgatgctggtacagatacatctctgcatactctgaatatgttcctagttgtgtattct Alignment from GeneWise GAAACATGCTCCTTTGCCTGTCCCCTGCTTGGCTGATGAAGGTGGCAACTCCAGGCCAAGAGGGTGAGGCAGTCCTGCTGGTCTCTAAGGCTGTGAGCTTCTATCCAGGGGGCCTGACATTCCTGGATGACTTTGTTCCCCCTCGGCATGCTACTTACTTCCTGGCAGGCCTGGGGCCAGAATCTGGCCGTGGCAAGGAGGCAGCAGAGCTGGCTCGGAATCTCACTTGCCCCACAGGAACCTCATCGGAGCTGTCCCAGCTGCTGGAGAACCGGCTGCTGATGAGGTGGTTGCTGTCCCAGCAGAGTGGTGTGGCCGTGCCAGCTACCCTGGCTTTCACTTATAGGCCTCCGGGGCTGCTTCGGGGAGGGGATGCCAGCCCTGGACTCCGGCTGGTGGAACTCAGTGGGAAGGAGGGCCAGGAAACACTGGTGAAAGAGGAAGTAGAGGCCTTTGTGCACTCCGAGGCCTTGGGTGATGCTTCACAGGTGGCTG tacgtagtcaatttcattgccttgcctgaactggtcatctttattaccagGAAATATGCTCCTCTGCCTGTCC---GCCTGGTTAATGAAAGTGGCAACACCAAGGCAGGAGGGTGAGGCGGTTTTACTGGTTTCTCAAGTTGTGAGTTTCTATCCAGGTGGTTTGACGTTTCTGGATGACTTTGTTCCACCTCGGCATGCTACTTACTTCCTGGCAGGTCTGGGGCCAGAATCTGGGCGTGGCAAGGAGGCAGCAGAGCTGGCCCGAAATCTTACTTGCCCTACAGGAACTTCATCAGAGCTGTCCCAGCTGCTAGAGAACCGGCTGCTCATGCGGTGGCTACTTTCCCAGCAGAGCAGTGTGGCTGTGCCTGCTACCCTAGCTTTCACTTATAGGCCTCCAGGACTGCTTCGGGGTGGGGATCCCAGCCCAGGACTCCGGCTGGTGGAGCTTAGTGGGAAGGAGGGCCAGGAAACACTTGTTAAAGAGGAAGTAGAGGCCTTTGTACATTCAGAGGCCTTGGGTGATGCCTCAAGG---GGCCgtttttcactgatgctggtacagatacatctctgcatactctgaatatgttcctagttgtgtattct #### Catsper1_ID926_3 --> 2 - 1 Original Alignment aaTGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---g gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagaaTGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAGTC---AAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCggtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from CESAR aaTGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---g gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagaaTGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAGTC---AAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCggtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from Spaln_aa2Genome AATGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---G gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagAATGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAGTC---AAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCGgtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from Spaln_nt2Genome AATGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---G gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagAATGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAG---TCAAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCGgtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from Pairagon AATGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---G gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagAATGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAG---TCAAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCGgtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from Exonerate_protein2genome AATGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---G gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagAATGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAGTC---AAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCGgtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from Exonerate_coding2genome AATGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTG---G gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagAATGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAGTC---AAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCGgtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg Alignment from GeneWise AATGGTACTTCATGGTCTTGGACTCCATCTTCCTCTCCATCTATGTACTAGAAGCAGTCCTCAAGCTAATTGCCCTGGGCCTGGAGTATTTTTATGACCCATGGAACAACCTGGAC- gtgagcagtgtagtcccagcctgtcccaaactctgttctgtgtctcacagAATGGTATTTCATGATCCTAGACTCCATCTTCCTCACCATCTTTGTACTAGAGGCAGTC---AAACTTATTGCTTTGGGCTTAGAGTATTTCTATGACCCGTCAAATAATCTGATCGgtaagtcaatacagctagtccataatgaagcgtttcgctggttcataatg #### Catsper1_ID928_5 --> 1 - 1 Original Alignment c------ATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCt ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagtCTAAAGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACtgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from CESAR c------ATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCt ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagtCTAAAGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACtgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from Spaln_aa2Genome GCTCAGCATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagTCTAAAGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from Spaln_nt2Genome CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagtctaaag-ATTTTGACTAGAGTCCAGGAAGTAGCTG---CCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from Pairagon CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagtctaaag-ATTTTGACTAGAGTCCAGGAAGTAGCTG---CCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from Exonerate_protein2genome CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagtctaaaGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from Exonerate_coding2genome CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagtctaaaGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta Alignment from GeneWise ----AGCATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatctgcttcaatgatgacttaactttctgttcctggtggcattcccagTCTAAAGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGGTCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtatgatgcacaatggaagttggatacaattattctaaatatgttaggta #### Catsper1_ID929_6 --> 2 - 1 Original Alignment tcCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAg gcGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagtcCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAAC---------ggtttgtaccgtttgtatgctaagccattgtgtctcctgtccactagctGC Alignment from CESAR tcCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAg gcGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagtcCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAACGGTTTGTACcgtttgtatgctaggttgtcgcttccttgtcttgacagctGC Alignment from Spaln_aa2Genome TCCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAG GCGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagTCCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAACGGTTTGTACCgtttgtatgctaagccattgtgtctcctgtccactagCTGC Alignment from Spaln_nt2Genome TCCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAG GCGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagTCCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAACGGTTTGTACCgtttgtatgctaagccattgtgtctcctgtccactagCTGC Alignment from Pairagon TCCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAGG----------------------------------------------CGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagTCCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAAC---------GGTTTGTACCGTTTGTATGCTAAGCCATTGTGTCTCCTGTCCACTAGCTGC Alignment from Exonerate_protein2genome TCCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAG GCGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagTCCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAACGGTTTGTACCgtttgtatgctaagccattgtgtctcctgtccactagCTGC Alignment from Exonerate_coding2genome TCCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAG GCGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagTCCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAACGGTTTGTACCgtttgtatgctaagccattgtgtctcctgtccactagCTGC Alignment from GeneWise TCCTCTTCTCTGTGGTTCTCCGAGCACTGTTTCAGGACTCAGACCCCAAGCGCTTCCAGAACATCTTTACCACACTCTTCACCCTGTTCACCATGCTCACCCTGGACGACTGGTCCCTCATCTACATAGACAACAGGGCCCAAG GCGC ttggactttccctttgctatgtcagatgtctgttctctcttgacccacagTCCTCTTCTCTGTGACTCTCCAAGCACTCTTCCAGGATCCAGATCCCAAGCGTTTCCAGAATGTCTTTATAACACTCTTCACCCTTTTCATGATGCTTAGCCTGGACGACTGGTCCCTTATCTACATAGAGAACGGTTTGTACCgtttgtatgctaagccattgtgtctcctgtccactagCTGC #### Ccdc88b_ID1824_25 --> 2 - 1 Original Alignment ggTCCTCGTCACCAGCACCCATGCGCCGCGTCCAGAGCTCTCTCTGCTTGGGAGATGAGACCCTGGCAGGTGGGCAGCGGCGGAGACTCAGTTCCCGGTTCCCTGGGGGGCGAAGCTCTGCGTCATTTAGTCCAGGGGACACCCCAAGGCAACGGTTCAGACAGCGAAGACCCGGCCCCCTGGGGGCACCCAGTACCCACAGCAAAg catggtgacttccctgatccatacaagattgtttttcttctgtgttccaggg---TCGTCACCAGCGCCCATGCACCAAATAGAGAGCTCCCTTTGCTTGGGAGACGAGACCCTAGCTGGTGGGCAGCGACGGAGTCTAAGTTCTCAGTTCTCTATTGGACAAAGTCCCGCTTCATTCAGTCCCAGT---ACTTCACAGCAATGGTTCAAACAGCAGAGGCCAGGCCCCCTTGGGGCACTGAGTACCTACAGCAAAggtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt Alignment from CESAR ggTCCTCGTCACCAGCACCCATGCGCCGCGTCCAGAGCTCTCTCTGCTTGGGAGATGAGACCCTGGCAGGTGGGCAGCGGCGGAGACTCAGTTCCCGGTTCCCTGGGGGGCGAAGCTCTGCGTCATTTAGTCCAGGGGACACCCCAAGGCAACGGTTCAGACAGCGAAGACCCGGCCCCCTGGGGGCACCCAGTACCCACAGCAAAg catcatggtgacttccctgatccatagattgtttttcttctgtgttccaggg---TCGTCACCAGCGCCCATGCACCAAATAGAGAGCTCCCTTTGCTTGGGAGACGAGACCCTAGCTGGTGGGCAGCGACGGAGTCTAAGTTCTCAGTTCTCTATTGGACAAAGTCCCGCTTCATTCAGTCCCAGT---ACTTCACAGCAATGGTTCAAACAGCAGAGGCCAGGCCCCCTTGGGGCACTGAGTACCTACAGCAAAggtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt Alignment from Spaln_aa2Genome GGTCCTCGTCACCAGCACCCATGCGCCGCGTCCAGAGCTCTCTCTGCTTGGGAGATGAGACCCTGGCAGGTGGGCAGCGGCGGAGACTCAGTTCCCGGTTCCCTGGGGGGCGAAGCTCTGCGTCATTTAGTCCAGGGGACACCCCAAGGCAACGGTTCAGACAGCGAAGACCCGGCCCCCTGGGGGCACCCAGTACCCACAGCAAAG catggtgacttccctgatccatacaagattgtttttcttctgtgttccagGG---TCGTCACCAGCGCCCATGCACCAAATAGAGAGCTCCCTTTGCTTGGGAGACGAGACCCTAGCTGGTGGGCAGCGACGGAGTCTAAGTTCTCAGTTCTCTATTGGACAAAGTCCCGCTTCATTCAGTCCCAGT---ACTTCACAGCAATGGTTCAAACAGCAGAGGCCAGGCCCCCTTGGGGCACTGAGTACCTACAGCAAAGgtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt Alignment from Spaln_nt2Genome GGTCCTCGTCACCAGCACCCATGCGCCGCGTCCAGAGCTCTCTCTGCTTGGGAGATGAGACCCTGGCAGGTGGGCAGCGGCGGAGACTCAGTTCCCGGTTCCCTGGGGGGCGAAGCTCTGCGTCATTTAGTCCAGGGGACACCCCAAGGCAACGGTTCAGACAGCGAAGACCCGGCCCCCTGGGGGCACCCAGTACCCACAGCAAAG catggtgacttccctgatccatacaagattgtttttcttctgtgttccagGG---TCGTCACCAGCGCCCATGCACCAAATAGAGAGCTCCCTTTGCTTGGGAGACGAGACCCTAGCTGGTGGGCAGCGACGGAGTCTAAGTTCTCAGTTCTCTATTGGACAAAGTCCCGCTTCATTCAGTCCCAG---TACTTCACAGCAATGGTTCAAACAGCAGAGGCCAGGCCCCCTTGGGGCACTGAGTACCTACAGCAAAGgtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt Alignment from Pairagon GGTCCTCGTCACCAGCACCCATGCGCCGCGTCCAGAGCTCTCTCTGCTTGGGAGATGAGACCCTGGCAGGTGGGCAGCGGCGGAGACTCAGTTCCCGGTTCCCTGGGGGGCGAAGCTCTGCGTCATTTAGTC-----------CAGGGGACACCCCAAGGCAACGGTTCAGACAGCGAAGACCCGGCCCCCTGGGGGCACCCAGTACCCACAGCAAAG catggtgacttccctgatccatacaagattgtttttcttctgtgttccagGG---TCGTCACCAGCGCCCATGCACCAAATAGAGAGCTCCCTTTGCTTGGGAGACGAGACCCTAGCTGGTGGGCAGCGACGGAGTCTAAGTTCTCAGTTCTCTATTGGACAAAGTCCCGCTTCATTCAGTCCCAGTACTTCACA--------------GCAATGGTTCAAACAGCAGAGGCCAGGCCCCCTTGGGGCACTGAGTACCTACAGCAAAGgtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt Alignment from Exonerate_protein2genome catggtgacttccctgatccatacaagattgtttttcttctgtgttccagggtcgtcaccagcgcccatgcaccaaatagagagctccctttgcttgggagacgagaccctagctggtgggcagcgacggagtctaagttctcagttctctattggacaaagtcccgcttcattcagtcccagtacttcacagcaatggttcaaacagcagaggccaggcccccttggggcactgagtacctacagcaaaggtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GGTCCTCGTCACCAGCACCCATGCGCCGCGTCCAGAGCTCTCTCTGCTTGGGAGATGAGACCCTGGCAGGTGGGCAGCGGCGGAGACTCAGTTCCCGGTTCCCTGGGGGGCGAAGCTCTGCGTCATTTAGTCCAGGGGACACCCCAAGGCAACGGTTCAGACAGCGAAGACCCGGCCCCCTGGGGGCACCCAGTACCCACAGCAAAG catggtgacttccctgatccatacaagattgtttttcttctgtgttccagGGTCGTCA---CCAGCGCCCATGCACCAAATAGAGAGCTCCCTTTGCTTGGGAGACGAGACCCTAGCTGGTGGGCAGCGACGGAGTCTAAGTTCTCAGTTCTCTATTGGACAAAGTCCCGCTTCATTCAGTCCC---AGTACTTCACAGCAATGGTTCAAACAGCAGAGGCCAGGCCCCCTTGGGGCACTGAGTACCTACAGCAAAGgtcagcggtgtcttattataattgtaatttcaatcgaagtatgaagttgt #### Ccdc88b_ID1827_22 --> 0 - 2 Original Alignment CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTAC---ct cttcaatggataggttaactaataaattcaggttttatgtttgttttcagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGCACAAACAGGGAGTTGCAAGAGTGTAGTTTGGAGAGT---GACCCCGTGCATTGTGAGCAGCCAGAATACCTGctgtactgccaacttaaggtcagattgatgctaccttaaggtcagattgatg Alignment from CESAR CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTAC---ct cttcaatggataggttaactaataaattcaggttttatgtttgttttcagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGCACAAACAGGGAGTTGCAAGAGTGTAGTTTGGAGAGT---GACCCCGTGCATTGTGAGCAGCCAGAATACCTGctgtactgccaacttaaggtcagattgatgctaccttaaggtcagattgatg Alignment from Spaln_aa2Genome CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTACCT cttcaatggataggttaactaataaattcaggttttatgtttgttttcagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGCACAAACAGGGAGTTGCAAGAGTGTAGTTTGGAGAGT---GACCCCGTGCATTGTGAGCAGCCAGAATACCTgctgtactgccaacttaaggtcagattgatgctaccttaaggtcagattgatg Alignment from Spaln_nt2Genome CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTACCTG-- cttcaatggataggttaactaataaattcaggttttatgtttgttttcagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGCACAAACAGGGAGTTGCAAGAGTGTAGTTTGGAGA---GTGACCCCGTGCATTGTGAGCAGCCAGAATACCTGCTgtactgccaacttaaggtcagattgatgctaccttaaggtcagattgatg Alignment from Pairagon CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTACCT----------------------------------------------------- cttcaatggataggttaactaataaattcaggttttatgtttgttttcagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGCACAAACAGGGAGTTGCAAGAGTGTAGTTTGGAGA---GTGACCCCGTGCATTGTGAGCAGCCAGAATACCTGCTGTACTGCCAACTTAAGGTCAGATTGATGCTACCTTAAGGTCAGATTGATG Alignment from Exonerate_protein2genome cttcaatggataggttaactaataaattcaggttttatgtttgttttcagctcttaacacagcttcatacagtacaaaaagaggagaataggcagcttttagtagaggtgaaggcttcaagccgcacaaacagggagttgcaagagtgtagtttggagagtgaccccgtgcattgtgagcagccagaatacctgctgtactgccaacttaaggtcagattgatgctaccttaaggtcagattgatg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTACCTG-- cttcaatggataggttaactaataaattcaggttttatgtttgttttcagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGCACAAACAGGGAGTTGCAAGAGTGTAGTTTGGAGAGT---GACCCCGTGCATTGTGAGCAGCCAGAATACCTGCTgtactgccaacttaaggtcagattgatgctaccttaaggtcagattgatg #### Ccdc88b_ID1828_21 --> 1 - 0 Original Alignment aGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGTGAG cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagaGCCCAAATGTTACTGACTGAGGTGACTCGAGGGTGTGGAGAGATCCAGGGAGAATGCGGGGAGCTGTGGGGTTGTCTATCAAGAATAGAGCTAGAGCGGGCACAACTTGAAATCCAGAGTGAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTAACACCA---------gtaagaaacagcgagggaaacaatgggtatataagcattcatacacaaat Alignment from CESAR aGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGTGAG cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagaGCCCAAATGTTACTGACTGAGGTGACTCGAGGGTGTGGAGAGATCCAGGGAGAATGCGGGGAGCTGTGGGGTTGTCTATCAAGAATAGAGCTAGAGCGGGCACAACTTGAAATCCAGAGTGAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTAACACCA---------gtaagaaacagcgagggaaacaatgggtatataagcattca Alignment from Spaln_aa2Genome AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTG------CGTGAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACA cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagAGCCCAAATGTTACTGACTGAGGTGACTCGAGGGTGTGGAGAGATCCAGGGAGAATGCGGGGAGCTGTGGGGTTGTCTATCAAGAATAGAGCTAGAGCGGGCACAACTTGAAATCCAGAGTGAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTAACACCAgtaagaaacagcgagggaaacaatgggtatataagcattcatacacaaat Alignment from Spaln_nt2Genome AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGC------TGCGTGAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACA cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagAGCCCAAATGTTACTGACTGAGGTGACTCGAGGGTGTGGAGAGATCCAGGGAGAATGCGGGGAGCTGTGGGGTTGTCTATCAAGAATAGAGCTAGAGCGGGCACAACTTGAAATCCAGAGTGAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTAACACCAgtaagaaacagcgagggaaacaatgggtatataagcattcatacacaaat Alignment from Pairagon AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACA cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagAGCCCAAATGTTACTGACTGAGGTGACTCGAGGGTGTGGAGAGATCCAGGGAGAATGCGGGGAGCTGTGGGGTTGTCTATCAAGAATAGAGCTAGAGCGGGCACAACTTGAAATCCAGAGTGAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTAACACCAgtaagaaacagcgagggaaacaatgggtatataagcattcatacacaaat Alignment from Exonerate_protein2genome cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagagcccaaatgttactgactgaggtgactcgagggtgtggagagatccagggagaatgcggggagctgtggggttgtctatcaagaatagagctagagcgggcacaacttgaaatccagagtgagcagctgtgtgtgtgggagtccaaccagcaattggatttgagtgcatgtcacctaacaccagtaagaaacagcgagggaaacaatgggtatataagcattcatacacaaat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTG------CGTGAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGTGAG cttaatctcaggtgactgaaaatctaagtctgccttctccctcccatcagAGCCCAAATGTTACTGACTGAGGTGACTCGAGGGTGTGGAGAGATCCAGGGAGAATGCGGGGAGCTGTGGGGTTGTCTATCAAGAATAGAGCTAGAGCGGGCACAACTTGAAATCCAGAGTGAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTAACA---------CCAgtaagaaacagcgagggaaacaatgggtatataagcattcatacacaaat #### Ccdc88b_ID1831_18 --> 0 - 0 Original Alignment AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG aagggctgtcacatcacaacgttaatatcctaaccttttttccccctaagAATGCCACATTAGTGGCAGAGAAAGTGGCTCTGCAGGGACAGTTACAGCATCTTGAGGGCCAGCTGGGTAGCCTACATGCTCGTGCACAGGAGTTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTG---gtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaacaat Alignment from CESAR AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG aagggctgtcacatcacaacgttaatatcctaaccttttttccccctaagAATGCCACATTAGTGGCAGAGAAAGTGGCTCTGCAGGGACAGTTACAGCATCTTGAGGGCCAGCTGGGTAGCCTACATGCTCGTGCACAGGAGTTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTG---gtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaac Alignment from Spaln_aa2Genome AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTG aagggctgtcacatcacaacgttaatatcctaaccttttttccccctaagAATGCCACATTAGTGGCAGAGAAAGTGGCTCTGCAGGGACAGTTACAGCATCTTGAGGGCCAGCTGGGTAGCCTACATGCTCGTGCACAGGAGTTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGgtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaacaat Alignment from Spaln_nt2Genome AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTG aagggctgtcacatcacaacgttaatatcctaaccttttttccccctaagAATGCCACATTAGTGGCAGAGAAAGTGGCTCTGCAGGGACAGTTACAGCATCTTGAGGGCCAGCTGGGTAGCCTACATGCTCGTGCACAGGAGTTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGgtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaacaat Alignment from Pairagon AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTG aagggctgtcacatcacaacgttaatatcctaaccttttttccccctaagAATGCCACATTAGTGGCAGAGAAAGTGGCTCTGCAGGGACAGTTACAGCATCTTGAGGGCCAGCTGGGTAGCCTACATGCTCGTGCACAGGAGTTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGgtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaacaat Alignment from Exonerate_protein2genome aagggctgtcacatcacaacgttaatatcctaaccttttttccccctaagaatgccacattagtggcagagaaagtggctctgcagggacagttacagcatcttgagggccagctgggtagcctacatgctcgtgcacaggagttgcttctacagagtcaacgggctcaagagcacagtagttgcttggtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaacaat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GGACTGTGGAGACCCAGAATGGACGGCTCATCGAAGTG---GAGCGAAATAATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTG AAGGGCTGTCACATCACAACGTTAATATCCTAACCTTTTTTCCCCCTAAGAATGCCACATTAGTGGCAGAGAAAGTGGCTCTGCAGGGACAGTTACAGCATCTTGAGGGCCAGCTGGGTAGCCTACATGCTCGTGCACAGGAGTTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGgtaaggagcttgggtgattgaatgggttgggtcatccaccttgaaacaat #### Ccdc88b_ID1838_11 --> 0 - 0 Original Alignment GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGCGAGGCCCATGCG tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGC------------gtaagcagtaaacaaacgctatagacagattgcaaagggttgtgaaggga Alignment from CESAR GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGCGAGGCCCATGCG tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGC------------gtaagcagtaaacaaacgctatagacagattgcaaagg Alignment from Spaln_aa2Genome GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGC tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGCgtaagcagtaaacaaacgctatagacagattgcaaagggttgtgaaggga Alignment from Spaln_nt2Genome GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGCGAGGCCCATGCG tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGCG-----TAAGCAgtaaacaaacgctatagacagattgcaaagggttgtga Alignment from Pairagon GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGC tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGCgtaagcagtaaacaaacgctatagacagattgcaaagggttgtgaaggga Alignment from Exonerate_protein2genome GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGCGAGGCCCATGCG tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGCGTAAGCAGTAAAcaaacgctatagacagattgcaaagggttgtgaaggga Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAGGAGCGGGTCCTTTCCGAGGCCCTGGAGGCCTCGAAGGTCCTGCTAGAGGAACAGCTGGAGGTTGCCCGAGAGCGCTCAGCCAGGCTGCATGAGACCCAGAGGGAGAACCTCCTGCTGCGCACGCGGTTGGGCGAGGCC- tgagaaccagggaggcttgatctctccatttcctgttacttatttttcagGAGAAGGAGGTCCTCTCCCAAGCTGTAGAGGCCTCAAATGGACTTCTTGAAGAACAGTTGGAAGTTGCGCATAAGCGTGCTGCAAGGCTGCATGAAACCCAGAGAGAAAATCTCTTGGTGCGCACACGATTGGGCGTAAGCAgtaaacaaacgctatagacagattgcaaagggttgtgaaggga #### Ccdc88b_ID1845_4 --> 0 - 1 Original Alignment GAGGAGCTACAGCTGCTGATCCTATCACCACCTCCAGACCTCCAGACAATGGGGTGTGACCCCTTCTCAg agagcccaggcacctagctcagacacattctaacccctgctcctttaaagGAAGAGCTACAGCTTTTAATATTATCTACATCACCAGACCTCCAG------------------------ggtgagtgttctaaccttgtctatcctaagtagtgtctcggcgcttcgcac Alignment from CESAR GAGGAGCTACAGCTGCTGATCCTATCACCACCTCCAGACCTCCAGACAATGGGGTGTGACCCCTTCTCAg agagcccaggcacctagctcagacacattctaacccctgctcctttaaagGAAGAGCTACAGCTTTTAATATTATCTACATCACCAGACCTCCAG------------------------ggtgagtgttctaaccttgtctatcctaagtagtgtctcggcgcttcgcac Alignment from Spaln_aa2Genome GAGGAGCTACAGCTGCTGATCCTATCACCACCTCCAGACCTCCAGACAAT agagcccaggcacctagctcagacacattctaacccctgctcctttaaagGAAGAGCTACAGCTTTTAATATTATCTACATCACCAGACCTCCAGGGTGAgtgttctaaccttgtctatcctaagtagtgtctcggcgcttcgcac Alignment from Spaln_nt2Genome GAGGAGCTACAGCTGCTGATCCTATCACCACCTCCAGACCTCCAGACAATGGGGTGTGACCCCTTCTC----AG agagcccaggcacctagctcagacacattctaacccctgctcctttaaagGAAGAGCTACAGCTTTTAATATTATCTACATCACCAGACCTCCAGGGTGAGTGTTCTAACCTTGTCTATCCTAAgtagtgtctcggcgcttcgcac Alignment from Pairagon GAGGAGCTACAGCTGCTGATCCTATCACCACCTCCAGACCTCCAGACAATGGGGTGTGACCCCTTCTCAG agagcccaggcacctagctcagacacattctaacccctgctcctttaaagGAAGAGCTACAGCTTTTAATATTATCTACATCACCAGACCTCCAG------------------------Ggtgagtgttctaaccttgtctatcctaagtagtgtctcggcgcttcgcac Alignment from Exonerate_protein2genome agagcccaggcacctagctcagacacattctaacccctgctcctttaaaggaagagctacagcttttaatattatctacatcaccagacctccagggtgagtgttctaaccttgtctatcctaagtagtgtctcggcgcttcgcac Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise -GAGCTACAGCTGCTGATCCTATCACCACCTCCAGACCTCCAGAC agagcccaggcacctagctcagacacattctaacccctgctcctttaaaggaagagctacagcttttaatattatctacatcaccagacctccagggtgagTGTTCTAACCTTGTCTATCCTAAGTAGTGTCTCGGCGCTTCGCAC #### Ccnj_ID8043_4 --> 2 - 2 Original Alignment atTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTGTTG------ct cctaatattaagcattctatactgtaggagtctttattttacatgcacagatTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTctgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from CESAR atTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTGTTG------ct cctaatattaagcattctatactgtaggagtctttattttacatgcacagatTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTctgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from Spaln_aa2Genome ATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTGTTGCTT----- cctaatattaagcattctatactgtaggagtctttattttacatgcacagATTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTCTgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from Spaln_nt2Genome ATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTGTTG------CT cctaatattaagcattctatactgtaggagtctttattttacatgcacagATTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTCTgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from Pairagon ATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTGTTG------CT cctaatattaagcattctatactgtaggagtctttattttacatgcacagATTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTCTgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from Exonerate_protein2genome ATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTG------TTGCT cctaatattaagcattctatactgtaggagtctttattttacatgcacagATTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTCTgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from Exonerate_coding2genome ATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTG------TTGCT cctaatattaagcattctatactgtaggagtctttattttacatgcacagATTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTCTgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat Alignment from GeneWise ATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCGTGTGTGGCTTCTTCGAGGATTATCCTTCGTCTGTCTCCAACGTGGCCCACGAGACTGCACCGTCTCACTGCCTACTCCTGGGACTTCTTGGTGCAGTGTATCGAACGGCTGTTGCTTGCT-- cctaatattaagcattctatactgtaggagtctttattttacatgcacagATTATGCCTTTCTGAATTATGCACCCTCCTTAATAGCAGCTGCATGTGTGGCCTTTTCCAGGATTATACTCCAACTGTCTCCAACCTGGCCTACAAGACTACACTGTTACACGGCATACTCCTGGGCCTTCTTGGTTCAGTGTATGGAATGGTTATCGAGTGCTCTgtaagtagagtcacatgattgaactcagactgccatggtgattgctgtat #### Ccs_ID661_7 --> 0 - 2 Original Alignment GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGag gTTGGCCT ggcagatgaatctgactccctcctttatagctttgccttgtcttacccag------------ATTGCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAaggtaagccatatcacaatcaattccttgcattatgtgtgccagaCTCTCAT Alignment from CESAR GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGag gTTGGCCT gtgcatatgaagggcagatgaatcttatagctttgccttgtcttacccag------------ATTGCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAaggtaagccatatcacaatcaaaactcctgggtttttttctcagaCTCTCAT Alignment from Spaln_aa2Genome GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAG GTTGGCCT ggcagatgaatctgactccctcctttatagctttgccttgtcttacccag------------ATTGCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAAGgtaagccatatcacaatcaattccttgcattatgtgtgccagACTCTCAT Alignment from Spaln_nt2Genome - -TTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAG GTTGGCCT GgcagatgaatctgactccctcctttatagctttgccttgtcttacccagATTGCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAAGgtaagccatatcacaatcaattccttgcattatgtgtgccagACTCTCAT Alignment from Pairagon -------------------------------------------------GATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAGGTTGGCC------------------------------------------T GGCAGATGAATCTGACTCCCTCCTTTATAGCTTTGCCTTGTCTTACCCAGATTGCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAAGGTAAGCCATATCACAATCAATTCCTTGCATTATGTGTGCCAGACTCTCAT Alignment from Exonerate_protein2genome ATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAG GTTGGCCT ggcagatgaatctgactccctcctttatagctttgccttgtcttacccagATTGCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAAGgtaagccatatcacaatcaattccttgcattatgtgtgccagACTCTCAT Alignment from Exonerate_coding2genome ggcagatgaatctgactccctcctttatagctttgccttgtcttacccagattgcccgcaccttggttattgatgagggagaagacgatgtgggctgggggggccaccctttatccaagattactgggaatttagagaaaaggtaagccatatcacaatcaattccttgcattatgtgtgccagactctcat Alignment from GeneWise GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAG GTTGGCCT ggcagatgaatctgactccctcctttatagctttgccttgtcttacccagATT------------GCCCGCACCTTGGTTATTGATGAGGGAGAAGACGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTAGAGAAAAGgtaagccatatcacaatcaattccttgcattatgtgtgccagACTCTCAT #### Cd274_ID6274_5 --> 2 - 1 Original Alignment tgAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT------g gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagtgAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGTAGTCggtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from CESAR tgAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT------g gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagtgAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGTAGTCggtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from Spaln_aa2Genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT------G gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagTGAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGTAGTCGgtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from Spaln_nt2Genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATG------ gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagTGAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGTAGTCGgtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from Pairagon TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATG------ gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagTGAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGTAGTCGgtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from Exonerate_protein2genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagTGAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATgtagtcggtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from Exonerate_coding2genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagTGAGGATGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATgtagtcggtaagaggataaagttcagtcattttggtggccatccaataccagaataa Alignment from GeneWise gtttgccctcactaacatccgaactcacgggtttacttttctgttttcagtgaggatgctggatgagaaatgcagtgttgagcatataagctcaaaaaaccggaatgtagtcggtaagaggataaagttcagtcattttggtggccatccaataccagaataa #### Cdc42bpg_ID1578_8 --> 0 - 0 Original Alignment ---------GACCACCTCCAGTTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagCCAACAGGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from CESAR ---------GACCACCTCCAGTTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagCCAACAGGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from Spaln_aa2Genome GACCACCTCCAG---------TTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagCCAACAGGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from Spaln_nt2Genome GACCACCTCCAG--TTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagccaacagGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from Pairagon -----------------------------------------------------------GACCACCTCCAGTTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA AGTCATCTTTATAGTTAGGTCCCTCCACATGTGTTCTTTGTACTGTCAAGCCAACAGGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from Exonerate_protein2genome AGGACCACCTCCAGTTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagccaacagGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from Exonerate_coding2genome agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagccaacaggtgaccatctccagtttcctgctgccgtcacagatgtgcctgctagtgcccgtgatctgatctgtcagctgttatgccgccaggaggagcaactaagccgtggtgcactggacgacttccacaagcatgcattctttgagggggttgactgggagaggctcacaaccagcacagcaccatatattcctgagcttcgaggcccaatggacacttcaaaccttgatgtggatgatgacaccctcaaccgctcagtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct Alignment from GeneWise ---------GACCACCTCCAGTTCCCTGCTGATGTGACTGATGTGCCTGCTAGTGCCCAGGACCTGATCCGACAGCTGCTGTGCCGTCAGGAGGAGCGGCTGGGCCGTGGTGGGCTGGACGACTTCCGGAAGCACCCCTTCTTTGAAGGGGTCGATTGGGAGAGGCTTGCAACCAGCACAGCGCCATACATCCCTGAGCTTCGAGGGCCGATGGACACCTCCAACTTCGACGTGGATGATGATACCCTCAACCGTCCA agtcatctttatagttaggtccctccacatgtgttctttgtactgtcaagCCAACAGGTGACCATCTCCAGTTTCCTGCTGCCGTCACAGATGTGCCTGCTAGTGCCCGTGATCTGATCTGTCAGCTGTTATGCCGCCAGGAGGAGCAACTAAGCCGTGGTGCACTGGACGACTTCCACAAGCATGCATTCTTTGAGGGGGTTGACTGGGAGAGGCTCACAACCAGCACAGCACCATATATTCCTGAGCTTCGAGGCCCAATGGACACTTCAAACCTTGATGTGGATGATGACACCCTCAACCGCTCAgtaagttgcagagaccattatgacacatttgtccaacaatgtactgagct #### Cdc42bpg_ID1595_25 --> 2 - 0 Original Alignment ccTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCG GTGCCGCGGC agtaacctcaacattatttaattcacatatgtcaactttttctctattagcaTGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGGG---------gtcagatgggatgaaaattcttgccttccatgtgccacagGTACGACAGC Alignment from CESAR ccTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCG G agtaacctcaacattatttaattcacatatgtcaactttttctctattagcaTGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGGG---------gtcagatgggatgaatctgaagcccctggtccttacacagG Alignment from Spaln_aa2Genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGC TTCCTGTCGG agtaacctcaacattatttaattcacatatgtcaactttttctctattagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGGGgtcagatgggatgaaaattcttgccttccatgtgccacag---------G Alignment from Spaln_nt2Genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCG GTGCCGCGGC agtaacctcaacattatttaattcacatatgtcaactttttctctattagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGG---------GgtcagatgggatgaaaattcttgccttccatgtgccacagGTACGACAGC Alignment from Pairagon CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCGGTGCCGCGG C agtaacctcaacattatttaattcacatatgtcaactttttctctattagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATG------------------GGgtcagatgggatgaaaattcttgccttccatgtgccacaggtacgacagC Alignment from Exonerate_protein2genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGC TTCCTGTCGGTGCCGCGGC agtaacctcaacattatttaattcacatatgtcaactttttctctattagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGGGgtcagatgggatgaaaattcttgccttccatGTGCCACAGGTACGACAGC Alignment from Exonerate_coding2genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGC TTCCTGTCGGTGCCGCGGC agtaacctcaacattatttaattcacatatgtcaactttttctctattagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGGGgtcagatgggatgaaaattcttgccttccatGTGCCACAGGTACGACAGC Alignment from GeneWise CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTC---------------------CTG-TCGGTGCCG---------CGGC agtaacctcaacattatttaattcacatatgtcaactttttctctattagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCAGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGAGTGCACCCCAAGAAGCGAACAGAGTCAGCCTATGATGGGGTCAGATGGGATGAAAATTCTTGCCTTCCATGTGCCACAGGTACGACAGC #### Cdc42bpg_ID1602_32 --> 0 - 1 Original Alignment ---GTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAg tggttgtcacattaggacattgagtggatatccgctctttctccctgcagAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAagtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from CESAR ---GTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAg tggttgtcacattaggacattgagtggatatccgctctttctccctgcagAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAagtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from Spaln_aa2Genome AAGGTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAG tggttgtcacattaggacattgagtggatatccgctctttctccctgcagAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAAgtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from Spaln_nt2Genome CTCAAGAAGGTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAG tggttgtcacattaggacattgagtggatatccgctctttctccctgcag------AAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAAgtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from Pairagon -------------------------------CCGCTC----------AAGAAGGTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAG TGGTTGTCACATTAGGACATTGAGTGGATATCCGCTCTTTCTCCCTGCAGAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAAgtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from Exonerate_protein2genome AAGGTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAG tggttgtcacattaggacattgagtggatatccgctctttctccctgcagAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAAgtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from Exonerate_coding2genome AAGGTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAG tggttgtcacattaggacattgagtggatatccgctctttctccctgcagAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAAgtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca Alignment from GeneWise AAGGTGAGACCCCTGAATCCAGAAGGCTCCTTGTTCCTTTATGGCACCGAGAAGGTCCGCCTGACCTACCTCAGGAATCCATTGGCAG tggttgtcacattaggacattgagtggatatccgctctttctccctgcagAAAGTGAGACCCCTCAATCCAGAAGGCTTGTTATTCCTTTATGGGACTGAAAAACTACGCCTGACTTACCTCAGAAACCCACTGGCAAgtaagtgtacacaatgccaattgactgtcagagcaataagtgaacaacca #### Cdc42bpg_ID1603_33 --> 2 - 2 Original Alignment agAAGGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCag agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacagaa------GAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTaggtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from CESAR agAAGGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCag actgtcagagcaataagtgaacaacgaacagctttgatgtcctttcacagaa------GAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTaggtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from Spaln_aa2Genome AGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCAG agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacagaagAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTAGgtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from Spaln_nt2Genome AGAAGGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCAG agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacag------AAGAGTTTGAGATTCCTGACCTGAC---AAACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTAGgtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from Pairagon AGAAGGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCAG agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacag------AAGAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTAGgtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from Exonerate_protein2genome GGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCAG agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacAGAAGAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTAGgtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from Exonerate_coding2genome GGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCAG agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacAGAAGAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTAGgtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa Alignment from GeneWise AGAAGGACGAGTTTGACATTCCCGACCTCACGGACAACAGCCGGCGCCAGCTGTTCCGCACCAAGAGCAAGCGCCGTTTCTTCTTCCGGGTGTCTGATGAGCTGCGACAGCAGCAGCGCAG agagcaataagtgaacaaccattcagaacagctttgatgtcctttcacagAA------GAGTTTGAGATTCCTGACCTGACA---AACAGCCGGCGACAACTCTTCCGGAGCAAAAGTAAGCGCCGTTTCTTCTTCCATGTGACTGACAAGCTACAACAGCAACAATGTAGgtaagttcctttgttacagtcctatgattcaacgattttctttacaagaa #### Cdc42bpg_ID1604_34 --> 1 - 0 Original Alignment gGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGGACCCGG acaccaataactaattgcagctatttattggtctttccgttctcttgcaggGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGG------gtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca Alignment from CESAR gGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGGACCCGG acaccaataactaattgcagctatttattggtctttccgttctcttgcaggGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGG------gtaattacagcgctggagtaggagatcacctaacctgtcacaaa Alignment from Spaln_aa2Genome GGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGG acaccaataactaattgcagctatttattggtctttccgttctcttgcagGGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGGgtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca Alignment from Spaln_nt2Genome GGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGG acaccaataactaattgcagctatttattggtctttccgttctcttgcagGGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGGgtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca Alignment from Pairagon GGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGG acaccaataactaattgcagctatttattggtctttccgttctcttgcagGGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGGgtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca Alignment from Exonerate_protein2genome GGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGG acaccaataactaattgcagctatttattggtctttccgttctcttgcagGGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGGgtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca Alignment from Exonerate_coding2genome GGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGG acaccaataactaattgcagctatttattggtctttccgttctcttgcagGGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGGgtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca Alignment from GeneWise GGAGATGCTGAAGGACCCTTTTGTGCGCTCCAAGTTCATCTCGCCGCCCACCAACTTCAACCACCTGGTGCACGTGGGCCCTACGGAGGGAAGGCCCAACACCAGGGATGGG acaccaataactaattgcagctatttattggtctttccgttctcttgcagGGAGATGCTGAAAGACCCCTTTGTGCGGTTCAAATTTATTCCACCACCAACCAACTTAATCCACCTGGTCCATGTGGGGCATACAGAGGGGAGGTCCAACACTAGGGATGGGgtaattacagcgctggagtaggagatcacctaacctgtcacaaagcttca #### Cdc42bpg_ID1605_35 --> 0 - 1 Original Alignment GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACCCAt aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGAC---tgtagggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from CESAR GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACCCAt aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGAC---tgtagggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from Spaln_aa2Genome GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGAC- aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGACTgtagggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from Spaln_nt2Genome GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACC aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGACTgtagggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from Pairagon GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACC aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGACTgtagggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from Exonerate_protein2genome GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACCCAT aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGACTGTAgggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from Exonerate_coding2genome GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACCCAT aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGACTGTAgggagtattcaggatagttctcagtgagatattcccgattatttcct Alignment from GeneWise GCTCAGGAACAGAAGAGCAGAGGTGCCCGCAGCTCCGGGCCGCAGCGGCCCCACAGCTTCTCAGAGGCATTTCGGCGGCCAGTGTCCACGGGCAGTGATGGTCTCCCTGGAGAAACAGACC aatgcaagagttccatgtagtctgctctattcgtccgtgggtctttgcagGCCCAGGAACAGAAGAGTAGTGGTGCCTGTAGCTCTGGACCACAACGGCCTCACAGCTTCTTAAAGGCATTGCAGCGGCCAGTGTCAACAGACAGTGATCGTCCACCAGGACAAACAGACTgtagggagtattcaggatagttctcagtgagatattcccgattatttcct #### Cdca5_ID1428_2 --> 2 - 0 Original Alignment ggCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG--- cagctggcctggtaatgggttatttggcgtgttttattgctttctggtaggaCCAAGGACTTTACTAACTCAGCCTTCAGAGTCACTAAAACACAAGCCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGATTgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from CESAR ggCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG--- cagctggcctggtaatgggttatttggcgtgttttattgctttctggtaggaCCAAGGACTTTACTAACTCAGCCTTCAGAGTCACTAAAACACAAGCCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGATTgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from Spaln_aa2Genome GGCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGGACA cagctggcctggtaatgggttatttggcgtgttttattgctttctggtagGACCAAGGACTTTACTAACTCAGCCTTCAGAGTCACTAAAACACAAGCCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGATTgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from Spaln_nt2Genome GGCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGGACA cagctggcctggtaatgggttatttggcgtgttttattgctttctggtagGACCAAGGACTTTACTAACTCAGCCTTCAGAGTCACTAAAACACAAGCCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGATTgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from Pairagon GGCCCAGGACTTCACTTACTAAGCCTTCGAAGTC-----------------GTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTG cagctggcctggtaatgggttatttggcgtgttttattgctttctggtagGACCAAGGACTTTACTAACTCAGCCTTCAGAGTCACTAAAACACAAGCCATGT-----------------TCAGACCTCACAAACTCATTTTCTGAAACCTGgcaacggattgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from Exonerate_protein2genome cagctggcctggtaatgggttatttggcgtgttttattgctttctggtaggaccaaggactttactaactcagccttcagagtcactaaaacacaagccatgttcagacctcacaaactcattttctgaaacctggcaacggattgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from Exonerate_coding2genome cagctggcctggtaatgggttatttggcgtgttttattgctttctggtaggaccaaggactttactaactcagccttcagagtcactaaaacacaagccatgttcagacctcacaaactcattttctgaaacctggcaacggattgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt Alignment from GeneWise GGGCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGGACA cagctggcctggtaatgggttatttggcgtgttttattgctttctggtaGGACCAAGGACTTTACTAACTCAGCCTTCAGAGTCACTAAAACACAAGCCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGATTgtatcaactgacttccctggtctgaaagcagctgcatacatcacaatttt #### Cdk2ap2_ID299_3 --> 0 - 1 Original Alignment GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGA------------------g gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACCTGTGGACTTAGACTGGggtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from CESAR GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGA------------------g gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACCTGTGGACTTAGACTGGggtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from Spaln_aa2Genome GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGA------------------G gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACCTGTGGACTTAGACTGGGgtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from Spaln_nt2Genome GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGAG-- gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACCTgtggacttagactggggtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from Pairagon ---------------------------------------------TACAGGCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGA------------------G GTGGAGCCCAACCCCTATTGGGGTTTAATGTACTCTGCCTTGCTCTGCAGGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACCTGTGGACTTAGACTGGGgtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from Exonerate_protein2genome GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGAG gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACctgtggacttagactggggtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from Exonerate_coding2genome GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGAG gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACctgtggacttagactggggtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt Alignment from GeneWise GCGATGAAGCCACCTGGTTCCCAGGGCTCTCAGAGCACCTACACGGACCTGCTGTCTGTCATAGAGGAGATGGGCAAAGAGATCCGGCCCACCTATGCTGGTAGCAAGAGTGCCATGGAGCGCCTGAAGAGA------------------G gtggagcccaacccctattggggtttaatgtactctgccttgctctgcagGCAATGAAGCCACCAGGTTCCCAGGGCTCTCAGCGCACCTTCACCGACCTGCTGTCTGTTATAGAGGAGATGGGCAAGGAAATCCGACCCACATATGCTGGTAGTAAAAGTTCCATGGACCGCCTGAAGAGACCTGTGGACTTAGACTGGGgtcagtgcattcaagggtaagccatgacaggacagcataattgaaaaagt #### Chuk_ID8920_8 --> 1 - 2 Original Alignment gCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTag ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagg---GAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTaggtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from CESAR gCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTag tggggcatggttcttggatgcactaccttaaatctgtgtgtctcccgcagg---GAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTaggtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from Spaln_aa2Genome TGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAG ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagGGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAGgtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from Spaln_nt2Genome TGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAG ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagGGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAGgtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from Pairagon TGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAG ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagGGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAGgtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from Exonerate_protein2genome TGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAG ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagGGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAGgtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from Exonerate_coding2genome TGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAG ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagGGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAGgtcagtgacactttgagtttgggaatatgcccctatctactcataagggc Alignment from GeneWise TGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAG ggcatggttcttggatgcactatgcccttaaatctgtgtgtctcccgcagGGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTAGgtcagtgacactttgagtttgggaatatgcccctatctactcataagggc #### Chuk_ID8922_6 --> 0 - 0 Original Alignment ------ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from CESAR ------ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from Spaln_aa2Genome TACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagatcatcacagTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from Spaln_nt2Genome A------CAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from Pairagon ------ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from Exonerate_protein2genome GGGAAGACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from Exonerate_coding2genome GGGAAGACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca Alignment from GeneWise ------ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG tcacaagtcttgtggaacttgatgacataactaccatgctcttctttcagATCATCACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtcagtaaatgacatgttagttctgattctgttacttcgttggtctttca #### Col17a1_ID10271_51 --> 2 - 1 Original Alignment gtGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAA---g ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccaggtGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAA---GAAAAGGGTGATAAAGCAggtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from CESAR gtGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAA---g ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccaggtGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAA---GAAAAGGGTGATAAAGCAggtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from Spaln_aa2Genome GTGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAA---G ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccagGTGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAA---GAAAAGGGTGATAAAGCAGgtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from Spaln_nt2Genome GTGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAAG ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccagGTGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAAGAAAAGGGTGATAAAGCAGgtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from Pairagon GTGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAAG ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccagGTGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAAGAAAAG------------Ggtgataaagcaggtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from Exonerate_protein2genome GTGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAAG ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccagGTGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAAGAAAAGGGTGATAAAGCAGgtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from Exonerate_coding2genome ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccaggtgacagggatccagctaggccacaaggctcaccagggcaacctggccctagagggaacaaagaaaagggtgataaagcaggtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta Alignment from GeneWise GTGACAGGGGCCCTGCTGGACCACGAGGTCCTCCAGGGCCACCCGGCCCCAGAGGGAACAAAGGAGAGAAAGGAGACAAAGGT- ttttgccccctaatcatcttcaggtatacatttcccctcatccttcccagGTGACAGGGATCCAGCTAGGCCACAAGGCTCACCAGGGCAACCTGGCCCTAGAGGGAACAAA---GAAAAGGGTGATAAAGCAGgtaattagtggaaatgagatggggtgcaggggcttagattgtgaaaacta #### Col17a1_ID10276_46 --> 2 - 1 Original Alignment gtTCTGGGATCAGCTTTGGGCATCCTGGC---CCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAg gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcaggt------CTTAGCTTTGGACATCCAGGCCCATCACCT---------------GCTGGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAggtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from CESAR gtTCTGGGATCAGCTTTGGGCATCCTGGCCCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAg actcgagcaggctcaaaaatcctccctgcatctgttttctcccttgtcaggt------CTTAGCTTTGGACATCCAGGCCCATCA---CCTGCT---------GGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAggtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from Spaln_aa2Genome GGATCAGCTTTGGGCATCCTGGCCCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAG gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcagGTCTTAGCTTTGGACATCCAGGCCCATCA------------CCTGCTGGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAGgtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from Spaln_nt2Genome ATC--AGCTTTGGGCATCCTGGCCCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAG gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcagGTCTTAGCTTTGGACATCCAGGCCCA-----------TCACCTG-CTGGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAGgtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from Pairagon GTTCTGGGATCAGCTTTGGGCATCCTGGCCCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAG gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcaggtcttag-------------CTTTGGACATCCAGGCCCATC-----------ACCTGCT-GGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAGgtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from Exonerate_protein2genome GGATCAGCTTTGGGCATCCTGGCCCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAG gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcagGTCTTAGCTTTGGACATCCAGGC------------CCATCACCTGCTGGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAGgtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from Exonerate_coding2genome gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcaggtcttagctttggacatccaggcccatcacctgctggaacttcatatgaaaagttattgtccatgcttaaaggtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg Alignment from GeneWise GGATCAGCTTTGGGCATCCTGGCCCACCGGGACCCCCTGGCCTGCCAGGAACATCCTACGAGGAGCTACTGACCATGCTCCGAG gcaggctcaaaaatcctcctgctaactgcatctgttttctcccttgtcagGTCTTAGCTTTGGACATCCAGGCCCA------------TCACCTGCTGGAACTTCATATGAAAAGTTATTGTCCATGCTTAAAGgtatgtcacaacccggaactatccatcaactcagaatggtctaaggggtg #### Col17a1_ID10282_40 --> 2 - 1 Original Alignment aa---ACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAg agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagtaAAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAggtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from CESAR aa---ACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAg agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagtaAAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAggtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from Spaln_aa2Genome GAAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagTAAAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAGgtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from Spaln_nt2Genome ---AAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagTAAAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAGgtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from Pairagon ---AAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagTAAAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAGgtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from Exonerate_protein2genome AAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagtaaAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAGgtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from Exonerate_coding2genome agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagtaaaaacattctttaggggccctccaggtccacctggccctccaggtccaaaaggggaccaaggtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta Alignment from GeneWise --GAAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG agccaatgttaagccctgagcaacctgcactctgtgggttctctttacagTAAAAACATTCTTTAGGGGCCCTCCAGGTCCACCTGGCCCTCCAGGTCCAAAAGGGGACCAAGgtgagtaggtagtgcaaaaactgccaagtgtgagcactagtatgagacta #### Col17a1_ID10284_38 --> 2 - 1 Original Alignment gg------CCTTCCATCCCAGGCCCGCCAGGACCCAGAGGTCCACCAg acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagggATTCTGCCTTCTACCCCAGGGCCACCCGGACCCCAAAGTCCACCAggtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from CESAR gg------CCTTCCATCCCAGGCCCGCCAGGACCCAGAGGTCCACCAg acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagggATTCTGCCTTCTACCCCAGGGCCACCCGGACCCCAAAGTCCACCAggtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from Spaln_aa2Genome GG------CCTTCCATCCCAGGCCCGCCAGGACCCAGAGGTCCACCAG acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagGGATTCTGCCTTCTACCCCAGGGCCACCCGGACCCCAAAGTCCACCAGgtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from Spaln_nt2Genome GG------CCTTCCATCCCAGGCCCGCCAGGACCCAGAGGTCCACCAG acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagGGATTCTGCCTTCTACCCCAGGGCCACCCGGACCCCAAAGTCCACCAGgtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from Pairagon ---------------------------------------------------------GCCTTCCATCCCAGGCCCGCCAGGACCCAGAGGTCCACCAG ACGATAGTAATGGAGGGAGATTCACAAGTAGGTCACTTTTGTCAACATAGGGATTCTGCCTTCTACCCCAGGGCCACCCGGACCCCAAAGTCCACCAGgtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from Exonerate_protein2genome GCCCGCCAGGACCCAGAGGTCCACCAG acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagggattctgccttctaccccagGGCCACCCGGACCCCAAAGTCCACCAGgtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from Exonerate_coding2genome acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagggattctgccttctaccccagggccacccggaccccaaagtccaccaggtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt Alignment from GeneWise -----GGGCCTTCCATCCCAGGCCCGCCAGGACCCAGAGGTCCACCAG acgatagtaatggagggagattcacaagtaggtcacttttgtcaacatagGGATTCTGCCTTCTACCCCAGGGCCACCCGGACCCCAAAGTCCACCAGgtgactgattgaaagggatgtgaggattaaggccatgtccaacaggaggt #### Col17a1_ID10293_29 --> 2 - 1 Original Alignment gtCCGGCTGGCGCTGATGGACAGCAAGGTTCCAGAg gatcagaaagcccattgatcataacacacttcctcccctgctctctccaggtCCAGCTGGCGCTGATGGACAACAA---------ggtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from CESAR gtCCGGCTGGCGCTGATGGACAGCAAGGTTCCAGAg gatcagaaagcccattgatcataacacacttcctcccctgctctctccaggtCCAGCTGGCGCTGATGGACAACAA---------ggtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from Spaln_aa2Genome GTCCGGCTGGCGCTGATGGACAGCAA- gatcagaaagcccattgatcataacacacttcctcccctgctctctccagGTCCAGCTGGCGCTGATGGACAACAAGgtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from Spaln_nt2Genome GTCCGGCTGGCGCTGATGGACAGCAAG gatcagaaagcccattgatcataacacacttcctcccctgctctctccagGTCCAGCTGGCGCTGATGGACAACAAGgtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from Pairagon GTCCGGCTGGCGCTGATGGACAGCAAG gatcagaaagcccattgatcataacacacttcctcccctgctctctccagGTCCAGCTGGCGCTGATGGACAACAAGgtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from Exonerate_protein2genome GTCCGGCTGGCGCTGATGGACAGCAAG gatcagaaagcccattgatcataacacacttcctcccctgctctctccagGTCCAGCTGGCGCTGATGGACAACAAGgtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from Exonerate_coding2genome gatcagaaagcccattgatcataacacacttcctcccctgctctctccaggtccagctggcgctgatggacaacaaggtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg Alignment from GeneWise gatcagaaagcccattgatcataacacacttcctcccctgctctctccaggtccagctggcgctgatggacaacaaggtgagacaaatcttcccttcccttgtagtttccttgatgactggttactg #### Col17a1_ID10301_21 --> 2 - 1 Original Alignment gt------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTg tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttaggtGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTggtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from CESAR gt------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTg tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttaggtGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTggtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from Spaln_aa2Genome GT------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTG tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttagGTGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTGgtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from Spaln_nt2Genome GTATCCCTGGGCCCCTGG------GCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTG tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttagGTGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTGgtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from Pairagon GT------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTG tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttagGTGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTGgtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from Exonerate_protein2genome GT------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTG tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttagGTGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTGgtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from Exonerate_coding2genome GT------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTG tcttttatgtaagggaaaatctgagtggccctcagttccttctctcttagGTGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTGgtgagtcccctatatacatgtttatttgttttgttccctttctaaataag Alignment from GeneWise CATGGGGAGTCAAGGACCTAAAGGAGACCGAGGCCTTCCTGGGACCCCAGGT------ATCCCTGGGCCCCTGGGCCACCCTGGCCCGGAAGGACCAAAGGGACAAAAAGGCAGCATTG TCTTTTATGTAAGGGAAAATCTGAGTGGCCCTCAGTTCCTTCTCTCTTAGGTGAATTAGTCCCAGGGCCATTGGGCCACCCTGGACCAGAAGGGCCAAAGGGACAGAAAGGCAGCATTGgtgagtcccctatatacatgtttatttgttttgttccctttctaaataag #### Coro1b_ID354_4 --> 2 - 0 Original Alignment gt------TGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagggGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgtttttgtgctgtttgtgtctccccagGA Alignment from CESAR gt------TGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagggGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgttttatggcaccttctttctcttcagGA Alignment from Spaln_aa2Genome GTGCAGGTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagGGGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgtttttgtgctgtttgtgtctccccagGA Alignment from Spaln_nt2Genome GT------TGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagGGGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgtttttgtgctgtttgtgtctccccagGA Alignment from Pairagon GT------TGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagGGGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgtttttgtgctgtttgtgtctccccagGA Alignment from Exonerate_protein2genome GTGCAGGTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagGGGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgtttttgtgctgtttgtgtctccccagGA Alignment from Exonerate_coding2genome GTGCAGGTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA GA atttagttcataataaactcatttgcacatttacattgtttcaattttagGGGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAgtgagaacaaatgagtatcctgtttttgtgctgtttgtgtctccccagGA Alignment from GeneWise GTGCAGGTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA------------------------------------------------GA atttagttcataataaactcatttgcacatttacattgtttcaattttagGGGATCTATGTGATAATGTGCTACTTATTTGGAATGTGGATGCCGCCGAAGACCTGTACCGTTTGGACAGTTTGCATCCCGACCTTGCTTATAATGTCAGTTGGAACCACATTGGAAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCAGTGAGAACAAATGAGTATCCTGTTTTTGTGCTGTTTGTGTCTCCCCAGGA #### Coro1b_ID357_7 --> 0 - 2 Original Alignment ---GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCag gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCC---CACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCcggtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from CESAR ---GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCag gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCcggtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from Spaln_aa2Genome GGCGATTCCAGCATC---CGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCCGgtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from Spaln_nt2Genome GGCG---ATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCCC---ACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCCGgtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from Pairagon ---GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCCC---ACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCCGgtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from Exonerate_protein2genome ---GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCCGgtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from Exonerate_coding2genome ---GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCCGgtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac Alignment from GeneWise ---GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG gatactaagggacattcctttaattactcctctctaccatggctggacagAGCGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCC---CACATCCAGTTCTTGATCACATTTGCCAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTGAAATAGCCCGgtaacaacaatcagtggttgtacatcagttatctcagtcttagttgaaac #### Cpsf7_ID2863_3 --> 0 - 2 Original Alignment TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGAGAATCGTGCAAATGGCCAGTCTAAAgg ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCA---------------------------gggtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from CESAR TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGAGAATCGTGCAAATGGCCAGTCTAAAgg ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCA---------------------------gggtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from Spaln_aa2Genome TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGA ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCAGGgtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from Spaln_nt2Genome TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGA ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCAGGgtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from Pairagon TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGAGAATCGTGCAAATGGCCAGTCTAAAGG ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGC---------------------------AGGgtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from Exonerate_protein2genome TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGA ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCAGGgtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from Exonerate_coding2genome TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGA ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCAGGgtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact Alignment from GeneWise TGGACCACAGACCAGCAGCTGATCCAGGTTATCCGCTCTATAGGAGTCTATGATGTGGTGGAGTTGAAATTTGCAGA ctgccaagtttgtcctgttatctgaactatgttctcaatcttattcgtagTGGACTACTGATCAGCAACTGATTCAGGTTCTACACTCTATAGGCATATATGACGTGGTGGAGTTGAAATTTGCAGGgtaagtatcaaaaccgtgggggatcccccataaggcgtatgttttggact #### Crtac1_ID8462_10 --> 2 - 0 Original Alignment gg---GGCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagggTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from CESAR gg---GGCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagggTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from Spaln_aa2Genome GGGGCGTAGTGACC---GACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagGGTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from Spaln_nt2Genome GG----GCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagGGTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from Pairagon ---GGGGCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagGGTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from Exonerate_protein2genome GG---GGCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagGGTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from Exonerate_coding2genome ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagggtggggtgtggtgactgattttgatggggatgggatgctagatttgatcttatcacatggaaggtccatagctcagcccttgtccattttctgtggtaatcaggtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga Alignment from GeneWise --GGGGGCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG ccctccttacccaaaaagtgatagcctgttcttcctatggggtcatccagGGTGGGGTGTGGTGACTGATTTTGATGGGGATGGGATGCTAGATTTGATCTTATCACATGGAAGGTCCATAGCTCAGCCCTTGTCCATTTTCTGTGGTAATCAGgtaagtaacacttttacccctacatgagaatgcaggtactacaggacaga #### Csf2ra_ID13430_10 --> 1 - 0 Original Alignment gTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAG ttaccacacgcatactacactacctgcaataatcaattttatattaccaggTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCT---gtaggtagtagccacaggctaccagaaattcaaatgggactggaccaaaa Alignment from CESAR gTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAG ttaccacacgcatactacactacctgcaataatcaattttatattaccaggTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCT---gtaggtagtagccacaggctaccagaaattcaaatgggactggacca Alignment from Spaln_aa2Genome GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCT ttaccacacgcatactacactacctgcaataatcaattttatattaccagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTgtaggtagtagccacaggctaccagaaattcaaatgggactggaccaaaa Alignment from Spaln_nt2Genome GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTG-AG ttaccacacgcatactacactacctgcaataatcaattttatattaccagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGTAGgtagtagccacaggctaccagaaattcaaatgggactggaccaaaa Alignment from Pairagon GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTG------------------------------------------------- ttaccacacgcatactacactacctgcaataatcaattttatattaccagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGTAGGTAGTAGCCACAGGCTACCAGAAATTCAAATGGGACTGGACCAAAA Alignment from Exonerate_protein2genome GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAG ttaccacacgcatactacactacctgcaataatcaattttatattaccagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGTAggtagtagccacaggctaccagaaattcaaatgggactggaccaaaa Alignment from Exonerate_coding2genome ttaccacacgcatactacactacctgcaataatcaattttatattaccaggttggaggtgacacgccgtctcttcccgccaatcccaggaattagggacaaggtgtctgatgatgtgcgagtgaaccctgtaggtagtagccacaggctaccagaaattcaaatgggactggaccaaaa Alignment from GeneWise GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAGACCCTCAGGAAGGACCTCCTGCAGCCC ttaccacacgcatactacactacctgcaataatcaattttatattaccagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGTAGGTAGTAGCCACAGGCTACCAGAAATTcaaatgggactggaccaaaa #### Csf2ra_ID13432_8 --> 0 - 1 Original Alignment GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCg ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAG------ggtaagggttaggcaattgttttgttttcatacaaatgatatatctattgt Alignment from CESAR GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCg ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGGGTGCAG------------ggtaagggttaggcaattgttttgttttcatacaaatgatatatctattgt Alignment from Spaln_aa2Genome GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCAT- ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGGGTGCAGGGTAAGGgttaggcaattgttttgttttcatacaaatgatatatctattgt Alignment from Spaln_nt2Genome GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCG ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG-GTGCAGGGTAAGGGTTAGgcaattgttttgttttcatacaaatgatatatctattgt Alignment from Pairagon GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGG ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGGgtgcagggtaagggttaggcaattgttttgttttcatacaaatgatatatctattgt Alignment from Exonerate_protein2genome GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATC ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGGGTGCAGGGTAAGGgttaggcaattgttttgttttcatacaaatgatatatctattgt Alignment from Exonerate_coding2genome ggcccacaaagatatgttctcactcccacttttcttttttttttttttaggccctggttgttgaggagacccgcctcactttccctagtcctgctccccacggatggcacagggtcaaagtccgagcaggtgatactaggatgaagcactgggggaaatgggtgcagggtaagggttaggcaattgttttgttttcatacaaatgatatatctattgt Alignment from GeneWise GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCG ggcccacaaagatatgttctcactcccacttttcttttttttttttttagGCCCTGGTTGTTGAGGAGACCCGCCTCACTTTCCCTAGTCCTGCTCCCCACGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGGGTGCAGGgtaagggttaggcaattgttttgttttcatacaaatgatatatctattgt #### Csf2ra_ID13433_7 --> 0 - 0 Original Alignment AGCGCAGAGCCAGGAAGCACACCCCGGAAG aaagcctgcctatataggacataaattaacttttcatgtttttctttaagAGCACAGAACCAGGAAGCACACCT------gtaggtaactcttagcacaaaacatggcctggttttaaaaaagccacaat Alignment from CESAR AGCGCAGAGCCAGGAAGCACACCCCGGAAG aaagcctgcctatataggacataaattaacttttcatgtttttctttaagAGCACAGAACCAGGAAGCACACCT------gtaggtaactcttagcacaaaacatggcctggttttaaaaaagc Alignment from Spaln_aa2Genome AGCGCAGAGCCAGGAAGCACACCC aaagcctgcctatataggacataaattaacttttcatgtttttctttaagAGCACAGAACCAGGAAGCACACCTgtaggtaactcttagcacaaaacatggcctggttttaaaaaagccacaat Alignment from Spaln_nt2Genome AGCGCAGAGCCAGGAAGCACACCCCGGAAG aaagcctgcctatataggacataaattaacttttcatgtttttctttaagAGCACAGAACCAGGAAGCACA--CCTGTAGgtaactcttagcacaaaacatggcctggttttaaaaaagccacaat Alignment from Pairagon AGCGCAGAGCCAGGAAGCACACCC aaagcctgcctatataggacataaattaacttttcatgtttttctttaagAGCACAGAACCAGGAAGCACACCTgtaggtaactcttagcacaaaacatggcctggttttaaaaaagccacaat Alignment from Exonerate_protein2genome AGCGCAGAGCCAGGAAGCACACCCCGGA aaagcctgcctatataggacataaattaacttttcatgtttttctttaagAGCACAGAACCAGGAAGCACACCTGTAGgtaactcttagcacaaaacatggcctggttttaaaaaagccacaat Alignment from Exonerate_coding2genome aaagcctgcctatataggacataaattaacttttcatgtttttctttaagagcacagaaccaggaagcacacctgtaggtaactcttagcacaaaacatggcctggttttaaaaaagccacaat Alignment from GeneWise aaagcctgcctatataggacataaattaacttttcatgtttttctttaagagcacagaaccaggaagcacacctgtaggtaactcttagcacaaaacatggcctggttttaaaaaagccacaat #### Csf2ra_ID13434_6 --> 2 - 0 Original Alignment agCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCAGTGGCAG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagagCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTTCAG------gtacaacacgactgaggcctcaattttctgggaaagcctgcctatatagg Alignment from CESAR agCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCAGTGGCAG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagagCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTT------CAGgtacaacacgactgaggcctcaattttctgggaaagcctgcctatatagg Alignment from Spaln_aa2Genome AGCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCAG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagAGCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTTCAGgtacaacacgactgaggcctcaattttctgggaaagcctgcctatatagg Alignment from Spaln_nt2Genome AGCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCAG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagAGCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTTCAGgtacaacacgactgaggcctcaattttctgggaaagcctgcctatatagg Alignment from Pairagon AGCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCA--------------------------------------------------- tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagAGCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTTCAGGTACAACACGACTGAGGCCTCAATTTTCTGGGAAAGCCTGCCTATATAGG Alignment from Exonerate_protein2genome AGCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCAG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagAGCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTTCAGgtacaacacgactgaggcctcaattttctgggaaagcctgcctatatagg Alignment from Exonerate_coding2genome GCATCCTTGACGGCCCGGG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagagcgccttggtcctccatgtgatgtcacagcagcctgtaattcttcccattgcactgtgtcttgggctccaccttccacttgggcatctctggcagcacgggattatcagtttgaggttcaggtacaacacgactgaggcctcaattttctggGAAAGCCTGCCTATATAGG Alignment from GeneWise AGCGACTCGGTCCCCCACGTGACGTCACCGCGTCCTGTAACTCTTCCCACTGCACCGTCTCGTGGGCCCCGCCCTCGACCTGGGCATCCTTGACGGCCCGGGACTTCCAGTTTGAGGTCCAG tcattgtcagtgtatttgtgtgcttcattaccctcctctttgtcttgaagAGCGCCTTGGTCCTCCATGTGATGTCACAGCAGCCTGTAATTCTTCCCATTGCACTGTGTCTTGGGCTCCACCTTCCACTTGGGCATCTCTGGCAGCACGGGATTATCAGTTTGAGGTTCAGgtacaacacgactgaggcctcaattttctgggaaagcctgcctatatagg #### Csf2ra_ID13435_5 --> 1 - 1 Original Alignment gGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTC------g gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagaGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGATTTGGggtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from CESAR gGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTC------g gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagaGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGATTTGGggtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from Spaln_aa2Genome GGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTC------G gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagAGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGATTTGGGgtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from Spaln_nt2Genome GGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTC------G gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagAGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGATTTGGGgtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from Pairagon GGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCT------CG gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagAGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGATTTGGGgtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from Exonerate_protein2genome GGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTCG gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagAGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGAtttggggtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from Exonerate_coding2genome GGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTC gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagAGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGatttggggtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc Alignment from GeneWise GGGTCACGACGTGGCGCGATGCATGGCCGACCCCGGGGATGACGTCATCACACAGTGCATTGCGAACGACTTGTCACTGCTGGGGAGTGAGGCCTACTTGGTCGTGACCGGTCGGAGCGGTGCGGGGCCAGTGCGGTTCCTGGACGACGTGGTGGCTACGAAGGCGCTC------G gccactatcttgggcctctgtcactctatgtgttttatgtttgtaaccagAGGTCATGATGTGCCACACTCCATGGCTGATCCCGGGGATGATGTGATGACCCTGTGCATTGCGAATGATCTATCCTTACTGGGGAGTAAGGCCTATTTAGTAGTTACTGGCCGAAGTGGGGCAGGGCCTGTGTGGTTCTTGGATGATGTGGTTGCTACAAAGGCACTGATTTGGGgtaacttcctgttcattggtgcatatacaatcacagcgtggacatggagc #### Csf2ra_ID13437_3 --> 0 - 1 Original Alignment ---CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAg atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagTACCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGggtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from CESAR ---CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAg atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagTACCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGggtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from Spaln_aa2Genome ---CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAA atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagTACCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGGgtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from Spaln_nt2Genome ---CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAG atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagTACCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGGgtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from Pairagon ---CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAG atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagTACCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGGgtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from Exonerate_protein2genome CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAG atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagtacCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGGgtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from Exonerate_coding2genome CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAG atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagtacCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGGgtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc Alignment from GeneWise ---CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAG atagaatgctctgcgaattaccttaaccccacaaatccatgtctcctcagTACCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGGgtaaggatagatgtcgtgcactccaggttacgcgtactagctatcatatc #### Ctsf_ID680_8 --> 0 - 1 Original Alignment GGC---ATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACCGGGGGACTCTGCTCTCCCTGTCAGAGCAGg cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGG---TTGATTCAA---------------------------ggtaggcatatgagccactctggatataagtttgcggtattcctctagttg Alignment from CESAR GGC---ATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACCGGGGGACTCTGCTCTCCCTGTCAGAGCAGg cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTTGATT------------------------------CAAggtaggcatatgagccactctggatataagtttgcggtattcctctagttg Alignment from Spaln_aa2Genome ---GGCATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACCGGGGGACTCTGCTCTCCCTGTCAGAGCAGGAG cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTTGATTCAAGGTAGGCATATGAGCCACTCTGGATATAAGTTTgcggtattcctctagttg Alignment from Spaln_nt2Genome GGCA---TGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACC GGG cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTTGATTCAAGgtaggcatatgagccactctggatataagtttgcggtattcctctagTTG Alignment from Pairagon ----------------------------------------------CCAGGGC---ATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACCGGGGGACTCTGCTCTCCCTGTCAGAGCAG--------------------------------------------------------- CCTCCTAGGAACCCATTAGGGGGCTCTGCTTTATCACCTGAACCTTCCAGAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTT------------------------------------GATTCAAGGTAGGCATATGAGCCACTCTGGATATAAGTTTGCGGTATTCCTCTAGTTG Alignment from Exonerate_protein2genome CAGGGCATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACC GGG cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTTGATTCAAGgtaggcatatgagccactctggatataagtttgcggtattcctctagTTG Alignment from Exonerate_coding2genome CAGGGCATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACC GGG cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTTGATTCAAGgtaggcatatgagccactctggatataagtttgcggtattcctctagTTG Alignment from GeneWise ---GGCATGTGTGGCTCCTGCTGGGCCTTTTCTGTCACAGGCAACGTGGAGGGCCAGTGGTTCCTGAACCGGGGGACTCTGCTCTCCCTGTCAGAGCAGGAGCTCTTG cctcctaggaacccattagggggctctgctttatcacctgaaccttccagAGCAGTATGTGCAGCTCTTGCTGGGCCTTCTCTGTCACTGGCAATGGCGAGGGCCAGTGGTTGATT---CAAGGTAGGCATATGAGCCACTCTGGATATAAGTTTGCGgtattcctctagttg #### Ctsf_ID681_9 --> 2 - 1 Original Alignment agCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTGg tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagagCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATA---------ggtaaactgtcatgctcgggcctagtccataggatgatagtggctaccatg Alignment from CESAR agCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTGg tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagagCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATA---------ggtaaactgtcatgctcgggcctagtccataggatgatagtggctaccatg Alignment from Spaln_aa2Genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTGGGA- tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagAGCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAGGTAAACTGTCATgctcgggcctagtccataggatgatagtggctaccatg Alignment from Spaln_nt2Genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAA tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagAGCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAGgtaaactgtcatgctcgggcctagtccataggatgatagtggctaccatg Alignment from Pairagon AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTGG tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagAGCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATA---------Ggtaaactgtcatgctcgggcctagtccataggatgatagtggctaccatg Alignment from Exonerate_protein2genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTT tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagAGCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAGGTAAACTgtcatgctcgggcctagtccataggatgatagtggctaccatg Alignment from Exonerate_coding2genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTT tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagAGCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAGGTAAACTgtcatgctcgggcctagtccataggatgatagtggctaccatg Alignment from GeneWise AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAA tcaggcaaactcctcaatagggttccttatcattgctctgtgattcacagAGCTCTCACATTGCGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAGgtaaactgtcatgctcgggcctagtccataggatgatagtggctaccatg #### Ctsf_ID685_13 --> 2 - 0 Original Alignment gcTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG GG cgtaagctctggtaattccttactattagacactatggtcccctccacaggtTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGTGAG---gtaaggagaaggaggtaaccttgggtcatcttatatttttctccctagGG Alignment from CESAR gcTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG cgtaagctctggtaattccttactattagacactatggtcccctccacaggtTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGTGAG---gtaaggagaaggaggtaaccttgctatatttgtttgtttgcttttca Alignment from Spaln_aa2Genome GCTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAG GA cgtaagctctggtaattccttactattagacactatggtcccctccacagGTTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGTGAGgtaaggagaaggaggtaaccttgggtcatcttatatttttctccctag-- Alignment from Spaln_nt2Genome GCTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAG GA cgtaagctctggtaattccttactattagacactatggtcccctccacagGTTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGTGAGgtaaggagaaggaggtaaccttgggtcatcttatatttttctccctag-- Alignment from Pairagon GCTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGG---------------------------------------------AGGG cgtaagctctggtaattccttactattagacactatggtcccctccacagGTTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGTGAGGTAAGGAGAAGGAGGTAACCTTGGGTCATCTTATATTTTTCTCCCTAGGG Alignment from Exonerate_protein2genome GCTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG GG cgtaagctctggtaattccttactattagacactatggtcccctccacagGTTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGT---GAGgtaaggagaaggaggtaaccttgggtcatcttatatttttctccctagGG Alignment from Exonerate_coding2genome GCTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG GG cgtaagctctggtaattccttactattagacactatggtcccctccacagGTTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGT---GAGgtaaggagaaggaggtaaccttgggtcatcttatatttttctccctagGG Alignment from GeneWise GCTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG GG cgtaagctctggtaattccttactattagacactatggtcccctccacagGTTCTAACATCCCTTACTGGGCAATCAAGAATAGCTGGGGAAGTGACTGGGGT---GAGgtaaggagaaggaggtaaccttgggtcatcttatatttttctccctagGG #### Ctsw_ID1024_2 --> 0 - 1 Original Alignment GATGCAGGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAg aggatgagaggagaatcatgacaaactaggcctctccccttgttttgcag------GGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAggtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from CESAR GATGCAGGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAg taaatcaggatgagaggagaatcatctaggcctctccccttgttttgcag------GGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAggtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from Spaln_aa2Genome GATGCAGGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAG aggatgagaggagaatcatgacaaactaggcctctccccttgttttgcag------GGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAGgtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from Spaln_nt2Genome GATGCAGGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAG aggatgagaggagaatcatgacaaactaggcctctccccttgttttgcag------GGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAGgtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from Pairagon GATGCAGGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAG aggatgagaggagaatcatgacaaactaggcctctccccttgttttgcag------GGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAGgtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from Exonerate_protein2genome GGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAG aggatgagaggagaatcatgacaaactaggcctctccccttgttttgcagGGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAGgtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from Exonerate_coding2genome GGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAG aggatgagaggagaatcatgacaaactaggcctctccccttgttttgcagGGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAGgtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa Alignment from GeneWise ---------------GATGCAGGTCCCCGGCCACTGGAGCTGAAGGAAGTCTTCAAGCTGTTCCAGATCCGGTTCAACCGGAGTTACTGGAACCCAGCAG aggatgagaggagaatcatgacaaactagGCCTCTCCCCTTGTTTTGCAGGGTCCCCGACCACTTGAGTTGAAGGAAGTCTTTAGACTGTTTGACATACGGCTCAACCAAAGCTACTGGAACCCAACAGgtgagtcaaggtatagacatttctggtacaactcctgttgttggctgaaa #### Cutc_ID8809_4 --> 2 - 1 Original Alignment gtGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTA------g tatgccacaggggtagctgaactctggcggattctctcattgacccttaggaGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGCTGGAGggtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc Alignment from CESAR gtGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTA------g tatgccacaggggtagctgaactctggcggattctctcattgacccttaggaGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGCTGGAGggtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc Alignment from Spaln_aa2Genome GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTA------G tatgccacaggggtagctgaactctggcggattctctcattgacccttagGAGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGCTGGAGGgtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc Alignment from Spaln_nt2Genome GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTA------G tatgccacaggggtagctgaactctggcggattctctcattgacccttagGAGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGCTGGAGGgtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc Alignment from Pairagon GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGT tatgccacaggggtagctgaactctggcggattctctcattgacccttagGAGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTgctggagggtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc Alignment from Exonerate_protein2genome GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTA tatgccacaggggtagctgaactctggcggattctctcattgacccttagGAGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGctggagggtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc Alignment from Exonerate_coding2genome GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAGCTCTTTGCCGCCCTCTGCCGGTCACTTTCCACAGAG tatgccacaggggtagctgaactctggcggattctctcattgacccttagGAGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGCTGGAGGGTATGTGTCTAGACACCAGCTAAAATACATgtgtaccatacaattccagc Alignment from GeneWise GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAGCTCTTTGCCGCCCTCTGCCGGTCACTTTCCACAGAG tatgccacaggggtagctgaactctggcggattctctcattgacccttagGAGTGCTGCAAGTGGTGACGCAGAGTGTCCATGTCCCAGTGTTTGTGATCATTCACCCACGAGGAGGTGACTTCCTACACTCAGACCAGGAAGTGGAAGTGATGATAGCTGATATTTGCCTAGCCAAGCTTTATGGTGCTGATGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAACTAAGTATATCTCTTGTGCTG------------------------------GAGGgtatgtgtctagacaccagctaaaatacatgtgtaccatacaattccagc #### Cyp26a1_ID7414_2 --> 0 - 0 Original Alignment ---CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagTACCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from CESAR ---CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagTACCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from Spaln_aa2Genome ---CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagTACCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from Spaln_nt2Genome ---CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagTACCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from Pairagon ---CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagTACCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from Exonerate_protein2genome CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagtacCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from Exonerate_coding2genome CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagtacCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa Alignment from GeneWise ---CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaatgatggccactttcatgttttttaattttaattttttagTACCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGTTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACTTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagtctgcaaggccaattgaagtaattactggaaggccattgctacaa #### Cyp26a1_ID7415_3 --> 0 - 0 Original Alignment ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG GGCGTGAAGGCGCGGAACCTTA atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagATTGAACATGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTGTTCCGTgtaccgtttgtgttttttcctatcccagGGTGTT---TCTTGTAATATAA Alignment from CESAR ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG GGCGTGAAGGCGCGGAACCTTA atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagATTGAACATGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTGTTCCGTgtaaccttaattcctactttaattttagGGTGTT---TCTTGTAATATAA Alignment from Spaln_aa2Genome ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGGGGCGTGAAGGCGCGGAACCTTATACAC atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagATTGAACATGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTGTTCCGT------------------GTACCGTTTgtgttttttcctatcccagggtg Alignment from Spaln_nt2Genome ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCT GTACCGGGGCGTGAAGGCGCGG atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagATTGAACATGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTT---CATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTgttccgtgtaccgtttgtgttttttcctatcccagG---------GTG-TTTCTTGT Alignment from Pairagon ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGGGGCGTGAAGGCGCGGAACCTT----------------------------------------------ATAC atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagATTGAACATGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTT---CATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTGTTCCG---------------------TGTACCGTTTGTGTTTTTTCCTATCCCAGGGTGTTTCTTGTAATATAATAC Alignment from Exonerate_protein2genome AACCTTATAC atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagattgaacatgtgataatgcatgcattcagcagggaagcactccagtgttatgtccctgtcatagctgaggaagtcagcagttgcttggaacagtggctatgctgtggtgaacatggtctccttgcgtatcctgaggtgaagcgccttatgttcattgctatgcgaatcctgctaggctgtcagcaaggttcagcaggaagtggggaggatgaacagcagctagtagagtcttttgaggaaatgacccgtaatcttgtttcccttcccattgatgtcccattcagtggtctgttccgtgtaccgtttgtgttttttcctatcccagggtgtttcttgtAATATAATAC Alignment from Exonerate_coding2genome GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagattgaacatGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTGTTCCGTgtaccgtttgtgttttttcctatcccagggtgtttcttgtaatataatac Alignment from GeneWise ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG GGCGTGAAGGCGCGGAACCTTA atcaggcacaaagcataggttgacaaactgtctctctgcctgggctacagATTGAACATGTGATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTCATAGCTGAGGAAGTCAGCAGTTGCTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGTTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTTGTTTCCCTTCCCATTGATGTCCCATTCAGTGGTCTGTTCCGTgtaccgtttgtgttttttcctatcccagGGTGTTTCTTGT---AATATAA #### Cyp2c39_ID7783_2 --> 0 - 1 Original Alignment TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTg tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGC---ggtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from CESAR TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTg tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGC---ggtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from Spaln_aa2Genome TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGC- tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGCGgtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from Spaln_nt2Genome TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGC---Ggtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from Pairagon TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGC---Ggtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from Exonerate_protein2genome TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGC---Ggtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from Exonerate_coding2genome TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGC---Ggtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat Alignment from GeneWise TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCC tgtagaaggtcagaattgttagtgtttgatccaattatttttttctgtagTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTCGTCCCACTGTTGTGCTATATGGGTATGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGGGGAAGCATCCCAATGGTAGATGAGATTAATACTGGCGgtgagcatgacattaagaggcaagttcaggtttgaggcgttgtaattaat #### Cyp2c50_ID7861_2 --> 0 - 1 Original Alignment TTATCAAAAGTTTAT---GGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGg ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAAT------ggtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca Alignment from CESAR TTATCAAAAGTTTAT---GGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGg ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAAT------ggtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca Alignment from Spaln_aa2Genome TTATCAAAAGTTTAT---GGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATG ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAATGgtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca Alignment from Spaln_nt2Genome TTATCAAAAGTTTATG---GCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAATGG--TGGgttctcagttagatttccaatgccagtaaaggggagtacgagtc Alignment from Pairagon TTATCAAAAGTTT---ATGGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATG ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAATGgtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca Alignment from Exonerate_protein2genome TTATCAAAAGTTTAT---GGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAAT------Ggtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca Alignment from Exonerate_coding2genome TTATCAAAAGTTTAT---GGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAAT------Ggtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca Alignment from GeneWise TTATCAAAAGTTTAT---GGCCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAAGCTCTGGTTGACCATGGGGAGGAGTTTGCTGGAAGAGGAAGGCTCCCAGTTTTTGATAAAGCTACTAAT- ctattacatggcagacagatatctcttgcagcttaatgtttttctcttagTTATCCAAAGTCTATGATGGTCCTGTGTATACACTGTATTTAGGTAAGAATCCTACTGTAGTATTACAGGGTTATGAGGCGGTGAGGGAATCGTTAGTTGACCATGGAGAAGAATTTGCTGGGAGAGAGAGACTACCTGTTTTTGATAAAGCTACCAATGgtgggttctcagttagatttccaatgccagtaaaggggagtacgagtcca #### Cyp2c50_ID7863_4 --> 2 - 0 Original Alignment gcTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG gcttccatacctagctttagtccaccactaatcgtctctaacctttataggc------TGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGGTTT---gtaaattcagatatttgggattacacccgtttgctgttattttaagtgtg Alignment from CESAR gcTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tgtctagcttccatacctagctttacactaatcgtctctaacctttataggc------TGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGGTTT---gtaaattcagatatttgggattacacccgtttgctgttattttaagt Alignment from Spaln_aa2Genome CCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTG gcttccatacctagctttagtccaccactaatcgtctctaacctttatagGCTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGGTTTgtaaattcagatatttgggattacacccgtttgctgttattttaagtgtg Alignment from Spaln_nt2Genome GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTG gcttccatacctagctttagtccaccactaatcgtctctaacctttatagG------CTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGgtttgtaaattcagatatttgggattacacccgtttgctgttattttaagtgtg Alignment from Pairagon GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTG gcttccatacctagctttagtccaccactaatcgtctctaacctttatagG------CTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGGTTTgtaaattcagatatttgggattacacccgtttgctgttattttaagtgtg Alignment from Exonerate_protein2genome ACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG gcttccatacctagctttagtccaccactaatcgtctctaacctttatAGGCTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGGTTT---gtaaattcagatatttgggattacacccgtttgctgttattttaagt Alignment from Exonerate_coding2genome ACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG gcttccatacctagctttagtccaccactaatcgtctctaacctttatAGGCTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGGTTT---gtaaattcagatatttgggattacacccgtttgctgttattttaagt Alignment from GeneWise GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG gcttccatacctagctttagtccaccactaatcgtctctaacctttatagGC------TGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCCGCAATGATATTCACTCAATTATTTTTGATGATCGATTCGAATATAAAGATCGGGATTTTCTGAATTTGATGGAAAAGTTAAATAAAATATCCAAAATAATGAGTATGCCATGG---TTTgtaaattcagatatttgggattacacccgtttgctgttattttaagtgtg #### Cyp2c54_ID7855_3 --> 2 - 1 Original Alignment gcATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT---------g ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcaggcATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCGGCAGCAAggtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from CESAR gcATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT---------g ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcaggcATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCGGCAGCAAggtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from Spaln_aa2Genome GCATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT---------G ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcagGCATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCGGCAGCAAGgtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from Spaln_nt2Genome GCATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT---------G ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcagGCATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCGGCAGCAAGgtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from Pairagon GCATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT---------G ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcagGCATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCGGCAGCAAGgtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from Exonerate_protein2genome GCATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAATG ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcagGCATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCggcagcaaggtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from Exonerate_coding2genome GCATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAATG ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcagGCATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCggcagcaaggtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact Alignment from GeneWise GCATTGGATTTAGTAATGGAAGTGTATGGAAAAACACGAGGCACTTCTCACTCATGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT---------G ctagccctgctgtattgccaggcggcttcatatgtcccatgtccttgcagGCATTGGATTTAGCAATGGAACCGTATGGAAGAACACCAGGCACTTCTCACTGATGACATTGTGGAATTTAGGTATGGGAAAAAGGAGTATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCCTGTGGAAGAACTGAGAAAGAGCAATCGGCAGCAAGgtaagtggaacaagggtgtggctaccaactgggttgcacaaattctgact #### Dagla_ID2759_11 --> 0 - 0 Original Alignment GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG acttcacttttgttacactaccacttgcaattgatttcttattgttgtag------CTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from CESAR GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG ctttacacttcacttttgttacacttgcaattgatttcttattgttgtag------CTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from Spaln_aa2Genome CTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG acttcacttttgttacactaccacttgcaattgatttcttattgttgtagCTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from Spaln_nt2Genome CTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG acttcacttttgttacactaccacttgcaattgatttcttattgttgtagCTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from Pairagon GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG acttcacttttgttacactaccacttgcaattgatttcttattgttgtag------CTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from Exonerate_protein2genome CTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG acttcacttttgttacactaccacttgcaattgatttcttattgttgtagCTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from Exonerate_coding2genome acttcacttttgttacactaccacttgcaattgatttcttattgttgtagctaactgatttaacaggtgatgcagagcaccttcctgcagagacacatagagttgcctggttggggcataaagtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa Alignment from GeneWise CTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG acttcacttttgttacactaccacttgcaattgatttcttattgttgtagCTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACATAGAGTTGCCTGGTTGGGGCATAAAgtacagcgttaactgatattccagtgtctcacagttgctctgatgctgaa #### Dagla_ID2760_10 --> 0 - 0 Original Alignment ---------GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttagGATATGTTAGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt Alignment from CESAR ---------GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttagGATATGTTAGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactaccac Alignment from Spaln_aa2Genome GTCTATGAAACTCCC---------TTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttagGATATGTTAGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt Alignment from Spaln_nt2Genome GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttaggatatgttagTTTATGAAAC-TCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt Alignment from Pairagon ---------GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttagGATATGTTAGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt Alignment from Exonerate_protein2genome GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttaggatatgttaGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt Alignment from Exonerate_coding2genome GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttaggatatgttaGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt Alignment from GeneWise ---------GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG ctcttcaaggtatatctgattaaccttcctgttactttcaccccatttagGATATGTTAGTTTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAAAAAGTAGTGGTCAGCATCAGGGGGAATTTATCCCCGAAAgtgcttgccattgtattcaactttacacttcacttttgttacactacctt #### Dak_ID2898_15 --> 1 - 0 Original Alignment gTATGGAAAGGCTGCACCAGGAGACAGGACAATG gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcaggTATGGAAAGGCTGCACCAGGAGACAGGACA---gtgccatggttgctttaccactttggctctcccctgtggtgctaagattt Alignment from CESAR gTATGGAAAGGCTGCACCAGGAGACAGGACAATG gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcaggTATGGAAAGGCTGCACCAGGAGACAGGACA---gtgccatggttgctttaccactttggctctcccctgtggtgctaatg Alignment from Spaln_aa2Genome GTATGGAAAGGCTGCACCAGGAGACAGGACA gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcagGTATGGAAAGGCTGCACCAGGAGACAGGACAgtgccatggttgctttaccactttggctctcccctgtggtgctaagattt Alignment from Spaln_nt2Genome GTATGGAAAGGCTGCACCAGGAGACAGGACA-----ATG gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcagGTATGGAAAGGCTGCACCAGGAGACAGGACAGTGCCATGgttgctttaccactttggctctcccctgtggtgctaagattt Alignment from Pairagon GTATGGAAAGGCTGCACCAGGAGACAGGACAAT------------------------------------------------ gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcagGTATGGAAAGGCTGCACCAGGAGACAGGACAGTGCCATGGTTGCTTTACCACTTTGGCTCTCCCCTGTGGTGCTAAGATTT Alignment from Exonerate_protein2genome GTATGGAAAGGCTGCACCAGGAGACAGGACAATG gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcagGTATGGAAAGGCTGCACCAGGAGACAGGACAGTGccatggttgctttaccactttggctctcccctgtggtgctaagattt Alignment from Exonerate_coding2genome gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcaggtatggaaaggctgcaccaggagacaggacagtgccatggttgctttaccactttggctctcccctgtggtgctaagattt Alignment from GeneWise gccactcgtgtcagcacctttggaggtacactgtgtgttcttttcttcaggtatggaaaggctgcaccaggagacaggacagtgccatggttgctttaccactttggctctcccctgtggtgctaagattt #### Dak_ID2904_9 --> 2 - 1 Original Alignment gcTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGg tgtctaggcatgctacaagcatgatcccgactttacttgtggaaaaataggt---TTAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTggtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct Alignment from CESAR gcTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGg gagtgtctaggcatgctacaagcatcccgactttacttgtggaaaaataggt---TTAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTggtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct Alignment from Spaln_aa2Genome GCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG tgtctaggcatgctacaagcatgatcccgactttacttgtggaaaaatagGT---TTAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTGgtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct Alignment from Spaln_nt2Genome GCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG tgtctaggcatgctacaagcatgatcccgactttacttgtggaaaaatagG---TTTAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTGgtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct Alignment from Pairagon GCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG tgtctaggcatgctacaagcatgatcccgactttacttgtggaaaaataggtttag---------TGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTGgtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct Alignment from Exonerate_protein2genome GCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG tgtctaggcatgctacaagcatgatcccgactttacttgtggaaaaatagGT---TTAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTGgtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG tgtctaggcatgctacaagcatgatcccgactttacttgtggaaaaatagGTTTA---GTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCTGGGAACTAGGTATCACTGCTGATGCTGCCATTCATTTGCTTGgtgagtaaccccatcaggcatccatatggaaaccctctaacgcctatgct #### Ddb1_ID2929_14 --> 1 - 1 Original Alignment cCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---g tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagtCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGggtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from CESAR cCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---g tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagtCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGggtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from Spaln_aa2Genome CCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---G tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagTCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGGgtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from Spaln_nt2Genome CCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---G tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagTCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGGgtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from Pairagon -----------------------------------------------CAGCCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---G TGTCAGGCACTTGTTTCTTTGTTTATTGTGTTTTCTTTACTTTTGGGCAGTCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGGgtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from Exonerate_protein2genome CCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---G tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagTCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGGgtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from Exonerate_coding2genome CCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGA---G tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagTCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGGgtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag Alignment from GeneWise CCACACAGAGATGGAACATGAAGTGGCATGCTTGGATATCACCCCATTAGGGGACAGCAATGGCCTCTCCCCACTTTGTGCCATTGGACTTTGGACAGACATCTCAGCTCGTATCCTGAAGCTCCCATCCTTTGAACTACTACACAAGGAGATGCTGGGTGGAGAG- tgtcaggcacttgtttctttgtttattgtgttttctttacttttgggcagTCACACAGAAATGGAACATGAAGTAGCATGTCTGGACACTACCCCGTTAGGGGATAGCAATGGTCTCTCCCTGCTTTGTGCCATTGGACTTTGGACAGATATCTCAGCTCGTATCTTGAGGCTCCCATCCTTTGAATTATTACATAAGGAGATGCTGGGTGGAATGGgtaagtcttttgtttatcctcaagacaacagcccagtcagggtgaacaag #### Ddb1_ID2934_19 --> 0 - 1 Original Alignment GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAA---GAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGAA------------------------g ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGAC---GAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGAGTTTGTTTTGTCTGGATTCTTGTCAtgtgagcaatgaccctttggggttaaaggcttggttgtagatctacaggtg Alignment from CESAR GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGAAg ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTG--agtttgttttgtctggattcttgtcatgtgagcaatgaccctttggggttaaaggcttggttgtagatctacaggtg Alignment from Spaln_aa2Genome GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGA AGTG- ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGAgtttgttttgtctggattcttgtcatgtgagcaatgaccctttggggttaaagGCTTGgttgtagatctacaggtg Alignment from Spaln_nt2Genome GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGAA ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGA-gtttgttttgtctggattcttgtcatgtgagcaatgaccctttggggttaaaggcttggttgtagatctacaggtg Alignment from Pairagon GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGA---------------------------------------------------------------------------- ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGAGTTTGTTTTGTCTGGATTCTTGTCATGTGAGCAATGACCCTTTGGGGTTAAAGGCTTGGTTGTAGATCTACAGGTG Alignment from Exonerate_protein2genome GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGAAG ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGAGTttgttttgtctggattcttgtcatgtgagcaatgaccctttggggttaaaggcttggttgtagatctacaggtg Alignment from Exonerate_coding2genome GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGAAG ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGAGTttgttttgtctggattcttgtcatgtgagcaatgaccctttggggttaaaggcttggttgtagatctacaggtg Alignment from GeneWise GCCCTGTCCAGCAGCGTCAGCTCCAGCAAACTTTTCTCCAGCAGTACGGCTCCTCACGAGACCTCCTTTGGAGAAGAAGTGGAGGTGCACAACCTCCTCATCATTGACCAGCACACCTTTGAAGTG ctcgaattgacttatccagattttttgacatagcccctccccctccccagGCTCTGTCTAGCAGTATCAGTTCCAGCAAACTTTTCTCCATCAGTACAGCCCCTCATGAAATGTCCTTTGGAGAAGAAGACGAGGTCCACAATCTCCTTATCAATGACCAACATACATTTGAGTTTgttttgtctggattcttgtcatgtgagcaatgaccctttggggttaaaggcttggttgtagatctacaggtg #### Ddb1_ID2936_21 --> 2 - 0 Original Alignment gaAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccaggaAAGCTT---ACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAAT------gtaagagagttggacaatggttttacactgaactctaatgacccacattt Alignment from CESAR gaAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccaggaAAGCTT---ACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAAT------gtaagagagttggacaatggttttacactgaactctaatgaccc Alignment from Spaln_aa2Genome GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAAT cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccagGAAAGCTT---ACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAATgtaagagagttggacaatggttttacactgaactctaatgacccacattt Alignment from Spaln_nt2Genome GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAAT cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccagGAAAGCT---TACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAATgtaagagagttggacaatggttttacactgaactctaatgacccacattt Alignment from Pairagon GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAAT cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccagGAAAGCT---TACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAATgtaagagagttggacaatggttttacactgaactctaatgacccacattt Alignment from Exonerate_protein2genome GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCA cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccagGAAAGCTT---ACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAATGTAAgagagttggacaatggttttacactgaactctaatgacccacattt Alignment from Exonerate_coding2genome GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCA cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccagGAAAGCTT---ACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGTACAAATGTAAgagagttggacaatggttttacactgaactctaatgacccacattt Alignment from GeneWise GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG cctgagtggaatcctagcaagcactggctctgcccttcttcccctcccagGAAAGCTT---ACTGTCATTGATAAGGAAGTAAAAGGGTCAGTGTACTCAATGGTTGATTTTAATGGGAAATTGTTGGCCAGT------ACAAATgtaagagagttggacaatggttttacactgaactctaatgacccacattt #### Dkk1_ID6483_2 --> 0 - 1 Original Alignment CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATg actgtgggatcaactgacctatcttacgagatgtatatcttttctttcag---TTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---GTTGAT------CAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATcgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from CESAR CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATg tcaactgtgggatcaactgacctatacgagatgtatatcttttctttcag---TTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---GTTGAT------CAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATcgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from Spaln_aa2Genome CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATG actgtgggatcaactgacctatcttacgagatgtatatcttttctttcag---TTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATCgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from Spaln_nt2Genome CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATG actgtgggatcaactgacctatcttacgagatgtatatcttttctttcag---TTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGC---------TGTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATCgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from Pairagon CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATG actgtgggatcaactgacctatcttacgagatgtatatcttttctttcag---TTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATCgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from Exonerate_protein2genome TACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATG actgtgggatcaactgacctatcttacgagatgtatatcttttctttcagTTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATCgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from Exonerate_coding2genome TACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATG actgtgggatcaactgacctatcttacgagatgtatatcttttctttcagTTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATCgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta Alignment from GeneWise TACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATG actgtgggatcaactgacctatcttacgagatgtatatcttttctttcagTTCCCTTGTGTTATAGATGAGGATTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCTGTTGAT---------CAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCAAGAATCgtagtggtaccccagtatctattgacaagttctatatctatgtaggtgta #### Dntt_ID8079_5 --> 0 - 0 Original Alignment GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from CESAR GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from Spaln_aa2Genome GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from Spaln_nt2Genome GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from Pairagon GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from Exonerate_protein2genome GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from Exonerate_coding2genome GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAA--- aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt Alignment from GeneWise GGAATTATTGAAGATGGAGAAAGTTCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAATCCTTCAAACTC aacagggagagggttataagatgatctcccccactccccgctccccacagGGAATCATTGAAGATGGGGATAGTCCTGAAGCTAAAGCTGTGTTAAATGATGAGCGATATAAGTCTTTCAAATACgtgagccacatgtcagggggaaagccccgcagaatgtagtggttgtgttt #### Dock8_ID5413_32 --> 0 - 1 Original Alignment GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATGATGCGCCGTCGCATTCCAg ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATG------------------ggtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg Alignment from CESAR GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATGATGCGCCGTCGCATTCCAg ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATG------------------ggtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg Alignment from Spaln_aa2Genome GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATG- ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATGGgtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg Alignment from Spaln_nt2Genome GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATGA ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATGGgtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg Alignment from Pairagon GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATGATGCGCCGTCGCATTCCAG ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATG------------------Ggtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg Alignment from Exonerate_protein2genome GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATGATGCGCCGTCGCATTCC ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATGGGTAAAATCCCAACACTgtaagacttgggaattaacaaaccttaacttatg Alignment from Exonerate_coding2genome ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagggaaagcagagttctgacaaagtcagtaaccaggtcctgcagaagtctagagatgtcaaggccaaactggaagaggccctgctccgtggtgaaggagcccgtggggagatgggtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg Alignment from GeneWise GGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCAAGAGACGTCAAGGCCAAGCTGGAAGAGGCCCTGCTCCGTGGGGAAGGAGCCCGTGGGGAGATG- ttgcagaagagacctagtaaactcaaagctttatcttactttgctttaagGGAAAGCAGAGTTCTGACAAAGTCAGTAACCAGGTCCTGCAGAAGTCTAGAGATGTCAAGGCCAAACTGGAAGAGGCCCTGCTCCGTGGTGAAGGAGCCCGTGGGGAGATGGgtaaaatcccaacactgtaagacttgggaattaacaaaccttaacttatg #### Dpf2_ID1305_8 --> 2 - 1 Original Alignment ccAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------g ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagccAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAggtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from CESAR ccAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------g ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagccAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAggtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from Spaln_aa2Genome CCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------G ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagCCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAGgtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from Spaln_nt2Genome CCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------G ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagCCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAGgtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from Pairagon CCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTC---------AG ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagCCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAGgtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from Exonerate_protein2genome CCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------G ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagCCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAGgtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from Exonerate_coding2genome CCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------G ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagCCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAGgtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt Alignment from GeneWise CCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTAGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCCGAGGAGCTAGTGTCCTGTTCCGACTGTGGCCGCTCA---------G ataacaaagtggggctcagcaaaaaagagccttctctcacttctgaccagCCAAGAAAGGACCTGATGGATTGGCCCTGCCTAACAACTACTGTGACTTCTGCCTTGGAGACTCAAAAATCAACAAGAAGACAGGGCAGCCTGAGGAGCTAGTGTCCTGTTCTGACTGTGGCCGCTCATTAACTCAAGgtgagtaacttactatacaccccatgccaaaggcttgactctatattgtt #### Dpf2_ID1309_5 --> 0 - 0 Original Alignment ------CGGATCATTGAACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagCTGCTCCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC Alignment from CESAR ------CGGATCATTGAACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagCTGCTCCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttctgccactgttttctgtttttcagGGGACAGGTGTC Alignment from Spaln_aa2Genome CGGATCATTGAA------CCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagCTGCTCCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC Alignment from Spaln_nt2Genome CGGATCATTGA------ACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagCTGCTCCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC Alignment from Pairagon ------CGGATCATTGAACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagCTGCTCCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC Alignment from Exonerate_protein2genome CGGATCATTGAACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagctgctcCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC Alignment from Exonerate_coding2genome CGGATCATTGAACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagctgctcCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC Alignment from GeneWise ------CGGATCATTGAACCCGATGACTTCCTTGATGACCTTGATGATGAGGACTATGAAGAAGATACGCCAAAGCGTCGGGGGAAGGGGAAGTCCAAG AGTAAGGGTGTG gtgatgagctctctgtgagctacctatgttgctatgttttcttgttacagCTGCTCCGGGTCATTGAACCTGATGACTTCTTTGATGACCTAGATGATGAGGACTATGATGAAGATACACCCAAGCGTCGGGGTAAGGGCAAGTCCAAGgtaagtagtttcttcttctgctatgtaccctttcccagGGGACAGGTGTC #### Dpp3_ID746_7 --> 0 - 2 Original Alignment ---GCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGag gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGaggtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from CESAR ---GCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGag gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGaggtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from Spaln_aa2Genome ---GCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGA gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGAGgtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from Spaln_nt2Genome --GGCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGAG gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGAGgtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from Pairagon ----------------------------------------------------GGCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGAG GAATATGTGGATGGATCAAAATGAAGATCCCCCGCCCTTTCTCTTTTCAGATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGAGgtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from Exonerate_protein2genome ---GCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGAG gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGAGgtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from Exonerate_coding2genome ---GCTTATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGAG gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGAGgtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa Alignment from GeneWise ------TATGCAGCCAACAGCCACCAGGAGCAAATGCTGGCTCAGTACGTGGAGAGCTTCACCCAGGGCTCCATTGAGGCCCATAAGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGCCCCATTGTAGAGAG gaatatgtggatggatcaaaatgaagatcccccgccctttctcttttcagATGGCGTATGCAGCCAACTGCTACCAGAAGCAGATGCTGTCCCAGTATGTGGAAAGCTTCACTGAAGGATCCATTGATGCCCATAAGAGGGGTTCCCATTTCTGGATCCAGGACAAAGGCCCAGTTGTAAAGAGgtaggtcatcactcaatctttccattcctggtttgttagcaagggtacaa #### Eef1g_ID2567_9 --> 2 - 0 Original Alignment gg---------------------ATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccaggtCCCATCTTCATGCGCACGGACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from CESAR gg---------------------ATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccaggtCCCATCTTCATGCGCACGGACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from Spaln_aa2Genome CTGGGATGTTTCAG------------------CGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccagGTCCCATCTTCATGCGCACGGACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from Spaln_nt2Genome GG---------------------ATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccagGTCCCATCTTCATGCGCACGGACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from Pairagon ------------------------------------------------------------------------GATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG GGTATGGGAATAAAGAGTTGGGGAGGACAGCTTCCCACACCCTTCTCCAGGTCCCATCTTCATGCGCACGGACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from Exonerate_protein2genome GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccaggtcccatcttcatgcgcacggACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from Exonerate_coding2genome GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccaggtcccatcttcatgcgcacggACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa Alignment from GeneWise --------------------GGGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG ggtatgggaataaagagttggggaggacagcttcccacacccttctccagGTCCCATCTTCATGCGCACGGACATGTTCCAACGGCTTGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAACTTGCCTATCCAgtaagtcctcaatatgagagattcatggtgggggcttaaaagttttgaaa #### Efemp2_ID1032_5 --> 2 - 1 Original Alignment acATAGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGg tccaagttggttggctaggctacaacctcaaattcattctttatttgaagac------GAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGggtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from CESAR acATAGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGg gatacatccaagttggttggctaggcctcaaattcattctttatttgaagac------GAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGggtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from Spaln_aa2Genome GACATAGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGG ttggttggctaggctacaacctcaaattcattctttatttgaa gACGAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGGgtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from Spaln_nt2Genome ATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGG tccaagttggttggctaggctacaacctcaaattcattctttatttgaagACGAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGGgtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from Pairagon ------------------------------------------------AGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGG TCCAAGTTGGTTGGCTAGGCTACAACCTCAAATTCATTCTTTATTTGAAGACGAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGGgtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from Exonerate_protein2genome ACATAGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGG tccaagttggttggctaggctacaacctcaaattcattctttatTTGAAGACGAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGGgtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from Exonerate_coding2genome ACATAGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGG tccaagttggttggctaggctacaacctcaaattcattctttatTTGAAGACGAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGGgtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg Alignment from GeneWise ACATAGATGAGTGTCGTTACCGCTATTGCCAGCATCGATGTGTGAACCTGCCGGGCTCTTTTCGATGCCAGTGTGAGCCAGGCTTCCAGTTGGGACCTAACAACCGCTCTTGTGTGG tccaagttggttggctaggctacaacctcaaattcattctttatttgaagAC------GAGTGCCGTTACCACTATTGCCAGCATCGATGTGTGATCCTACCAGGCTCGTTCCGATGTCAATGTGAGCCAGGTTTCCAATTAGGCCCTAACATTCGTTCTTGTGTGGgtaaaacagcgtgtcccaaaggtctttaacctttgagtggaaccactatg #### Efemp2_ID1033_6 --> 2 - 1 Original Alignment at------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCg tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagatTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTggtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from CESAR at------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCg tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagatTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTggtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from Spaln_aa2Genome AT------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCG tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagATTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTGgtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from Spaln_nt2Genome AT------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCG tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagATTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTGgtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from Pairagon AT------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCG tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagATTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTGgtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from Exonerate_protein2genome AT------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCG tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagATTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTGgtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from Exonerate_coding2genome AT------GTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCG tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagATTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTGgtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt Alignment from GeneWise -----GATGTGAATGAGTGTGACATGGGAGCCCCATGTGAGCAGCGCTGCTTCAACTCCTATGGGACCTTCCTGTGTCGCTGTAACCAGGGCTATGAGCTGCACCGGGATGGCTTCTCCTGCAGCG tgaaatccaaaactttcactttctatctctttttaccctctcatcatcagATTTTTTCGTTAATGAATGTGACATGGGAGCACCTTGTGAGCAGCGTTGTTTCAATTCATATGGGACCTTTTTGTGCCGGTGTAACCAGGGCTATGAGCTACACTGGGATGGCTTCTCCTGCAGTGgtaccagtcaactgagatatcccctatatgctacacaacataaatttgtt #### Ehbp1l1_ID1220_15 --> 0 - 1 Original Alignment CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCA------g tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTggtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca Alignment from CESAR CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCA------g tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTggtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca Alignment from Spaln_aa2Genome CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCA------G tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTGgtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca Alignment from Spaln_nt2Genome CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCA------G tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTGgtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca Alignment from Pairagon CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAAT----------------------------------------------------------- tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTGGTAATGCCCCCTAGTTTCATCTGTGCTTAAAACCCAATACAATTGAGACA Alignment from Exonerate_protein2genome CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCA------G tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTGgtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca Alignment from Exonerate_coding2genome tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagcatcggttacaggacacaagccagtatgtgtgtgcagagcaacaagcccttgagcaggaacagggacaggttgatggcagggcccctgaagtgcagagacaatttcggagcctgatggaatcactccttggtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca Alignment from GeneWise CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAGGTGCC- tgaggtttaggtgaggcaacctgtcctcccacctgcccacacctgcctagCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCCCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCACTCCTTGgtaatgccccctagtttcatctgtgcttaaaacccaatacaattgagaca #### Ehbp1l1_ID1221_14 --> 2 - 0 Original Alignment gt------GGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccaggtAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from CESAR gt------GGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccaggtAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from Spaln_aa2Genome GT------GGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccagGTAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from Spaln_nt2Genome GT------GGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccagGTAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from Pairagon GT------GGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccagGTAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from Exonerate_protein2genome GT------GGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccagGTAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from Exonerate_coding2genome tcagcagtggcaggatgggaatggtgattgctttctccttataaacccaggtaaccgggggccaccacctactgaaaagtcatctcgtagcttggaagaagagacagggctggtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt Alignment from GeneWise -----GGTGGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG tcagcagtggcaggatgggaatggtgattgctttctccttataaacccagGTAACCGGGGGCCACCACCTACTGAAAAGTCATCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtactgctacattgattggtggtccttgctttcctgaggtttaggt #### Ehbp1l1_ID1227_8 --> 2 - 2 Original Alignment ct------GCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAag agatggcaatccaaacctctaaaagctaatgtttctctccattctattagctATCGAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCTGCCCCAGTAAGTGCCCCTGCACCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACCGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGAACTCCACCTGAGCCAaagtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from CESAR ct------GCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAag agatggcaatccaaacctctaaaagctaatgtttctctccattctattagctATCGAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCTGCCCCAGTAAGTGCCCCTGCACCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACCGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGAACTCCACCTGAGCCAaagtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from Spaln_aa2Genome CT------GCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG agatggcaatccaaacctctaaaagctaatgtttctctccattctattagCTATCGAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCTGCCCCAGTAAGTGCCCCTGCACCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACCGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGAACTCCACCTGAGCCAAAgtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from Spaln_nt2Genome CT------GCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG agatggcaatccaaacctctaaaagctaatgtttctctccattctattagCTATCGAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCTGCCCCAGTAAGTGCCCCTGCACCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACCGCCATGACTGATGG---AGTGGGGCATGAGACCCTAGAGCCCCCAGGAACTCCACCTGAGCCAAAgtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from Pairagon ----------------------------------------------------------GCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAG-----------------------GTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG AGATGGCAATCCAAACCTCTAAAAGCTAATGTTTCTCTCCATTCTATTAGCTATCGAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCTGCCCCAGTAAGTGCCCCTGCACCCCAAGTTAGAGCAATCCGGGGCCAAGGG-----------------------------GATCCAACCGCCATGACTGATGGAGTGGGGCATGAGACCCTAGAGCCCCCAGGAACTCCACCTGAGCCAAAgtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from Exonerate_protein2genome agatggcaatccaaacctctaaaagctaatgtttctctccattctattagctatcgaagctagaccctctagtgctgaaaagacaagtcctgccccagtaagtgcccctgcaccccaagttagagcaatccggggccaaggggatccaaccgccatgactgatggagtggggcatgagaccctagagcccccaggaactccacctgagccaaagtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from Exonerate_coding2genome agatggcaatccaaacctctaaaagctaatgtttctctccattctattagctatcgaagctagaccctctagtgctgaaaagacaagtcctgccccagtaagtgcccctgcaccccaagttagagcaatccggggccaaggggatccaaccgccatgactgatggagtggggcatgagaccctagagcccccaggaactccacctgagccaaagtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg Alignment from GeneWise -----GCTGCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG agatggcaatccaaacctctaaaagctaatgtttctctccattctattagCTATCGAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCTGCCCCAGTAAGTGCCCCTGCACCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACCGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGAACTCCACCTGAGCCAAAgtgagcatcatcacagcttctcaggcagggttgcaccattgcagtgttgg #### Ehbp1l1_ID1228_7 --> 2 - 1 Original Alignment atCTGTCTCGAGAGCTGAAGACACTCTGTGAAGAAGAAGATGAAGGCCACATACGGCCCCAGCAGGCAg ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagat---TCATGTGAGTTGAAGAGACTCTGTGAGGAGGAAGACGAAGGTCACATACGTCCCCAGCAGTCAggttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt Alignment from CESAR atCTGTCTCGAGAGCTGAAGACACTCTGTGAAGAAGAAGATGAAGGCCACATACGGCCCCAGCAGGCAg agtccctttgtatgactttgttccttttctgctttgcctctaccctgcagat---TCATGTGAGTTGAAGAGACTCTGTGAGGAGGAAGACGAAGGTCACATACGTCCCCAGCAGTCAggttagtctagtaatgggatgagatggcaatccaaacctctaaaagctagt Alignment from Spaln_aa2Genome ATCTGTCTCGAGAGCTGAAGACACTCTGTGAAGAAGAAGATGAAGGCCACATACGGCCCCAGCAGGCAG ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagAT---TCATGTGAGTTGAAGAGACTCTGTGAGGAGGAAGACGAAGGTCACATACGTCCCCAGCAGTCAGgttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt Alignment from Spaln_nt2Genome ATCTGTCTCGAGAGCTGAAGACACTCTGTGAAGAAGAAGATGAAGGCCACATACGGCCCCAGCAGGCAG ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagAT---TCATGTGAGTTGAAGAGACTCTGTGAGGAGGAAGACGAAGGTCACATACGTCCCCAGCAGTCAGgttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt Alignment from Pairagon ATCTGTCTCGAGAGCTGAAGACACTCTGTGAAGAAGAAGATGAAGGCCACATACGGCCCCAGCAGGCAG ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagAT---TCATGTGAGTTGAAGAGACTCTGTGAGGAGGAAGACGAAGGTCACATACGTCCCCAGCAGTCAGgttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt Alignment from Exonerate_protein2genome ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagattcatgtgagttgaagagactctgtgaggaggaagacgaaggtcacatacgtccccagcagtcaggttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt Alignment from Exonerate_coding2genome ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagattcatgtgagttgaagagactctgtgaggaggaagacgaaggtcacatacgtccccagcagtcaggttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt Alignment from GeneWise ATCTGTCTCGAGAGCTGAAGACACTCTGTGAAGAAGAAGATGAAGGCCACATACGGCCCCAGCAGGCAG ccctttgtatgactttgttcctgaatttctgctttgcctctaccctgcagAT---TCATGTGAGTTGAAGAGACTCTGTGAGGAGGAAGACGAAGGTCACATACGTCCCCAGCAGTCAGgttagtctagtaatgggatgagatggcaatccaaacctctaaaagctatt #### Ehbp1l1_ID1230_5 --> 0 - 2 Original Alignment GAGTCCAAGGGACAGCGGAAGGTACTGGCCACAGTTGATGTGAACCTAGCCCACCATGCAGGGCCTGTGCCTGCTCAGGTTCCACTTCGACTGCGGCTGAAGCCCAAATCTGTGAAGGTGGTGCATGCCGAACTGAGCCTCACCCTTTCTGGGGTGCTGCTGCGAGAAGGCCGTGCCac tacaacagcccatcttcacatttctcccccctctctccgcccatcttcagGAGTCAAAAGGACAGCGGAAAGTTTTAGCTGCAGTGGGTGTCATT------CATCATGCAGGTCCCCTACCTGGCCAGATCTCACTTCAATTGCGGCAGAAGCCCAAGTCCATCAAAGTTGTACACGCTGAGCTTACCCTCACACTCGCTGTC---CTTCTACAAGAAGGCCGT---atgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from CESAR GAGTCCAAGGGACAGCGGAAGGTACTGGCCACAGTTGATGTGAACCTAGCCCACCATGCAGGGCCTGTGCCTGCTCAGGTTCCACTTCGACTGCGGCTGAAGCCCAAATCTGTGAAGGTGGTGCATGCCGAACTGAGCCTCACCCTTTCTGGGGTGCTGCTGCGAGAAGGCCGTGCCac tacaacagcccatcttcacatttctcccccctctctccgcccatcttcagGAGTCAAAAGGACAGCGGAAAGTTTTAGCTGCAGTGGGTGTC------ATTCATCATGCAGGTCCCCTACCTGGCCAGATCTCACTTCAATTGCGGCAGAAGCCCAAGTCCATCAAAGTTGTACACGCTGAGCTTACCCTCACACTCGCT---GTCCTTCTACAAGAAGGCCGT---atgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from Spaln_aa2Genome GAGTCCAAGGGACAGCGGAAGGTACTGGCCACAGTTGATGTGAACCTAGCCCACCATGCAGGGCCTGTGCCTGCTCAGGTTCCACTTCGACTGCGGCTGAAGCCCAAATCTGTGAAGGTGGTGCATGCCGAACTGAGCCTCACCCTTTCTGGGGTGCTGCTGCGAGAAGGCCGTGC tacaacagcccatcttcacatttctcccccctctctccgcccatcttcagGAGTCAAAAGGACAGCGGAAAGTTTTAGCTGCAGTGGGTGTC------ATTCATCATGCAGGTCCCCTACCTGGCCAGATCTCACTTCAATTGCGGCAGAAGCCCAAGTCCATCAAAGTTGTACACGCTGAGCTTACCCTCACACTCGCT---GTCCTTCTACAAGAAGGCCGTATgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from Spaln_nt2Genome GAGTCCAAGGGACAGCGGAAGGTACTGGCCACAGTTGATGTGAACCTAGCCCACCATGCAGGGCCTGTGCCTGCTCAGGTTCCACTTCGACTGCGGCTGAAGCCCAAATCTGTGAAGGTGGTGCATGCCGAACTGAGCCTCACCCTTTCTGGGGTGCTGCTGCGAGAAGGCCGT----GCCACG- tacaacagcccatcttcacatttctcccccctctctccgcccatcttcagGAGTCAAAAGGACAGCGGAAAGTTTTAGCTGCAGTGGGTGTCA------TTCATCATGCAGGTCCCCTACCTGGCCAGATCTCACTTCAATTGCGGCAGAAGCCCAAGTCCATCAAAGTTGTACACGCTGAGCTTACCCTCACACTCGCT---GTCCTTCTACAAGAAGGCCGTATGTGCCAAGCgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from Pairagon GAGTCCAAGGGACAGCGGAAGGTACTGGCCACAGTTGATGTGAACCTAGCCCACCATGCAGGGCCTGTGCCTGCTCAGGTTCCACTTCGACTGCGGCTGAAGCCCAAATCTGTGAAGGTGGTGCATGCCGAACTGAGCCTCACCCTTTCTGGGGTGCTGCTGCGAGAAGGCC tacaacagcccatcttcacatttctcccccctctctccgcccatcttcagGAGTCAAAAGGACAGCGGAAAGTTTTAGCTGCAGTGGGTGTCA------TTCATCATGCAGGTCCCCTACCTGGCCAGATCTCACTTCAATTGCGGCAGAAGCCCAAGTCCATCAAAGTTGTACACGCTGAGCTTACCCTCACACTCGCT---GTCCTTCTACAAGAAGGCCgtatgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from Exonerate_protein2genome tacaacagcccatcttcacatttctcccccctctctccgcccatcttcaggagtcaaaaggacagcggaaagttttagctgcagtgggtgtcattcatcatgcaggtcccctacctggccagatctcacttcaattgcggcagaagcccaagtccatcaaagttgtacacgctgagcttaccctcacactcgctgtccttctacaagaaggccgtatgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from Exonerate_coding2genome tacaacagcccatcttcacatttctcccccctctctccgcccatcttcaggagtcaaaaggacagcggaaagttttagctgcagtgggtgtcattcatcatgcaggtcccctacctggccagatctcacttcaattgcggcagaagcccaagtccatcaaagttgtacacgctgagcttaccctcacactcgctgtccttctacaagaaggccgtatgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca Alignment from GeneWise GAGTCCAAGGGACAGCGGAAGGTACTGGCCACAGTTGATGTGAACCTAGCCCACCATGCAGGGCCTGTGCCTGCTCAGGTTCCACTTCGACTGCGGCTGAAGCCCAAATCTGTGAAGGTGGTGCATGCCGAACTGAGCCTCACCCTTTCTGGGGTGCTGCTGCGAGAAGGCCGTGC tacaacagcccatcttcacatttctcccccctctctccgcccatcttcagGAGTCAAAAGGACAGCGGAAAGTTTTAGCTGCAGTGGGTGTC------ATTCATCATGCAGGTCCCCTACCTGGCCAGATCTCACTTCAATTGCGGCAGAAGCCCAAGTCCATCAAAGTTGTACACGCTGAGCTTACCCTCACACTCGCT---GTCCTTCTACAAGAAGGCCGTATgtgccaagcgtacctttgtgcaggcagttttacagtgaggctgggcagca #### Eif1ad_ID950_3 --> 2 - 2 Original Alignment ggGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACtg gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcaggg---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAAtggtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from CESAR ggGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACtg aatgatgcatcatgctgctctacacaagttcccttccaaacaaatttcaggg---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAAtggtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from Spaln_aa2Genome GGGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACTG gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcagGGTTTCTCATTGTTGAACCT---TTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAATGgtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from Spaln_nt2Genome GGGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACTG gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcagGG---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAATGgtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from Pairagon GGGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACTG gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcagGG---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAATGgtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from Exonerate_protein2genome GGGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACTG gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcagGG---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAATGgtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from Exonerate_coding2genome GGGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACTG gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcagGG---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAATGgtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga Alignment from GeneWise GGGATTTCCTCATTGTTGACCCTATTGAAGAAGGAGAAAAAGTGAAGGCTGAGATCTCTTTTGTGCTCTGCAAGAACCATGTCCGCTCTCTACAGAAGGAGGGTCACTG gatgcatcatgctgctctacacaaaaagttcccttccaaacaaatttcagGG---TTTCTCATTGTTGAACCTTTTGAAGGTGGTGAGAAAGTCAAGGCAGAGATTTTGTTTGTACTCTGCAAGAACCATGTCCACACCCTGCAAAAGGAGGGCCAATGgtgagccagtctccctgtgcccctgctcagtgaagtagttaggttgtcga #### Eif3a_ID13327_3 --> 0 - 2 Original Alignment ---------GTAAACATTAAATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGag ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagCACACACCAGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACaggtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from CESAR ---------GTAAACATTAAATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGag ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagCACACACCAGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACaggtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from Spaln_aa2Genome GTAAACATTAAATCTTTA---------GAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGAG ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagCACACACCAGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACAGgtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from Spaln_nt2Genome GTAAACATTAA---------ATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGAG ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagCACACACCAGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACAGgtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from Pairagon ---------GTAAACATTAAATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGAG ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagCACACACCAGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACAGgtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from Exonerate_protein2genome GTAAACATTAAATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGAG ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagcacacaccaGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACAGgtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from Exonerate_coding2genome GTAAACATTAAATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGAG ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagcacacaccaGTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACAGgtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac Alignment from GeneWise --AACATTAAATCTTTAGAAGATGTTGTTAGGGCATATTTGAAATTAGCAGAGGAAAAAACAGAAGCTGCTAAAGAAGAGTCCCAACAAATGGTGTTAGATATAGAAGATCTGGATAATATTCAGACTCCTGAGAG ccttagactaggcaggaccccttctattaaaccttcttcctctcctgcagcacacaccagTAAACATTAAGTCTTTAAAGGACGTTGTTAGGGCATATTTGAAGTTAGCAGAGGAAAAAACAGAAGCTGCTAGAGAAGAGTCTCAACAAATGGTGTTGGATTTAGAAGATCTGGATAATATCCAGACTCCTGACAGgtatgtcccaggacactaatctcacatttgcaaatcaataaacatgttac #### Eml3_ID2503_3 --> 1 - 2 Original Alignment cAGCATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACac gCCCCGAAGAAATTCTTCCTCCTCC gtgagcgtaagtagaattatcccaattttatgttgtgctttaatttgcagc---ATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGAATGTTCAGATacgtttgaaactccttcctcccatcagaCCCCGAAGAAATTCTTTGTCCTCA Alignment from CESAR cAGCATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACac gCCCCGAAGAAATTCTTCCTCCTCC gtaagatgagtaagtagaattatccttttatgttgtgctttaatttgcagc---ATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGAATGTTCAGATacgtgaatgtccttttcctttgtatagaCCCCGAAGAAATTCTTTGTCCTCA Alignment from Spaln_aa2Genome CAGCATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACACG-------------------------CCCCGAAGAAATTCTTCCTCCTCC gtgagcgtaagtagaattatcccaattttatgttgtgctttaatttgcagC---ATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGAATGTTCAGATACGTTTGAAACTCCTTCCTCCCATCAGaCCCCGAAGAAATTCTTTGTCCTCA Alignment from Spaln_nt2Genome CAG--- CATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACAC GCCCCGAAGAAATTCTTCCTCCTCC GTGAGCgtaagtagaattatcccaattttatgttgtgctttaatttgcagCATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGA----------ATgttcagatacgtttgaaactccttcctcccatcagACCCCGAAGAAATTCTTTGTCCTCA Alignment from Pairagon ----------------------------------------------GCAGCATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACACG-------------------------CCCCGAAGAAATTCTTCCTCCTCC GTGAGCGTAAGTAGAATTATCCCAATTTTATGTTGTGCTTTAATTTGCAGCATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGAATGTTCAGATACGTTTGAAACTCCTTCCTCCCATCAGACCCCGAAGAAATTCTTTGTCCTCA Alignment from Exonerate_protein2genome CAGCATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACACGCCCCGAAGAAATTCTTCCTCCTCCTCCTCCCCCTC gtgagcgtaagtagaattatcccaattttatgttgtgctttaatttgCAGCATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGAATGTTCAGATACG---TTTGAAACTCCTTCCTCCCATCAGACCCCGAAgaaattctttgtcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CAGCATCACAGTCCCTCCAGGACTGCCACCTACATGCAGCCCTTCCTTGGTGACCAGAGGCACCCAAACGGAAGAAGAATTGGAGATTGTTCCATCCTCTGGACCCCCTGGCCTGAGCAATGGTCCTCCAGCTCTTCAGGGGGGCAGTGAAGAACCTAGTGGGACCCAGTCTGAAGGAGGGTGCAGCAGCAGCAGTGGGGCAGGCTCCCCTGGCCCCCCAGGAATCCTCAGGCCGGTGCAGCCTCTTCAGCGTTCTGACACG---------------------------CCCCGAAGAAATTCTTCCTCCT gtgagcgtaagtagaattatcccaattttatgttgtgctttaatttgcagC---ATAACAGTCCCACCGGGGCGGCCACCAATCAGTAGTCCTTCCCTGCTTACAAAAGGCACACAAACTAAAGAAGAGTTGGAGATTGTTCCTTCCTCTGGACCACCTGGTCTAAGCAATGGCCCACCAGCTCTACAAGGGAGCAGCAAAGAACCTACTGGAATCCAATTACAAGGTGGTTGCCGCAGCAGTAGTGGATCAGGCTCACCAGGGCCTCCAGGAATCCTCAGGCCGGTGCAGCCGCTTGAATGTTCAGATACGTTTGAAACTCCTTCCTCCCATCAGA--CCCCGAAGAAATTCTTTGTCCT #### Eml3_ID2512_11 --> 0 - 0 Original Alignment AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG atggtcttgggctcaaacaggtgtaccaaaaatactgatttgcctttcag------------------------------------------GACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from CESAR AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG tggcttcagggctcaaacaggtgtaccaaaaatactgatttgcctttcag------------------------------------------GACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from Spaln_aa2Genome GACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG atggtcttgggctcaaacaggtgtaccaaaaatactgatttgcctttcagGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from Spaln_nt2Genome GACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG atggtcttgggctcaaacaggtgtaccaaaaatactgatttgcctttcagGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from Pairagon AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG atggtcttgggctcaaacaggtgtaccaaaaatactgatttgcctttcag------------------------------------------GACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from Exonerate_protein2genome AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG atggtcttGGGCTCAAACAGGTGTACCAAAAATACTGATTTGCCTTTCAGGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from Exonerate_coding2genome atggtcttgggctcaaacaggtgtaccaaaaatactgatttgcctttcaggacagcagttgtattgttactagtggaaaatcacatgttcacttttggaattggagtggtggtacaggggctcctggaaatggaatccttgcacggaagcaggatgttcttggggtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg Alignment from GeneWise GACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG atggtcttgggctcaaacaggtgtaccaaaaatactgatttgcctttcagGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGAAATGGAATCCTTGCACGGAAGCAGGATGTTCTTGGGgtgagacgggtaagatagacaaacgcatggtataatcacaacatactgcg #### Eml3_ID2514_13 --> 2 - 0 Original Alignment agACCTACACGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG catgaaaccacaaatgctcgttttcatctgcgtgggggctgtttctgcagaa---------ATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg Alignment from CESAR agACCTACACGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG actacaatccatgaaaccacaaatgatctgcgtgggggctgtttctgcagaa---------ATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg Alignment from Spaln_aa2Genome AGACCTACACGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG catgaaaccacaaatgctcgttttcatctgcgtgggggctgtttctgcagAA---------ATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg Alignment from Spaln_nt2Genome CGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG catgaaaccacaaatgctcgttttcatctgcgtgggggctgtttctgcagAAATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg Alignment from Pairagon AGACCTACACGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG catgaaaccacaaatgctcgttttcatctgcgtgggggctgtttctgcagA---------AATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg Alignment from Exonerate_protein2genome AGACCTACACGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG catgaaaccacaaatgctcgttttcatctgcgtgggggctgTTTCTGCAGAAATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AGACCTACACGATCGTGGCCCAGGCCCATGCTCACGAGGGGTCCATCTTTGCCCTGTGTCTCCGCCGGGATGGGACAGTGCTGAGTGGTGGTGGGCGGGACCGACGACTGGTGCAGTGGGGGCCCGGGTTGGTGGCCCTCCAGGAGGCAGAG catgaaaccacaaatgctcgttttcatctgcgtgggggctgtttctgcagAA---------ATTGTGGCCCAACCGCATGCTCATGAGGAGTGCTTCTTTGTACTCTGTCTTCATCAGGATGGAACAGTACTCACTGGTGGTGGGTGGCATAGACGTCTAGTGCAGTGGGGGCCTGGGCTGGTCGCACTCCAGGAGGCAGAAgtagggcctgatctgggccccaacaacaggggtggatgtggagacatggg #### Eml3_ID2517_16 --> 0 - 2 Original Alignment GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGG---ag tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCaggtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata Alignment from CESAR GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGG---ag tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCaggtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata Alignment from Spaln_aa2Genome GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGGAGG-- tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCAGgtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata Alignment from Spaln_nt2Genome GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGG---AG tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCAGgtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata Alignment from Pairagon GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGG---AG tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCAGgtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata Alignment from Exonerate_protein2genome GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGG---AG tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCAGgtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAGACGGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTTGTAGGACTGAACACAGGGAGG-- tcgaaatacataatcatccatatctagtttgatctctttctttttgaaagGAGACAGGTTTATGTGCTGACTTCCACCCAAGTGGGGCAGTTGTGGTCATAGGACTGAACACTGGGGTCAGgtatgtgagtcaacaccatggaaactaaagagggtatccgtccagggata #### Eml3_ID2519_18 --> 2 - 0 Original Alignment atGGGTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gtttaataaagatatgatagcagtaacatcattttacttctgctctgcagat------TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga Alignment from CESAR atGGGTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gattcagtttaataaagatatgataacatcattttacttctgctctgcagat------TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga Alignment from Spaln_aa2Genome ATGGGTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gtttaataaagatatgatagcagtaacatcattttacttctgctctgcagAT------TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga Alignment from Spaln_nt2Genome GTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gtttaataaagatatgatagcagtaacatcattttacttctgctctgcagAT--TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga Alignment from Pairagon ATGGGTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gtttaataaagatatgatagcagtaacatcattttacttctgctctgcagAT------TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga Alignment from Exonerate_protein2genome ATGGGTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gtttaataaagatatgatagcagtaacatcattttacttctgctctgcagAT------TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ATGGGTTGTACCTGGCTATTGGTTCCCATGACAACATGATCTACATCTATAGTGTTTCCAGTTGTGGCACTAAGTCCAGCCGCTTTGGCAGATGTATG gtttaataaagatatgatagcagtaacatcattttacttctgctctgcagAT------TACCTCGCACTAGGTTCACATGATAATATGATTTATATATACAGTATTTCCAGTTGTGGTACCAAATCTACCCACTTTGGAAGGTGTATGgtaagacacgtgcggcctgaacatccacagaacttagaaacccactgtga #### Exosc1_ID8332_7 --> 0 - 1 Original Alignment ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAg tggttatataagaaaggtcaaacactgacacagcggctccttctttgcag---TCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAggtaggacagtaactaaacctgctgtcccagaaaggttgtctaagaaaatc Alignment from CESAR ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAg taatggttatataagaaaggtcaaatgacacagcggctccttctttgcag---TCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAggtaggacagtaactaaacctgctgtcccagaaaggttgtcttgtctttct Alignment from Spaln_aa2Genome ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG tggttatataagaaaggtcaaacactgacacagcggctccttctttgcagTCGCTAGGGGCTGCACAG---TCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAGgtaggacagtaactaaacctgctgtcccagaaaggttgtctaagaaaatc Alignment from Spaln_nt2Genome TCCCTAGGCGATGCACAGTCCAATTACCTGCTG---ACTACTGCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG tggttatataagaaaggtcaaacactgacacagcggctccttctttgcagTCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAGgtaggacagtaactaaacctgctgtcccagaaaggttgtctaagaaaatc Alignment from Pairagon ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTA---CTGCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG tggttatataagaaaggtcaaacactgacacagcggctccttctttgcag---TCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAGgtaggacagtaactaaacctgctgtcccagaaaggttgtctaagaaaatc Alignment from Exonerate_protein2genome TCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG tggttatataagaaaggtcaaacactgacacagcggctccttctttgcagTCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAGgtaggacagtaactaaacctgctgtcccagaaaggttgtctaagaaaatc Alignment from Exonerate_coding2genome TCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG tggttatataagaaaggtcaaacactgacacagcggctccttctttgcagTCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAGgtaggacagtaactaaacctgctgtcccagaaaggttgtctaagaaaatc Alignment from GeneWise -----------------TCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACTGCT---GAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAGGT------------------------------------------------ tggttatataagaaaggtcaaacactgacacagCGGCTCCTTCTTTGCAGTCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACTACTGCTGCTGAAAATGAGCTGGGTGTTGTAGTGGCCCACAGTGAGGCAGGTAGGACAGTAACTAAACCTGCTGTCCCAGAAAGGTTGTCTAAGAAAATC #### Fads1_ID2688_2 --> 0 - 0 Original Alignment GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGAAT------ ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTT---CTTGGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAATAATGCTgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt Alignment from CESAR GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGAAT------ ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTTCTT---GGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAATAATGCTgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt Alignment from Spaln_aa2Genome GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGAAT------ ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTTCTT---GGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAATAATGCTgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt Alignment from Spaln_nt2Genome GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGAATAAAGCG ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTA---TCTTCTTGGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAATAATGCTgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt Alignment from Pairagon GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGAATAAAGCGCTAA---------------------------------------------- ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTTC---TTGGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAATAATGCTGTAATGCAATAGACCCTGAAAATTAGGGATGCTGTCGTTGCACTAGTAGT Alignment from Exonerate_protein2genome GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGA ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTTCTT---GGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAataatgctgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt Alignment from Exonerate_coding2genome GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGA ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTTCTT---GGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAataatgctgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt Alignment from GeneWise GATCCTTTTGTGGCATTCCACATCAACAAGGGTCTTGTGAGAAAGTATATGAACTCTCTTCTGATTGGAGAGCTGGCTCCGGAGCAACCCAGCTTTGAACCCACCAAGAATAAAGCG ttcattctcatttccatcagttttcattatcctgtttttcttcttttcagGATCCTTTTGTGGCATTCCACTTCAACAAGGGTCTTGTGAGAAAATATATGAACTATCTTCTT---GGGGAGCTAGCTCCCGAGCAACCCAGCTTTGAACCCACCAAGAATAATGCTgtaatgcaatagaccctgaaaattagggatgctgtcgttgcactagtagt #### Fads1_ID2689_3 --> 0 - 0 Original Alignment ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from CESAR ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from Spaln_aa2Genome AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from Spaln_nt2Genome ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCC---CATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from Pairagon ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCC---CATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from Exonerate_protein2genome ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from Exonerate_coding2genome ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttagGTCAAAGTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac Alignment from GeneWise CGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcttagttaggctgaagttcacaaattttcctgttttgttccctttttaggtcaaagTAATATCTGATGAGTTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAACCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCTCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCTCCGTTCAGgtgagtcccacctctcagcctaaaccacaaatattgaagagtgtttgtac #### Fads1_ID2690_4 --> 0 - 0 Original Alignment GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACC---TCGACATGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG--------- ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGAGGGACTCTgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac Alignment from CESAR GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG--------- ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGAGGGACTCTgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac Alignment from Spaln_aa2Genome GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG--------- ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGAGGGACTCTgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac Alignment from Spaln_nt2Genome GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG--------- ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGAGGGACTCTgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac Alignment from Pairagon GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG-------------------------- ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGAGGGACTCTGTACAGACTGAAGTTATgtcaggatatcattaagtctttgctcatctgac Alignment from Exonerate_protein2genome GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGagggactctgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac Alignment from Exonerate_coding2genome GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGagggactctgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac Alignment from GeneWise GCTCAGGCAGGTTGGCTACAGCATGACTTTGGGCACCTGTCAGTCTTTGGCACCTCGACA---TGGAATCACCTGCTACATCATTTTGTGATTGGCCACCTGAAG--------- ttttgactccagcattggtgtctaggggccgtgttcatgcctgcctgcagGGTCAGGCAGGTTGGCTACAGCATGAGTTTGGGCGTTTGTCACTTTTTGGCACCTCATCAATGTGGAATTACCTGCTCCACCATTTTGTGATTGGACACCTAAAGAGGGACTCTgtacagactgaagttatgtcaggatatcattaagtctttgctcatctgac #### Fads1_ID2695_9 --> 1 - 0 Original Alignment gTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accttattacttgctctgcaatgttttttaagacttgtgctccattgtagg---------AGCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from CESAR gTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accaccagaaccttattacttgctcttttaagacttgtgctccattgtagg---------AGCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from Spaln_aa2Genome CAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accttattacttgctctgcaatgttttttaagacttgtgctccattgtaggagCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from Spaln_nt2Genome AAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accttattacttgctctgcaatgttttttaagacttgtgctccattgtagGAGCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from Pairagon GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accttattacttgctctgcaatgttttttaagacttgtgctccattgtagG---------AGCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from Exonerate_protein2genome AAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accttattacttgctctgcaatgttttttaagacttgtgctccattgtagGAGCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from Exonerate_coding2genome accttattacttgctctgcaatgttttttaagacttgtgctccattgtaggagcaactggtttgtgtgggtgacacaaatgaatcatatctccatgcacattgatccagataggaatgtggactgggtctcaacacaggtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat Alignment from GeneWise CAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accttattacttgctctgcaatgttttttaagacttgtgctccattgtaggagCAACTGGTTTGTGTGGGTGACACAAATGAATCATATCTCCATGCACATTGATCCAGATAGGAATGTGGACTGGGTCTCAACACAGgtgagttgtagtgtacccagctgtgaagcttcagagttcatatcatgaat #### Fads3_ID2662_5 --> 0 - 0 Original Alignment GGCTTTTCCGCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcag---------GCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat Alignment from CESAR GGCTTTTCCGCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG tgcacacttgcacacaacaatgcaaccttgtcacccctaccccgcctcag---------GCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggatttcgt Alignment from Spaln_aa2Genome GCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcagGCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat Alignment from Spaln_nt2Genome GCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcagGCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat Alignment from Pairagon GGCTTTTCCGCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcag---------GCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat Alignment from Exonerate_protein2genome GCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcagGCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat Alignment from Exonerate_coding2genome GCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcagGCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat Alignment from GeneWise GCCCACTGGTGGAATTTCCGCCACTTCCAGCACCATGCCAAACCCAACATCTTCCACAAAGACCCAGATGTGACTGTCGCACCTGTCTTCCTCCTGGGGGAGTCATCTGTGGAG gcacacaacaatgcaagcagacactccttgtcacccctaccccgcctcagGCCCACTGGTGGAATTTCCAGCACTTGAAGCATCATGCCAAGCCCAACATATTCCACAAAGACCCTGATGTAACTGTTACACCTGTCTTCCTACTTGGTGTATCATCTGTGGAAgtaagtaggtccctgcaatctacaggatgtttctttcccctggttattat #### Fads3_ID2663_6 --> 0 - 1 Original Alignment ---TATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGa caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTggtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from CESAR ---TATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGa caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTggtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from Spaln_aa2Genome TATGGCAAG---AAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGA caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTGgtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from Spaln_nt2Genome --GTATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGA caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTGgtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from Pairagon ----------------------------------------------------GTATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGA CAATCTACAGGATGTTTCTTTCCCCTGGCTTTTTCATTTTTTTCGTCAAGGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTGgtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from Exonerate_protein2genome ---TATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGA caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTGgtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from Exonerate_coding2genome ---TATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGA caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTGgtagggggtgccagcacgatttattggtggcagttggcagccctaacaga Alignment from GeneWise ---TATGGCAAGAAGAAACGCAGATACCTGCCCTACAACCACCAGCATCTATACTTCTTCCTGA caatctacaggatgtttctttcccctggctttttcatttttttcgtcaagGTGTATGGCAAGAAGAAACAACGATACCTGCCATACAATCATCAACATCTATACTTTTTCCTTGgtagggggtgccagcacgatttattggtggcagttggcagccctaacaga #### Fads3_ID2666_9 --> 1 - 0 Original Alignment gGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcaggGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACAT------------------------------gtgggtttcttgtgtgctgaagtgcatactggtttcagaacggcctgtta Alignment from CESAR gGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcaggGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACAT------------------------------gtgggtttcttgtgtgctga Alignment from Spaln_aa2Genome GGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAGCTGGCAGCCACC tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcagGGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGTGGGTTTCTTGTGTGCTGAAGTGCATACTGGTTTCAGAACGgcctgtta Alignment from Spaln_nt2Genome GGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCAT tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcagGGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATgtgggtttcttgtgtgctgaagtgcatactggtttcagaacggcctgtta Alignment from Pairagon GGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCAT tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcagGGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATgtgggtttcttgtgtgctgaagtgcatactggtttcagaacggcctgtta Alignment from Exonerate_protein2genome GGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCAT tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcagGGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATgtgggtttcttgtgtgctgaagtgcatactggtttcagaacggcctgtta Alignment from Exonerate_coding2genome tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcagggtcttggagagccagtggtttgtgtggatcacacagatgaaccatatccccaagaagataggacatgtgggtttcttgtgtgctgaagtgcatactggtttcagaacggcctgtta Alignment from GeneWise GGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG tgagtcatcttgatcgaatgattcaatatgcttttgtctccctcctgcagGGTCTTGGAGAGCCAGTGGTTTGTGTGGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGTG---------GGTTTCTTGTGTGCTGAAgtgcatactggtttcagaac #### Fam160b1_ID12352_3 --> 2 - 0 Original Alignment atGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTATACACCTTAGGGAAAGCCGAC aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagatGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAG---CAATCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTA---------------------gtattatcctcctcaccttggtctggtgatgatcgtgttgagcactagtg Alignment from CESAR atGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTATACACCTTAGGGAAAGCCGAC aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagatGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAGCAA---TCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTA---------------------gtattatcctcctcaccttggtctggtga Alignment from Spaln_aa2Genome ATGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTATACACC---------------TTAGGGAAAGCCGAC aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagATGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAGCAA---TCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTAGTATTATCCTCCTCACCTTGGTCTGGTGATGATCGTgttgagcactagtg Alignment from Spaln_nt2Genome ATGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTA aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagATGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAGC---AATCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTAgtattatcctcctcaccttggtctggtgatgatcgtgttgagcactagtg Alignment from Pairagon ATGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTA aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagATGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAGC---AATCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTAgtattatcctcctcaccttggtctggtgatgatcgtgttgagcactagtg Alignment from Exonerate_protein2genome ATGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTATACACCTTAGG aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagATGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAG---CAATCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTAGTATTATCCTCctcaccttggtctggtgatgatcgtgttgagcactagtg Alignment from Exonerate_coding2genome ATGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTATACACCTTAGG aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagATGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAG---CAATCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTAGTATTATCCTCctcaccttggtctggtgatgatcgtgttgagcactagtg Alignment from GeneWise ATGATAAAGCCCCAGTGACCGACACAAACATCCCATCCCACCTGGAACAGATGTTAGACATCCTGGTCCAAGAAGAAAATGAGCGGGAATCTGGAGAGACAGGGCCATGCATGGAATACCTGCTCCATCACAAGATCTTGGAAACGTTATACACCTTA---------------GGGAAAGCCGAC aatgagtgtgcacttgccctcaccatgcttctgttcccttctctggctagATGATAAGGCCCCAGTAACAGACACCAACCTATCATGCCACCTGGAACAGATGCTAGACATACTGGTCCAAGAGGAAAATGAG---CAATCTGGGGAGACTGGGCCTTGCATTGAATATTTACTGCATCACAAGATCTTGGAAACATTAGTATTATCCTCCTCACCTTGGTCTGGTGATGATCGTgttgagcactagtg #### Fam160b1_ID12356_7 --> 0 - 2 Original Alignment ------GACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGgg agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtagGCTCACGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGgggtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from CESAR ------GACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGgg agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtagGCTCACGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGgggtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from Spaln_aa2Genome GACGGCCGGATA------GCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGGG agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtagGCTCACGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGGGgtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from Spaln_nt2Genome G-TCCTGACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGGG agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtagGCTCACGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGGGgtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from Pairagon ------GACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGGG agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtagGCTCACGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGGGgtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from Exonerate_protein2genome GACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGGG agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtaggctcacGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGGGgtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from Exonerate_coding2genome GACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGGG agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtaggctcacGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGGGgtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg Alignment from GeneWise ------GACGGCCGGATAGCTGTGAAGGCCTGCGAGGGCTTGATGCTCTTGGTGAGCCTACCGGAGCCTGCGGCTGCCAAGTGCCTTGCTCAGAGCACCTGCCTGTGCGAGCTGCTGACCGGCAGACTCACCTCCCTGTACAAGGCTCTACCTCAGTCAGTGGACCCCTTAGACATTGAAACCGTGGAGGCAGTTAACTGGGG agaagaagaaatgcggctatagcccttctgtatcctgctttctgctgtagGCTCACGATGGCCGGATAGCTGTAAAGGCTTGCAAGGGTTCCATGCTCTTAGCAAGCCTACCAGAGCCTGCAGCAGCCAAGTGCCTTGCTCAGAGCACTTGCCTATGTGAGCTGCTCACTGGAAGACTCACTTCCTTGTACAAGTCATTACCACAGTCAGTAGACCCTCTAGACATTGAAACAGTGGAGGCAGTGAACTGGGGgtgagcatcaattcgatagacttcttggacaatcgactgcttagactgtg #### Fam160b1_ID12357_8 --> 1 - 0 Original Alignment gTTGGACTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagg------TCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from CESAR gTTGGACTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG atttttccatttgcatctggttatacctacattcttttcattcttctcagg------TCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from Spaln_aa2Genome GTTGGACTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagG------TCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from Spaln_nt2Genome CTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagGTCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from Pairagon GTTGGACTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagG------TCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from Exonerate_protein2genome CTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagGTCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from Exonerate_coding2genome CTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagGTCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca Alignment from GeneWise GTTGGACTCATACAGCCATAAAGAAGACGCTTCGGCGTTCCCGGGGAAGCGGGCCTTAATTTCATTTCTTTCCTGGTTCGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAG ccatttgcatctggttataactttccctacattcttttcattcttctcagG------TCTTACAGCCACAAAGAAGATACATCAGCGTTCCCAGGGAAGCGGGCCTTGATTGCGTTTCTTTCCTGGTTTGATTACTGTGATCAGCTCATCAAGGAGGCACAAAAGgtgagcagcataatcttctgcttatgcacaccaaactgttcttaccttca #### Fas_ID6925_6 --> 2 - 1 Original Alignment gtCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTCCACTTg atagttgagaatactagccacctgtcctttattttatttcttgatcttagctCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGATT------ggtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from CESAR gtCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTCCACTTg atagttgagaatactagccacctgtcctttattttatttcttgatcttagctCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGATT------ggtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from Spaln_aa2Genome GTCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATT- atagttgagaatactagccacctgtcctttattttatttcttgatcttagCTCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGATTGgtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from Spaln_nt2Genome GTCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTCCACTTG atagttgagaatactagccacctgtcctttattttatttcttgatcttagCTCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGA------TTGgtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from Pairagon GTCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTCCACTTG atagttgagaatactagccacctgtcctttattttatttcttgatcttagCTCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGA------TTGgtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from Exonerate_protein2genome GTCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTC atagttgagaatactagccacctgtcctttattttatttcttgatcttagCTCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGATTGgtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from Exonerate_coding2genome GTCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTC atagttgagaatactagccacctgtcctttattttatttcttgatcttagCTCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGATTGgtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc Alignment from GeneWise GTCCCAGAAATCGCCTATGGTTGTTGACCATCCTTGTTTTGTTAATTC atagttgagaatactagccacctgtcctttattttatttcttgatcttagCTCCCAGAAATTGCCTGTGGTTGTTGACCATCCTTGTTTTGCTGATTGgtgggtcacttcaggaatgttcagagattattacagtagtgtgaggaggc #### Fas_ID6926_7 --> 2 - 0 Original Alignment taTTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT cagcaatatgacatcggctggggttcgcatactgtttatttattctttagta---------------TACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTgtgagcatctagtgcaatacagtgattctctttccaatactcccaatcaa Alignment from CESAR taTTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT atcgtcaactattcacagcaatatgcgcatactgtttatttattctttagta---------------TACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTgtgagcatctagtgcaatacagtgattctctttccaatactcccaatcaa Alignment from Spaln_aa2Genome TATTTATATATCGA---AAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT cagcaatatgacatcggctggggttcgcatacTGTTTATTTATTCTTTAGTATACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTgtgagcatctagtgcaatacagtgattctctttccaatactcccaatcaa Alignment from Spaln_nt2Genome AGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT cagcaatatgacatcggctggggttcgcatactgtttatttattctttagTATACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTgtgagcatctagtgcaatacagtgattctctttccaatactcccaatcaa Alignment from Pairagon TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT cagcaatatgacatcggctggggttcgcatactgtttatttattctttagTA---------------TACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTgtgagcatctagtgcaatacagtgattctctttccaatactcccaatcaa Alignment from Exonerate_protein2genome TATTTATATATCGA---AAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGTGAAACCATACCAATGAATGCCTCAA cagcaatatgacatcggctggggttcgcatacTGTTTATTTATTCTTTAGTATACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTGTGAGCATCTAGTGCAATACAGTGAttctctttccaatactcccaatcaa Alignment from Exonerate_coding2genome TATTTATATATCGA---AAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGTGAAACCATACCAATGAATGCCTCAA cagcaatatgacatcggctggggttcgcatacTGTTTATTTATTCTTTAGTATACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTGTGAGCATCTAGTGCAATACAGTGAttctctttccaatactcccaatcaa Alignment from GeneWise TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGTGAAACCATACC cagcaatatgacatcggctggggttcgcatactgtttatttattctttagTA---------------TACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCCAGAACCTCAAGTCGTGTGAGCATCTAgtgcaatacagtgattctctttccaatactcccaatcaa #### Fgf8_ID9566_3 --> 0 - 0 Original Alignment ---------GAAGGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagAGAACAGGTGGAGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from CESAR ---------GAAGGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagAGAACAGGTGGAGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from Spaln_aa2Genome ---------GAAGGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagAGAACAGGTGGAGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from Spaln_nt2Genome GA--AGGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagagaacagGTGGAGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from Pairagon AGGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagagaacaggtggAGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from Exonerate_protein2genome GCCTGCGCTGGGCAG GGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG GCCTGCGCTTGGTAGggagccaacatcctggtggctgcatttctttgcagagaacaggtggaggccctggtggggggcctgcgcttggcagGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from Exonerate_coding2genome GGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagagaacaggtggaGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt Alignment from GeneWise GGCCCGGGCGGGGGGCCTGCGCTGGGCAGGGAGCCCACTTCCCTGCTCCGAGCTGGCCGGGAGCCCCAGGGTGTTTCCCAACAG gcctgcgcttggtagggagccaacatcctggtggctgcatttctttgcagagaacaggtggaGGCCCTGGTGGGGGGCCTGCGCTTGGCAGGGAGCCGACCTCCCTGCTCCGAGCTGGTCGGGAACCTCAAGGGGTTTCCCAACAAgtgagcagttagagagatggggaagattcctccattttaggccctgggtt #### Fibp_ID1008_5 --> 1 - 1 Original Alignment gGATTACGCAGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAg aagagagagaaacataatatgttctgattctgcccgcttccctgttgcaga---------TCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAggtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from CESAR gGATTACGCAGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAg ttcaagcataagagagagaaacatagattctgcccgcttccctgttgcaga---------TCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAggtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from Spaln_aa2Genome GGATTACGCAGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAG aagagagagaaacataatatgttctgattctgcccgcttccctgttgcagA---------TCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAGgtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from Spaln_nt2Genome TACGCAGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAG aagagagagaaacataatatgttctgattctgcccgcttccctgttgcag-----ATCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAGgtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from Pairagon GGATTACGCAGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAG aagagagagaaacataatatgttctgattctgcccgcttccctgttgcag---------ATCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAGgtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from Exonerate_protein2genome AGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAG aagagagagaaacataatatgttctgattctgcccgcttccctgttgcagATCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAGgtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from Exonerate_coding2genome AGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAG aagagagagaaacataatatgttctgattctgcccgcttccctgttgcagATCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAGgtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt Alignment from GeneWise GGATTACGCAGCCATCGTCTTTTTTGCCAACAACCGCTTTGAAACAGGAAAGAAAAAGCTGCAGTACCTGAGCTTTGGGGACTTTGCCTTCTGTGCAGAGCTTATGATCCAGAACTGGACCCTTGGAGCCGTCGGTGAGGCCCCCACTGACCCAG aagagagagaaacataatatgttctgattctgcccgcttccctgttgcagA---------TCCATTGTTTTCTTTGCCAATAATGACTTTGAAACCGGGAAAAAAAGGCTGCAGCACCTAAGCTTTGAGGCCTTTGCCTTTCGTGCAGAACTTATGATCCAGAACTGGACCCTTGGGACCATTGGTGAGGCTCCAACTGATCCAGgtgagcgtaattgataaggccccaactgatccaggtacacaaactcttgt #### Fibp_ID1009_6 --> 2 - 2 Original Alignment acTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGag cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagacCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTGGAC---aggtgagtagcgcaggagtgttagtagcagaacttactgtactcagtctaca Alignment from CESAR acTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGag cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagacCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTGGAC---aggtgagtagcgcaggagtgttagtagcagaacttactgtactcagtctaaa Alignment from Spaln_aa2Genome ACTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGAGC cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagACCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTGGACAGg tgagtagcgcaggagtgttagtagcagaacttactgtactcagtct Alignment from Spaln_nt2Genome ACTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGAG cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagACCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTG---GACAGgtgagtagcgcaggagtgttagtagcagaacttactgtactcagtctaca Alignment from Pairagon ACTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAG------------------------------------------------- cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagACCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTGGACAGGTGAGTAGCGCAGGAGTGTTAGTAGCAGAACTTACTGTACTCAGTCTACA Alignment from Exonerate_protein2genome ACTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGAG cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagACCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTG---GACAGgtgagtagcgcaggagtgttagtagcagaacttactgtactcagtctaca Alignment from Exonerate_coding2genome ACTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGAG cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagACCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTG---GACAGgtgagtagcgcaggagtgttagtagcagaacttactgtactcagtctaca Alignment from GeneWise ACTCTCAGGTGGACGACATGGATGTGGACTTAGATAAGGAGTTTCTCCAAGACTTGAAGGAGCTCAAGGTTCTCGTGGCTGACAAGGACCTCCTGGACCTGCATAAGAG cacatgaatagcccagatggttgtgcatacgctgctctccccatcctcagACCCCCAGGTGGACTACATGGATGTTGACCTAGACAAAGAATTCCTCCAAGACTTCAAGGAGCTTAAGGTTCTTGTGGCTGACAAGGACCTCCTGGATCTG---GACAGgtgagtagcgcaggagtgttagtagcagaacttactgtactcagtctaca #### Fibp_ID1011_8 --> 0 - 0 Original Alignment AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTTGTGGACCTCGTGGAGAAG TTTGTGG cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAG------TGCAACAAAGATGTTAGAGTCTTGTTT------------------gtaagaagcagttagaatcgaaccccctgctttctgtgcacagTTTGTAG Alignment from CESAR AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTTGTGGACCTCGTGGAGAAG cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAG------TGCAACAAAGATGTTAGAGTCTTGTTT------------------gtaagaagcagttagaatttgccccctcctta Alignment from Spaln_aa2Genome AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTT GTGGACC cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAG------TGCAACAAAGATGTTAGAGTCTTGTTTgtaagaagcagttagaatcgaaccccctgctttctgtgcacag------- Alignment from Spaln_nt2Genome AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTTGTGGACCTCGTGGAGAA cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAG-TG-----CAACAAAGATGTTAGAGTCTTGTTTGT-------AAGAAGCAgttagaatcgaaccccctgctttctgtgcacag Alignment from Pairagon AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATT-----------------------------------TGTGGACCTCGTGGAG cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAG------TGCAACAAAGATGTTAGAGTCTTGTTTGTAAGAAGCAGTTAGAATCGAACCCCCTGCTTTCTGTGCAC--------- Alignment from Exonerate_protein2genome AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTTGTG cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAGTGC------AACAAAGATGTTAGAGTCTTGTTTGTAagaagcagttagaatcgaaccccctgctttctgtgcacagtttgtag Alignment from Exonerate_coding2genome AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTTGTG cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAGTGC------AACAAAGATGTTAGAGTCTTGTTTGTAagaagcagttagaatcgaaccccctgctttctgtgcacagtttgtag Alignment from GeneWise AATCTGTCTCGGGGGCTGGTGAACGTGGCTGCCAAGCTGACCCACAATAAGGATGTCAGAGACCTATTTGTG-GACCTCGTGGAG------------------------AAGTTTGTGG cacatacagaatctggaggaaatcggggacgtcttcccctctctccacagAATCTTTCTAGAGGCCTGATAAACGTGGCTGCCAAGTGC------AACAAAGATGTTAGAGTCTTGTTTGTAAGAAGCAGTTAGAATCGAACCCCCTGCTTTCTGTGCACAGTTTGTAG #### Fkbp2_ID1947_2 --> 0 - 2 Original Alignment GGAAAGCTAGAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGgg cgttcaagcggttataggcgatgttttgcaacactcattttgtgtctcag------------------------------AGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAgggtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from CESAR GGAAAGCTAGAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGgg acattctttcctcatcgttgatgttttgcaacactcattttgtgtctcag------------------------------AGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAgggtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from Spaln_aa2Genome GGAAAGCTAGAAGATGGGACG---GAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGGG cgttcaagcggttatagGCGATGTTTTGCAACACTCATTTTGTGTCTCAGAGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAGGgtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from Spaln_nt2Genome AGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGGG cgttcaagcggttataggcgatgttttgcaacactcattttgtgtctcagAGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAGGgtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from Pairagon GGAAAGCTAGAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGGG cgttcaagcggttataggcgatgttttgcaacactcattttgtgtctcag------------------------------AGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAGGgtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from Exonerate_protein2genome GGAAAGCTA---GAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGGG cgttcaagcggttatagGCGATGTTTTGCAACACTCATTTTGTGTCTCAGAGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAGGgtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from Exonerate_coding2genome GGAAAGCTA---GAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGGG cgttcaagcggttatagGCGATGTTTTGCAACACTCATTTTGTGTCTCAGAGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAGGgtatggttggcatacaatctaagttgcaattgctgtagtaaaggtatttt Alignment from GeneWise GGAAAGCTAGAAGATGGGACGGAGTTT------GACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGCTGGGACCAGGGGCTGCTGGGGATGT tcaagcggttatagGCGATGTTTTGCAAC---ACTCATTTTGTGTCTCAGAGCAGCCTACCACAGAACCAGCCCTTTATTTTCTCCCTTGGCACTGGCCAGGTTATCAAGGGTTGGGACCAGGGTCTACTAGGGTATGgttggcatacaatctaagttgcaattgctgtagtaaaggtatttt #### Fth1_ID2624_3 --> 0 - 0 Original Alignment AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCAC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGACCTC---gttgatagcttcaataggctgcatatagatgggttgccatcatgaggaga Alignment from CESAR AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCAC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGACCTC---gttgatagcttcaataggctgcatatagatgggttgccatcatgagg Alignment from Spaln_aa2Genome AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGACCTCgttgatagcttcaataggctgcatatagatgggttgccatcatgaggaga Alignment from Spaln_nt2Genome AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCAC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGA---CCTCgttgatagcttcaataggctgcatatagatgggttgccatcatgaggaga Alignment from Pairagon AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGACCTCgttgatagcttcaataggctgcatatagatgggttgccatcatgaggaga Alignment from Exonerate_protein2genome AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCAC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGACCTCGTTgatagcttcaataggctgcatatagatgggttgccatcatgaggaga Alignment from Exonerate_coding2genome AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCAC tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGACCTCGTTgatagcttcaataggctgcatatagatgggttgccatcatgaggaga Alignment from GeneWise AAACCAGACCGTGATGACTGGGAGAGCGGGCTGAATGCAATGGAGTGTGCACTGCACTTGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCACTTA tgtattgggggtttaatgattatgacacccatggattattgtttccacagAAGCCTGAACGTGAGGATTGGGAGAGTGGGCTAAATGGAATAGAATGCGCACTCCACTTGGAAAAGAGTGTAAACCAGTCCCTACTGGAGCTGCATGAACTAGCAACTGATAAGAATGAC------CTCgttgatagcttcaataggctgcatatagatgggttgccatcatgaggaga #### Ganab_ID2468_7 --> 1 - 0 Original Alignment gCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgtaacagg------TCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from CESAR gCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG cagtgaatgtccaaattttactatatgaagcgtcctctgtcttgtaacagg------TCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from Spaln_aa2Genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgtaacagG------TCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from Spaln_nt2Genome ATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgtaacagGTCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from Pairagon GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgtaacagG------TCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from Exonerate_protein2genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgTAACAGGTCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from Exonerate_coding2genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgTAACAGGTCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat Alignment from GeneWise GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG atgtccaaattttactatagttaaatgaagcgtcctctgtcttgtaacagG------TCAAAAGACCCTGCAGAGGGCAATGGGGCCCAGCCTGAGGCAACACCTGGGGATGGTGACAAGgtatggtgaatgtgcaatttttacatctttaggaggcggcaagtgggtat #### Ganab_ID2469_8 --> 0 - 1 Original Alignment CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTAT---------g ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGAATGGAAAggcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from CESAR CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTAT---------g ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGAATGGAAAggcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from Spaln_aa2Genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTAT---------G ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGAATGGAAAGgcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from Spaln_nt2Genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATG--------- ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGAATGGAAAGgcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from Pairagon CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATG--------- ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGAATGGAAAGgcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from Exonerate_protein2genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATG ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGaatggaaaggcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from Exonerate_coding2genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATG ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGaatggaaaggcaagaaagtagccttgatgctaattttggaattgacatgtcttagatcc Alignment from GeneWise CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTAT------------------------------------------------G ctttaggaggcggcaagtgggtatgaataggccccttgctccctccacagCCAGAGGAGACCCAAGAAAAGGCTGAGAAAGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCAAGCCTTATGAATGGAAAGGCAAGAAAGTAGCCTTGATGCTAATTTTGGAATTGACATgtcttagatcc #### Ganab_ID2471_10 --> 1 - 0 Original Alignment gGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG--- atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagaGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTGTT---CTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACACA------AAGAAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag Alignment from CESAR gGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagaGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTGTT---CTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACACA---AAGAAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag Alignment from Spaln_aa2Genome GGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagAGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTGTT---CTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACACA---AAGAAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag Alignment from Spaln_nt2Genome GGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagAGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTG---TTCTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACA---CAAAGAAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag Alignment from Pairagon GGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGA-------------------------------------------------------- atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagAGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTG---TTCTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACAC-------AAAGAAAGTCTGTCGTAGATATGTGAGATATGAGGTCTGCCTTAAACATCTCATCAG Alignment from Exonerate_protein2genome GGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagAGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTGTT---CTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACACAAAG---AAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag Alignment from Exonerate_coding2genome GGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagAGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTGTT---CTGGCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACACAAAG---AAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag Alignment from GeneWise GGGCGGTGAGCCGTACCGCCTGTACAATTTGGATGTGTTCCAGTATGAGCTGAACAACCCCATGGCTCTATATGGGTCTGTGCCTGTGCTCCTGGCACACAGCTTTCATCGAGACCTGGGCATCTTCTGGCTTAATGCTGCTGAGACTTGGGTTGATATATCCTCCAACACGGCTGGGAAG atttttttcagataagaaatcttcatgtccctgtggcgcaccccttccagAGGTGGTGAGCCATATCGTTTGTACAACTTAGATGTATTACAGTACGAGCTAAATAACCCAACAGCACTCTATGGGTCGGTACCTGTTCTG---GCACACAGCTTCCATCGAGACCTGGGAATCTTCTGGCTCAATGCAGCTGAGACTTGGGTTGATATATCATCTAACACAAAG---AAAgtctgtcgtagatatgtgagatatgaggtctgccttaaacatctcatcag #### Ganab_ID2473_12 --> 2 - 0 Original Alignment ggACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcaccagcaggc------ACATTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from CESAR ggACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG aagcatttatactcttaccaaagatttttttgctctgggttcaccagcaGGC---ACATTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from Spaln_aa2Genome GGACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcaccagcagGCACA------TTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from Spaln_nt2Genome GGACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcaccagcagGCA------CATTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from Pairagon GGACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcaccagcagGCA------CATTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from Exonerate_protein2genome GGACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcacCAGCAGGCACATTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from Exonerate_coding2genome GGACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcacCAGCAGGCACATTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg Alignment from GeneWise --GGGACCCAGGCATTGCCCCCACTCTTCTCCCTCGGCTATCACCAGAGTCGCTGGAACTACCGGGATGAGGCTGATGTTTTGGAAGTGGATCAGGGTTTTGATGATCACAACATGCCTTGTGATGTCATTTGGTTGGACATTGAACATGCTGATGGCAAGCGGTACTTCACTTGGGACCCCACCCGATTTCCTCAGCCCCTCAATATGCTTGAGCACTTGGCTTCCAAGAGGCGGAAG catttatactcttaccaaaccagatttttttgctctgggttcaccagCAGGCACA------TTACCCCCCCCCTCATCCCTTGGCTACCATCAAAGTCGCTGGAACTACTGTGATGAAGCAGATACCTTGGAGGTTGGCCAGGGTTTTGACGATCATAACATGCCCTGTGATGTTATATGGTTGGATGTCGAACATGCTGATGGGAAGAGGTACTTTACCTGGGATCCCACCCAATTCCCCCAGCCACTTAATATGCTTGATCACTTGACTTCAAAGCGACGGAAGgtgagtgatgttacagctatccatattttttgtccagggttgggaattgg #### Ganab_ID2474_13 --> 0 - 1 Original Alignment CTGGTGGCCATTGTGGACCCCCACATCAAGGTA------GACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCA---------g gc gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTTAAAGTAGACTCTGGCTACCAGGTT---CATGAATTGCAA---------------ATCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAATTAAAGATggtgagttccatgaccaatgaagtttttcccctgatggggaggggacaggc Alignment from CESAR CTGGTGGCCATTGTGGACCCCCACATCAAG------GTAGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCA---------g gc gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTTAAAGTAGACTCTGGCTACCAGGTTCATGAA------------------TTGCAAATCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAATTAAAGATggtgagttccatgaccaatgaagttttgcctttctcctttccattgcaggc Alignment from Spaln_aa2Genome CTGGTGGCCATTGTGGACCCCCACATC------AAGGTAGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCA---------G GC gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTTAAAGTAGACTCTGGCTACCAGGTTCATGAA------------------TTGCAAATCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAATTAAAGATGgtgagttccatgaccaatgaagtttttcccctgatggggaggggacagGC Alignment from Spaln_nt2Genome CTGGTGGCCATTGTGGACCCCCACATCAAGGT------AGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCA---------G GC gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTTAAAGTAGACTCTGGCTACCAGGTTC---ATGAATTGCAAA---------------TCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAATTAAAGATGgtgagttccatgaccaatgaagtttttcccctgatggggaggggacagGC Alignment from Pairagon CTGGTGGCCATTGTGGACCCCCACATCAAG------GTAGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGC---------------------------------------------------------CAGGC gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTTAAAGTAGACTCTGGCTACCAGGTTCAT---GAATTGCAAA---------------TCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAATTAAAGATGGTGAGTTCCATGACCAATGAAGTTTTTCCCCTGATGGGGAGGGGACAGGC Alignment from Exonerate_protein2genome CTGGTGGCCATTGTGGACCCCCACATCAAGGTAGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCAG GC gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTT------------AAAGTAGACTCTGGCTACCAGGTTCATGAATTGCAAATCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAAttaaagatggtgagttccatgaccaatgaagtttttcccctgatggggaggggacagGC Alignment from Exonerate_coding2genome CTGGTGGCCATTGTGGACCCCCACATCAAGGTAGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCAG GC gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTT------------AAAGTAGACTCTGGCTACCAGGTTCATGAATTGCAAATCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAAttaaagatggtgagttccatgaccaatgaagtttttcccctgatggggaggggacagGC Alignment from GeneWise CTGGTGGCCATTGTGGACCCCCACATC------AAGGTAGACTCTGGCTACCGAGTTCACGAAGAATTGCGAAACCATGGGCTGTATGTTAAAACTCGGGATGGCTCTGATTACGAGGGCTGGTGCTGGCCA---------G GC gaattggcattgtaacctaaacaattccttcctaatcttcctcatcctagCTAGTTGCTACTGTGGACCCACATATCAAGGTTAAAGTAGACTCTGGCTACCAGGTTCATGAA------------------TTGCAAATCAAGACTCGGGATGGCTCTGACTACGAAGGCTGGAGTTGGCCAATTAAAGATGgtgagttccatgaccaatgaagtttttcccctgatggggaggggacagGC #### Ganab_ID2477_16 --> 0 - 1 Original Alignment CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAGCGCTTTg accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAG------ggtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from CESAR CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAGCGCTTTg accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAG------ggtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from Spaln_aa2Genome CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAG- accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAGGgtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from Spaln_nt2Genome CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAGC accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAGGgtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from Pairagon CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAGCGCTTTG accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAG------Ggtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from Exonerate_protein2genome CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAGC accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAGGgtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from Exonerate_coding2genome accaggaagcctggtttagattttttttaagaccacttttgttctttcagcatatggcaaccactgatggcctgatacagtgttcaggaggggttgagcgttcatttgtgttgagtcggtccttttcttcagggttccagggtaagtggaggcttaaactagcatcaacactctactcacttctggttaac Alignment from GeneWise CACATGGCGACTGCTGATGGGCTAATACAGCGCTCTGGGGGCATAGAGCGTCCCTTTGTCCTGAGTAGGGCTTTCTTCTCAGGCTCCCAGC accaggaagcctggtttagattttttttaagaccacttttgttctttcagCATATGGCAACCACTGATGGCCTGATACAGTGTTCAGGAGGGGTTGAGCGTTCATTTGTGTTGAGTCGGTCCTTTTCTTCAGGGTTCCAGGgtaagtggaggcttaaactagcatcaacactctactcacttctggttaac #### Ganab_ID2478_17 --> 2 - 1 Original Alignment ga------GCTGTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAg cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcaggaGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAggtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from CESAR gaGCT------GTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAg cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcaggaGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAggtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from Spaln_aa2Genome GA------GCTGTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAG cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcagGAGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAGgtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from Spaln_nt2Genome GAGCT------GTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAG cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcagGAGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAGgtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from Pairagon GA------GCTGTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAG cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcagGAGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAGgtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from Exonerate_protein2genome GA------GCTGTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAG cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcagGAGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAGgtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from Exonerate_coding2genome GA------GCTGTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAG cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcagGAGCTCAGGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAGgtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac Alignment from GeneWise ---GTGTGGACAGGGGACAACACTGCCGAATGGGATCATTTGAAGATCTCTATCCCTATGTGTCTCAGCCTGGCACTGGTGGGGCTTTCCTTCTGTGGAG cagtgactaatatcttgtcggcgtagtcaaaacattttggtttgtttcaggagctcagGCTGTGTGGGCAGGGGACAACACTGCTGAATGGGATCATTTGAAGATCTCTATCCATATGTGCCTCAGCTTGGCATTGGTGGGGCTGTCATTCTGTGGAGgtaagtgcagttatcatctgggctcttgcattgggttggtgtgttggtac #### Ganab_ID2484_23 --> 0 - 2 Original Alignment GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCT---ag ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTaggtaagttttatgccctgcctccattttctggacctgtttgactgggttgc Alignment from CESAR GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCT---ag ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTaggtaagttttatgccctgcctccattttctggacctgtgttctgctctcct Alignment from Spaln_aa2Genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGTTC ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTAGgtaagttttatgccctgcctccattttctggacctgtttgactgggttgc Alignment from Spaln_nt2Genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGTTCAG ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGT--AGgtaagttttatgccctgcctccattttctggacctgtttgactgggttgc Alignment from Pairagon GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCT------------------------------------------------------- ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTAGGTAAGTTTTATGCCCTGCCTCCATTTTCTGGACCTGTTTGACTGGGTTGC Alignment from Exonerate_protein2genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGTTC ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTAGgtaagttttatgccctgcctccattttctggacctgtttgactgggttgc Alignment from Exonerate_coding2genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGTTC ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTAGgtaagttttatgccctgcctccattttctggacctgtttgactgggttgc Alignment from GeneWise GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGT-- ataggtagacagaccacactgtctgttggcatgtctggtgacctccctagGGTACTGCACAGGGAGAGCTATTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTTGTAGgtaagttttatgccctgcctccattttctggacctgtttgactgggttgc #### Gbf1_ID9800_19 --> 0 - 0 Original Alignment ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagAAAAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa Alignment from CESAR ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagAAAAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa Alignment from Spaln_aa2Genome AGTTGTAAT---GGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagAAAAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa Alignment from Spaln_nt2Genome A---GTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagAAAAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa Alignment from Pairagon ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagAAAAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa Alignment from Exonerate_protein2genome AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagaaaAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa Alignment from Exonerate_coding2genome AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAGGAATTTCGCAAAAACCTAAAAGGTGTGAATGGAGGCAAGGACTTTGAGCAAGA aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagaaaAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTA---GAAGTAAGGGCAGGATTTTTGTCTATTCAGGACAGCACCACTCAACAGCTTAA Alignment from GeneWise ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG aggtaaacatttcattttgcggtttacactgcttgcttgtcccatgccagAAAAGCTGCAATGGCTCTCCTTTTGCCAATAGTGGTGCCTGTTCTGCACTAGCCTACACTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtaagggcaggatttttgtctattcaggacagcaccactcaacagcttaa #### Gbf1_ID9803_22 --> 1 - 0 Original Alignment gAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttaga------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from CESAR gAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG cttggacatgtgcaccaggtgtttcctttgttctttcattctgcttttaga------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from Spaln_aa2Genome GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttagA------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from Spaln_nt2Genome TGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttagAGCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from Pairagon GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttag------AGCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from Exonerate_protein2genome GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttagA------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from Exonerate_coding2genome GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttagA------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc Alignment from GeneWise GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG catgtgcaccaggtgtttcctgatactttgttctttcattctgcttttagA------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtatgaaactaccaagtaaactaatcagaggttaatgctgcacatcatcc #### Gbf1_ID9807_26 --> 0 - 0 Original Alignment ------CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from CESAR ------CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from Spaln_aa2Genome CAATGT------GACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from Spaln_nt2Genome CAATGTGACCCAG------AAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from Pairagon ------CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from Exonerate_protein2genome ------CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from Exonerate_coding2genome ------CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca Alignment from GeneWise ------CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG atagccaagatacctattcaaaagggctcttgcctgtttctgtcttacagCCTACCCAGTGCGACCCAGAAAAGATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCTCTGCAGGAACTCATGAAGgtaccctatgaacagatcatggaaaaatagaattatactggtgcagtgca #### Gbf1_ID9808_27 --> 0 - 2 Original Alignment GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAAC---ag agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCaggtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg Alignment from CESAR GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAAC---ag agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCaggtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg Alignment from Spaln_aa2Genome GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAACAGG-- agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCAGgtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg Alignment from Spaln_nt2Genome GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAAC---AG agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCAGgtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg Alignment from Pairagon GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAAC------------------------------------------------------- agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCAGGTATCCTAAGTTGGCCTGTAGAAGTCACAAGAATACCTCCCAAAGAGATG Alignment from Exonerate_protein2genome GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAAC---AG agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCAGgtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg Alignment from Exonerate_coding2genome GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAAC---AG agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCAGgtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg Alignment from GeneWise GCTCTGGTCTCAGTGACACCAGATGAAGAGACATATGACGAAGAAGATGCTGCTTTCTGTCTAGAGATGCTGCTAAGGATCGTGTTAGAGAACAGG-- agtgtgctagaatcccagcccctttaatctatgtttttatttgtttgcagTCTCTGGTCTCTGTAGCCCCTGATGAAGAGACATATGATGAAGAAGATGCTGCTTTCTGTCTTGAAATGCTGCTAAGGATTGTTCTAGAGAACTGCAGgtatcctaagttggcctgtagaagtcacaagaatacctcccaaagagatg #### Gbf1_ID9812_31 --> 0 - 1 Original Alignment GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAATGGT---------------------g tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTGTCTGGGATTCCTATGCCAggtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga Alignment from CESAR GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAATGGT---------------------g tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTGTCTGGGATTCCTATGCCAggtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga Alignment from Spaln_aa2Genome GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAATGGT---------------------G tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTGTCTGGGATTCCTATGCCAGgtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga Alignment from Spaln_nt2Genome GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAATGGTG- tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTgtctgggattcctatgccaggtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga Alignment from Pairagon GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAATGGT------------------------------------------------------------------------ tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTGTCTGGGATTCCTATGCCAGGTGAGTTTTCCTTAACACCAGTGCAGCATGAGTGACATGGAGGAATTAGA Alignment from Exonerate_protein2genome GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAATGGTGGGT tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTGTctgggattcctatgccaggtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga Alignment from Exonerate_coding2genome tcttagtatcactcctaacctgaaatatctggcccctcatttccccccaggtggggaaggatgatattgataattccaagccaggggcagggttcagtaagccaggtacttctccactagttaaccagtatagcctcacagtaggcttggatctgggcccacatgacactaagtccttacttaagtgtgttgaatctctgtcctttattatcaaagatgctgcgcacatcacacctgataattttgaactgggagtcaagaccctctgtatctttgtagaggccagtctgaatgatctgtctgggattcctatgccaggtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga Alignment from GeneWise GTGGGGAAGGATGACATTGATAACTCCAAACCAGGAGCAGGGCTCAGCAGGCCAGGCCCTTCACCCCTGGTCAACCAGTACAGCCTTACAGTGGGCCTGGATCTGGGCCCACACGACACTAAGTCCCTGCTTAAGTGTGTGGAGTCACTGTCCTTCATTGTCCGAGATGCTGCTCACATCACCCCTGACAACTTTGAACTCTGCGTCAAGACTCTCCGCATCTTTGTAGAAGCCAGTCTGAAT------GGTGGGTGCAAGTCCCAG- tcttagtatcactcctaacctgaaatatctggcccctcatttccccccagGTGGGGAAGGATGATATTGATAATTCCAAGCCAGGGGCAGGGTTCAGTAAGCCAGGTACTTCTCCACTAGTTAACCAGTATAGCCTCACAGTAGGCTTGGATCTGGGCCCACATGACACTAAGTCCTTACTTAAGTGTGTTGAATCTCTGTCCTTTATTATCAAAGATGCTGCGCACATCACACCTGATAATTTTGAACTGGGAGTCAAGACCCTCTGTATCTTTGTAGAGGCCAGTCTGAATGATCTGTCTGGGATTCCTATGCCAGgtgagttttccttaacaccagtgcagcatgagtgacatggaggaattaga #### Gif_ID3278_2 --> 2 - 1 Original Alignment ctGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACAGTGCA---------------------g agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagctGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACCATG---ATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAGTGCAGTGTTTGGACACTTCAATCATggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from CESAR ctGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACAGTGCA---------------------g agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagctGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACC---ATGATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAGTGCAGTGTTTGGACACTTCAATCATggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from Spaln_aa2Genome CTGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGAC- agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagCTGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACCATG---ATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAgtgcagtgtttggacacttcaatcatggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from Spaln_nt2Genome CTGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACAGTGCAG- agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagCTGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACCA---TGATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAGTGCAGTgtttggacacttcaatcatggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from Pairagon CTGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACAGTGCAG--------------------- agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagCTGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACCA---TGATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAGTGCAGTGTTTGGACACTTCAATCATGgtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from Exonerate_protein2genome CTGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACA agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagCTGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACC---ATGATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAgtgcagtgtttggacacttcaatcatggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from Exonerate_coding2genome CTGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACA agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagCTGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACC---ATGATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAgtgcagtgtttggacacttcaatcatggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa Alignment from GeneWise CTGTGCCCCCAGATCAGCAACCCTGGGTCGATGGCCTACAAGCGCTCATGGAGAACTCGGTGACTGACTCAGACTTCCCAAACCCCAGCATCCTGATTGCCATGAACCTGGCCGGCGCCTACAACGTGGAGGCCCAGAAACTCCTGACTTACCAGCTCATGGCCAGTGACAGTGCA-- agtcattctgtggagctgcacacagtagaatgtcctgggtcttcccacagCTGTTCCCCTAGATCAACATCCTTGGGTTGAAGGCTTACAAACACTCATGGAAAACTCAGTAACTGACTCCGACTTCCCTAACCCAACC---ATGATTGCCAAGAACCTGGCTGGTGCATACATTGTGGGGCCTCAAAAACTCCTGACTTACCAACTAATGGCCAGTGAAAGTGCAGTgtttggacacttcaatcatggtaaatcactaagggtacatttttaccatgagtcttttatgttcgcccaa #### Gif_ID3279_3 --> 2 - 1 Original Alignment acCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCA------a tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagacTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACTCTG---AGGAAAATGGAAAACTGGTCACCTTCAGTCATCagtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from CESAR acCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCA------a tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagacTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAGTCATCagtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from Spaln_aa2Genome ACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAAGCCCGG tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagACTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACTCTGAGGAAA---ATGGAAAACTGGTCACCTTCAGTCATCAgtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from Spaln_nt2Genome ACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCA------A tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagACTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACTCT---GAGGAAAATGGAAAACTGGTCACCTTCAGTCATCAgtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from Pairagon ACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCA------A tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagACTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAGTCATCAgtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from Exonerate_protein2genome ACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagACTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAGtcatcagtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from Exonerate_coding2genome ACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagACTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAGtcatcagtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg Alignment from GeneWise ACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCA------A tcctacctctgttttgtgtagtttctctcttcttctttttttaactacagACTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTGTCTACTCTG---AGGAAAATGGAAAACTGGTCACCTTCAGTCATCAgtaagagtggcttgtggggccattgacagggagagatgttatgcatgacg #### Gldc_ID6402_13 --> 1 - 0 Original Alignment cTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCACAGCATGATCCCACTG cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagtTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAGTATG---------gtatgagcacatcggcgggtctgacttgttaccatgtacattggtatcta Alignment from CESAR cTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCACAGCATGATCCCACTG cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagtTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAGTATG---------gtatgagcacatcggcgggtctgacttgttaccatgtacat Alignment from Spaln_aa2Genome GCTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCACAGCAT cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagTTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAGTATGgtatgagcacatcggcgggtctgacttgttaccatgtacattggtatcta Alignment from Spaln_nt2Genome CTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCACAGCATGATCCCA cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagTTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAGTATGGTATGAgcacatcggcgggtctgacttgttaccatgtacattggtatcta Alignment from Pairagon CTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCACAGCATG cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagTTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAGTATGgtatgagcacatcggcgggtctgacttgttaccatgtacattggtatcta Alignment from Exonerate_protein2genome CTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCACAGCATG cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagTTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAGTATGgtatgagcacatcggcgggtctgacttgttaccatgtacattggtatcta Alignment from Exonerate_coding2genome CTATCACTC cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagttaccacttagaaactaaccttgtcccatacatgaagagattggaaaaccgagatatttccctcttacacagtatggtatgagcacatcggcgggtctgacttgttaccatgtacatTGGTATCTA Alignment from GeneWise CTATCACTCAGAAACTAATCTTGTCCGGTATATGAAGAAACTGGAGAACAAAGACATCTCCCTCGTTCAC- cctgtggagtggctaatctctgtgtttaccatcgacccccacttccccagTTACCACTTAGAAACTAACCTTGTCCCATACATGAAGAGATTGGAAAACCGAGATATTTCCCTCTTACACAgtatggtatgagcacatcggcgggtctgacttgttaccatgtacattggtatcta #### Got1_ID8751_4 --> 2 - 0 Original Alignment agAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatataccagag---CATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from CESAR agAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG agtttctatccccattaatagtggacacagtttttctgttaatataccagag---CATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from Spaln_aa2Genome AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatataccagAG---CATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from Spaln_nt2Genome AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatataccagAG---CATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from Pairagon AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatataccagAG---CATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from Exonerate_protein2genome AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatatacCAGAGCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from Exonerate_coding2genome AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatatacCAGAGCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc Alignment from GeneWise --CATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG ttctatccccattaatagtggataacacagtttttctgttaatataccagAGCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtgagggaagataagaatagatgcccaagcttagtgcaggagggttttcc #### Gpr137_ID1886_5 --> 0 - 0 Original Alignment GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG--- gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTC---TTTTGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from CESAR GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG--- gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from Spaln_aa2Genome GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG--- gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from Spaln_nt2Genome GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG--- gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCT---TTTGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from Pairagon GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG--- gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCT---TTTGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from Exonerate_protein2genome GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG--- gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from Exonerate_coding2genome GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGcgagtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc Alignment from GeneWise GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTGAGC gggctaacagggttgcgcattaacaaatctgttgaccctgtgacctttagGCAGATCTGGTCAATGACCTAGTGAACAAAGGATACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGCGAgtgagaaacatgtggccctcagtagagatgtgctgtccaacctaaaggcc #### Gpr137_ID1887_4 --> 0 - 0 Original Alignment GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAG--- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATAGGG---CCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatcca Alignment from CESAR GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAG--- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATAGGG---CCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatctg Alignment from Spaln_aa2Genome GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAG--- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATA---GGGCCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatcca Alignment from Spaln_nt2Genome GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAG--- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATAGGG---CCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatcca Alignment from Pairagon GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGAC-------------------------------------------------------- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATAGGG---CCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCGTAAGTTATATTGCATTCTGGGCTAACAGGGTTGCGCATTAACAAATCCA Alignment from Exonerate_protein2genome GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAG--- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATA---GGGCCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatcca Alignment from Exonerate_coding2genome GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAG--- tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATA---GGGCCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatcca Alignment from GeneWise GGGACCAGCGTGTGTCAGGCAGCTGCTATAGGGGGTGCCATGGTCCTTCTCTATGCCAGCCGGGCCTGTTACAACCTGGCAGCTCTGGCCTTGGCCCCTCGGAGCCGGCTAGATGCCTTCGATTACGACTGGTACAACGTATCTGACCAGGCA tgtaaacgtacctagaatgctgggaccaagtgaaaatgtatcgtttgcagGGAACAAGTGTATGTCAGGTAGCAGCAATAGGG---CCCATGATTTTGATTTATGCCAGCAGGGCCTGCTACAACCTGGCAGCCTTGGCCTTGGCACCTCAGAGTCGGTTAGATGCTTTTGATTATGACTGGTATAATGTCTCAGACCAAGGCgtaagttatattgcattctgggctaacagggttgcgcattaacaaatcca #### Gpr137_ID1888_3 --> 1 - 0 Original Alignment gCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG--- ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccaggCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGT------GCTCTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGTTAgtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from CESAR gCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG--- ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccaggCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGTTAgtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from Spaln_aa2Genome GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG--- ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccagGCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGTTAgtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from Spaln_nt2Genome GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAA ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccagGCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAgttagtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from Pairagon GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG--- ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccagGCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGTTAgtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from Exonerate_protein2genome GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccagGCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGttagtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from Exonerate_coding2genome GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccagGCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGttagtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct Alignment from GeneWise GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAGGGG ggttggctatagctgctgcaaggtgtcccctgacctcatttgtgttccagGCTGGCTGTTCAAGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTTTATCATGCCAGCGTCAGCAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCTCTT------GCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACGACCAGCATCTACTTAGATGCAAAGTTAgtgagtgtgtaatatagatgtggcattgttggatttgtggacagaattct #### Gucy2g_ID11571_20 --> 2 - 0 Original Alignment ctCTCCGGATTCACGTTTCCCAGAGCACCGCAGGAGCTCTTCTAGCAGCAGGGGGGTACCATCTGCAAAAGAGA---GGCACCATT------TCAGTCAAG--- ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagctCTCCGTATTCATATTTCACACAGTACTTCTGGTGCTCTTCTGGCAGCAGGGGGGTACCCACTGCAAGAGAGAGGCAGCACTGTTTCTGTATCTGTGAAAGGAgtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from CESAR ctCTCCGGATTCACGTTTCCCAGAGCACCGCAGGAGCTCTTCTAGCAGCAGGGGGGTACCATCTGCAAAAGAGAGGC---ACCATTTCAGTCAAG ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagctCTCCGTATTCATATTTCACACAGTACTTCTGGTGCTCTTCTGGCAGCAGGGGGGTACCCACTGCAAGAGAGAGGCAGCACTGTTTCTGTATCTgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from Spaln_aa2Genome CTCTCCGGATTCACGTTTCCCAGAGCACCGCAGGAGCTCTTCTAGCAGCAGGGGGGTACCATCTGCAAAAGAGAGGC---ACCATTTCAGTCAAG ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagCTCTCCGTATTCATATTTCACACAGTACTTCTGGTGCTCTTCTGGCAGCAGGGGGGTACCCACTGCAAGAGAGAGGCAGCACTGTTTCTGTATCTgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from Spaln_nt2Genome CTCTCCGGATTCACGTTTCCCAGAGCACCGCAGGAGCTCTTCTAGCAGCAGGGGGGTACCATCTGCAAAAGAGAGGCACCA---TTTCAGTCAAG ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagCTCTCCGTATTCATATTTCACACAGTACTTCTGGTGCTCTTCTGGCAGCAGGGGGGTACCCACTGCAAGAGAGAGGCAGCACTGTTTCTGTATCTgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from Pairagon CTCTCCGGATTCACGTTTCCCAGAGCACCGCAGGAGCTCTTCTAGCAGCAGGGGGGTACCATCTGCAAAAGAGAGGCACCATT ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagCTCTCCGTATTCATATTTCACACAGTACTTCTGGTGCTCTTCTGGCAGCAGGGGGGTACCCACTGCAAGAGAGAGGCAGCACTgtttctgtatctgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from Exonerate_protein2genome ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagctctccgtattcatatttcacacagtacttctggtgctcttctggcagcaggggggtacccactgcaagagagaggcagcactgtttctgtatctgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from Exonerate_coding2genome ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagctctccgtattcatatttcacacagtacttctggtgctcttctggcagcaggggggtacccactgcaagagagaggcagcactgtttctgtatctgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa Alignment from GeneWise CTCTCCGGATTCACGTTTCCCAGAGCACCGCAGGAGCTCTTCTAGCAGCAGGGGGGTACCATCTGCAAAAGAGAGGC---ACCATTTCAGTCAAG ggattgaaaatattgggttgatacaacgccttgctttacttcccgttcagCTCTCCGTATTCATATTTCACACAGTACTTCTGGTGCTCTTCTGGCAGCAGGGGGGTACCCACTGCAAGAGAGAGGCAGCACTGTTTCTGTATCTgtgaaaggagtaagactgggcctgtttgtgctcagcattaaaaaaatctaaaccttgaa #### Hectd2_ID7146_4 --> 1 - 0 Original Alignment gGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagg------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from CESAR gGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG cctaagtttgcctacctctttttggtctccctgacacccccattccccagg------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from Spaln_aa2Genome GGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagG------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from Spaln_nt2Genome GGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagG------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from Pairagon GGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagG------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from Exonerate_protein2genome GGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagG------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from Exonerate_coding2genome GGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagG------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag Alignment from GeneWise GGAAGATTTAGAAAAAGCTGAGGCCACAGGGAATTGGAAGACAGTACATGCTTTTTATATAACAGCATTTGATTCTTTCACAGAACTAAACACTGCATTTAAG tttgcctacctctttttggttctcatctccctgacacccccattccccagG------CTAGAAAAAGCTGAAGCTACAGGGAACTGGAAAGCAGTACATGCTTTCTATATTACGGCATTTGATTCCTTTACAGAGCTAAACACTGCATTTAAGgtgagtatacaaaaaaaagttgcctctcactttttggttgtacacaaaag #### Hectd2_ID7162_18 --> 2 - 0 Original Alignment agTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG--------- tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagagTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from CESAR agTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG--------- tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagagTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from Spaln_aa2Genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG--------- tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagAGTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from Spaln_nt2Genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAAT tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagAGTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATgtactacaaggtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from Pairagon AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG--------- tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagAGTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from Exonerate_protein2genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATGCTGCTTCGT tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagAGTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from Exonerate_coding2genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATGCTGCTTCGT tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagAGTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca Alignment from GeneWise AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG--------- tgttctccttttagacccaatgtccttctgctgtgtgtttgtctcttcagAGTACATTCAACTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCAGAGTGTGTGTGCTTCCAATGCATTGATGTACTACAAGgtgagtttagatttcaattgaatgggtccaataattgataactaatccca #### Hells_ID7708_15 --> 0 - 0 Original Alignment ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTCAAG---------------gtaagttcaactaaaagtaagctacaatatatttatgctgtctgtccagt Alignment from CESAR ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTC---------------AAGgtaagttcaactaaaagtaagctacaatatatttatgctgtctgtccagt Alignment from Spaln_aa2Genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAA gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTCAAGgtaagttcaactaaaagtaagctacaatatatttatgctgtctgtccagt Alignment from Spaln_nt2Genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGT-CACAAG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTCAAGGTAAGTTCAACTAAAAgtaagctacaatatatttatgctgtctgtccagt Alignment from Pairagon ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACT---------------CAAGgtaagttcaactaaaagtaagctacaatatatttatgctgtctgtccagt Alignment from Exonerate_protein2genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAGG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTCAAGGTAAGTTCAACTAAAAgtaagctacaatatatttatgctgtctgtccagt Alignment from Exonerate_coding2genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAGG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTCAAGGTAAGTTCAACTAAAAgtaagctacaatatatttatgctgtctgtccagt Alignment from GeneWise ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gttacattcaaatctacaagctgtcattgacttgccttctttcttattagAATGATGAAGAGTTTGTAACAAACTCTGGGAGGTTCCTAATTTCAGATCGAATGCTGCCAGAACTC---------------AAGgtaagttcaactaaaagtaagctacaatatatttatgctgtctgtccagt #### Hif1an_ID9067_5 --> 0 - 2 Original Alignment GTGGACTTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACtg catgtgtgaaatgacagcttgtctcctgcactatactcccactgccctag------TTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATtggtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from CESAR GTGGACTTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACtg ttgccacatgtgtgaaatgacagctctgcactatactcccactgccctag------TTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATtggtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from Spaln_aa2Genome TTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACTG catgtgtgaaatgacagcttgtctcctgcactatactcccactgccctagTTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATTGgtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from Spaln_nt2Genome TTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACTG catgtgtgaaatgacagcttgtctcctgcactatactcccactgccctagTTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATTGgtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from Pairagon GTGGACTTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACTG catgtgtgaaatgacagcttgtctcctgcactatactcccactgccctag------TTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATTGgtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from Exonerate_protein2genome GTGGACTTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACTG catgtgtgaaatgacagcttgtctcctgcactatactcccactgCCCTAGTTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATTGgtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from Exonerate_coding2genome GTGGACTTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACTG catgtgtgaaatgacagcttgtctcctgcactatactcccactgCCCTAGTTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATTGgtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt Alignment from GeneWise TTTGACAATCCTGACTACGAGAGGTTCCCCAATTTCCGAAATGTGGTTGGTTATGAGACAGTGGTTGGCCCTGGGGATGTTCTTTACATCCCAATGTACTG catgtgtgaaatgacagcttgtctcctgcactatactcccactgccctagTTTGATAATCCAGACTATGAGAGGTTCCCCAACTTTCGTAATGTGGTTGGCTATGAGACAGTGGTTGGCCCTGGGGATGTACTATACATCCCCATGTATTGgtaaggtgcaaatgaatgaagcagtgctttcacctccctacaatggtatt #### Hnrnpul2_ID2404_8 --> 0 - 0 Original Alignment ---GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagATGGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from CESAR ---GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagATGGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from Spaln_aa2Genome GTGATTCTGATGGTG---GGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagATGGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from Spaln_nt2Genome ---GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagATGGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from Pairagon ---GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagATGGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from Exonerate_protein2genome GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagatgGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from Exonerate_coding2genome GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagatgGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct Alignment from GeneWise ---GTGATTCTGATGGTGGGACTTCCTGGATCTGGAAAGACCCAGTGGGCACTGAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTTCTCACGCAAATGAGG tagtagttaacctaataatgctcataatacaccccctctgcccataccagATGGTGATTCTGATGGTGGGAGTCCCTGGATCAGCAAAGACGCAGTGGGCACTAAAATACGCAAAAGACAACCCTGAGAGAAGATACAATGTTCTGGGAGCTGAGACTGTCCTCACGCAAATGAGGgtaagaaatttatcaggttttatgagcagaattggtaaaagtcataatct #### Hnrnpul2_ID2409_13 --> 0 - 0 Original Alignment GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAAT------------------------------------gtgagaatgaaacagggatcagaagaaagagataggtggcggtacggatg Alignment from CESAR GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTAC------------------------------AAATACAAT------gtgagaatgaaacagggatcagaagaaagagataggtggcggta Alignment from Spaln_aa2Genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAAC---------------------AGATACAGAGACTATTACAGACAATACAA tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATGTGAGAATGAAACAGGGATCAGAAGAAAGAGATAGGTGGCGGTACGGATG Alignment from Spaln_nt2Genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACA-GATACAGAGACT---ATTACAGACAATACAACCG-GGAT tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATGTGAGAATGAAACAGGGATCAGAAGAAAGAGATAGGTGGCGgtacggatg Alignment from Pairagon GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACA------------------------------------ATgtgagaatgaaacagggatcagaagaaagagataggtggcggtacggatg Alignment from Exonerate_protein2genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAAC tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATgtgagaatgaaacagggatcagaagaaagagataggtggcggtacggatg Alignment from Exonerate_coding2genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAAC tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATgtgagaatgaaacagggatcagaagaaagagataggtggcggtacggatg Alignment from GeneWise GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tcttaaatgcctataatggattgagcttgggtgtcatcccctccctccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATAC------------------------------------AATgtgagaatgaaacagggatcagaagaaagagataggtggcggtacggatg #### Hoga1_ID8380_3 --> 2 - 0 Original Alignment ccACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG------ agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagctATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGACAACCgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from CESAR ccACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG------ agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagctATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGACAACCgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from Spaln_aa2Genome CCACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG------ agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagCTATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGACAACCgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from Spaln_nt2Genome CCACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAGG----- agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagCTATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGACAACCgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from Pairagon CCACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG------ agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagCTATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGACAACCgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from Exonerate_protein2genome CCACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagCTATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGacaaccgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from Exonerate_coding2genome TCCACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcaGCTATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGacaaccgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta Alignment from GeneWise CCACGCAAGCCACAGTAGAGATGACTGTCAGCATGGCTCAGGTGGGTGCTGATGTCGCCATGGTGGTGACCCCTTGTTACTATCGTGGCCGCATGAGCAGCGCTGCCCTCATTCACCACTACACCAAG------ agtagattaacatatcaagtggtggctgtcccctgatttctcctgagcagCTATGCAAGCTACAGTAGATATGACTGTCAGCATGGCTCAAGTTGGTGTTGATGTCGCCATGGTGGTGACTCCATGTTACTATCATGGCCATATGAGCAGTGCAGCAATTATCCACCACTACACTAAGACAACCgtaaacaggaatggttgagatatgctttaagtattgattgaaggaagcta #### Hoga1_ID8381_4 --> 0 - 0 Original Alignment GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGAGAT------ taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from CESAR GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGA------GAT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from Spaln_aa2Genome GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGA------GAT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from Spaln_nt2Genome GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGAG------AT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from Pairagon GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGG------AGAT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from Exonerate_protein2genome GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGA------GAT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from Exonerate_coding2genome GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGA------GAT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca Alignment from GeneWise GTTGCTGACGTTTCTCCAATCCCTGTGGTGTTGTACAGTGTCCCAGCCAATACGGGGCTAGAGCTACCTGTGGATGCCGTGGTTACATTGTCTCAGCACCCAAATATCATCGGCTTGAAGGACAGTGGTGGA------GAT taaacaggggttgacatggtaaatgcctcctcctctgactttgcttccagATTGCTGATGTTCCCCCAATCCCCGTAGTGTTATACAGTGTCCCAGCCAATACAGGACTAGAGCTACCTGTGGATGCTGTGGTCACATTGTCTCAACACCCAAACATTATTGGCCTGAAGGTCAGTGGTGGAGGTCCAGATgtgagatgctatagggtccgatttgctcaagcaacctcaacctcaggtca #### Hps1_ID8620_8 --> 0 - 1 Original Alignment GACACAGACAGCATCTCCCTCCCTGAAGAGTACTTCACTCCTGCTCCTTCCCCAGGCGATCAGAGTTCA---------------g tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttagGATACTGAT---AATTCC---CCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGT------GGTCCAAAATTCCCGGTGCAGggtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from CESAR GACACAGACAGCATCTCCCTCCCTGAAGAGTACTTCACTCCTGCTCCTTCCCCAGGCGATCAGAGT---------TCAg tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttagGATACTGATAAT---TCC---CCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGTGGTCCAAAATTCCCGGTGCAGggtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from Spaln_aa2Genome GACACAGACAGCATCTCCCTCCCTGAAGAGTACTTCACTCCTGCTCCTTCCCCAGGCGAT---------CAGAGTTCAG tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttagGATACTGATAATTCC------CCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGTGGTCCAAAATTCCCGGTGCAGGgtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from Spaln_nt2Genome GACACAGACAGCATCTCCCTCCCTGAAGAGTACTTCACTCCTGCTCCTTCCCCAGGCGATC--AGAGTTCAG tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttagGATACTGATA--AT-TC---CCCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGTGGTCCAAAATTCCCGgtgcagggtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from Pairagon ----------------------------------------------------------------CCCTGAAGAGTACTTCACTCCTGCTCCTTCCC-----------------------CAGG TGGTAAGCAAACTACGGTGTATTCTCTGCACATGCAGTGTCCTTCCTTAGGATACTGATAATTCCCCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGTGGTCCAAAATTCCCGGTGCAGGgtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from Exonerate_protein2genome GACACAGACAGCATCTCCCTCCCTGAAGAGTACTTCACTCCTGCTCCTTCCCCAGGCGATCAGAGTTCAGGTA tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttagGATACTGAT------AATTCCCCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGTGGTCCAAAATTCCCGGtgcagggtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from Exonerate_coding2genome tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttaggatactgataattccccggaagagtatttcactccctctcctcccccaagtggtccaaaattcccggtgcagggtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga Alignment from GeneWise GACACAGACAGCATCTCCCTCCCTGAAGAGTACTTCACTCCTGCTCCTTCCCCAGGC- tggtaagcaaactacggtgtattctctgcacatgcagtgtccttccttagGATACTGATAATTCC------CCGGAAGAGTATTTCACTCCCTCTCCTCCCCCAAGTGgtccaaaattcccggtgcagggtgagtggagtgggtgtggcaccttactatgtcacttagttaagtacaga #### Hps1_ID8621_7 --> 0 - 0 Original Alignment ------------------------AGGAGACCCAAGAGCAGCCAAAACATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAGGGAGACA tatgcgatgcatttctgcttgctcatgactcctctgtcctgtgtctgcagTCCTTTGAAGGTTACGGCCAAACAAGGCATCCAAAGAGA---------------------CAAACCAGGAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAgtgaggcctaagctggtaagcaaactacggtgtattctctgccattgtgt Alignment from CESAR AGGAGACCCAAGAGCAGCCAAAACATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAGGGAGACA cacagtactgtatgcgatgcatttctgcttgctcagtcctgtgtctgcagtcctttgaagGTTACGGCCAAA------CAAGGCA-TCCAAAGAGACAAACCAGGAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAgtgaggcctaagctggtaagcaaactacggtgtattctctgcacatgcag Alignment from Spaln_aa2Genome AGGAGACCCAAGAGCAGCCAAAAC---ATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAGGGAGACA tatgcgatgcatttctgcttgctcatgactcctctgtcctgtgtctgcagTCCTTTGAAGGTTACGGCCAAACAAGGCATCCAAAGAGACAAACCAGGAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAgtgaggcctaagctggtaagcaaactacggtgtattctctgccattgtgt Alignment from Spaln_nt2Genome GAGACCCAAGAGCAGCCAAAACATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAGGGAGACA tatgcgatgcatttctgcttgctcatgactcctctgtcctgtgtctgcagtcctttgaagGTTAC----GGCCAAACAAGGCAT-CCAAAGAGACAAACCAGGAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAgtgaggcctaagctggtaagcaaactacggtgtattctctgccattgtgt Alignment from Pairagon GGAGGAGGATAGCGACAGCCCTCAGAGGAGACCCAAGAGCAGCCAAAACATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAGGGAGACAGACACAGACAGCATCTCCCT------------------------------ tatgcgatgcatttctgcttgctcatgactcctctgtcctgtgtctgcagtcctttgaaggttacggccaaacaaggcatccaaagagacaaaccag---------------------------------------------------------------------GAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAG------------------TGAGGCCTAAGCTGGTAAGCAAACTACGGTG Alignment from Exonerate_protein2genome TGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGAGGAGGAGGATAGCGACAGCCCTCAGAGGAGA---CCCAAGAGCAGCCAAAACATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAG TATGCGATGCATTTCTGCTTGCTCATGACTCCTCTGTCCTGTGTCTGCAGTCCTTTGAAGGTTACGGCCAAACAAGGCATCCAAAGAGACAAACCAGGAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAGTGAGGCCTAAGCTGGTAAGCAAACTACGGTGTATTCTCTGCCATTGTGT Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---AGGAGACCCAAGAGCAGCCAAAACATCCCAGTGCAGCAGGCAAGGAGCCAGAGCACCTCAGTCCCCACCAGGAGTTCCAGGGAGACA tatgcgatgcatttctgcttgctcatgactcctctgtcctgtgtctgcagTCCTTTGAAGGTTACGGCCAAACAAGGCATCCAAAGAGACAAACCAGGAGCCAGAGTACCTCAGTACCTGCCAGGGGTTGTAAGGAAACAgtgaggcctaagctggtaagcaaactacggtgtattctctgccattgtgt #### Hps1_ID8622_6 --> 1 - 0 Original Alignment cCATGGTGCGAGCACCCTGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGAGGAGGAGGATAGCGACAGC---CCTCAG taacaacccaagctcctattctgttcttttcttctttacacctcttccagc------GCAAGCACTCTATGTCCAGAAGATTTTCTT---------CTCCTAGTTCATGACCCACAGCCTTCACCAGCCATGACAGAGGAAGAGGGGGAGCAAGAAGATGGTCCCAGCAGTCCACAGgtaaatgcaaagcccagaattgtgattgactacctatcagaaggagctgg Alignment from CESAR cCATGGTGCGAGCACCCTGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGAGGAGGAGGATAGC---GACAGCCCTCAG ccaccctaacaacccaagctcctatcttttcttctttacacctcttccagc------GCAAGCACTCTATGTCCAGAAGATTTTCTT---------CTCCTAGTTCATGACCCACAGCCTTCACCAGCCATGACAGAGGAAGAGGGGGAGCAAGAAGATGGTCCCAGCAGTCCACAGgtaaatgcaaagcccagaattgtgattgactacctatcagaaggagctgg Alignment from Spaln_aa2Genome CCATGGTGCGAGCACCCTGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGAGGAGGAGGAT---AGCGACAGCCCTCAGAGGAGACCCAAGAGCAGCCAA taacaacccaagctcctattctgttcttttcttctttacacctcttccagC------GCAAGCACTCTATGTCCAGAAGATTTTCTT---------CTCCTAGTTCATGACCCACAGCCTTCACCAGCCATGACAGAGGAAGAGGGGGAGCAAGAAGATGGTCCCAGCAGTCCACAGGTAAATGCAAAGCCCAGAATTgtgattgactacctatcagaaggagctgg Alignment from Spaln_nt2Genome TGCGAGCACCCTGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGAGGAGGAGGATAGCGACAGCCCTCAGAGGAG taacaacccaagctcctattctgttcttttcttctttacacctcttccagCGCAAGCACTCTATGTCCAGAAGATTTTC---------TTCTCCTAGTTCATGACCCACAGCCTTCACCAGCCATGACAGAGGAAGAGGGGGAGCAAGAAGATGGTCCCAGCAGTC--CACAGgtaaatgcaaagcccagaattgtgattgactacctatcagaaggagctgg Alignment from Pairagon CCATGGTGCGAGCACCCTGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGA taacaacccaagctcctattctgttcttttcttctttacacctcttccagcgcaagcactctatgtccagaagattttcttctcctagttcatgacccacagccttcaccagCCATG-----------------------------------------------------------------------------ACAGAGGAAGAGGGGGAgcaagaagatggtcccagcagtccacaggtaaatgcaaagcccagaattgtgattgactacctatcagaaggagctgg Alignment from Exonerate_protein2genome taacaacccaagctcctattctgttcttttcttctttacacctcttccagcgcaagcactctatgtccagaagattttcttctcctagttcatgacccacagccttcaccagccatgacagaggaagagggggagcaagaagatggtcccagcagtccacaggtaaatgcaaagcccagaattgtgattgactacctatcagaaggagctgg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCATGGTGCGAGCACCCTGCGCCCCGCAGACCTCCTGGCGCTCATCCTTCTGGTGCAGGACCTCCAGCCCTCCCCAGGAACCACAGAGGAGGAGGAGGAGGAGGAGGATAGC---GACAGCCCTCAGAGGAGACCCAAGAGCAGCCAA taacaacccaagctcctattctgttcttttcttctttacacctcttccagC------GCAAGCACTCTATGTCCAGAAGATTTTCTT---------CTCCTAGTTCATGACCCACAGCCTTCACCAGCCATGACAGAGGAAGAGGGGGAGCAAGAAGATGGTCCCAGCAGTCCACAGGTAAATGCAAAGCCCAGAATTgtgattgactacctatcagaaggagctgg #### Il33_ID6363_6 --> 2 - 0 Original Alignment gc------GACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagggCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from CESAR gc------GACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagggCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from Spaln_aa2Genome GCGACGGTGTGGAT------GGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagGGCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from Spaln_nt2Genome GC------GACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagGGCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from Pairagon G------CGACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagGGCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from Exonerate_protein2genome GC------GACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagGGCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from Exonerate_coding2genome GC------GACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagGGCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa Alignment from GeneWise -----GGCGACGGTGTGGATGGGAAGAAGCTGATGGTGAACATGAGTCCCATCAAAGACACAGACATCTGGCTGCATGCCAACGACAAGGACTACTCCGTGGAG cccctaaataaacacctagctcacatttcctttgcacttatgtctttcagGGCAAAATGATGGTGTGGATGGGAAGAAGCTAATGGTGAAGATGAGTCCAATTAAAGACACAGACATCTGGCTGCACGCCAATGACAAGGACTACCCAGTGGAGgtaaggggaagatactctaataaccctgatggatccttttcttcatataa #### Incenp_ID2605_14 --> 1 - 0 Original Alignment gGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAAGAGGAAG tttattggtaactagcagactactacttctgacatcaccacttgctgtaggGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAAGCAG---gtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from CESAR gGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAAGAGGAAG tttattggtaactagcagactactacttctgacatcaccacttgctgtaggGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAAG---CAGgtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from Spaln_aa2Genome GGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAAGAGGAAG tttattggtaactagcagactactacttctgacatcaccacttgctgtagGGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAAG---CAGgtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from Spaln_nt2Genome GGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAAGAGGAAG tttattggtaactagcagactactacttctgacatcaccacttgctgtagGGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAA---GCAGgtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from Pairagon GGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAA tttattggtaactagcagactactacttctgacatcaccacttgctgtagGGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAAgcaggtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from Exonerate_protein2genome GGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAAGAGGAAG tttattggtaactagcagactactacttctgacatcaccacttgctgtagGGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAAGCAGGTActgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from Exonerate_coding2genome tttattggtaactagcagactactacttctgacatcaccacttgctgtagggagatgcaagagagagaaaaggccttgagactccagaaagaacggctccaaaaggaacttggggaaaagaagcaggtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc Alignment from GeneWise GGAGATGCAGGAGAGAGAGAAAGCCCTGCGACTCCAAAAGGAACGACTTCAGAAGGAACTGGAGGAGAAGAAGAGGAAG tttattggtaactagcagactactacttctgacatcaccacttgctgtagGGAGATGCAAGAGAGAGAAAAGGCCTTGAGACTCCAGAAAGAACGGCTCCAAAAGGAACTTGGGGAAAAGAAG---CAGgtactgagggcggccctgcagacatatattctgcagagtaaagtctgatc #### Incenp_ID2608_11 --> 1 - 0 Original Alignment g---AAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcaggCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from CESAR g---AAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcaggCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from Spaln_aa2Genome GCTGAAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcagGCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from Spaln_nt2Genome G---AAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcagGCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from Pairagon ------------------------------------------------------AAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG CCATTCAGAATTTGCAGAGACTCTTTGTTTTGATGGTTTTGATGTTTCAGGCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from Exonerate_protein2genome G---AAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcagGCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from Exonerate_coding2genome G---AAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcagGCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat Alignment from GeneWise -CTGAAGCGTGAAGAGCGCCTCCGCAAGGTGTTGCAGGCCCGTGAGAGGGTGGAACAGATGAAGGAGGAAAAGAAGAAGCAGATTGAGCAGAAGTTTGCTCAGATTGATGAGAAGACAGAAAAG ccattcagaatttgcagagactctttgttttgatggttttgatgtttcagGCCAAAGCGTGAAGAGCGGCTCCGCAAGGTGCTGCAAGCGCGTGAGAGGGTAGAACAAATGAAAGAAGAGAGGAAGAAGCAGATTGAGCAGAAGTTTGCTCAAATTGATGAGAAGACAGAAAAAgtagcccggccatataagatagcgacgcagagcagtgccttcttttggat #### Incenp_ID2611_8 --> 1 - 0 Original Alignment g---------AGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagaGGGGACCGAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCAGCC------CCACCCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from CESAR g---------AGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagaGGGGACCGAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCAGCC------CCACCCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from Spaln_aa2Genome GTGTCAGGAGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagagGGGACCGAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCAGCC------CCACCCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from Spaln_nt2Genome GTGTCAGGAGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagagGGGACCGAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTT---CAGCC---CCACCCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from Pairagon GTGTCAGGAGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTT---CCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagagGGGACCGAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCAGCCCCAC---------CCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from Exonerate_protein2genome GAGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagaggggaccgAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCA------GCCCCACCCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from Exonerate_coding2genome GAGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCCTGTCCAGCCAACAAG atggcagtgatgacgagtaatattctagtactctttgctatcccttttagaggggaccgAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCA------GCCCCACCCAACAAAgtaagtgtctgctcatcttttatgcccttattctggattctatccaagca Alignment from GeneWise -------AGGAGGAAACGCAGTTACAAACAGGCAATAAGTGAACCGGATGAGGAGCAACTGGAAGATGAAGAACTGCAGCCCTGCCAGAATAAGACCCCTTCCCCACCC------------------TGTCCAGCC-------------------------------- atggcagtgatgacgagtaatattctagtactctttgctatcccttttagAGGGGACCGAAGGAAGCGTAGTTACAAAAAGGCTACAGGCAAGCCTGATGAGGATCAGCTGGAAGATGAAGACCGTAAGCCATGTCAGAATAAAACACTTTCAGCCCCACCCAACAAAGTAAGTGTCTGCTCATCTTTTATGCCCTTATTCTGGATTCTATCCAAGCA #### Kat5_ID1109_13 --> 1 - 0 Original Alignment tGAGATCAGTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttttgtttcagt---------GAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from CESAR tGAGATCAGTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG tgtgctatgatctcacaggtgtatagcttctttcactttttttgtttcagt---------GAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from Spaln_aa2Genome TGAGATCAGTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttttgtttcagT---------GAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from Spaln_nt2Genome GTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttttgtttcag-TGAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from Pairagon TGAGATCAGTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttttgtttcag---------TGAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from Exonerate_protein2genome TGAGATCAGTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttTTGTTTCAGTGAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from Exonerate_coding2genome TGAGATCAGTGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttTTGTTTCAGTGAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt Alignment from GeneWise TGAAATCACTAGTATCAAGAAAGAAGATGTCATCTCCACACTGCAGTATCTCAACCTCATCAATTACTACAAG atctcacaggtgtatactgagcatggcttctttcactttttttgtttcagTGAAATTACTAGTATTAAGAAAGAAGATGTCATCTCTACGTTGCAGTATCTCAACCTAATCAATTACTACAAGgtaaacgggcataatccaattgaagcaaaaacttgcttatacttaggtgt #### Kat5_ID1110_12 --> 2 - 2 Original Alignment gcTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATC---------------aa tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaaggcTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCCCCTGTCTTCATTaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from CESAR gcTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATC---------------aa tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaaggcTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCCCCTGTCTTCATTaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from Spaln_aa2Genome GCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAATGAG tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaagGCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCCCCTgtcttcattaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from Spaln_nt2Genome GCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA---- tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaagGCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCCCCTgtcttcattaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from Pairagon GCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATC---------------AA tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaagGCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCCCCTGTCTTCATTAAgtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from Exonerate_protein2genome GCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaagGCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCccctgtcttcattaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from Exonerate_coding2genome GCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaagGCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCccctgtcttcattaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat Alignment from GeneWise GCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAATGAG tgagcctataccaggagaaggagcaggacttcctttctttgttttaaaagGCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCTGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGTCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCTCCCCTgtcttcattaagtaagtgagggagcaaatcagtaggatgtgctatgatctcacaggtgtat #### Kat5_ID1114_8 --> 0 - 0 Original Alignment GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGC------gtgagcttacgaggtgatttagacatcagagtggcttagtgcgagtaatg Alignment from CESAR GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGC------gtgagcttacgaggtgatttagacatcagagtggcttagtgcga Alignment from Spaln_aa2Genome GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGC tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCgtgagcttacgaggtgatttagacatcagagtggcttagtgcgagtaatg Alignment from Spaln_nt2Genome GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGC tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCgtgagcttacgaggtgatttagacatcagagtggcttagtgcgagtaatg Alignment from Pairagon GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGC tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCgtgagcttacgaggtgatttagacatcagagtggcttagtgcgagtaatg Alignment from Exonerate_protein2genome GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCGTGAGCttacgaggtgatttagacatcagagtggcttagtgcgagtaatg Alignment from Exonerate_coding2genome GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCGTGAGCttacgaggtgatttagacatcagagtggcttagtgcgagtaatg Alignment from GeneWise GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG tccccccagtgtactcacccgctgacacttcatcattaccatcttgacagGATCCTCAGGATAGCTCAGATGGTATACCAACAGCTCCACAAATGACAGGTAGCCTAGTGTCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGTCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAG------CGCgtgagcttacgaggtgatttagacatcagagtggcttagtgcgagtaatg #### Kat5_ID1115_7 --> 0 - 0 Original Alignment ---------AATGGGTCAGCCCGTAGG---GCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagTACCACTATAATGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from CESAR ---------AATGGGTCAGCCCGTAGG---GCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagTACCACTATAATGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from Spaln_aa2Genome -------AATGGGTCAGCCCGTAGG---GCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagTACCACTATAATGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from Spaln_nt2Genome ---------AATGGGTCAGCCCGTAG---GGCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagTACCACTATAATGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from Pairagon ---------AATGGGTCAGCCCGTAG---GGCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagTACCACTATAATGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from Exonerate_protein2genome AATGGGTCAGCCCGTAGGGCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagtaccactataatGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from Exonerate_coding2genome AATGGGTCAGCCCGTAGGGCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagtaccactataatGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg Alignment from GeneWise ---------AATGGGTCAGCC---CGTAGGGCAGTGGCAGCCCAGCCTGGACGGAAGCGGAAATCTAATTGCTTGGGCACTGATGAG cctgtaaagtcgcatgcatgctgtatgtccactagttcattttgctgcagTACCACTATAATGGGTCAACTTGTCGAGCGGCTGTAGCAGCTCAGGCTGGATGGAAATGTAAGTCAAACTGCTTGGGCACTGATGAGgtgaggcaaggcacccaagcagggttggatgtagatttgatttctgattg #### Kat5_ID1116_6 --> 0 - 0 Original Alignment AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAG--------- tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGAGCGGCCCCgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from CESAR AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAG--------- tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGAGCGGCCCCgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from Spaln_aa2Genome AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAGAATGGGTCA tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGAGCGGCCCCgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from Spaln_nt2Genome AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAGA-------- tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGAGCGGCCCCgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from Pairagon AAACGGAAGGTGGAGGTGGTTTCACCA--------GCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAG--------- tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTG--------GTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGAGCGGCCCCgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from Exonerate_protein2genome AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAG tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGagcggccccgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from Exonerate_coding2genome AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAG tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGagcggccccgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt Alignment from GeneWise AAACGGAAGGTGGAGGTGGTTTCACCAGCAACCCCAGTGCCCAGCGAGACAGCCCCAGCCTCGGTTTTCCCTCAGAATGGGTCA tcatcttcataccagctgttgtgtcttctatggcacccttccccttacagAAACGGAAAATTGAGGTAGTTTCACCAACTGGTTTGGTGCCTAGGGAGACAGCTGCAGTCTCTGTTTTCCCTCAGAGCGGCCCCgtgaggcttcaactgcttccttagagttatttcagtttggtttttgcctt #### Kat5_ID1117_5 --> 0 - 0 Original Alignment ---CCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttcttttt Alignment from CESAR ---CCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttctatgg Alignment from Spaln_aa2Genome GTGCCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttcttttt Alignment from Spaln_nt2Genome GTGCCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttcttttt Alignment from Pairagon ---CCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAAC--------------------------------------------------- tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCGTGCTTTGCAAAAACGGTCATCTTCATACCAGCTGTTGTGTCTTCTTTTT Alignment from Exonerate_protein2genome GTGCCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttcttttt Alignment from Exonerate_coding2genome GTGCCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttcttttt Alignment from GeneWise ---CCGGCCTCCGCCCAGGCCAGCGGGAAGACCTTGCCAATCCCGGTCCAGATCACACTCCGCTTCAACCTGCCCAAGGAGCGGGAGGCCATCCCAGGTGGCGAGCCTGACCAGCCGCTCTCCTCCAGCTCCTGCCTGCAACCCAACCACCGCTCAACG tcacatggtatccctcaattccatgccttgaagtcttttacttttcttagCTACCGGCCTCAGCCCAGGCCAGCGGGAAGACATTGCCAATCCCAGTCCAGATCATCCTCCGCTTCAACTTGCCCAAGGAGCGGGAGGCCATCCCAGGTGATGAGCCTGACCAGCCACTCTCCTCTAGCTCCTGCCTACAACCCAATCACCGCTCAATCgtgctttgcaaaaacggtcatcttcataccagctgttgtgtcttcttttt #### Kcnip2_ID9603_9 --> 0 - 0 Original Alignment AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTC------------------gtaagtaaatgcaagagcgactcggcgaagatagggggttagggtttgaa Alignment from CESAR AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTC------------------gtaagtaaatgcaagagcgactcggcgaagat Alignment from Spaln_aa2Genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAA------CAG gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCGTAAGTAAATGCAAGAGCGACTCGgcgaagatagggggttagggtttgaa Alignment from Spaln_nt2Genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTC gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCgtaagtaaatgcaagagcgactcggcgaagatagggggttagggtttgaa Alignment from Pairagon AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTC gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCgtaagtaaatgcaagagcgactcggcgaagatagggggttagggtttgaa Alignment from Exonerate_protein2genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCGTAAGTAAATGCAAGAGCgactcggcgaagatagggggttagggtttgaa Alignment from Exonerate_coding2genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCGTAAGTAAATGCAAGAGCgactcggcgaagatagggggttagggtttgaa Alignment from GeneWise AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAGGAC gtttccctcaacttgccttgtaactgagctctcttcgtgcttccctacagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCGTAAGTAAATGCAAGAGCGACtcggcgaagatagggggttagggtttgaa #### Kcnip2_ID9604_8 --> 0 - 0 Original Alignment ---GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccagGATGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from CESAR GAA---ATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccagGATGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from Spaln_aa2Genome GAAATGCTCGAC---ATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccagGATGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from Spaln_nt2Genome GAA---ATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccagGATGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from Pairagon ---GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccagGATGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from Exonerate_protein2genome GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccaggatGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from Exonerate_coding2genome GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccaggatGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac Alignment from GeneWise ---GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgtggggtgttctgctaccctttggctcccactcctctccagGATGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTATCCTGCACTCCGGGAGGAAGCCCCACGGGAACATGTGGAAAGCTTCTTCCAAgtaagtgttgcgtcttctggaatagcgggatatatgcagagtcactccac #### Kcnip2_ID9605_7 --> 0 - 0 Original Alignment GACTTTGTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccag------GTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGA---TATTGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from CESAR GACTTTGTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG atcgattattatgcagtgtcttaaggattccaattctgcctttcctccag------GTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGA---TATTGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from Spaln_aa2Genome GACTTTGTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccag------GTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGA---TATTGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from Spaln_nt2Genome GTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccagGTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGA---TATTGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from Pairagon GACTTTGTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccag------GTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGAT---ATTGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from Exonerate_protein2genome GTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccagGTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGATAT---TGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from Exonerate_coding2genome GTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccagGTGGCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGATAT---TGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc Alignment from GeneWise GACTTTGTGGCTGGTTTGTCAGTGATTCTTCGGGGAACCATAGATGATAGACTGAACTGGGCTTTCAACTTATATGACCTCAACAAGGATGGCTGTATCACGAAGGAG tattatgcagtgtcttaagtgcctggattccaattctgcctttcctccagGTG------GCAGGTTTGTCAGTGATCCTTCGAGCAACTATAGATGACAGATAT---TGGGCTTTCAATTTATATGACCTCAATAAGGATGGCTGTATCACAAGGGAGgtgtgttgcaactccagatttcggtgacattagggccagttttgaatcgc #### Kcnip2_ID9606_6 --> 2 - 0 Original Alignment acTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG--- gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagacTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAATTAgtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from CESAR acTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG--- gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagacTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAATTAgtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from Spaln_aa2Genome ACTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG--- gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagACTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAATTAgtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from Spaln_nt2Genome ACTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG--- gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagACTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAATTAgtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from Pairagon ACTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG--- gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagACTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAATTAgtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from Exonerate_protein2genome ACTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagACTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAAttagtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from Exonerate_coding2genome ACTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAG gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagACTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAAttagtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact Alignment from GeneWise ACTCCAGCAACTACGCTACTTTTCTCTTCAATGCCTTTGACACCAACCATGATGGCTCTGTCAGTTTTGAGGAC gcatggaatagccaagagaaccaggcaatctttctcctctcttccctcagACTCCAGCAACTATGCTACTTTCCTCTTCAATGCCTTTGACACCAACCATGATGGCTCAGTTAGTTTTGAATTAgtacggcaagaaaaaaagcatgctaaggaaaccaaccatcctctctaact #### Kcnip2_ID9607_5 --> 0 - 1 Original Alignment GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGA---g agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAggtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa Alignment from CESAR GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGA---g agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAggtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa Alignment from Spaln_aa2Genome GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGA---G agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAGgtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa Alignment from Spaln_nt2Genome GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGA---G agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAGgtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa Alignment from Pairagon GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGG------------------------------------------------------- agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAGGTGTGTCACAGGCATAGTGGGAAGATGTAAGCATGGAATAGCCAAGAGAA Alignment from Exonerate_protein2genome GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAA---GGAG agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAGgtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa Alignment from Exonerate_coding2genome GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAA---GGAG agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAGgtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa Alignment from GeneWise GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAGAC- agagtaaaagtgcctctaggttatattgatgtcattcaacatttctttagGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAACAAGgtgtgtcacaggcatagtgggaagatgtaagcatggaatagccaagagaa #### Kcnip2_ID9609_3 --> 2 - 1 Original Alignment ca------TTAGCTGCCCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAg gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagcaCACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAggtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from CESAR ca------TTAGCTGCCCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAg gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagcaCACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAggtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from Spaln_aa2Genome CATTAGCTGCCCCA------GCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAG gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagCACACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAGgtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from Spaln_nt2Genome CATTAGCTGC------CCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAG gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagCACACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAGgtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from Pairagon C------ATTAGCTGCCCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAG gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagCACACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAGgtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from Exonerate_protein2genome GTGAAACATTAGCTGCCCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAG gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagCACACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAGgtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from Exonerate_coding2genome GTGAAACATTAGCTGCCCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAG gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagCACACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAGgtaagatagaccctggggtgttattggttgataccaaatttaggacccag Alignment from GeneWise -----ACATTAGCTGCCCCAGCCTCCCTCCGCCCCCACAGACCCCGCCCGCTGGACCCAG gactgggtctcagtttgcttgcccaattctcacaacccccctctacacagCACACTTATTAGCTGCCCCAGCCTCCCTTCGCCCCCATAGACCCCGACCACTGGACCCAGgtaagatagaccctggggtgttattggttgataccaaatttaggacccag #### Kcnk4_ID1877_3 --> 2 - 0 Original Alignment TTTTCTCGGGGACCATCATCACTACCATCg gcTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGATG---CTG---CTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATctgtaagttctcctccatctagtc---------tccttgcaggtTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGAGGC------AAAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttgtacttg Alignment from CESAR CAGCGCCTTCTTTTTCTCGGGGACCATCATCACTAC gcTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGATG------CTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG CAGTGCCTTTCTTTTTTCAGGATCTATTGTGACAAAtctcctccatctagtctccttgcaggtTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGA------GGCAAAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttgtacttg Alignment from Spaln_aa2Genome TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGATG------CTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtaagttctcctccatctagtctccttgcagGTTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGA------GGCAAAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttgtacttg Alignment from Spaln_nt2Genome TTTTCTCGGGGACCATCATCACTACCATCG-------------------------------GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGATGCTGCTGGCG------GGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTGTAAGTTCTCCTCCATCTAGTCTCCTTGCAGGTTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGAGGCA------AAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttg Alignment from Pairagon TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGATGCTGCTGGCG------GGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtaagttctcctccatctagtctccttgcagGTTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGAGGCA------AAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttg Alignment from Exonerate_protein2genome TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTG------TTCGGGATGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtaagttctcctccatctagtctccttgcagGTTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGA------GGCAAAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttgtacttg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTG------TTCGGGATGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtaagttctcctccatctagtctccttgcagGTTATGGAAATATACTCCTACATACCAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCAGTATGTGGGATAGGGCTGTTGCTTCTAGGAGTTGGGGACCAGCTAGGCTCTTCACTGCGTCGAGGC------AAAATTGGAGCAATCTTCTCAgtaaacacctgtgcctgatttttgtacttg #### Kdm2a_ID518_3 --> 2 - 2 Original Alignment atTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATA---aa gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagatTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCaggtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from CESAR atTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATA---aa gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagatTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCaggtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from Spaln_aa2Genome ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAG-- gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagATTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCAGgtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from Spaln_nt2Genome ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATA---AA gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagATTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCAGgtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from Pairagon ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATA gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagATTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCgtcaggtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from Exonerate_protein2genome ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATA---AA gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagATTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCAGgtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from Exonerate_coding2genome ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATA---AA gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagATTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCAGgtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa Alignment from GeneWise ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAG-- gataatcaccaatcttacagaggtgtttacagatcactgtctgctttcagATTTTAATGATGAATATTTACAACAGGGTGGGCTGAGGCACCACCTTACCTTTAAGAATGCAGATGGACTTGGAATCGTCAGgtgagtcctctgggtcataatgctatgataattgggatgcatagtaaaaa #### Kif20b_ID6998_3 --> 0 - 0 Original Alignment ------------------------------------GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGTGGCA---------CAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagTTTTCTATAGGCTCTGGTCCTAATGGAGACATCCCT------GTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTA---CGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from CESAR ---------GGCTGT---------------------GTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagTTTTCTATAGGCTCTGGTCCTAATGGAGACATCCCTGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from Spaln_aa2Genome GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagttttctataggctctggtcctaatggagacATCCCTGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from Spaln_nt2Genome GGCTG--TGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagttttctataggctctggtcctaatggagACATCCCTGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from Pairagon -------------------------------------------------------------------------------------TGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG CTGGCTATAAACACAGTGTCTCTTGAGATCTGTTGATGTTTTGTTTTCAGTTTTCTATAGGCTCTGGTCCTAATGGAGACATCCCTGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from Exonerate_protein2genome CTGAGGGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagttttctataggctctggtcctaatgGAGACATCCCTGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from Exonerate_coding2genome GTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagttttctataggctctggtcctaatggagacatccctGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga Alignment from GeneWise ---------GGCTGT---------------------GTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtgtctcttgagatctgttgatgttttgttttcagTTTTCTATAGGCTCTGGTCCTAATGGAGACATCCCTGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGATCCACAGAGTATGCTAGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCATGTACAGGAATTTAGCTTTTCTAAAgtgagcgtaagtatggtggattgaccacactgaatgctctatcaagagga #### Kif20b_ID7002_7 --> 2 - 1 Original Alignment gaCACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------g attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagggCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAACAGG---------CCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAggtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from CESAR gaCACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------g attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagggCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAAC---------AGGCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAggtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from Spaln_aa2Genome GACACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------G attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagGGCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAAC---------AGGCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAGgtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from Spaln_nt2Genome GACACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------G attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagGGCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAACAG---------GCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAGgtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from Pairagon GACACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAA------AG attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagGGCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAACAG---------GCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAGgtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from Exonerate_protein2genome GACACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------G attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagGGCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAAC---------AGGCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAGgtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from Exonerate_coding2genome GTTACCATACATAATGACAGTTATGACGTTCTTTGTGGACACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------G attttaaggtttgCTTTGCAGTTGAACTACGTAACCCTTTTTCCTTCCAGGGCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAAC---------AGGCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAGgtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt Alignment from GeneWise GACACTTAACAAACTCTTTGACTATCCCAGAATTTGAAGAATCCGTGAACAGTTGTGACCAGTCCAGTCTGAATGTGGATAATATAAAGTATTCTGTGTGGGTTTCTTTCTTTGAAATTTACAATGAAAGTATTTACGATTTGTTTGTTCCTGTGTCCTCTAAGTTTCAAAAGAGAAAAATGTTACGACTTTCCCAAGATATAAAGGGCTATTCTTTTATAAAA------G attttaaggtttgctttgcagttgaactacgtaaccctttttccttccagGGCACTTTACAAACTCTTTGACTATTCCAGAGTTTGAGGAACCTGTCAAC---------AGGCCAAGTTTAAATGTAGATAATATAAAGTATTCTGTGTGGGTCTCATTTTTTGAAATCTATAACAAAAGTATATTC---TTGTTTGTGCCTGTTTCTTCCAAGTTTCAAAAGAGAAAAATGTTACGAATTGCTCAGGACATAAAGGGATATTCTTTTATTAAAATCTCAGgtaaggccatcttgttaaagagggagcatatgttacaactatttcacatt #### Klc2_ID854_12 --> 0 - 0 Original Alignment ------GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGGG ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagAAACTCGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCT---CCTGAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTgtattcgcataacaaatctcttttgagcctgaatctgacccctcccccct Alignment from CESAR ------GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGGG ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagAAACTCGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCT---CCTGAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTgtattcgcataacaaatctcttttgagcctgcccacttcttcttggtaca Alignment from Spaln_aa2Genome ------GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGGG ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagAAACTCGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCT---CCTGAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTgtattcgcataacaaatctcttttgagcctgaatctgacccctcccccct Alignment from Spaln_nt2Genome ------GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGGG ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagAAACTCGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCTC---CTGAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTgtattcgcataacaaatctcttttgagcctgaatctgacccctcccccct Alignment from Pairagon -----------------------------------GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGG--------------------------------------------------- ttcttgtgtatatttttgcagGGCCTAATTTTTGTTTGTTTTTTTCTAAGAAACTCGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCTC---CTGAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTGTATTCGCATAACAAATCTCTTTTGAGCCTGAATCTGACCCCTCCCCCCT Alignment from Exonerate_protein2genome GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGGG ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagaaactcGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCT---CCTGAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTgtattcgcataacaaatctcttttgagcctgaatctgacccctcccccct Alignment from Exonerate_coding2genome ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagaaactcggcctagaccctgccagtcagacaaaggtcatcaagctattaaaggatggtagcagtggacacagccagtgccgtggtagtagagatgtgattgggcctcctgagttagatttggaagagtcagagccaatggctcattggggtggtgtattcgcataacaaatctcttttgagcctgaatctgacccctcccccct Alignment from GeneWise ------GGCCTGGATCCTGCCAGCCAGACCAAGGTGGTAGAACTGTTAAAAGATGGCAGTGGTGGACGAGGACACCGCCGTGGCAGCAGAGATGTGGCTGGGCCTCAATCTGAGTCGGACCTGGAGGAGTCAGGGCCTGCAGCTGAGTGGAGTGGG ttcttgtgtatatttttgcagggcctaatttttgtttgtttttttctaagAAACTCGGCCTAGACCCTGCCAGTCAGACAAAGGTCATCAAGCTATTAAAGGATGGTAGCAGTGGACACAGCCAGTGCCGTGGTAGTAGAGATGTGATTGGGCCTCCT---GAGTTAGATTTGGAAGAGTCAGAGCCAATGGCTCATTGGGGTGGTgtattcgcataacaaatctcttttgagcctgaatctgacccctcccccct #### Klc2_ID859_7 --> 0 - 0 Original Alignment GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG------ atgttatacagcaccaaaactaggaacttgaacttttttcttcattccagGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGAGCAGAgtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from CESAR GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG------ atgttatacagcaccaaaactaggaacttgaacttttttcttcattccagGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGAGCAGAgtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from Spaln_aa2Genome AAGGTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTGGCT--- atgttatacagcaccaaaactaggaacttgaacttttttcttcattccag---GTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGAGCAGAgtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from Spaln_nt2Genome AAGGTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTGG----- atgttatacagcaccaaaactaggaacttgaacttttttcttcattccag---GTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGAGCAGAgtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from Pairagon AAGGTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG------ atgttatacagcaccaaaactaggaacttgaacttttttcttcattccag---GTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGAGCAGAgtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from Exonerate_protein2genome GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG atgttatacagcaccaaaactaggaacttgaacttttttcttcattccagGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGagcagagtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from Exonerate_coding2genome GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG atgttatacagcaccaaaactaggaacttgaacttttttcttcattccagGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGagcagagtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat Alignment from GeneWise ------------------------AAGGTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTGGCTTCC atgttatacagcaccaaaactagGAACTTGAACTTTTTTCTTCATTCCAGGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTTAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACTTGAGCAGAgtaagttgtaatgtgatgaattctaaaagatgacaccacccattttgaat #### Ldb1_ID9693_7 --> 0 - 0 Original Alignment GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC--- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct Alignment from CESAR GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC--- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct Alignment from Spaln_aa2Genome GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC--- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct Alignment from Spaln_nt2Genome GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC--- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct Alignment from Pairagon GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC----------------------------------------------------- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGGTGGAGTGATCCCAGCCCCACCTGATCTAAGGGCTTTGGAGTCCACATCT Alignment from Exonerate_protein2genome GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC--- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct Alignment from Exonerate_coding2genome GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCAC--- tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct Alignment from GeneWise GTGTGTGTGGAAGGCCGGTTGTACCTGGAGTTCATGTTTGACGACATGATGCGGATAAAGACGTGGCACTTCAGCATCCGGCAACACAGAGAGCTCATCCCCAGAAGTATCCTGGCCATGCACGCC tttgaggaaatcaccaaagcaagggtagctgatttttttctgtgttttagGTCTGTGTAGAAGGACGGCTGTACTTGGAGTTCATGTTTGATGACATGATGCGGATAAAGACATGGCACTTCAGCATCCAGCAACACAGTGAACTTATTCCAAGAAGTATCCTGGCGATGCACCAGgtggagtgatcccagccccacctgatctaagggctttggagtccacatct #### Ldb1_ID9694_6 --> 2 - 0 Original Alignment ccATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG------ ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagccATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGGGTGGAgtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from CESAR ccATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG------ ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagccATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGGGTGGAgtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from Spaln_aa2Genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG------ ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGGGTGGAgtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from Spaln_nt2Genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG- ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGGgtggagtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from Pairagon CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG------ ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGGGTGGAgtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from Exonerate_protein2genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGggtggagtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from Exonerate_coding2genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggttctgggtgagatgctttctctctttttccatgtttgtctcattttagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGggtggagtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc Alignment from GeneWise ----------------------------------------------------ATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG------ GGTTCTGGGTGAGATGCTTTCTCTCTTTTTCCATGTTTGTCTCATTTTAGCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAAGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTACCCAGGGTGGAgtatgaaaagtgtagggatagcataacctgataccatgagaggcaacacc #### Ldb1_ID9695_5 --> 0 - 1 Original Alignment GAGTGTGACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATa agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttag------GATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACagtgagttggttctgggtgagatgctttctctctttcctttatctcacccc Alignment from CESAR GAGTGTGACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATa aggatgagaggttgatgggggtgtgatggaccatgctttctaatctttag------GATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACagtgagttggttctgggtgagatgctttctctctttttccatgtttgtctc Alignment from Spaln_aa2Genome GAGTGTGACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATA agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttag------GATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACAgtgagttggttctgggtgagatgctttctctctttcctttatctcacccc Alignment from Spaln_nt2Genome GACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATA agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttagGATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACAgtgagttggttctgggtgagatgctttctctctttcctttatctcacccc Alignment from Pairagon GAGTGTGACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATA agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttag------GATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACAgtgagttggttctgggtgagatgctttctctctttcctttatctcacccc Alignment from Exonerate_protein2genome GACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATA agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttagGATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACAgtgagttggttctgggtgagatgctttctctctttcctttatctcacccc Alignment from Exonerate_coding2genome GACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATA agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttagGATAATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACAgtgagttggttctgggtgagatgctttctctctttcctttatctcacccc Alignment from GeneWise GAGTGTGACAATCTCTGGTGGGATGCTTTCACAACTGAGTTCTTTGAAGATGACGCCATGCTGACCATCACTTTCTGCTTGGAGGATGGACCAAAGAGATATACC------------------------------------------------ agaggttgatgggggtgtgtctcgtatggaccatgctttctaatctttagGAT------AATCTTTGGTGGGATGCTTTCACAACTGAGTTCTTTGAGGATGATACCATGCTCACTTTAAACTTTTGTTTGAAAGATGGGCCAAACAGGTACAGTGAGTTGGTTCTGGGTGAGATGCTTTCTCTCTTTCCTTTATCTCACCCC #### Ldb1_ID9696_4 --> 1 - 0 Original Alignment gAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG ttggctacatatgtccacacacctatttagggctgtttcttcccctgcaggAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAAT---------gtaagtcagtctgctgaagatgagaggttgatggggaccaccttcactat Alignment from CESAR gAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG ttggctacatatgtccacacacctatttagggctgtttcttcccctgcaggAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAAT---------gtaagtcagtctgctgaagatgagaggttgattctcgtatg Alignment from Spaln_aa2Genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAGGAG ttggctacatatgtccacacacctatttagggctgtttcttcccctgcagGAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAATGTAAGTCAGTCTgctgaagatgagaggttgatggggaccaccttcactat Alignment from Spaln_nt2Genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGAC ttggctacatatgtccacacacctatttagggctgtttcttcccctgcagGAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAA-TGTAAgtcagtctgctgaagatgagaggttgatggggaccaccttcactat Alignment from Pairagon GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAAC ttggctacatatgtccacacacctatttagggctgtttcttcccctgcagGAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAATgtaagtcagtctgctgaagatgagaggttgatggggaccaccttcactat Alignment from Exonerate_protein2genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAAC TG ttggctacatatgtccacacacctatttagggctgtttcttcccctgcagGAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAATgtaagtcagtctgctgaagatgagaggttgatggggaccaccttcactAT Alignment from Exonerate_coding2genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAAC TG ttggctacatatgtccacacacctatttagggctgtttcttcccctgcagGAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAATgtaagtcagtctgctgaagatgagaggttgatggggaccaccttcactAT Alignment from GeneWise GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACA-------------------------------------------- ttggctacatatgtccacacacctatttagggctgtttcttcccctgcagGAGGCACAGTCCATATGGTAATCAGACTGATTATAGGATATTTGAGCTAAACAAGCGGCGTCAGAATGTAAGTCAGTCTGCTGAAGATGAGAGGTTGATGGGGACCACCTTCACTAT #### Lipa_ID6938_5 --> 2 - 0 Original Alignment gtTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAAG--------- ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcaggtTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAAGTCGCGAGgtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from CESAR gtTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAAG--------- ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcaggtTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAAGTCGCGAGgtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from Spaln_aa2Genome GTTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAAG--------- ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcagGTTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAAGTCGCGAGgtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from Spaln_nt2Genome GTTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAA---------G ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcagGTTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAAGTCGCGAGgtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from Pairagon GTTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCA---------AG ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcagGTTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAAGTCGCGAGgtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from Exonerate_protein2genome GTTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAAG ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcagGTTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAagtcgcgaggtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from Exonerate_coding2genome GTTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAAG ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcagGTTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAagtcgcgaggtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt Alignment from GeneWise GTTTCATAGCTTTTTCACAGATGCCTGAGTTGGCAAAGAAGATTAAAATGTTTTTAGTCTTGGCTCCCGTGTTGTCTCTCAATTTTGCTTCAGGCCCGCTACTTCAATTGGGACGCTTGCCAGACCCTCTTCTCAAG--------- ggtagggatggctcaagctaaggtcaatagcttgccttccttgtgtgcagGTTTCATAGCTTTTTCACAAATGCCTGAGTTAGCTAAAAAGATCAAAATGTTTTTAGCACTGACCCCAGTATTGTCTCTCAATTTTGCTTCCAGCCCGTTATTACAGTCAGGCCACTTGCCCGATCCATTGCTCAAAAGTCGCGAGgtgagtgagttgatattttaagcacctgattctcaatagtaagtgtctgt #### Lipo1_ID6826_7 --> 0 - 0 Original Alignment AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAG--- attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from CESAR AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAG--- attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from Spaln_aa2Genome AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAGGTA attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from Spaln_nt2Genome AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAG--- attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from Pairagon AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAG--- attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from Exonerate_protein2genome AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAGGTA attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from Exonerate_coding2genome AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAGGTA attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa Alignment from GeneWise AGCCGCCTTGATGTGTATGTAAAGCTCAATCTAGCAGGAACATCAGTAAAAGTTCTTATACATTATAATCAGGTA attcaacaatgtttgactggaatacttgacctcctcttttctgattgcagAGCCGCCTTAAAGTGTATGTTACGCTCAATCTAGCTGGTACATCAGTAAAAGTTCTTATTCATTATAATCAGACCgtgggtcattactagtgtcctgtccatgcctggaccttctgtgttagcaa #### Loxl4_ID8568_7 --> 2 - 0 Original Alignment ggCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTAT------GAGCGGACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAGAACAAG aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagggCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTTCAGA------gtaagcgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from CESAR ggCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTATGAGCGG------ACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAGAACAAG aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagggCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTTC------AGAgtaagcgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from Spaln_aa2Genome GGCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTAT------GAGCGGACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAGAACAAG aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagGGCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTTCAGAGTAAGCgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from Spaln_nt2Genome GGCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTATGAGCGGA------CCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAGAACAAG- aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagGGCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTT-CAGAGTAAGCgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from Pairagon GGCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTATGAGCGG------ACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAGA aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagGGCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTT-CAGAgtaagcgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from Exonerate_protein2genome GGCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTAT------GAGCGGACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAG aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagGGCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTTCAGAgtaagcgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from Exonerate_coding2genome GGCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTAT------GAGCGGACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAG aagaaataaaggaatggagaggcatctctgtacgggggttgtttttgcagGGCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTTCAGAgtaagcgtacggcacactctattcaagtttcaggtttccctgccaattgt Alignment from GeneWise -------------------------------------------------GGGCTAGGACCCATCCACCTGAGTGAGGTGCGCTGCCGGGGGTAT------GAGCGGACCCTGGGTGACTGCCTTGCCCTGGAAGGGTCCCAGAATGGTTGTCAACATGCAAACGACGCTGCTGTCAGGTGCAACATCCCAGACATGGGCTTCCAGAACAAG AAGAAATAAAGGAATGGAGAGGCATCTCTGTACGGGGGTTGTTTTTGCAGGGCTAGGA---ATCCATCTGAGTGAAGTACAATGCAGGGGGTATGAACGGGAGCGTGCCTTGGGTGACTGCCTTGCCCTGGAAGGGTCACCAAACAGTTGTCAGCATGCAAATGGTGCCACTATCAGGTGCAATATTCCAGATATAGGCTTCAGAGTAAGCgtacggcacactctattcaagtttcaggtttccctgccaattgt #### Ltbp3_ID1252_4 --> 0 - 1 Original Alignment ---TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGt ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGtgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from CESAR ---TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGt ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGtgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from Spaln_aa2Genome CCTTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGT ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from Spaln_nt2Genome CCTTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGT ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from Pairagon CCTTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGT ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from Exonerate_protein2genome CCTTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGT ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from Exonerate_coding2genome CCTTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGT ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTgtaagagcataacatggacttacaatttttctgatcatgattagtagttg Alignment from GeneWise ---TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGT ccattccaaccatcaagctggtgctgatctttttcttttcccatttacagCCATGTGGCAGCAACCCTTTGCCTGGTCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTgtaagagcataacatggacttacaatttttctgatcatgattagtagttg #### Ltbp3_ID1253_5 --> 2 - 1 Original Alignment at---------------------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGg taccaagcttactctctcttttcactatcagaataattttcttcttttagatTCCATCGTGACCGACTTCGATACAGGAGTACAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGggtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from CESAR at---------------------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGg taccaagcttactctctcttttcactatcagaataattttcttcttttagatTCCATCGTGACCGACTTCGATACAGGAGTACAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGggtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from Spaln_aa2Genome GGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccaagcttactctctcttttcactatcagaataattttcttcttttagattccatcgtgaccgacttcgatacagGAGTACAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from Spaln_nt2Genome GGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccaagcttactctctcttttcactatcagaataattttcttcttttagattccatcgtgaccgacttcgatacagGAGTACAAAAGCCTGGACCTGTTCGAGG---GGTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from Pairagon ---------------------ATACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccaagcttactctctcttttcactatcagaataattttcttcttttagATTCCATCGTGACCGACTTCGATACAGGAGTACAAAAGCCTGGACCTGTTCGAGG---GGTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from Exonerate_protein2genome ATACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccaagcttactctctcttttcactatcagaataattttcttcttttagattccatcgtgaccgacttcgATACAGGAGTACAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from Exonerate_coding2genome ATACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccaagcttactctctcttttcactatcagaataattttcttcttttagattccatcgtgaccgacttcgATACAGGAGTACAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg Alignment from GeneWise --------------------TATACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccaagcttactctctcttttcactatcagaataattttcttcttttagATTCCATCGTGACCGACTTCGATACAGGAGTACAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGTCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgtgagcatcaccaatgaccgaagcttccattaattgggcaataattgttg #### Ltbp3_ID1254_6 --> 2 - 1 Original Alignment at---------ATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTg caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagacCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAggtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from CESAR at---------ATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTg caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagacCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAggtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from Spaln_aa2Genome AT---------ATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTG caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagACCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAGgtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from Spaln_nt2Genome A---------TATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTG caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagACCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAGgtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from Pairagon A---------TATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTG caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagACCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAGgtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from Exonerate_protein2genome AT---------ATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTG caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagACCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAGgtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from Exonerate_coding2genome AT---------ATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTG caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagACCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAGgtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt Alignment from GeneWise --------GATATCAACGAATGTGCGATGCCTGGCATGTGTCGCCATGGTGACTGCCTCAACAACCCTGGCTCTTATCGCTGTGTCTGCCCGCCCGGTCATAGCTTGGGTCCCTCGCGCACACAGTGCATTG caggattgattgtttcttgtttcaagtgtgtgcgctgcttccttgtgtagACCACTTTACTATAAATGAATGTGTGATGCCTGGGATGTGTCGTCATGGGGATTGTCTGACCAACCCTGGCTCTTTCCACTGTGTCTGCCCACCTGGTCATAGTCTAGGTCCTTTCCGCAAACAGTGTATAGgtaagctcaagaatgagtttggattgactaaaggggagcagatgggtggt #### Ltbp3_ID1261_13 --> 2 - 1 Original Alignment atGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGg gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagatGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTC------ggtgagagtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from CESAR atGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGg gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagatGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGA------CTCggtgagagtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from Spaln_aa2Genome ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagATGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCGGTGAGAgtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from Spaln_nt2Genome ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCG-CTCG gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagATGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCGgtgagagtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from Pairagon ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCG-CTCG gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagATGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCGgtgagagtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from Exonerate_protein2genome ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagATGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCGGTGAGAgtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from Exonerate_coding2genome gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagatgtaaccgggtgtggggctgagccctgtggccctgggaaaggtatctgtatgactactggtggatcatataattgtcattgcaaccggggctaccgccttcatgtaggtgcagggggccgactcggtgagagtccagacacttgggcagcacacacctttgtgcatttctgacac Alignment from GeneWise ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG gatgtgactgatcaattctagacatatccactgtggcttcccgcggacagATGTAACCGGGTGTGGGGCTGAGCCCTGTGGCCCTGGGAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCGGTGAGAgtccagacacttgggcagcacacacctttgtgcatttctgacac #### Ltbp3_ID1268_20 --> 2 - 1 Original Alignment ag------GTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAg gctatagcttagcagatattaattggaattctctctccgtgtcttcctagagTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAggtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from CESAR ag------GTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAg gctatagcttagcagatattaattggaattctctctccgtgtcttcctagagTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAggtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from Spaln_aa2Genome AGGTGGAGCAGCCCCAC------CACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAG gctatagcttagcagatattaattggaattctctctccgtgtcttcctagAGTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAGgtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from Spaln_nt2Genome AG------GTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAG gctatagcttagcagatattaattggaattctctctccgtgtcttcctagAGTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAGgtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from Pairagon AG------GTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAG gctatagcttagcagatattaattggaattctctctccgtgtcttcctagAGTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAGgtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from Exonerate_protein2genome AG------GTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAG gctatagcttagcagatattaattggaattctctctccgtgtcttcctagAGTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAGgtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from Exonerate_coding2genome gctatagcttagcagatattaattggaattctctctccgtgtcttcctagagtggctagtggagcagcctcagcataagaaggaatgctaccttaactttgatgacgcagtgttcagtgacagcatactagccactaatgttactcaacaggaatgctgctgctctctgggagcaggatggggagaccactgtgaaatctatccctgtcctatattcagctcaggtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat Alignment from GeneWise -----GAGGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAG gctatagcttagcagatattaattggaattctctctccgtgtcttcctagAGTGGCTAGTGGAGCAGCCTCAGCATAAGAAGGAATGCTACCTTAACTTTGATGACGCAGTGTTCAGTGACAGCATACTAGCCACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCAGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATATTCAGCTCAGgtaacttaatgctgattctcagtcctatcagtcaggcctgggtcagtcat #### Ltbp3_ID1270_22 --> 2 - 1 Original Alignment acATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGCGTGg aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagacACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGT---ggtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc Alignment from CESAR acATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGCGTGg aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagacACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGT---ggtaaggggttagactacttttccaatcaaggaaaacagcttaacccctgc Alignment from Spaln_aa2Genome ACATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGC- aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagACACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGTGgtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc Alignment from Spaln_nt2Genome ACATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGCG aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagACACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGTGgtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc Alignment from Pairagon ACATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGCG aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagACACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGTGgtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc Alignment from Exonerate_protein2genome ACATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGCG aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagACACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGTGgtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc Alignment from Exonerate_coding2genome aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagacactgatgaatgcatattgtttggggcagagatctgtaaggagggtaaattcgtgaacatgcagcctggctatgagtgctattgcaagcagggcttctatttcgatggtaatcttttagagtgtggtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc Alignment from GeneWise ACATCGACGAATGCATATTGTTTGGGGCAGAGATCTGCAAGGAGGGCAAGTGTGTGAACACGCAGCCCGGCTACGAGTGCTACTGCAAGCAGGGCTTCTACTACGATGGCAACCTGCTGGAGTGCG aaatctgagtgttagcccactggcacctcagccggtgctcctctccacagACACTGATGAATGCATATTGTTTGGGGCAGAGATCTGTAAGGAGGGTAAATTCGTGAACATGCAGCCTGGCTATGAGTGCTATTGCAAGCAGGGCTTCTATTTCGATGGTAATCTTTTAGAGTGTGgtaaggggttagactacttttccaatcaaggaaaacagctgtaacagttc #### Ltbp3_ID1271_23 --> 2 - 1 Original Alignment acGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGATG------g ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagatTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGggtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from CESAR acGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGATG------g ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagatTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGggtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from Spaln_aa2Genome ACGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGATG------G ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagATTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGGgtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from Spaln_nt2Genome ACGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGATG------G ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagATTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGGgtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from Pairagon ACGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGAT------GG ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagATTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGGgtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from Exonerate_protein2genome ACGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGATG------G ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagATTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGGgtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from Exonerate_coding2genome ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagatttggatgagtgcttagatgagtctaactgcaggaatggggtatttgaaaatacacatggtggctaccgctgtgcatgtacaccaccaactgaatatagctcagctcaacatcaatgttcaagccctgaggcgatgattccgggtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct Alignment from GeneWise ACGTGGATGAGTGCTTGGATGAGTCTAACTGCAGGAACGGAGTGTGTGAGAACACACGTGGCGGCTACCGCTGTGCCTGCACGCCGCCGGCAGAGTACAGTCCCGCACAGCGCCAGTGTCTGAGCCCGGAGGAGATG------G ttttccaatcaaggaaaacagctgtttaacccctgcctctctctctgcagATTTGGATGAGTGCTTAGATGAGTCTAACTGCAGGAATGGGGTATTTGAAAATACACATGGTGGCTACCGCTGTGCATGTACACCACCAACTGAATATAGCTCAGCTCAACATCAATGTTCAAGCCCTGAGGCGATGATTCCGGgtaagccgttagaaaacaagcctcacaactcctgtaccttaagtgctgct #### Ltbp3_ID1272_24 --> 2 - 1 Original Alignment agCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACCg ggTCCCAGTGC atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagag---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGGG---CAGTGCAGACCATGTCCCCCACGTGGTACTggtaaagagattcgaaggttgggtcttcccttctcctcagggTCCCAGTGC Alignment from CESAR agCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACCg ggTCCCAGTGC ataatagcatattcctcttgtttctcaccttgtattgctttgtattatagag---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGGG---CAGTGCAGACCATGTCCCCCACGTGGTACTggtaaagagattcgaaggatgactccccctggccctgcagggTCCCAGTGC Alignment from Spaln_aa2Genome AGCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACCG GGTCCCAGTGC atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagAG---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGGG---CAGTGCAGACCATGTCCCCCACGTGGTACTGgtaaagagattcgaaggttgggtcttcccttctcctcagGGTCCCAGTGC Alignment from Spaln_nt2Genome AGCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACCG GGTCCCAGTGC atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagAG---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGG---GCAGTGCAGACCATGTCCCCCACGTGGTACTGgtaaagagattcgaaggttgggtcttcccttctcctcagGGTCCCAGTGC Alignment from Pairagon AGCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACCG GGTCCCAGTGC atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagAG---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGG---GCAGTGCAGACCATGTCCCCCACGTGGTACTGgtaaagagattcgaaggttgggtcttcccttctcctcagGGTCCCAGTGC Alignment from Exonerate_protein2genome AGCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACCG GGTCCCAGTGC atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagAG---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGGG---CAGTGCAGACCATGTCCCCCACGTGGTACTGgtaaagagattcgaaggttgggtcttcccttctcctcagGGTCCCAGTGC Alignment from Exonerate_coding2genome atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagaggccccagaaagatgtgaagtatgctggggacagcaaggagaagatggtatgtgtatgggccccctagtgggacctgccctcacttttgatgactgttgttgccgtcaaggccgtgggtgggggcagtgcagaccatgtcccccacgtggtactggtaaagagattcgaaggttgggtcttcccttctcctcagggtcccagtgc Alignment from GeneWise AGCACGCCCCAGAGAGACGTGAAGTGTGCTGGGGCCAGCGAGGAGAGGACGGCATGTGTATGGGGCCCCTGGCGGGACCTGCCCTCACTTTTGATGACTGCTGCTGCCGCCAGGGCCGCGGCTGGGGTACCCAGTGCAGACCGTGCCCGCCACGTGGCACC---------------------------------------GGGTCCCAGTGC atagcatattcctcttgtttctcaacaccttgtattgctttgtattatagAG---GCCCCAGAAAGATGTGAAGTATGCTGGGGACAGCAAGGAGAAGATGGTATGTGTATGGGCCCCCTAGTGGGACCTGCCCTCACTTTTGATGACTGTTGTTGCCGTCAAGGCCGTGGGTGGGGG---CAGTGCAGACCATGTCCCCCACGTGGTACTGGTAAAGAGATTCGAAGGTTGGGTCTTCCCTTCTCCTCAGGGTCCCAGTGC #### Macrod1_ID2053_8 --> 2 - 0 Original Alignment gc---TACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcaggcAAATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from CESAR gc---TACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcaggcAAATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from Spaln_aa2Genome GC---TACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcagGCAAATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from Spaln_nt2Genome GC---TACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcagGCAAATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from Pairagon GCACCGGCTGCGCTCAGTGGCTTTCCCGTGCATCTCCACAGGCGTGTTTGGCTACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcagGCA-----------------------------------------------AATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from Exonerate_protein2genome TTGGCTACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcagGCAAATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from Exonerate_coding2genome gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcaggcaaataccccaatgaggaggctgcagaggtagtgctggtttcattgcaggaatggttggagcaacacaaggacaaggtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg Alignment from GeneWise TTGGCTACCCCAATGAGGAGGCTGCAGAAGTAGTGCTGGCTTCGCTGCGGGAATGGCTGGAGCAGCACAAGGACAAG gaggtggtgggacgcaatatggatttacccttcctctctcctgccttcagGCAAATACCCCAATGAGGAGGCTGCAGAGGTAGTGCTGGTTTCATTGCAGGAATGGTTGGAGCAACACAAGGACAAGgtgagaccaaattcatgacaggagtttcattagatgaagaggttttattg #### Macrod1_ID2054_9 --> 0 - 1 Original Alignment GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTA------------------g ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTACCATACCACAAAATCACCggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt Alignment from CESAR GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTA------------------g ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTACCATACCACAAAATCACCggtgagtataagtagctcttgtacttgaagagacccaacctccgtatctct Alignment from Spaln_aa2Genome GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTACCAtaccacaaaatcaccggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt Alignment from Spaln_nt2Genome GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTACCAtaccacaaaatcaccggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt Alignment from Pairagon GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTACCAtaccacaaaatcaccggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt Alignment from Exonerate_protein2genome GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTA ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTAccataccacaaaatcaccggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt Alignment from Exonerate_coding2genome ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctaggtggatcgactcattatctgtgtatgcttggagaaagaagagggcatttacagggaacatcttccacattatttcccagtaccataccacaaaatcaccggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt Alignment from GeneWise GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatagggtcaaagtttaagtaaaatattcccttctgtttctagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCACATTATTTCCCAGTACCAtaccacaaaatcaccggtgagtataagtagctcttgtacttgaagagacccaactggctttctttt #### Map3k11_ID1204_5 --> 0 - 1 Original Alignment GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGCGA------CGGCGCGAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGAGCGC------GAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATGCCCCTG---------g ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAggtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from CESAR GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGCGA------CGGCGCGAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGAGCGC------GAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATGCCCCTG---------g ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAggtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from Spaln_aa2Genome GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGCGA------CGGCGCGAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGAGCGC------GAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATGCCCCTG---------G ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAGgtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from Spaln_nt2Genome GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGCGACGGCGC------GAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGA------GCGCGAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATGCC-------CCTG--G ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAGgtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from Pairagon GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGC------GACGGCGCGAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGA------GCGCGAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATG---------------- ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAGgtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from Exonerate_protein2genome GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGCGA------CGGCGCGAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGAGCGC------GAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATG---------CCCCTGG ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAGgtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from Exonerate_coding2genome ctacattgtgagttgatggctatgtactagccagatgttgttcccctcaggaactccttagtcaagaggaagaattgacatgggctgcatgtgtgcagtggtctcaggcagaacagctccagctgagccgccatgagcatttgctggcgcaatgggagctagaggtttttgaacaactgcctgcactgacattactactccagcaggtggatcgagaacaggcacatgtacaccgacggcaggccacctccgaactgagccagctccgagccagagatagtgaagaacgggtcagcatgactttacctccagcaggtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa Alignment from GeneWise GAACTACTGAGCCGGGAGGAGGAACTGACGCGCGCTGCACGTGAGCAGCGGTCCCAGGCGGAGCAGCTGCGA------CGGCGCGAGCACCTGCTGGCGCAGTGGGAGCTGGAGGTGTTCGAGCGC------GAGCTGACGCTGCTACTGCAGCAGGTGGACCGAGAACGGCCGCACGTGCGCCGCCGCCGGGGCACCTTCAAGCGGAGCAAACTCCGAGCAAGGGACGGCGGAGAACGCATCAGCATG---------CCCCTGG ctacattgtgagttgatggctatgtactagccagatgttgttcccctcagGAACTCCTTAGTCAAGAGGAAGAATTGACATGGGCTGCATGTGTGCAGTGGTCTCAGGCAGAACAGCTCCAGCTGAGCCGCCATGAGCATTTGCTGGCGCAATGGGAGCTAGAGGTTTTTGAACAACTGCCTGCACTGACATTACTACTCCAGCAGGTGGATCGAGAACAGGCACATGTACACCGACGGCAGGCCACCTCCGAACTGAGCCAGCTCCGAGCCAGAGATAGTGAAGAACGGGTCAGCATGACTTTACCTCCAGCAGgtaagcgctgtgactccaagcagtggcattaaggattactgctttgcaaa #### Mark2_ID2108_13 --> 2 - 0 Original Alignment ccGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG agtatggtgccttgggggacatttttcaccccgccctctttgcactgcagct---------ATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTACT---GCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from CESAR ccGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG gtgacatagagtatggtgccttgggtcaccccgccctctttgcactgcagct---------ATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTACT---GCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from Spaln_aa2Genome GCCGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG ccttgggggacatttttcaccccgccctctttgcactgca gCTATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTACT---GCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from Spaln_nt2Genome CCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG agtatggtgccttgggggacatttttcaccccgccctctttgcactgcagCTATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAG---ACTACTGCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from Pairagon CCGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG agtatggtgccttgggggacatttttcaccccgccctctttgcactgcag---------CTATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTA---CTGCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from Exonerate_protein2genome CCGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG agtatggtgccttgggggacatttttcaccccgccctctttGCACTGCAGCTATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTACT---GCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from Exonerate_coding2genome CCGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG agtatggtgccttgggggacatttttcaccccgccctctttGCACTGCAGCTATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTACT---GCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc Alignment from GeneWise CCGTCCCTGCCATTCCCACCTCGAATTCCTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAAGAGACAGGGCGGAAAGCCAGCAGCACCGCCAAAGTGCCTGCCAGCCCTCTGCCTGGCCTGGACAGGAAGAAGACCACTCCTGCCCCCTCCACG agtatggtgccttgggggacatttttcaccccgccctctttgcactgcagCT---------ATTCCCACCTCCAATTCCTATTCTAAAAAGACTCAGACTAACAATGCAGAAAACAAGCGCCCTGAGGAGGAAACAGGACGAAGAGCCAGCAGCACTGCCAAGGTGCCCACGAGCCCATTGCCGGGCCTGGATAGGAAGAAGACTACT---GCACCATCTACAgtcagtcctacagttactctcccagagactaagtgcactactttagaggc #### Mark2_ID2111_10 --> 0 - 1 Original Alignment CAAATTATG---------------AAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACA---------g tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagCAAATCATGGAGGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGATGCCTACggtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat Alignment from CESAR CAAATT---------------ATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACA---------g tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagCAAATCATGGAGGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGATGCCTACggtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat Alignment from Spaln_aa2Genome CAAATT---------------ATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAGAG tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagCAAATCATGGAGGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGATgcctacggtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat Alignment from Spaln_nt2Genome CAAATTATG---------------AAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAGA-------- tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagCAAATCATGGAGGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGATGCCTACGgtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat Alignment from Pairagon CAAATT---------------ATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGAC------------------------------------------------------------- tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagCAAATCATGGAGGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGATGCCTACGGTAAAGCTGTGTGGTGCTGCATGTCTGAGGTAGGGCCACGTTGTGTTAAT Alignment from Exonerate_protein2genome AGAGGCACTTTAGAGCAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAG tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagCAAATCATGGAGGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGatgcctacggtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat Alignment from Exonerate_coding2genome tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagcaaatcatggaggatcagtggatgaaagatcagtggatgaatgttgggcatgaggatgttgaactaaagatttatgtgcaaccctttcctgactatagggcaccacggcaaacagatgcctacggtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat Alignment from GeneWise ---CAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAGAG------- tttgaaaatagttacattttgctctctgtgcttgtgttttttgactgtagcaaatcatggagGATCAGTGGATGAAAGATCAGTGGATGAATGTTGGGCATGAGGATGTTGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGCACCACGGCAAACAGATGCCTACGgtaaagctgtgtggtgctgcatgtctgaggtagggccacgttgtgttaat #### Mark2_ID2115_6 --> 2 - 0 Original Alignment gaGAGGTGTTTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cctccatgaaacaacgccttcttgtaacccttgacctccatcaccttcaggt---------GATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from CESAR gaGAGGTGTTTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cagaacttccctccatgaaacaacgaacccttgacctccatcaccttcaggt---------GATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from Spaln_aa2Genome TTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cctccatgaaacaacgccttcttgtaacccttgacctccatcaccttcagGTGATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from Spaln_nt2Genome GAGAGGTGTTTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cctccatgaaacaacgccttcttgtaacccttgacctccatcaccttcagG---------TGATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from Pairagon GAGAGGTGTTTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cctccatgaaacaacgccttcttgtaacccttgacctccatcaccttcagG---------TGATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from Exonerate_protein2genome GAGAGGTGTTTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cctccatgaaacaacgccttcttgtaacccttgacctccatCACCTTCAGGTGATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from Exonerate_coding2genome cctccatgaaacaacgccttcttgtaacccttgacctccatcaccttcaggtgattatttagtggctcatggcaggatgaaagaaaaggaggctcgagccaaataccaccaggtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac Alignment from GeneWise TTGATTACCTAGTGGCCCATGGCAGGATGAAAGAAAAAGAAGCTCGAGCCAAATTTCGCCAG cctccatgaaacaacgccttcttgtaacccttgacctccatcaccttcagGTGATTATTTAGTGGCTCATGGCAGGATGAAAGAAAAGGAGGCTCGAGCCAAATACCACCAGgtgagaatttggcaccagtgtgagaatacagaatgtgaaagcatctccac #### Men1_ID1614_5 --> 0 - 2 Original Alignment AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCTGGAAag acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCAC------aggtgagaacctcaagatcagaggaatcaataagtattggaatcag Alignment from CESAR AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCTGGAAag acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCAC------aggtgagaacctcaagatcagaggaatcaataagtattggaatc Alignment from Spaln_aa2Genome AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCT acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCACAGgtgagaacctcaagatcagaggaatcaataagtattggaatcaggata Alignment from Spaln_nt2Genome AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCTGG acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCA--CAGgtgagaacctcaagatcagaggaatcaataagtattggaatcaggata Alignment from Pairagon AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCTGGAAAG acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCAC------AGgtgagaacctcaagatcagaggaatcaataagtattggaatc Alignment from Exonerate_protein2genome AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCTGGAAAG acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCAC------AGgtgagaacctcaagatcagaggaatcaataagtattggaatc Alignment from Exonerate_coding2genome AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCTGGAAAG acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCAC------AGgtgagaacctcaagatcagaggaatcaataagtattggaatc Alignment from GeneWise AAGCTGCTCTGGCTGCTGTATGACCTCGGACATCT acacaatatccgggttgagtacaaaatctccacaactgccaccattctccctgcagAAGTTGCTTTGGCTGCTGTATGACCTGGGGCACAGgtgagaacctcaagatcagaggaatcaataagtattggaatcaggata #### Men1_ID1618_9 --> 0 - 0 Original Alignment ---------GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from CESAR ---------GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from Spaln_aa2Genome GGCACCCAGGGCCAAGGT---------TCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from Spaln_nt2Genome GGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagtgggatattggtacacagGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from Pairagon ---------GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from Exonerate_protein2genome ---------GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from Exonerate_coding2genome ---------GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa Alignment from GeneWise ---------GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG agaactagaaggggagaaatccctttaattgccactctctctttccaaatttgcagTGGGATATTGGTACACAGGGACAAGGCTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTACGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAAgtgagtgggtatcgaaggacagagagaacagtcctatatgggaa #### Mrpl11_ID769_4 --> 2 - 2 Original Alignment ggAAAGAGGTGGCAGGCCTGGTGAGTTTGAAGCAC---GTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATTGGCTCTGCCCGTTCCCTGGGCATTCGAGTGGTGAAG---ga caaggcaccaaggaccaaatatccctcagattcattctcctctcccacagggAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCT---------TCTGTT------TCTGCCCGTTCTTTGAGCGTTTGGGTGGTGAAGACCgagtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata Alignment from CESAR ggAAAGAGGTGGCAGGCCTGGTGAGTTTGAAGCAC---GTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATTGGCTCTGCCCGTTCCCTGGGCATTCGAGTGGTGAAG---ga caaggcaccaaggaccaaatatccctcagattcattctcctctcccacagggAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCTTCTGTT---------------TCTGCCCGTTCTTTGAGCGTTTGGGTGGTGAAGACCgagtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata Alignment from Spaln_aa2Genome GGAAAGAGGTGGCAGGCCTGGTGAGTTTGAAG---CACGTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATTGGCTCTGCCCGTTCCCTGGGCATTCGAGTGGTGAAGGAC-- caaggcaccaaggaccaaatatccctcagattcattctcctctcccacagGGAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCTTCTGTT---------------TCTGCCCGTTCTTTGAGCGTTTGGGTGGTGAAGACCGAgtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata Alignment from Spaln_nt2Genome GGAAAGAGGTGGCAGGCCTGGTGAGTTTGAAGCAC---GTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATTGGCTCTGCCCGTTCCCTGGGCATTCGAGTGGTGAAG---GA caaggcaccaaggaccaaatatccctcagattcattctcctctcccacagGGAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCT----TCTGTT-----------TCTGCCCGTTCTTTGAGCGTTTGGGTGGTGAAGACCGAgtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata Alignment from Pairagon No alignment No alignment Alignment from Exonerate_protein2genome GGAAAGAGGTGGCAGGCCTGGTGAGTTTGAAG---CACGTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATT caaggcaccaaggaccaaatatccctcagattcattctcctctcccacagGGAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCTTCTGTTTCTGCCCGTTCTttgagcgtttgggtggtgaagaccgagtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata Alignment from Exonerate_coding2genome TTACTTTTTGAAGGCAGCTGCTGGGATCGAGAAGGGGGCCCGGCATACAGGGAAAGAGGTGGCAGGCCTGGTGAGTTTGAAG---CACGTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATT CAAGGCACCAAGGACCAAATATCCCTCAGATTCATTCTCCTCTCCCACAGGGAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCTTCTGTTTCTGCCCGTTCTttgagcgtttgggtggtgaagaccgagtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata Alignment from GeneWise GGAAAGAGGTGGCAGGCCTGGTGAGTTTGAAG---CACGTATATGAGATTGCCTGTGTCAAAGCTAAGGATGATGCTTTTGCCATGCAAGATGTGCCCCTGTCTTCTGTGGTCCGTTCCATCATTGGCTCTGCCCGTTCCCTGGGCATTCGAGTGGTGAAGGAC-- caaggcaccaaggaccaaatatccctcagattcattctcctctcccacagGGAAAGAGGTGGCGGGCTTAGTGAGTCTGAGGCAGTATGTATTCAAGATCTCATGTGTCGAAGCTAAAGAAGAGGCTTTTGCCATGCAAGATGTGCCCTTGTCATCTTCTGTT---------------TCTGCCCGTTCTTTGAGCGTTTGGGTGGTGAAGACCGAgtaagttgtatgacaggaaggttaataaattgtctatttgatgggaaata #### Mrpl16_ID3289_2 --> 2 - 1 Original Alignment atTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAa aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagatGCT---GCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACA------agtaaacgcacattgtaccctgaggattactacataactccagctatgcct Alignment from CESAR atTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAa aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagatGCT---GCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACA------agtaaacgcacattgtaccctgaggattactacataactccagctatgcct Alignment from Spaln_aa2Genome ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagATGCT---GCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACAAGTAAACgcacattgtaccctgaggattactacataactccagctatgcct Alignment from Spaln_nt2Genome ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTT aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagATGCT---GCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACAAgtaaacgcacattgtaccctgaggattactacataactccagctatgcct Alignment from Pairagon ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagATGCT---GCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAAC------AAgtaaacgcacattgtaccctgaggattactacataactccagctatgcct Alignment from Exonerate_protein2genome ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgAAGATGCTGCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACAAGTAAACgcacattgtaccctgaggattactacataactccagctatgcct Alignment from Exonerate_coding2genome GCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagatgctGCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACAAGTAAACgcacattgtaccctgaggattactacataactccagctatgcct Alignment from GeneWise ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTT aaggggtgtgagcacctatataaacctcaagtttctgtctgtctttgaagATGCT---GCAACTCTTCCCACCAGTGATGGTCTAAAAACTCTTTTCCCTGTTCCAACAAgtaaacgcacattgtaccctgaggattactacataactccagctatgcct #### Mta2_ID2533_6 --> 0 - 1 Original Alignment GACTGCTTTTTTTACTCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGg gcactaaatcacactgagtgcgtggcgttcacctgctgctttctttctag---------------TCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGggtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from CESAR GACTGCTTTTTTTACTCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGg agaccattaatatcagcactaaatccgttcacctgctgctttctttctag---------------TCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGggtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from Spaln_aa2Genome TCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGG gcactaaatcacactgagtgcgtggcgttcacctgctgctttctttctagTCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGGgtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from Spaln_nt2Genome TCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGG gcactaaatcacactgagtgcgtggcgttcacctgctgctttctttctagTCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGGgtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from Pairagon GACTGCTTTTTTTACTCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGG gcactaaatcacactgagtgcgtggcgttcacctgctgctttctttctag---------------TCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGGgtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from Exonerate_protein2genome GACTGCTTTTTTTACTCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGG gcactaaatcacactgagtgcgtggcgttcacctgCTGCTTTCTTTCTAGTCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGGgtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from Exonerate_coding2genome GACTGCTTTTTTTACTCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGG gcactaaatcacactgagtgcgtggcgttcacctgCTGCTTTCTTTCTAGTCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGGgtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat Alignment from GeneWise TCACTGGTGTTTGATCCTGTGCAGAAGACACTTCTGGCTGATCAAGGGGAGATCAGAGTTGGTTGCAAATTCCAAGCTGAGATCCCAGATCGTTTGGCAGAGG gcactaaatcacactgagtgcgtggcgttcacctgctgctttctttctagTCATTGGTGTATGAGCCTGTGCAGAAAACACTACTCACAGATCAAGGGGAGAGCAGGGTTGGTTGCACATTCCAAGCTGCAATTCCAGATCATTTGGCAGAGGgtaagtaaaagtctggcttgaatataatttgttctctcaactatatcaat #### Mta2_ID2534_7 --> 2 - 2 Original Alignment ga---------------GAATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCcg gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttaggaAAGTCACTCTGTGTAGAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTcggtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from CESAR ga---------------GAATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCcg gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttaggaAAGTCACTCTGTGTAGAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTcggtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from Spaln_aa2Genome AATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCCG gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttaggaaagtcactctgtgtagAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTCGgtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from Spaln_nt2Genome AATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCCG gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttaggaaagtcactctgtgtagAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTCGgtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from Pairagon G---------------AGAATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCCG gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttagGAAAGTCACTCTGTGTAGAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTCGgtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from Exonerate_protein2genome AATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCCG gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttaggaaagtcactctgtgtagAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTCGgtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from Exonerate_coding2genome AATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCCG gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttaggaaagtcactctgtgtagAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTCGgtactgaaaggttaggaggacacataggtgcactacatcttattctggat Alignment from GeneWise --------------GGAGAATCAGATAATCGAAACCAACAGAAGATGGAGATGAAAGTCTGGGACCCAGACAACCCTCTCACAGACCGGCAGATTGATCAGTTTCTCGTGGTGGCCCG gtgcaacttctacagcccaaagaggttcaaatatgtaattactattttagGAAAGTCACTCTGTGTAGAGTCAGATAACAGAAACCAACAGATGATGGAGATGAAAGTCTGGGACCCAGGAAATCCACTTACAGACCAGCAGAATGACCAGTTCCTAATTGTGGCTCGgtactgaaaggttaggaggacacataggtgcactacatcttattctggat #### Mta2_ID2536_9 --> 0 - 0 Original Alignment ---------------------------------------------TTCCATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagAAAAATATCCGACAAAGGGATAACTCACACTGTAGGAATCATCCTTTTCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga Alignment from CESAR caagaactcaggagcctacattagtgctgttcagtgttcctcctgtgtagg Alignment from Spaln_aa2Genome AGATATCACTCTGTTCCATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagaaaaatatccgacaaagggataactcacactgtagGAAT---CATCCTTTTCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga Alignment from Spaln_nt2Genome GATATCACTCTGTTCCATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagaaaaatatccgacaaagggataactcacactgtagGA-ATCA-TCCTTTTCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga Alignment from Pairagon ----------TTCCATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagaaaaatatccgacaaagggataactcacactgtagGAATCATCCTTTTCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga Alignment from Exonerate_protein2genome CATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagaaaaatatccgacaaagggataactcacactgtaggaatcatccttttCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga Alignment from Exonerate_coding2genome TTCCATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagaaaaatatccgacaaagggataactcacactgtaggaatcatcctTTTCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga Alignment from GeneWise ----------TTCCATGCCATGGATACCTTGCAAAGGAATGGCTATGACTTGGCCAAGGCTATGTCAACCCTAGTACCACAGGGAGGCCCGGTGCTCTGTCGGGATGAGATGGAGGAATGGTCTGCTTCTGAAGCCATGCTGTTTGAAGAGGCTCTGGAGAAGTACGGGAAGGATTTCAATGATATCCGCCAGGACTTT agggtaaaaagcacatcaaaactctcaacctattttatttgttttccaagaaaaatatccgacaaagggataactcacactgtagGAATCATCCTTTTCACGCTATGGATACCCTGCAAAAGAATGGATATGACCTAGCCAAGGCTATGACAACCCTCGTACCACAGGGAGGTCCAGTTCTTTGCCAAGATGAGATGGGGGAATGGTCTGCTTCAGAAGCCATGCTAGTTGAAGAAGCTTTGGAGAAGTATGGAGAAGATTTTAATGACATCCACCAAGACTTTgtgagtgatcaagaccaaggagtgaaagaacaatgatgatactaaaaaga #### Mta2_ID2540_13 --> 2 - 0 Original Alignment cc---ACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagcaATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from CESAR cc---ACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagcaATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from Spaln_aa2Genome CCACACAGTCTGCCCAG---TGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagCAATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from Spaln_nt2Genome CCA---CACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagCAATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from Pairagon C---CACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagCAATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from Exonerate_protein2genome CC---ACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagCAATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from Exonerate_coding2genome CC---ACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagCAATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga Alignment from GeneWise --ACCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA gaatcactgtaatacagtaattcttttaatttttgtcttttttattccagCAATGACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACGCAGCTAGAAGGAGCAGCTCGGATAACAACCgtaagggtgagtgtgtctggagcgaccataagaactgaaggtaaggaaga #### Mus81_ID1042_14 --> 0 - 2 Original Alignment GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC---------ag atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATGAACTGTaggtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from CESAR GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC---------ag atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATGAACTGTaggtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from Spaln_aa2Genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAGT-------- atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATGAACTGTAGgtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from Spaln_nt2Genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAGT---- atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATGAACTgtaggtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from Pairagon GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAG----- atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATGAACTgtaggtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from Exonerate_protein2genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAG atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATgaactgtaggtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from Exonerate_coding2genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAG atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATgaactgtaggtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca Alignment from GeneWise GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC---------AG atgaatggaatgagctctgtttcacaagtactgatgcctcccatccccagGCTCAGTCTGTGCGGGAGGTAATTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCATGAACTGTAGgtgatgtacttacagtacatgtgaccccttctaccacagctagtgataca #### Mus81_ID1046_10 --> 2 - 0 Original Alignment aaAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagagAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAG---gtgagtctgatgtgacatagttaggattaactacttctgttatctagggc Alignment from CESAR aaAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagagAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAG---gtgagtctgatgtgacatagttaggattaactacttctgttatctag Alignment from Spaln_aa2Genome AAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGCTTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagAGAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGgtgagtctgatgtgacatagttaggattaactacttctgttatctagggc Alignment from Spaln_nt2Genome AAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGCTTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagAGAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGgtgagtctgatgtgacatagttaggattaactacttctgttatctagggc Alignment from Pairagon AAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCG---CTTTCGGGAGCAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagAGAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGgtgagtctgatgtgacatagttaggattaactacttctgttatctagggc Alignment from Exonerate_protein2genome AAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGCTTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagAGAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGgtgagtctgatgtgacatagttaggattaactacttctgttatctagggc Alignment from Exonerate_coding2genome AAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGCTTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagAGAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGgtgagtctgatgtgacatagttaggattaactacttctgttatctagggc Alignment from GeneWise AAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGCTTTCGGGAGCAGAAG ggggagcattagtagtggaaatccacaaccaatttttctttgtggatcagAGAGACCTGGGGAGTTAGTCCTAGATCACATTGTTGAACATAAGAGGATTGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGgtgagtctgatgtgacatagttaggattaactacttctgttatctagggc #### Mus81_ID1047_9 --> 1 - 1 Original Alignment gGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAg agcctagatcagcctgcatatgccaaatccctctgatcattatatttcagt---GGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAggtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from CESAR gGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAg gggagcctagatcagcctgcatatgaatccctctgatcattatatttcagt---GGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAggtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from Spaln_aa2Genome GGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAG agcctagatcagcctgcatatgccaaatccctctgatcattatatttcagT---GGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAGgtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from Spaln_nt2Genome GGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAG agcctagatcagcctgcatatgccaaatccctctgatcattatatttcag---TGGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAGgtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from Pairagon GGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAG agcctagatcagcctgcatatgccaaatccctctgatcattatatttcag---TGGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAGgtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from Exonerate_protein2genome GGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAG agcctagatcagcctgcatatgccaaatccctctgatcattatatttcagT---GGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAGgtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from Exonerate_coding2genome GGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAG agcctagatcagcctgcatatgccaaatccctctgatcattatatttcagT---GGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAGgtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa Alignment from GeneWise GGCAGGACACAGGCCAGAAATGCTCCGAGAGTTACAAAGGCTGCGTGTGCCCCACACCGTACGCAAGCTACACGTTGGAGACTTTGTGTGGGTGGCACAGGAGACCAGGCCCAGAGACCCAG agcctagatcagcctgcatatgccaaatccctctgatcattatatttcagT---GGCCACCGTCCAGAAATGCTCCATGAGTTGCAAAGGCTCCATGTGCCCCACACTGTACGTAAACTACATGTTGGAGACTTTGTATGGGTTGCACAGGAGACTCGTCCTAGAGACCCAGgtaagcttatttaggaatcatttgctgggggggagcattagtagtggaaa #### Mus81_ID1048_8 --> 1 - 2 Original Alignment tGGCACCACCGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAgg ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagt------AGTGAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGgggtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from CESAR tGGCACCACCGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAgg atcaaaggggacacaatgtgatatcctgaagcatttctgttttgtttcagtAGT------GAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGgggtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from Spaln_aa2Genome TGGCACCACCGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAGG ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagT------AGTGAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGGGgtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from Spaln_nt2Genome TGGCACCACCGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAGG ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagT------AGTGAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGGGgtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from Pairagon TGGCACCACCGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAGG ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagtagT---------GAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGGGgtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from Exonerate_protein2genome CGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAGG ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagtagTGAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGGGgtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from Exonerate_coding2genome CGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAGG ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagtagTGAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGGGgtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat Alignment from GeneWise TGGCACCACCGAGGGGGCCGTCCAGCAGAGACCACTGGAGCTAAGGCCTAGCGAGTACAGAGTGCTGTTGTGTGTGGACATTGGCGAAACCAGAGG ggggacacaatgtgatatcaattggctgaagcatttctgttttgtttcagT------AGTGAGGGCGCTGTCCAACAAAGATCACTGGAATTATGGCCAAGTGTGTACAGGGTGCTGGTGTGTACGGATATCCGGAAAACCAGGGGgtatgcacaccagggtggcatgtaggaatggcttagagggtctcgtgaat #### Mus81_ID1052_4 --> 0 - 0 Original Alignment GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTG--- attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGGATgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac Alignment from CESAR GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTG--- attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGGATgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac Alignment from Spaln_aa2Genome GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTGAAT attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGGATgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac Alignment from Spaln_nt2Genome GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTG--- attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGGATgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac Alignment from Pairagon GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTG------------------------------------- attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGGATGTACAAGGAGACATGTTTTACTGGCCATGAGGTAgtgggaggaaaaccac Alignment from Exonerate_protein2genome GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTG attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGgatgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac Alignment from Exonerate_coding2genome attccctgcaagaactctatgtatcatgattttgcttcctgtttatttaggtgctcacccagtcccaagcaggaagtaccagtgttggttactggccagcgcagaactcaggggctcaagaagttttactacaactatacagggagcatctggatgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac Alignment from GeneWise GTTCCCACCCAGCCTCAAGCAGGAAGCACCAGTGTTGGCTATTGGCCAGCTCAGAACTCAGGTGCTCGAGAGATCCTGCTGCAACTCTACAGGGAGCACCTGAAT attccctgcaagaactctatgtatcatgattttgcttcctgtttatttagGTGCTCACCCAGTCCCAAGCAGGAAGTACCAGTGTTGGTTACTGGCCAGCGCAGAACTCAGGGGCTCAAGAAGTTTTACTACAACTATACAGGGAGCATCTGGATgtacaaggagacatgttttactggccatgaggtagtgggaggaaaaccac #### Mus81_ID1053_3 --> 2 - 0 Original Alignment gtGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA--- atgttgtaatttggagttccacacattccatgatcttctctcctctccaggaGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from CESAR CCACACGCGTTTCGTGTTTCAAA gtGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA--- CCATACACGATTTGTATTCCAGAagttccatgatcttctctcctctccaggaGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from Spaln_aa2Genome GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA--- atgttgtaatttggagttccacacattccatgatcttctctcctctccagGAGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from Spaln_nt2Genome GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCAG-- atgttgtaatttggagttccacacattccatgatcttctctcctctccagGAGACCATGCCCCTA---CACCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from Pairagon GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA--- atgttgtaatttggagttccacacattccatgatcttctctcctctccagGAGACCATGCCCCTA---CACCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from Exonerate_protein2genome GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA--- atgttgtaatttggagttccacacattccatgatcttctctcctctccagGAGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from Exonerate_coding2genome atgttgtaatttggagttccacacattccatgatcttctctcctctccaggagaccatgcccctacaccatctgggaaaaagggtgccggcaaaggtccgcctgagcaggtacaagaaccttctatgccaggggtaagtaagctagaccaattatagggaaacctatgacttattttaataaa Alignment from GeneWise GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCAGTT atgttgtaatttggagttccacacattccatgatcttctctcctctccagGAGACCATGCCCCTACA---CCATCTGGGAAAAAGGGTGCCGGCAAAGGTCCGCCTGAGCAGGTACAAGAACCTTCTATGCCAGGGgtaagtaagctagaccaattatagggaaacctatgacttattttaataaa #### Myrf_ID2714_23 --> 1 - 2 Original Alignment g------CTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGaa gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagaGTAAAGCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGaagtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from CESAR g------CTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGaa gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagaGTAAAGCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGaagtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from Spaln_aa2Genome TTGCAGGCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAA gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagAGTAAAGCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGAAgtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from Spaln_nt2Genome GCTTGGCAAC------TTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAA gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagAGTAAAGCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGAAgtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from Pairagon ------GCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAA gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagAGTAAAGCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGAAgtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from Exonerate_protein2genome GCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAA gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagagtaaaGCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGAAgtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from Exonerate_coding2genome gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagagtaaagcttggcaacttcacataccatatccctgtaagtagcagcacaccgctacacctcagcctcaccctgcaaatgaagtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca Alignment from GeneWise ---GGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAA gatcttggggaggtgacacgagtggcttatctggtctcacttattcctagagtaaagCTTGGCAACTTCACATACCATATCCCTGTAAGTAGCAGCACACCGCTACACCTCAGCCTCACCCTGCAAATGAAgtaggtgaaagctacttacctcaccgacaaatgtaaagttaatccaaaca #### Myrf_ID2721_16 --> 1 - 0 Original Alignment c---------CATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagcTCTCCATCTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from CESAR c---------CATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagcTCTCCATCTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from Spaln_aa2Genome CCATGCAGGG---------AGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagCTCTCCATCTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from Spaln_nt2Genome C---------CATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagCTCTCCATCTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from Pairagon C---------CATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagCTCTCCATCTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from Exonerate_protein2genome CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagctctccatcTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from Exonerate_coding2genome CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagctctccatcTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGgcaagtcggtccaacagccacatacacttctacccattcatagagttgcc Alignment from GeneWise -------AGCCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAGTCATCG-- ggaaagatccgcaggtgttttatgcattttctccttctgtctctctgtagCTCTCCATCTCATGCTGGTAGTGAATTTAGTAGGACTGGCAGTGTCCCTCACAAAAAAAGGCCCCCCAGGCTTGCCAATAAGGCAAGTCGgtccaacagccacatacacttctacccattcatagagttgcc #### Myrf_ID2722_15 --> 0 - 2 Original Alignment GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTC---------ag tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGATGGGGACaggtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg Alignment from CESAR GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTC---------ag tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGATGGGGACaggtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg Alignment from Spaln_aa2Genome GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAGC-------- tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGATGGGGACAGgtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg Alignment from Spaln_nt2Genome GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTC---------AG tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGATGGGGACAGgtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg Alignment from Pairagon GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTT-------------------------------------------------------------- tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGATGGGGACAGGTGAGCCAACAAACAATATGGACAGTAGACTAAGGTAAGAAGAGGAGGGG Alignment from Exonerate_protein2genome GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGAtggggacaggtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg Alignment from Exonerate_coding2genome GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGAtggggacaggtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg Alignment from GeneWise GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTC---------AG tggtgggtggataaaatgagcagttcccgttcctataatcacatttacagGAGCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCGATGGGGACAGgtgagccaacaaacaatatggacagtagactaaggtaagaagaggagggg #### Myrf_ID2723_14 --> 2 - 0 Original Alignment gt---GTCATCGCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCCAAT---GGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagggTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from CESAR gt---GTCATCGCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCC---AATGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagggTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from Spaln_aa2Genome GTGTCATCGCCCAGGAAGTG---AAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCC---AATGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagGGTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from Spaln_nt2Genome GTGTCATC---GCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCCAA---TGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagGGTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from Pairagon -------CATCGCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGC---CAATGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagGGTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from Exonerate_protein2genome GT---GTCATCGCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCC---AATGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagGGTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from Exonerate_coding2genome GT---GTCATCGCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCC---AATGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagGGTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt Alignment from GeneWise --GGTGTCATCGCCCAGGAAGTGAAGGAGATCCTGCCTGAAGCTGTGAAGGACACAGGGGATGTAGTCTTTGCC---AATGGGAAAACCATAGAGAACTTCCTTGTAGTGAACAAG gcctggtaaagtagagtgttgactgcagctctatttgtgcttttccacagGGTGCATCCTTGCGCGGGAGGTGAAGGTGATTCTGCCTGAAGCTGTGGAGGACACAGGGGATGTTGTCTTCACAAAAAATGGAAAAAGTATAAAGAACTTCCTAGTAGTGAACAAAgtgagcttacaggatctgcagcttaggcatggtatcttgcatctagctgt #### Myrf_ID2732_6 --> 1 - 1 Original Alignment aCTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAg gc actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagaCTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCC------ggtgagattataaaggccccattcagattgtttttttccatgtatgtaggg Alignment from CESAR aCTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAg gc actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagaCTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCC------ggtgagattataaaggccccattcagttgttttaaactgaaattcccaggg Alignment from Spaln_aa2Genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCC- TCC actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagACTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCCGgtgagattataaaggccccattcagattgtttttttccatgtatgta Alignment from Spaln_nt2Genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAG GC actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagACTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCC------GgtgagattataaaggccccattcagattgtttttttccatgtatgtagGG Alignment from Pairagon ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCC---------------TCCCC---------------------------AGGC actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagACTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCCGGTGAGATTATAAAGGCCCCATTCAGATTGTTTTTTTCCATGTATGTAGGG Alignment from Exonerate_protein2genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCT CCCCAGGC actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagACTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCCGgtgagattataaaggccccattcagattgtttttttccatgtATGTAGGG Alignment from Exonerate_coding2genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCT CCCCAGGC actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagACTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCCGgtgagattataaaggccccattcagattgtttttttccatgtATGTAGGG Alignment from GeneWise ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCA------------------------------------------GGC actactctagtgacaaggaggaatgaaggctcacttgcattgtctttcagACTACCACCACACCCTTCCAAGAAGAGGAAGCATTCTGAAACACCCCCCAACACACTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTGACAACCTTACCGCTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACATAAAGGCCCACTCTCACCTGATACTGGATCACTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCCCCAGGTGCACCCGGTGAGATTATAAAGGCCCCATTCAGATTGTTTTTTTCCATGTATGTAGGG #### Naaladl1_ID1444_3 --> 2 - 0 Original Alignment tgGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACTCCAAAG aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagttGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGACC------gtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt Alignment from CESAR tgGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACTCCAAAG gagtatcagaagtcactaggcagcacactccttacttggtctgtctgcagttGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGACC------gtatatcatgcttaacgatttaagatggtttcctccctaaattg Alignment from Spaln_aa2Genome TGGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACT aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagTTGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGACCgtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt Alignment from Spaln_nt2Genome TGGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACTC aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagTTGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGAC-Cgtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt Alignment from Pairagon TGGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACT aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagTTGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGACCgtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt Alignment from Exonerate_protein2genome TGGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACT aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagTTGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGACCgtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt Alignment from Exonerate_coding2genome TGGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACT aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagTTGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGGACCgtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt Alignment from GeneWise TGGGCCCCAATGGAACAACCTTCCACTCCTTCCAACCCTTCGAGAAGAATCTGACCGGGGAGCAGGCGGGGCCCAATGTATTGCAACCTTATGCTGCCTACGCTCCCCCTGGGACTCCAAAG aactatcagaagtcactaggcagcacactccttacttggtctgtctgcagTTGGCCCCAATGGAACAACGTTCCACTCCTTTCAACCTTTCAAAAGGAATATAATTGGAGAGCAGGCAGGGCCTAATGCATTGCAACCATATGCTGCCTATGCTCCTCCAGGG------ACCgtatatcatgcttaacgatttaagatggtttcctccctaaattgctgggt #### Naaladl1_ID1448_7 --> 1 - 1 Original Alignment tGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTg ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagtGACATCAGAGTCCGTGTTCACAATAGATTAGAACTTAGAATTTCCACAAATGTGCTTGGA------------------------ggtgtgtctattaacactcccctcttctgcgtccctaatagtaaattctgt Alignment from CESAR tGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTg ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagtGACATCAGAGTCCGTGTTCACAATAGATTAGAACTTAGAATTTCCACAAATGTGCTTGGA------------------------ggtgtgtctattaacactcccctcttctgcgtccctaatagtaaattctgt Alignment from Spaln_aa2Genome TGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGT ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagTGACATCAGAGTCCGTGTTCACAATAGATTAGAACTTAGAATTTCCACAAATGTgcttggaggtgtgtctattaacactcccctcttctgcgtccctaatagtaaattctgt Alignment from Spaln_nt2Genome TGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCAT CATCCAGGGG ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagTGACATCAGAGTCCGTGTTCACAATAGATTAGAACTTAGAATTTCCACAAATGTGCTTGG-AGgtgtgtctattaacactcccctcttctgcgtccctaatagTAAATTCTGT Alignment from Pairagon ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagtgacatcagagtccgtgttcacaatagattagaacttagaatttccacaaatgtgcttggaggtgtgtctattaacactcccctcttctgcgtccctaatagtaaattctgt Alignment from Exonerate_protein2genome TGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCA ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagTGACATCAGAGTCCGTGTTCACAATAGATTAGAACTTAGAATTTCCACAAATGTGCTTGGAGgtgtgtctattaacactcccctcttctgcgtccctaatagtaaattctgt Alignment from Exonerate_coding2genome ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagtgacatcagagtccgtgttcacaatagattagaacttagaatttccacaaatgtgcttggaggtgtgtctattaacactcccctcttctgcgtccctaatagtaaattctgt Alignment from GeneWise TGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATC-- ttgtattataactagtcaataatagctctcacatgatctttgtgttgtagTGACATCAGAGTCCGTGTTCACAATAGATTAGAACTTAGAATTTCCACAAATGTGCTTGGAGGTGTgtctattaacactcccctcttctgcgtccctaatagtaaattctgt #### Naaladl1_ID1454_13 --> 1 - 0 Original Alignment cCTGGGCACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACCTATGACCGG attaaggtccagggagactctttttacacccttgctgtctgtccccacagcCTT---------GGGGCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACC---------gtaatttaagctccattggtttgtggcatggcaacaaaaggggactagta Alignment from CESAR cCTGGGCACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACCTATGACCGG attaaggtccagggagactctttttacacccttgctgtctgtccccacagcCTT---------GGGGCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACC---------gtaatttaagctccattggtttgtggcatggcaacaaaagg Alignment from Spaln_aa2Genome CCTGGGCACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACC attaaggtccagggagactctttttacacccttgctgtctgtccccacagC---------CTTGGGGCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACCgtaatttaagctccattggtttgtggcatggcaacaaaaggggactagta Alignment from Spaln_nt2Genome CCTGGGCACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACC attaaggtccagggagactctttttacacccttgctgtctgtccccacagCCT--------TGGG-GCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACCgtaatttaagctccattggtttgtggcatggcaacaaaaggggactagta Alignment from Pairagon CCTGGGCACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACC attaaggtccagggagactctttttacacccttgctgtctgtccccacagC---------CTTGGGGCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACCgtaatttaagctccattggtttgtggcatggcaacaaaaggggactagta Alignment from Exonerate_protein2genome CCTGGGCACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACCTATGA attaaggtccagggagactctttttacacccttgctgtctgTCCCCACAGCCTTGGGGCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACCGTAATttaagctccattggtttgtggcatggcaacaaaaggggactagta Alignment from Exonerate_coding2genome attaaggtccagggagactctttttacacccttgctgtctgtccccacagccttggggctggtagtgactatgcagcatttgttcacttcgcaggcatcacatctatggattttgcttataccgtaatttaagctccattggtttgtggcatggcaacaaaaggggactagta Alignment from GeneWise ------------------------------------------------ACACTGGGCGCTGGCAGTGACTATGCCGCATTCGTTCACTTCCTGGGCATCACGTCCATGGACCTTGCCTACACC ATTAAGGTCCAGGGAGACTCTTTTTACACCCTTGCTGTCTGTCCCCACAGCCTTGGGGCTGGTAGTGACTATGCAGCATTTGTTCACTTCGCAGGCATCACATCTATGGATTTTGCTTATACCgtaatttaagctccattggtttgtggcatggcaacaaaaggggactagta #### Naaladl1_ID1456_15 --> 2 - 1 Original Alignment gtTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGg gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacaggcTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGAAT---------ggtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from CESAR gtTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGg gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacaggcTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGAAT---------ggtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from Spaln_aa2Genome GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAAC- gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacagGCTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGAATGgtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from Spaln_nt2Genome GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATC gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacagGCTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGA--ATGgtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from Pairagon GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGG gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacagGCTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGAAT---------Ggtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from Exonerate_protein2genome GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACA gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacagGCTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGAATGgtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from Exonerate_coding2genome gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacaggctttagtagccagcaggctgttgcccggactgctgggagtgtgcttctccagctcagtgatagcctcttcctgcccctaaatgttagtgactatagtgagaccttgcaaagttttcttcaggcagcacaagaagcccttggtactcaattagaaaagcagaatggtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca Alignment from GeneWise GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAAC- gaaggtgaaacttggatttggtctctattagccaccatcttgtcttacagGCTTTAGTAGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTGCAAAGTTTTCTTCAGGCAGCACAAGAAGCCCTTGGTACTCAATTAGAAAAGCAGAATGgtgagtcccttatacccaaacatcttgagcccccagcggtggaatctaca #### Naaladl1_ID1458_17 --> 1 - 2 Original Alignment tCCTCTGCAGGTACGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACag tagcccaatgaacagaacgtatcccttttcctggggatcgtccctgctagt---------GTTCAGATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACaggtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from CESAR tCCTCTGCAGGTACGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACag agagatacatagcccaatgaacagattttcctggggatcgtccctgctagt---------GTTCAGATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACaggtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from Spaln_aa2Genome TCCTCTGCAGGTACGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACAG tagcccaatgaacagaacgtatcccttttcctggggatcgtccctgctagT---------GTTCAGATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACAGgtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from Spaln_nt2Genome TA--CGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACAG tagcccaatgaacagaacgtatcccttttcctggggatcgtccctgctagTGTTCAGATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACAGgtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from Pairagon TCCTCTGCAGGTACGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACAG tagcccaatgaacagaacgtatcccttttcctggggatcgtccctgctagtgttcag----------------ATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACAGgtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from Exonerate_protein2genome TCCTCTGCAGGTACGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACAG tagcccaatgaacagaacgtatcccttttcctggggatcgtCCCTGCTAGTGTTCAGATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACAGgtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from Exonerate_coding2genome tagcccaatgaacagaacgtatcccttttcctggggatcgtccctgctagtgttcagatggttaatgatcaactaatgctattagagtgtgcatttctgaacccaagggcattcccagaggagaggcattacaggtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac Alignment from GeneWise TCCTCTGCAGGTACGAATGGTCAATGACCAGCTGATGCTCTTAGAACGGGCATTCCTGAACCCAAGGGCTTTCCCAGAGGAGAGGCACTACAG tagcccaatgaacagaacgtatcccttttcctggggatcgtccctgctagT---------GTTCAGATGGTTAATGATCAACTAATGCTATTAGAGTGTGCATTTCTGAACCCAAGGGCATTCCCAGAGGAGAGGCATTACAGgtgagtcagtgtaaattgagctgccgacttgcttagaactagagttcaac #### Ndufv1_ID275_7 --> 2 - 0 Original Alignment gtGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCG--- ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttataggtGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCC---ACATTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAATC---ATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from CESAR gtGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCG--- ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttataggtGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCACA---TTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAATC---ATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from Spaln_aa2Genome GTGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCG ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttatagGTGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCACA---TTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAATCATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from Spaln_nt2Genome GTGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCGA ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttatagGTGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCA---CATTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAA---TCATGGATCGTTTGGgtgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from Pairagon GTGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCG--- ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttatagGTGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCA---CATTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAA---TCATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from Exonerate_protein2genome GTGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCG ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttatagGTGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCACA---TTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAATCATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from Exonerate_coding2genome GTGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCG ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttatagGTGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCACA---TTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAATCATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt Alignment from GeneWise GTGGTGTCACAGGTGGCTGGGACAACCTCCTTGCTGTGATTCCTGGTGGCTCATCTACTCCACTGATTCCCAAATCTGTGTGTGAGACCGTGCTAATGGACTTCGATGCACTGGTGCAGGCTCAGACAGGCCTGGGCACGGCTGCAGTTATTGTTATGGATCGCTCGACA ggggtgcttgcaaagaatgcttcttacatttattgtaatgtctcttatagGTGGTGTAACAGGCGGCTGGGACAATCTGCTTGCTGTGACACCAGGTGGATCATCCACA---TTAATTCCCAAATCTGTTTGTGAGACAGTGCTAATGGATTTTGATGCTCTAGTGCAGGCTCAGACAGGGCTGGGAACAGCCACAGTAATC---ATGGATCGTTTGGGTgtgagtggtcataagcaccctcatgcttgtcactatgatgtgtgtttttt #### Ndufv1_ID276_6 --> 2 - 1 Original Alignment gaGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCT---------g gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcaggaGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGAACGGGTGggtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from CESAR gaGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCT---------g gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcaggaGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGAACGGGTGggtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from Spaln_aa2Genome GAGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCT---------G gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcagGAGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGAACGGGTGGgtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from Spaln_nt2Genome GAGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCTG----- gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcagGAGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGAACGGgtgggtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from Pairagon GAGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCTG----- gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcagGAGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGAACGGgtgggtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from Exonerate_protein2genome GAGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCTG gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcagGAGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGaacgggtgggtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from Exonerate_coding2genome GAGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCTG gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcagGAGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGaacgggtgggtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa Alignment from GeneWise GAGTGTTTGGATGCCCCACAACTGTGGCCAATGTGGAGACAGTGGCTGTGTCCCCCACCATTTGCCGTCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGAGAACGCAATTCAGGTACCAAATTGTTTAACATCTCTGGCCATGTCAACCACCCCTGCACTGTGGAGGAAGAGATGTCTGTGCCACTGAAAGAGCTGATTGAGAAACATGCT---------G gatggtgcttgattatgactcagttaatcaatccctgtgtgtcttttcagGAGTGTTTGGCTGTCCCACCACTGTGACCAATGTTAAAACAGTGGCTGTGTCCCCCACAATCTGTCGCCGTGGGGGCACCTGGTTTGCTGGCTTTGGCCGGGAGCACAATTCAGGTACAAAATTGTTCAACATCTTTGGCCATGTCAACCGCCCATGCACTGTGGAGGAAGAGATGGCAGTACCCCTCAAGGAGCTGATTGAGAAACATACTGAACGGGTGGgtacgactttagccaattaaaggtcagggcatcagaggggtgcttgcaaa #### Nfkb2_ID9824_2 --> 0 - 1 Original Alignment GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAg tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCT------ggtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from CESAR GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAg tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCT------ggtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from Spaln_aa2Genome GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCT- tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCTGgtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from Spaln_nt2Genome GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTG tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCTGgtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from Pairagon GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTG tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCTGgtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from Exonerate_protein2genome GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTG tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCTGgtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from Exonerate_coding2genome GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTG tagccaatttatcccttaataccactacttgtctgctcctttccatgtagGGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCTGgtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg Alignment from GeneWise GACAATTGCTACGATCCAGGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTG tagccaatttatcccttaataccactacttgtctgctcctttccatgtag------------------GGGCTAGACGGAATCCCAGATTATGAAGATTTTGAATTCAGCCCAACCATAGGTGAACCTAATGACCCAGCACCTGgtaaactaataagagtatacggaggcttttcaattgaggagtttgaggtg #### Nfkb2_ID9825_3 --> 2 - 0 Original Alignment ctGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagctGATGGACCCTATCTTGTGATTGTGGAACAA---------gtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from CESAR ctGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagctGATGGACCCTATCTTGTGATTGTGGAA---------CAAgtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from Spaln_aa2Genome CTGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAA ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagCTGATGGACCCTATCTTGTGATTGTGGAACAAGTAATTgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from Spaln_nt2Genome CTGATGGCCCCTATCTGGTGATTGTGGAACAGCCCA ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagCTGATGGACCCTATCTTGTGATTGTGGAACA----Agtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from Pairagon CTGATGGCCCCTATCTGGTGATTGTGGAACAG ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagCTGATGGACCCTATCTTGTGATTGTGGAACAAgtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from Exonerate_protein2genome CTGATGGCCCCTATCTGGTGATTGTGGAACAG ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagCTGATGGACCCTATCTTGTGATTGTGGAACAAgtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from Exonerate_coding2genome CTGATGGCCCCTATCTGGTGATTGTGGAACAG ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagCTGATGGACCCTATCTTGTGATTGTGGAACAAgtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg Alignment from GeneWise ctgtttttgggattagtaaaagggggaaactgtggtcatctttcttgcagctgatggaccctatcttgtgattgtggaacaagtaattgtagagatcatctaataagtcaaataaggcagtaaatcaatagg #### Nfkb2_ID9827_5 --> 0 - 2 Original Alignment ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCT---------ca ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAAcagtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from CESAR ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCT---------ca ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAAcagtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from Spaln_aa2Genome ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCAA-------- ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAACAgtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from Spaln_nt2Genome ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCT-CAATTTAATA ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAACAgtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from Pairagon ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCT---------CA ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAACAgtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from Exonerate_protein2genome ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCAATTTAATAA ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAACAgtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from Exonerate_coding2genome ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCAATTTAATAA ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAACAgtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc Alignment from GeneWise ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCT---------CA ggcctgtggggcactcagctatatagaatattccttttcttcttttccagATATGTAACTATGAGGGACCCAGAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCAGGCAAGCAGTGTTCAGAAGTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTGCCCCTGAACAgtaagccgcttaacagtcttggagctaatccaagggatatctggatgtcc #### Nfkb2_ID9828_6 --> 1 - 1 Original Alignment aTTTAATAATCTGGGTGTCCTGCATGTAACCAAGAAGAACATGATGGAGATTATGATCCAGAAACTTCAGAGGCAGCGTCTCCGCTCCAAGCCTCAGGGCCTTACAg ataggtgacactgtataatttatccagaagcttctgccttgcctttgcaggTTCAACAATTTCGGC------CATGTAACCAAAAAGAACATGATGGAGATAATGATACAAAGACTGCAC------------------------------------ggtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg Alignment from CESAR aTTTAATAATCTGGGTGTCCTGCATGTAACCAAGAAGAACATGATGGAGATTATGATCCAGAAACTTCAGAGGCAGCGTCTCCGCTCCAAGCCTCAGGGCCTTACAg ataggtgacactgtataatttatccagaagcttctgccttgcctttgcaggTTCAACAATTTCGGC------CATGTAACCAAAAAGAACATGATGGAGATAATGATA---------------CAAAGACTGCAC---------------------ggtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg Alignment from Spaln_aa2Genome ATTTAATAATCTGGGTGTCCTGCATGTAACCAAGAAGAACATGATGGAGATTATGATCCAGAAACTTCAGA ataggtgacactgtataatttatccagaagcttctgccttgcctttgcagGTTCAACAATTTCGGC------CATGTAACCAAAAAGAACATGATGGAGATAATGATACAAAGACTGCACGgtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg Alignment from Spaln_nt2Genome ATTTAATAATCTGGGTGTCCTGCATGTAACCAAGAAGAACATGATGGAGATTATGATCCAGAAACTTCAGA ataggtgacactgtataatttatccagaagcttctgccttgcctttgcagGTTCAACAATTTCGG------CCATGTAACCAAAAAGAACATGATGGAGATAATGATACAAAGACTGCACGgtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg Alignment from Pairagon ATTTAATAATCTGGGTGTCCTGCATGTAACCAAGAAGAACATGATGGAGATTATGATCCAGA----------------------------------------------------------- ataggtgacactgtataatttatccagaagcttctgccttgcctttgcagGTTCAACAATTTCGGC------CATGTAACCAAAAAGAACATGATGGAGATAATGATACAAAGACTGCACGGTATCTAACAGAATGTGTCTTGGATGGTGCTCATAAACATGAAACAGTTG Alignment from Exonerate_protein2genome ataggtgacactgtataatttatccagaagcttctgccttgcctttgcaggttcaacaatttcggccatgtaaccaaaaagaacatgatggagataatgatacaaagactgcacggtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg Alignment from Exonerate_coding2genome ataggtgacactgtataatttatccagaagcttctgccttgcctttgcaggttcaacaatttcggccatgtaaccaaaaagaacatgatggagataatgatacaaagactgcacggtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg Alignment from GeneWise ATTTAATAATCTGGGTGTCCTGCATGTAACCAAGAAGAACATGATGGAGATTATGATCCAGAAACTTCAGA ataggtgacactgtataatttatccagaagcttctgccttgcctttgcagGTTCAACAATTTCGGC------CATGTAACCAAAAAGAACATGATGGAGATAATGATACAAAGACTGCACGgtatctaacagaatgtgtcttggatggtgctcataaacatgaaacagttg #### Nfkb2_ID9829_7 --> 2 - 1 Original Alignment agGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGC---a agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagagGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCagtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from CESAR agGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGC---a agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagagGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCagtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from Spaln_aa2Genome AGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGC---A agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagAGGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCAgtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from Spaln_nt2Genome AGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGC---A agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagAGGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCAgtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from Pairagon AGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAG---CA agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagAGGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCAgtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from Exonerate_protein2genome AGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGC---A agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagAGGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCAgtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from Exonerate_coding2genome AGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGC---A agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagAGGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCAgtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc Alignment from GeneWise AGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCAAG- agggcaatttattacttgccctacccatgtcctgaatctcgatgttgcagAGGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCTTCAgtaaaactgacctgcacaaacataagcaataagatttcagttgaaaggtc #### Nfkb2_ID9830_8 --> 2 - 1 Original Alignment agTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAAAA---------g agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagaaTCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAGGGAGTACggtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from CESAR agTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAAAA---------g agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagaaTCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAGGGAGTACggtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from Spaln_aa2Genome AGTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAAAA---------G agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagAATCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAGGGAGTACGgtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from Spaln_nt2Genome AGTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAA---------AAG agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagAATCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAGGGAGTACGgtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from Pairagon AGTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAA---------AAG agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagAATCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAGGGAGTACGgtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from Exonerate_protein2genome AGTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAAAAG agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagAATCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAgggagtacggtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from Exonerate_coding2genome AGTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAAAAG agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagAATCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAgggagtacggtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa Alignment from GeneWise AGTCTCCAGGGGCCTCGAACCTGAAGATCTCCCGAATGGACAAGACAGCGGGTTCCGTGCGCGGTGGAGACGAAGTTTATTTGCTCTGTGATAAGGTGCAAAAA---------G agattgacgcccgcaagtcaatcaagccgcacctgcttttcttcccacagAATCTTCAGGGGGTTTGAATTTGAAGATTTCTGAGATGGACAAGGCTGCTGGGTCAGTGCAGGGGGGAGATGAGGTTTATTTGCTCTGTGAAAGGGTGCAAAGGAGGGAGTACGgtgagggtgtgtctaggctagttctactttggcagactgtaatggtgaaa #### Nfkb2_ID9831_9 --> 2 - 0 Original Alignment acGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccggttgcctttcagat------------CAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from CESAR acGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG acctgcctctgtaccttcatatcaccgatctgtggccggttgcctttcagat------------CAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from Spaln_aa2Genome ACGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccggttgcctttcagAT------------CAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from Spaln_nt2Genome TTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccggttgcctttcagATCAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from Pairagon ACGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccggttgcctttcagA------------TCAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from Exonerate_protein2genome ACGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccgGTTGCCTTTCAGATCAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from Exonerate_coding2genome ACGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccgGTTGCCTTTCAGATCAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat Alignment from GeneWise ACGACATTGAGGTTCGGTTCTATGAGGATGATGAGAATGGATGGCAAGCCTTTGGGGACTTCTCTCCCACAGACGTTCATAAACAG accttcatatcactgatcttcccctcgatctgtggccggttgcctttcagAT------------CAATTCTATGAGGATGATGAGAATGGGTGGCAAGCCTTTGGGGACTTCTCTTCCACAGATGTATATAAACAGgtgagtcaactgaacataattcatattccctgtggtgagtacatgtacat #### Nfkb2_ID9841_19 --> 0 - 1 Original Alignment ---GTG---AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAg tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAggtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from CESAR GTG------AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAg tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAggtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from Spaln_aa2Genome GTGAAGACTCTGCTGCTA------AATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAG tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAGgtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from Spaln_nt2Genome GTG------AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAG tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAGgtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from Pairagon GT------GAAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAG tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAGgtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from Exonerate_protein2genome GTG------AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAG tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAGgtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from Exonerate_coding2genome tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcaggttgtgaaaaaaacactacttctaaacactgctcagaattccacagagccacccttggcccccccgacgccagtaggtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa Alignment from GeneWise GTG------AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAG tgatagggagagatacccccccattaggcctctgtgtgtgtctcttgcagGTTGTGAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCCCCGACGCCAGTAGgtacaactgcatgccatggcttgcaggggagggattgagggctttcttaa #### Noc3l_ID7660_15 --> 0 - 1 Original Alignment GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTTCTGGACAAg gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCTT---------ggtcagtaacaccatcacttcattctgccaccctttcatctgatggtgcta Alignment from CESAR GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTTCTGGACAAg gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCTT---------ggtcagtaacaccatcacttcattctgccaccctttaaaaaatctgtttgt Alignment from Spaln_aa2Genome GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTT- gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCTTGgtcagtaacaccatcacttcattctgccaccctttcatctgatggtgcta Alignment from Spaln_nt2Genome GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTTCTGGACA gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCT---TGGTCAgtaacaccatcacttcattctgccaccctttcatctgatggtgcta Alignment from Pairagon GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTTCTGGACA---------------------------------------------- gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCT---TGGTCAGTAACACCATCACTTCATTCTGCCACCCTTTCATCTGATGGTGCTA Alignment from Exonerate_protein2genome GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTT gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCTTGgtcagtaacaccatcacttcattctgccaccctttcatctgatggtgcta Alignment from Exonerate_coding2genome GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTT gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCTTGgtcagtaacaccatcacttcattctgccaccctttcatctgatggtgcta Alignment from GeneWise GAGCTAAGTTATCAAGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATATTCTTT gggatagaatgcatggagtttaattgggccatgtgagttcctctcttcagGAACTTAGTTATCATGAAAGTCTCCACTGTGTTCAAACTGCTTTTCATGTTCTTGgtcagtaacaccatcacttcattctgccaccctttcatctgatggtgcta #### Npm3_ID9578_2 --> 2 - 0 Original Alignment gtTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG caggatgtgcctagaaggcgcttcctgcttcttgtccttttgatttgcaggt---------TCTGATCACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc Alignment from CESAR gtTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG gacttggttcaggatgtgcctagaatgcttcttgtccttttgatttgcaggt---------TCTGATCACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc Alignment from Spaln_aa2Genome GTTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG caggatgtgcctagaaggcgcttcctgcttcttgtccttttgatttgcagGTTCTGAT---------CACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc Alignment from Spaln_nt2Genome GTTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG caggatgtgcctagaaggcgcttcctgcttcttgtccttttgatttgcagGTTCTGA---------TCACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc Alignment from Pairagon GTTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG caggatgtgcctagaaggcgcttcctgcttcttgtccttttgatttgcagGTTCTGA---------TCACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc Alignment from Exonerate_protein2genome GTTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG caggatgtgcctagaaggcgcttcctgcttcttgtccttttGATTTGCAGGTTCTGATCACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGGTTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATG caggatgtgcctagaaggcgcttcctgcttcttgtccttttgatttgcagGT---------TCTGATCACACACGTTCATTCACTTTCAATGTTGCAGAGGAAGATGACACAGAGCAGGTGCTTGCGTTGAACATGgtaggtggtgcaagaaaatttggttcagcacacccttggtcttatctttc #### Nrxn2_ID1761_12 --> 2 - 1 Original Alignment gtAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGg gacttcctgctgatttctctattgcccttcttctacctcttcacctctaggt---------GAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGggtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from CESAR gtAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGg tgcataagagacttcctgctgatttccttcttctacctcttcacctctaggt---------GAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGggtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from Spaln_aa2Genome GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG gacttcctgctgatttctctattgcccttcttctacctcttcacctctagGT---------GAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGgtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from Spaln_nt2Genome GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG gacttcctgctgatttctctattgcccttcttctacctcttcacctctagGT---------GAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGgtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from Pairagon GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG gacttcctgctgatttctctattgcccttcttctacctcttcacctctagGT---------GAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGgtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from Exonerate_protein2genome CCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG gacttcctgctgatttctctattgcccttcttctacctcttcacctctagGTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGgtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from Exonerate_coding2genome CCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG gacttcctgctgatttctctattgcccttcttctacctcttcacctctagGTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGgtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt Alignment from GeneWise GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG gacttcctgctgatttctctattgcccttcttctacctcttcacctctagGT---------GAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGgtaggtggttgagactgcccctgtggttgggagtcctgctcaatctcatt #### Nudt22_ID1971_4 --> 1 - 0 Original Alignment gTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagg---AGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from CESAR gTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG gattatgggaatgcaacactatcctatactcttgttttgatcccctctagg---AGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from Spaln_aa2Genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagG---AGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from Spaln_nt2Genome CAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagGAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from Pairagon CAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagGAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from Exonerate_protein2genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagG---AGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from Exonerate_coding2genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagG---AGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac Alignment from GeneWise GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG tatgggaatgcaacactatcctagcatactcttgttttgatcccctctagG---AGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAAGCCCACGAATCTACAGGAATCATCTTTGTGGAAACGCAGgtaccagagtttagctctgtttggcacctggattatttaaggctattaac #### Nudt8_ID267_2 --> 1 - 0 Original Alignment tTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGATGTA---ATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTATGACCGG ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagtTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTTG---GTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCAT------gtgcgtttctagaagcttttcaggtgaggaagcttttcaatagaaaaagt Alignment from CESAR tTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGAT---GTAATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTATGACCGG ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagtTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTTG---GTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCAT------gtgcgtttctagaagcttttcaggtgaggaagcttttcaataga Alignment from Spaln_aa2Genome TTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGATGTAATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTAT ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagTTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTTGGTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCATgtgcgtttctagaagcttttcaggtgaggaagcttttcaatagaaaaagt Alignment from Spaln_nt2Genome TTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGATGT---AATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTAT ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagTTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTT---GGTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCATgtgcgtttctagaagcttttcaggtgaggaagcttttcaatagaaaaagt Alignment from Pairagon TTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGA---TGTAATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTAT ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagTTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTT---GGTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCATgtgcgtttctagaagcttttcaggtgaggaagcttttcaatagaaaaagt Alignment from Exonerate_protein2genome TTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGAT---GTAATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTATGACCGG ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagTTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTTG---GTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCATGTGCGTttctagaagcttttcaggtgaggaagcttttcaatagaaaaagt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TTTCCCAGGCGGTAAGTGTGATCCCGACGACCAAGATGTA---ATACATACGGCCCTTCGGGAGACTCAGGAGGAGCTGGGCCTAGAGGTGCCCAAGGAGCACGTGTGGGGTGTCCTGCAGCCAGTGTAT ttgattggtctaggccacgtaaacattatttcttgctgtttctcttacagTTTTCCAGGTGGTAAGTGTGACCCTGATGACCGAGATGTTGTAATACACACTGCACTGCAGGAGACACAAGAGGAGTTAGACTTG---GTACCCAAGGAGCAAGTCTGGGGAGTGTTGCAACCTGTGCATgtgcgtttctagaagcttttcaggtgaggaagcttttcaatagaaaaagt #### Nxf1_ID2345_5 --> 0 - 0 Original Alignment TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATC---CAGGATCGAGAAAACAGAAGG ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGA---gtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc Alignment from CESAR TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGAAGG ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGA---gtgagtagcgcagccaaaattagagaatggactggtcgtatctactt Alignment from Spaln_aa2Genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGA ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGAgtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc Alignment from Spaln_nt2Genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGA ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGAgtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc Alignment from Pairagon TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGA ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGAgtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc Alignment from Exonerate_protein2genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATCCAGGATCGAGAAAACAGAAGG ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGAgtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc Alignment from Exonerate_coding2genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATCCAGGATCGAGAAAACAGAAGG ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGAgtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc Alignment from GeneWise TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATC---CAGGATCGAGAAAACAGAAGG ttgagtagcctcatccggtgaggaatatagtgttcatcttctttcctcagTTTCATCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAAC---AGAgtgagtagcgcagccaaaattagagaatggactggtcgtatctacttttc #### Nxf1_ID2346_6 --> 0 - 0 Original Alignment ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAG--- caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from CESAR ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAG--- caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from Spaln_aa2Genome ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAG--- caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from Spaln_nt2Genome ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAGCTG caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from Pairagon ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAA---- caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from Exonerate_protein2genome ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAG--- caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from Exonerate_coding2genome ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAG--- caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg Alignment from GeneWise ATATCTATCATCATCAATGCTTCTGCTCCACCCTACACTGTACAGAATGAACTGAAGCCCGAACAAATAGAGCAGCTCAAGCTG caaatgtaaaaatgcagcaactgtcctgggtggtgctgttgattctacagATATCTATCATAATCAATACTTCTGCCCCGGCCTACACTGTGCAGAACAAAGTAGAGGCAGAACAAATAGAGCAGCTCAAACACgtaagcttgcatatgtctaccccctgaaatctctagggaaagttaaactg #### Nxf1_ID2347_7 --> 0 - 1 Original Alignment CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCTCAGACCCAg cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGC---------ggtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc Alignment from CESAR CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCTCAGACCCAg cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGC---------ggtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc Alignment from Spaln_aa2Genome CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGC- cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGCGgtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc Alignment from Spaln_nt2Genome CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCT-------------------------------CAGACCCAG cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGCGGTCAGTCATTGCCAGATCGCCCAATGAACAGATTATTGAGgtagtaaatc Alignment from Pairagon CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCTCAGACCCAG cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGC---------Ggtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc Alignment from Exonerate_protein2genome CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCT cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGCGgtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc Alignment from Exonerate_coding2genome CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCT cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGCGgtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc Alignment from GeneWise CTGATCATGAGCAAACGATATGATGGCAACCAACAAGCACTTGACCTCAAGGGGCTCCGCT cactaacctcaggttaaaagtgtctaggttttgttttttttaattttcagACTGTCATGAGCAAACAGTATGACAGTAATCAACAAGCACTGGACCTTAAGCAGCTTCGCGgtcagtcattgccagatcgcccaatgaacagattattgaggtagtaaatc #### Nxf1_ID2356_16 --> 2 - 0 Original Alignment cc---------CAGCGGTTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACA gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagccTGGTTTGACCAGCGATTCTGC---CTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAgtaagcgtctgcttgatggttatctgtttaattgagaccaaaaagtgagg Alignment from CESAR cc---------CAGCGGTTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACA gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagccTGGTTTGACCAGCGATTCTGC---CTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAgtaagcgtctgcttgatggttatctgtttaattgagaccaaaaagtgagg Alignment from Spaln_aa2Genome TTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACA gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagcctggtttgaccagCGATTCTGCCTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAgtaagcgtctgcttgatggttatctgtttaattgagaccaaaaagtgagg Alignment from Spaln_nt2Genome CC---------CAGCGGTTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACA gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagCCTGGTTTGACCAGCGATTCTG---CCTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAgtaagcgtctgcttgatggttatctgtttaattgagaccaaaaagtgagg Alignment from Pairagon C---------CCAGCGGTTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACA gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagCCTGGTTTGACCAGCGATTCTG---CCTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAgtaagcgtctgcttgatggttatctgtttaattgagaccaaaaagtgagg Alignment from Exonerate_protein2genome CCCAGCGGTTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACAAGCACATTACTGTGTTTTTCTGTCAATGGAGTCTTCAAGGAAG gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagcctggtttgACCAGCGATTC---TGCCTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAGTAAGC---GTCTGCTTGATGGTTATCTGTTTAATTGAGACCAaaaagtg Alignment from Exonerate_coding2genome gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagcctggtttgaccagcgattctgcctaaagcatacacgtttgaatgtagttgcctttcttaatgctttacccaaaactcaacatgacgtcaatgcatttgtagtagacataagtgcacagacagtaagcgtctgcttgatggttatctgtttaattgagaccaaaaagtgagg Alignment from GeneWise --------ACCCAGCGGTTCCGACTCTTAAAGCATACACGTCTTAATGTCGTTGCCTTCCTCAATGAGTTACCCAAAACTCAACATGACGTTAACGCCTTCGTGGTAGATATAAGTGCCCAAACAAGCACATTACTGTGTTTTTCTGTC- gaatttaggggtttaattctaaagcttgttttgtccctttattttttcagCCTGGTTTGACCAGCGATTC---TGCCTAAAGCATACACGTTTGAATGTAGTTGCCTTTCTTAATGCTTTACCCAAAACTCAACATGACGTCAATGCATTTGTAGTAGACATAAGTGCACAGACAGTAAGCGTCTGCTTGATGGTTATCTgtttaattgagaccaaaaagtgagg #### Opalin_ID8090_5 --> 0 - 0 Original Alignment GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctag------GAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCCA---ATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from CESAR GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgcatatgagtatcactcttttggaatcatcaacttctgtctctcctag------GAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCCA---ATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from Spaln_aa2Genome GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctag------GAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCCA---ATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from Spaln_nt2Genome GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctag------GAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCC---AATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from Pairagon GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctag------GAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCC---AATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from Exonerate_protein2genome GAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctagGAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCCA---ATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from Exonerate_coding2genome GAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctagGAGATCCCATGTGAAATTGCAGAGCTCTTTGACAATCCA---ATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata Alignment from GeneWise ---CCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG atgagtatcactcttttggatagttaatcatcaacttctgtctctcctaggagATCCCATGTGAAATTGCAGAGCTCTTTGACAATCCA---ATATCTGAGgtcagtgtacgtgacagcttgtaagtactgatatgcttgtcagacaaata #### Otub1_ID2060_6 --> 0 - 0 Original Alignment ---------TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagCAATTTGCGTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAA---------------AGTCAGGAGgtaaggcctaccccagcacctgtactgaggccttcctttttttagtatga Alignment from CESAR ---------TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagCAATTTGCGTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGT---------------CAGGAGgtaaggcctaccccagcacctgtactgaggccttcctttttttagtatga Alignment from Spaln_aa2Genome ---------TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCA gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagCAATTTGCGTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTAAGGCCTACCCCAgcacctgtactgaggccttcctttttttagtatga Alignment from Spaln_nt2Genome CGTTCATGGA-------CCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACT-----GTTAAGGAGTTCTGCCAGCAG-- gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagCAATTTGCGTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTAAGGCCTAC-CCCAGCACCTgtactgaggccttcctttttttagtatg Alignment from Pairagon ---------------------------------------------------------CGTTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG GACCATCTCAATACTTTGTCATACCCTGTATTTTGCCTTTTCTTTTGAAGCAATTTGCGTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAA---------------GTCAGGAGgtaaggcctaccccagcacctgtactgaggccttcctttttttagtatga Alignment from Exonerate_protein2genome TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagcaatttgcgTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTAAGGCCTACCCCAgcacctgtactgaggccttcctttttttagtatga Alignment from Exonerate_coding2genome TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagcaatttgcgTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTAAGGCCTACCCCAgcacctgtactgaggccttcctttttttagtatga Alignment from GeneWise ---------TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG gaccatctcaatactttgtcataccctgtattttgccttttcttttgaagCAATTTGCGTTCATGGATTTTATTGAGCGTGTGGAGAAGAAGACCTCTGTTGCTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGCTAACCTCAGGCTATGTCCAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGT---------------CAGGAGgtaaggcctaccccagcacctgtactgaggccttcctttttttagtatga #### Pacs1_ID876_18 --> 2 - 2 Original Alignment agCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAGGCATAAGtt tttgaggtatactggaacactactcttactaatgtgttttgctttttcagaaCCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGC---------ttgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from CESAR agCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAGGCATAAGtt tttgaggtatactggaacactactcttactaatgtgttttgctttttcagaaCCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGC---------ttgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from Spaln_aa2Genome AGCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAG tttgaggtatactggaacactactcttactaatgtgttttgctttttcagAACCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGCTTgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from Spaln_nt2Genome AGCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAG tttgaggtatactggaacactactcttactaatgtgttttgctttttcagAACCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGCTTgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from Pairagon AGCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAGGCATAAGTT tttgaggtatactggaacactactcttactaatgtgttttgctttttcagAACCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGC---------TTgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from Exonerate_protein2genome AGCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAG tttgaggtatactggaacactactcttactaatgtgttttgctttttcagAACCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGCTTgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from Exonerate_coding2genome tttgaggtatactggaacactactcttactaatgtgttttgctttttcagaaccactagatgtggtgggtcatgtgatgctgtacatcaatggttctataacaacacaccagcttcctatcacagaagctatgctgacctgcttgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact Alignment from GeneWise AGCCACTGGACGTGGTGGGTCGTGTGATGCAGTATGTCAATGGAGCTACCACAACACACCAGCTGCCTGTGGCTGAAGCCATGTTGACCTGCAG tttgaggtatactggaacactactcttactaatgtgttttgctttttcagAACCACTAGATGTGGTGGGTCATGTGATGCTGTACATCAATGGTTCTATAACAACACACCAGCTTCCTATCACAGAAGCTATGCTGACCTGCTTgtgggtccacaggggagctgatgagaactttcaggagaccaggttacact #### Pacs1_ID877_17 --> 2 - 1 Original Alignment gtTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCAGTGTCA---------g atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcaggcTCACATCCTGTAGCC------ATAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGGTGTCATACGTTGACggtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from CESAR gtTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCAGTGTCA---------g atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcaggcTCACATCCTGTAGCC------ATAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGGTGTCATACGTTGACggtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from Spaln_aa2Genome GTTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCAGTGTCA---------G atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcagGCTCACATCCTGTAGCC------ATAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGGTGTCATACGTTGACGgtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from Spaln_nt2Genome GTTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCAGTGTCA---------G atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcagGCTCACATCCTGTAGCCA------TAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGGTGTCATACGTTGACGgtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from Pairagon GTTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCAGTGTCA---------G atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcagGCTCACATCCTGTAGCCA------TAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGGTGTCATACGTTGACGgtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from Exonerate_protein2genome GTTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCA atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcagGCTCACATCCTGTAGCC------ATAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGgtgtcatacgttgacggtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from Exonerate_coding2genome atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcaggctcacatcctgtagccataggctctgtggacagcaggtatagcagtacttttctagatcctgcatcaaaagatctattcagccagtcagagcccctggtgtcatacgttgacggtgggtcccattagtagcagtttgctacctttggtactatctcctatgac Alignment from GeneWise GTTCTCATCCAGTGGCCAAATACTTGGGCTCAGTAGATAGTAGATATAGCAGCACCTTTCTTGATTCTGCCTGGAGAGACCTATTCAGTCGCTCAGAGCCTCCAGTGTCA---------G atgctaattgtatgtttggaatgagtaacattccctgttcctgtgtgcagGCTCACATCCTGTAGCC------ATAGGCTCTGTGGACAGCAGGTATAGCAGTACTTTTCTAGATCCTGCATCAAAAGATCTATTCAGCCAGTCAGAGCCCCTGGTGTCATACGTTGACGgtgggtcccattagtagcagtttgctacctttggtactatctcctatgac #### Pacs1_ID881_13 --> 1 - 0 Original Alignment c---AAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagtGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from CESAR c---AAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagtGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from Spaln_aa2Genome C----AAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagTGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from Spaln_nt2Genome CAAGGTGGA---AGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagTGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from Pairagon ---CAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagTGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from Exonerate_protein2genome C---AAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagTGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from Exonerate_coding2genome C---AAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagTGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac Alignment from GeneWise -AGCAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcccccatccactcttctgtccaacagTGCCAAGGTGGAAGGGACACACACACCTCCACAGAAAAGAAGTACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAACGAACTAATAGTGCTGACAGTGAGAAGTCACCAGATCTGGGCCACAGCATACAGgtgggagtgttgtggttgatgcttttggaaaactaagtgattgaagttac #### Pacs1_ID888_6 --> 2 - 0 Original Alignment atCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagac---GCCCCAGACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from CESAR atCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG accggattttgttaaactctcctgcaaatccctccctccctccctcccagac---GCCCCAGACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from Spaln_aa2Genome ATCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagACGCCCCAGACATC---GACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from Spaln_nt2Genome ATCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagA---CGCCCCAGACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from Pairagon ATCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagA---CGCCCCAGACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from Exonerate_protein2genome ATCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagAC---GCCCCAGACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from Exonerate_coding2genome ATCGCTCCCCAGATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagAC---GCCCCAGACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac Alignment from GeneWise ATATTGACAACTACTCTGAAGAAGAGGAGGAAAGCTTCTCCTCAGAGCAGGAAGGCAGTGACGACCCATTGCATGGGCAG ggattttgttaaactctcctgcagtaaatccctccctccctccctcccagacgccccagACATCGACAATTATTCAGAGGAGGAGGAGGAAAGCTTCTTCTCAGCACAGGATGACACTGATGAACCACTGCATGGACAAgtaagtatttgacagtgtggcagtgtacaatttgaaacagggtgaggcac #### Pcgf6_ID10082_5 --> 2 - 1 Original Alignment gaGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCT------g ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagaaGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCATCGGggtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from CESAR gaGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCT------g ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagaaGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCATCGGggtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from Spaln_aa2Genome GAGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCT------G ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagAAGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCATCGGGgtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from Spaln_nt2Genome GAGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCT------G ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagAAGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCATCGGGgtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from Pairagon GAGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCT------G ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagAAGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCATCGGGgtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from Exonerate_protein2genome GAGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCTG ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagAAGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCatcggggtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from Exonerate_coding2genome GAGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCTG ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagAAGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCatcggggtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa Alignment from GeneWise GAGAAAAAAAGCAAATGCATGACTTCTATAAAGAAAGAGGTCTAGAAGTCCCCAAGCCT------G ggccataggtgaagcattctgtgtgcatatattcttgttctctcccccagAAGAAAAGAAACAAATGCATGACTTCTATAAAGAAAGAGGTCTTGAAGTCCCAAAGCCTCATCGGGgtatgtagggctgtttcttcttgtttggatgtgttttgacagaccaataa #### Pcgf6_ID10084_3 --> 2 - 2 Original Alignment tt---------------TGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAag tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagttTGGACTTTTCCAATGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAaggtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from CESAR tt---------------TGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAag tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagttTGGACTTTTCCAATGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAaggtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from Spaln_aa2Genome TT---------------TGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAAG tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagTTTGGACTTTTCCAATGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAAGgtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from Spaln_nt2Genome TTTG---------------TAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAAG tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagTTTGGACTTTTCCAATGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAAGgtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from Pairagon TT---------------TGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAAG tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagTTTGGACTTTTCCAATGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAAGgtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from Exonerate_protein2genome TTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAAG tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagtttggacttttccaaTGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAAGgtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from Exonerate_coding2genome TTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAAG tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagtttggacttttccaaTGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAAGgtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc Alignment from GeneWise --------------TTTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGTAACAGATGCCCAAAATGCAACATAGTTGTCCACCAGACTCAGCCTCTTTATAATATAAG tataatattaagtaacaatcataaagtaacccttggcctgctgcccacagTTTGGACTTTTCCAATGTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAATAGATGCCCAAAGTGCAACATAGTTGTCCACCAAACTCAGCCTCTTTATAATATAAGgtgagtaggtatggacctgcttcaaactatttcgttcattgttacagtcc #### Pcnxl3_ID1159_34 --> 2 - 0 Original Alignment gcAGCAGTGAGCAGCCCCTCCCACCAGGTCCTAGCTGGGGACCACGGCCTTCCCTCAGTGGCTCTGGTGATGGGCGGCCCCCTCCTCTGCTGCAGTGGCCTCCCCCTCGGCTCCCTGGACCACCCCCTGCTTCACCTGCTCCCACTGAGGGTCCCCGGCCCTCAAGACCTTCTGGCCCTGCTCTCCTCAATTCTGAGGGACCCAGTGGGAAGTGGAGTCTGGGGGGTCGGAAGGGACTGGGAGGACCTGATGGGGAGCCAGCCTCAGGGAGCCCCAAAGGAGGCACCCCCAAATCTCAG agactgcaagcgccatagactggccgggttttgtggacttatgcttgcaggc------------------------------AGCTGGGGACCAAGGCCCTCACTAATTGGCTCTGGAGATGGGCAGCCCCGTTCTCTTTTACAGTGGCCGCCCCCTCGGCTCCAAGGACCACCTCCAGTTTCACCTGTCCCCACTGATGGACCTCAGCCCTCACGACTTTCGGGCCCTGCTCTCCTTAATTCAGAGGGACCCAGTGGGAAGTGGAGTTTGGGGGGTCAGAAGGGCCTGGAAGGATCTGATGGGGAACCTGCTTCTGGGAGCCCAAAAGGTGGTAGACCCAAGTCTCAGgtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from CESAR gcAGCAGTGAGCAGCCCCTCCCACCAGGTCCTAGCTGGGGACCACGGCCTTCCCTCAGTGGCTCTGGTGATGGGCGGCCCCCTCCTCTGCTGCAGTGGCCTCCCCCTCGGCTCCCTGGACCACCCCCTGCTTCACCTGCTCCCACTGAGGGTCCCCGGCCCTCAAGACCTTCTGGCCCTGCTCTCCTCAATTCTGAGGGACCCAGTGGGAAGTGGAGTCTGGGGGGTCGGAAGGGACTGGGAGGACCTGATGGGGAGCCAGCCTCAGGGAGCCCCAAAGGAGGCACCCCCAAATCTCAG aaaattatgaactgaaatgttggccgggttttgtggacttatgcttgcaggc------------------------------AGCTGGGGACCAAGGCCCTCACTAATTGGCTCTGGAGATGGGCAGCCCCGTTCTCTTTTACAGTGGCCGCCCCCTCGGCTCCAAGGACCACCTCCAGTTTCACCTGTCCCCACTGATGGACCTCAGCCCTCACGACTTTCGGGCCCTGCTCTCCTTAATTCAGAGGGACCCAGTGGGAAGTGGAGTTTGGGGGGTCAGAAGGGCCTGGAAGGATCTGATGGGGAACCTGCTTCTGGGAGCCCAAAAGGTGGTAGACCCAAGTCTCAGgtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from Spaln_aa2Genome CCCACCAGGTC CTAGCTGGGGACCACGGCCTTCCCTCAGTGGCTCTGGTGATGGGCGGCCCCCTCCTCTGCTGCAGTGGCCTCCCCCTCGGCTCCCTGGACCACCCCCTGCTTCACCTGCTCCCACTGAGGGTCCCCGGCCCTCAAGACCTTCTGGCCCTGCTCTCCTCAATTCTGAGGGACCCAGTGGGAAGTGGAGTCTGGGGGGTCGGAAGGGACTGGGAGGACCTGATGGGGAGCCAGCCTCAGGGAGCCCCAAAGGAGGCACCCCCAAATCTCAG AGACTGCAAGCgccatagactggccgggttttgtggacttatgcttgcagGCAGCTGGGGACCAAGGCCCTCACTAATTGGCTCTGGAGATGGGCAGCCCCGTTCTCTTTTACAGTGGCCGCCCCCTCGGCTCCAAGGACCACCTCCAGTTTCACCTGTCCCCACTGATGGACCTCAGCCCTCACGACTTTCGGGCCCTGCTCTCCTTAATTCAGAGGGACCCAGTGGGAAGTGGAGTTTGGGGGGTCAGAAGGGCCTGGAAGGATCTGATGGGGAACCTGCTTCTGGGAGCCCAAAAGGTGGTAGACCCAAGTCTCAGgtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from Spaln_nt2Genome AGGTC CTAGCTGGGGACCACGGCCTTCCCTCAGTGGCTCTGGTGATGGGCGGCCCCCTCCTCTGCTGCAGTGGCCTCCCCCTCGGCTCCCTGGACCACCCCCTGCTTCACCTGCTCCCACTGAGGGTCCCCGGCCCTCAAGACCTTCTGGCCCTGCTCTCCTCAATTCTGAGGGACCCAGTGGGAAGTGGAGTCTGGGGGGTCGGAAGGGACTGGGAGGACCTGATGGGGAGCCAGCCTCAGGGAGCCCCAAAGGAGGCACCCCCAAATCTCAG AGACTgcaagcgccatagactggccgggttttgtggacttatgcttgcagGCAGCTGGGGACCAAGGCCCTCACTAATTGGCTCTGGAGATGGGCAGCCCCGTTCTCTTTTACAGTGGCCGCCCCCTCGGCTCCAAGGACCACCTCCAGTTTCACCTGTCCCCACTGATGGACCTCAGCCCTCACGACTTTCGGGCCCTGCTCTCCTTAATTCAGAGGGACCCAGTGGGAAGTGGAGTTTGGGGGGTCAGAAGGGCCTGGAAGGATCTGATGGGGAACCTGCTTCTGGGAGCCCAAAAGGTGGTAGACCCAAGTCTCAGgtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from Pairagon GCAGCAGTGAGCAGCCCCTCCCACCAGGTCCTAGCTGGGGACCACGGCCTTCCCTCAGTGGCTCTGGTGATGGGCGGCCCCCTCCTCTGCTGCAGTGGCCTCCCCCTCGGCTCCCTGGACCACCCCCTGCTTCACCTGCTCCCACTGAGGGTCCCCGGCCCTCAAGACCTTCTGGCCCTGCTCTCCTCAATTCTGAGGGACCCAGTGGGAAGTGGAGTCTGGGGGGTCGGAAGGGACTGGGAGGACCTGATGGGGAGCCAGCCTCAGGGAGCCCCAAAGGAGGCACCCCCAAATCTCAG agactgcaagcgccatagactggccgggttttgtggacttatgcttgcagGC------------------------------AGCTGGGGACCAAGGCCCTCACTAATTGGCTCTGGAGATGGGCAGCCCCGTTCTCTTTTACAGTGGCCGCCCCCTCGGCTCCAAGGACCACCTCCAGTTTCACCTGTCCCCACTGATGGACCTCAGCCCTCACGACTTTCGGGCCCTGCTCTCCTTAATTCAGAGGGACCCAGTGGGAAGTGGAGTTTGGGGGGTCAGAAGGGCCTGGAAGGATCTGATGGGGAACCTGCTTCTGGGAGCCCAAAAGGTGGTAGACCCAAGTCTCAGgtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from Exonerate_protein2genome agactgcaagcgccatagactggccgggttttgtggacttatgcttgcaggcagctggggaccaaggccctcactaattggctctggagatgggcagccccgttctcttttacagtggccgccccctcggctccaaggaccacctccagtttcacctgtccccactgatggacctcagccctcacgactttcgggccctgctctccttaattcagagggacccagtgggaagtggagtttggggggtcagaagggcctggaaggatctgatggggaacctgcttctgggagcccaaaaggtggtagacccaagtctcaggtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from Exonerate_coding2genome agactgcaagcgccatagactggccgggttttgtggacttatgcttgcaggcagctggggaccaaggccctcactaattggctctggagatgggcagccccgttctcttttacagtggccgccccctcggctccaaggaccacctccagtttcacctgtccccactgatggacctcagccctcacgactttcgggccctgctctccttaattcagagggacccagtgggaagtggagtttggggggtcagaagggcctggaaggatctgatggggaacctgcttctgggagcccaaaaggtggtagacccaagtctcaggtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac Alignment from GeneWise ----------------------------------CCCCTCCCACCAGGTCCTAGCTGGGGACCACGGCCTTCCCTCAGTGGCTCTGGTGATGGGCGGCCCCCTCCTCTGCTGCAGTGGCCTCCCCCTCGGCTCCCTGGACCACCCCCTGCTTCACCTGCTCCCACTGAGGGTCCCCGGCCCTCAAGACCTTCTGGCCCTGCTCTCCTCAATTCTGAGGGACCCAGTGGGAAGTGGAGTCTGGGGGGTCGGAAGGGACTGGGAGGACCTGATGGGGAGCCAGCCTCAGGGAGCCCCAAAGGAGGCACCCCCAAATCTCAG AGACTGCAAGCGCCATAGACTGGCCGGGTTTTGTGGACTTATGCTTGCAGGCAGCTGGGGACCAAGGCCCTCACTAATTGGCTCTGGAGATGGGCAGCCCCGTTCTCTTTTACAGTGGCCGCCCCCTCGGCTCCAAGGACCACCTCCAGTTTCACCTGTCCCCACTGATGGACCTCAGCCCTCACGACTTTCGGGCCCTGCTCTCCTTAATTCAGAGGGACCCAGTGGGAAGTGGAGTTTGGGGGGTCAGAAGGGCCTGGAAGGATCTGATGGGGAACCTGCTTCTGGGAGCCCAAAAGGTGGTAGACCCAAGTCTCAGgtgggcaggacctcatggtaaagaggcgtcctcagtgacaaggtggttac #### Pcnxl3_ID1160_33 --> 1 - 1 Original Alignment a---CTTCATAAG---GGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAg tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcaggGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAggtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg Alignment from CESAR a---CTTCAT---AAGGGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAg tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcaggGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAggtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggcaa Alignment from Spaln_aa2Genome A---CTTCAT---AAGGGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAG tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcagGGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAGgtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg Alignment from Spaln_nt2Genome GAGACTTCATAAG---GGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAG tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcagGGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAGgtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg Alignment from Pairagon GAGACTTCAT---AAGGGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAG tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcagGGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAGgtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg Alignment from Exonerate_protein2genome GGAGAGACTTCATAAGGGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAG tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcagGGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAGgtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg Alignment from Exonerate_coding2genome tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcagggaacttcataagaagggttgtggtgccggctgcaatagtggaggtaatcttgatgatgcagattgtggtcggggtggtggcttggcttccctcggcaaccatcctcccttggttcaccctacgccagacaatgtggcaggtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg Alignment from GeneWise -AGACTTCATAAG---GGCTGTGGCGCTGGCTGTAATAGCGGAGGGAATGTGGATGACTCGGACTGTGGTGGGGGTGGCGGCCTGACCTCCCTCAGCAATCATCCGCCCTTGGCACACCCTACGCCTGAAAATGCAGCAG tatgtttacgtgcttcacctcatgcagcgactcttctggtggtctttcagGGAACTTCATAAGAAGGGTTGTGGTGCCGGCTGCAATAGTGGAGGTAATCTTGATGATGCAGATTGTGGTCGGGGTGGTGGCTTGGCTTCCCTCGGCAACCATCCTCCCTTGGTTCACCCTACGCCAGACAATGTGGCAGgtagaggcaagatcttaagaaaattatgaactgaaatgttggccgggatg #### Pcnxl3_ID1163_30 --> 1 - 0 Original Alignment cCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT------CACCAG cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagcTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCAT---gtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttgt Alignment from CESAR cCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT---CACCAG cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagcTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATgtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttcc Alignment from Spaln_aa2Genome CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT---CACCAG cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagCTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATgtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttgt Alignment from Spaln_nt2Genome CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTTCACCAG--- cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagCTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATgtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttgt Alignment from Pairagon CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTTCAC-------------------------------------------------------- cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagCTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATGTAAGAAGCATAATTGAGCAGTGTAGGAGCAGGTGTCTCCTTTACCTTGT Alignment from Exonerate_protein2genome CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT---CACCAG cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagCTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATgtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttgt Alignment from Exonerate_coding2genome cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagcttagagcccttcctgtatgacctgcgagctctgtttaagggagatttcaggatcacctctccccgtgatgagtgggacatagatttattgcaccaggttgtggcaccaggggtacgtatggccctaaagcttcatcatcatgtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttgt Alignment from GeneWise CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTTCACCAGGAC cctcaatgatcctttgaaatggagaggcttctccttttttcctattccagCTTAGAGCCCTTCCTGTATGACCTGCGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCTCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATgtaagaagcataattgagcagtgtaggagcaggtgtctcctttaccttgt #### Pcnxl3_ID1168_25 --> 1 - 1 Original Alignment cACTAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAg tacaaggcagcaggtaactcatgttttttcacttatttattgcctcccagt---AAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAggtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from CESAR cACTAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAg tcttacaaggcagcaggtaactcatttttcacttatttattgcctcccagt---AAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAggtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from Spaln_aa2Genome CACTAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAG tacaaggcagcaggtaactcatgttttttcacttatttattgcctcccagT---AAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAGgtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from Spaln_nt2Genome CAC TAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAG tacaaggcagCAGgtaactcatgttttttcacttatttattgcctcccagTAAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAGgtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from Pairagon CACTAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAG tacaaggcagcaggtaactcatgttttttcacttatttattgcctcccag---TAAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAGgtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from Exonerate_protein2genome CACTAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAG tacaaggcagcaggtaactcatgttttttcacttatttattgcctcccagT---AAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAGgtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from Exonerate_coding2genome tacaaggcagcaggtaactcatgttttttcacttatttattgcctcccagtaaacctgtagaccactctaacactcggcttgtgacacaactggaccggaatccaggtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt Alignment from GeneWise CACTAAACGTGTGGACCATTCTAACACTCGCCTAGTGACACAGCTGGACCGGAACCCAG tacaaggcagcaggtaactcatgttttttcacttatttattgcctcccagT---AAACCTGTAGACCACTCTAACACTCGGCTTGTGACACAACTGGACCGGAATCCAGgtaagttacagctggccccagttctgaaagcaacacaatgcacttacttt #### Pcnxl3_ID1178_15 --> 2 - 1 Original Alignment GTGGCCACTg tg------TTCACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAg GTGGCAACTggtgaggcacctcaagataattgtttcttttgtttcatcagtaTTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAggtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from CESAR GTGGCCACTg tg------TTCACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAg GTGGCAACTggtgagtcacctcaagataattgtttcttttgtttcatcagtaTTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAggtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from Spaln_aa2Genome GTGGCCACTG TG------TTCACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAG GTGGCAACTGgtgaggcacctcaagataattgtttcttttgtttcatcagTATTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAGgtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from Spaln_nt2Genome GTGGCCACTG TGTT------CACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAG GTGGCAACTGgtgaggcacctcaagataattgtttcttttgtttcatcagTATTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAGgtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from Pairagon GTGGCCACTGT----------------------------------------------GTTCACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAG GTGGCAACTGGTGAGGCACCTCAAGATAATTGTTTCTTTTGTTTCATCAGTATTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAGgtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from Exonerate_protein2genome GTGGCCACTG TG------TTCACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAG GTGGCAACTGgtgaggcacctcaagataattgtttcttttgtttcatcagTATTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAGgtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from Exonerate_coding2genome gtggcaactggtgaggcacctcaagataattgtttcttttgtttcatcagtattgaatttcaccttatgctttccctttgtcttcctgctggggctcctgcctcaggtcaacacctgcctgacatacctctcggaacaaattgatatgcatggttttggaggcacaggtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat Alignment from GeneWise GTGGCCACT- -----GTGTTCACCTTATGCTTTCCGTTCGTCTTCCTCCTGGGCCTCCTGCCCCAGGTCAACACCTGCCTCATGTACCTCCTGGAGCAGATAGACATGCATGGCTTTGGAGGCACAG GTGGCAACTGgtgaggcacctcaagataattgtttcttttgtttcatcagTATTGAATTTCACCTTATGCTTTCCCTTTGTCTTCCTGCTGGGGCTCCTGCCTCAGGTCAACACCTGCCTGACATACCTCTCGGAACAAATTGATATGCATGGTTTTGGAGGCACAGgtgagatgtgctcggaaaggtctaggccatgaatattacatgtaccaaat #### Pcnxl3_ID1188_5 --> 2 - 1 Original Alignment acATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAACTGa gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagacATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAA---agtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from CESAR acATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAACTGa gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagacATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAA---agtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from Spaln_aa2Genome ACATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAA- gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagACATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAAAgtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from Spaln_nt2Genome ACATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAACTGA gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagACATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAA---Agtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from Pairagon ACATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAACTGA gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagACATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAA---Agtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from Exonerate_protein2genome ACATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAAC gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagACATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAAAgtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from Exonerate_coding2genome CCAGGTTTCGGAGTTGCTGCCCCGGATGGAGGATTCTGGGCCCCTCAGAGACATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAAC GCAATACAAAGAGGAAATGGCATGACAAGTCTTTTTGTTTTTTAAACAAGACATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAAAgtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa Alignment from GeneWise ACATCAAGGAGCTGGTACGGGAACAGGGCAGCAACAACGTGATCGTGACCTCTGCCGATCGAGAAATGCTGAAGCTCAGCTCCCAAGAGAAAC gcaatacaaagaggaaatggcatgacaagtctttttgttttttaaacaagACATTAAAGAGCTGGTACGGGAGCAGAGCAGTAACAATATAATTGTTACGTCTGCAGGCCGTGAAATGCTGAGGCTCAGCTCTAAGGAGAAAAgtatgtagttgaaatgttggaagctgttcttaaagggtgaacacccttaa #### Pcx_ID553_3 --> 2 - 0 Original Alignment gt---------GAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggagggggtctttcttctctcctcactcaggtCTTATTCATGAGATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from CESAR gt---------GAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggagggggtctttcttctctcctcactcaggtCTTATTCATGAGATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from Spaln_aa2Genome GTGAGATTGCCATC---------CGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggagggggtctttcttctctcctcactcagGTCTTATTCATGAGATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from Spaln_nt2Genome GT---------GAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggagggggtctttcttctctcctcactcagGTCTTATTCATGAGATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from Pairagon ------------------------------------------------------------TGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG TGGTGGTTCCTATCCCCAGGGGAGGGGGTCTTTCTTCTCTCCTCACTCAGGTCTTATTCATGAGATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from Exonerate_protein2genome GT---------GAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggagggggtctttcttctctcctcactcagGTCTTATTCATGAGATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from Exonerate_coding2genome tggtggttcctatccccaggggagggggtctttcttctctcctcactcaggtcttattcatgagattgctatccgcgtctttcgtgcttgcagagaacttggcatccgcacagtagctgtgtattcagaacaggatacagggctaacacacaggcagaaaacagatgagggttaccttcttggtcgtggccttgcacctgtccaaacctatttgcacattccagacatcattagggtttcgaaggtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt Alignment from GeneWise ---GCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggagggggtctttcttctctcctcactcaggtcttattcatgagATTGCTATCCGCGTCTTTCGTGCTTGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCAGAACAGGATACAGGGCTAACACACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTTGCACCTGTCCAAACCTATTTGCACATTCCAGACATCATTAGGGTTTCGAAGgtgagaatcaattatctttacagggggagagaaaagtcccactcatttgt #### Pcx_ID554_4 --> 0 - 1 Original Alignment GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCA---------------------------g attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAACA---GACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAACGATGCAGTGGCTCTGCGAGTACACggtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from CESAR GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCA---------------------------g attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAACA---GACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAACGATGCAGTGGCTCTGCGAGTACACggtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from Spaln_aa2Genome GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATC---GCTGCAG attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAACA---GACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAACGatgcagtggctctgcgagtacacggtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from Spaln_nt2Genome GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCAGGCGTTCCAGTGG-TCCCCG-GCACG-G attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAA---CAGACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAACGATGCAGTGGCTCTGCGAGTACACGgtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from Pairagon GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCAGGCGTTCCAGTGG--------------- attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAAC---AGACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAACGATGCAGTGGCTCTGCGAGTACACGgtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from Exonerate_protein2genome GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCAG attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAACA---GACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAacgatgcagtggctctgcgagtacacggtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from Exonerate_coding2genome attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacaggaaaatggtgaagatgcagtgcatccaggttatggttttctctctgagcaggcggattttgcccaggcctgccaggacactggagtccgattcattggaccaagcccagaggtgatacttaaaacagacagggtagaagcccaggctgttgccatagatgcaaacgatgcagtggctctgcgagtacacggtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt Alignment from GeneWise GAAAATGGTGTAGATGCGGTGCATCCTGGCTATGGGTTCCTCTCAGAGCGAGCAGACTTTGCCCAGGCCTGCCAAGATGCTGGAGTCCGGTTCATTGGTCCAAGCCCAGAGGTGGTCCGCAAGATGGGAGACAAGGTGGAAGCCCGGGCCATTGCCATCGCTGCA---------------------------G attgcacatgtcagatcaatgaacacttctctgttttcttcttcaaacagGAAAATGGTGAAGATGCAGTGCATCCAGGTTATGGTTTTCTCTCTGAGCAGGCGGATTTTGCCCAGGCCTGCCAGGACACTGGAGTCCGATTCATTGGACCAAGCCCAGAGGTGATACTTAAAACA---GACAGGGTAGAAGCCCAGGCTGTTGCCATAGATGCAAACGATGCAGTGGCTCTGCGAGTACACGgtaagttaccaaacagaacattaaatttaaatcaggagtacaggtgtttt #### Pcx_ID555_5 --> 2 - 0 Original Alignment gcGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcaggtGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTAT---GATGGAGGTCATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from CESAR gcGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcaggtGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTAT---GATGGAGGTCATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from Spaln_aa2Genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTAT---GATGGAGGTCATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from Spaln_nt2Genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGG-CTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCT-TTATTTTCAATGCAGCTTA---TGATGGAGGTCATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from Pairagon GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTAT---GATGGAGGTCATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from Exonerate_protein2genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTAT---GATGGAGGTCATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from Exonerate_coding2genome aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcaggtgccccggtagttcctggaacagagtcccccatcagctccctatatgaagcccatgagttcactaacacctatgatcctccctttattttcaatgcagcttatgatggaggtcatgacatgagggttgtgcagagctatgagtacaaggtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat Alignment from GeneWise GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG------ aatttaaatcaggagtacaggtgttttgtttcttttcttcctgttttcagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCACTAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGATGGAGGT---CATGACATGAGGGTTGTGCAGAGCTATGAGTACAAGgtaggaagggcagcaaagggtagggtggtcatggcagggccagtgtttat #### Pcx_ID563_12 --> 2 - 1 Original Alignment gaCATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAg ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcagga---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAggtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc Alignment from CESAR gaCATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAg actctttgaaattgggaaaacagtgtgtgttgttttgtactttctttcagga---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAggtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc Alignment from Spaln_aa2Genome GACATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAG ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcagGA---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAGgtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc Alignment from Spaln_nt2Genome GACATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAG ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcagGA---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAGgtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc Alignment from Pairagon GACATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAG ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcagGA---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAGgtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc Alignment from Exonerate_protein2genome GACATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAG ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcagGA---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAGgtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc Alignment from Exonerate_coding2genome GACATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGC ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcaggagttatggtcaatggacctatctcaccaatcccagtcaatgtgacgcctagtcctgtagatgctgctgttccagcagtccctatagGTAAGGTATAATATACCTTCTGAGTGAGAAGGTGTGTCAGAGACAGCATC Alignment from GeneWise GACATGTCATGGTGAATGGCCCTACCACTCCAATCCCTGTCAATGTGAGCCCCAGTCCTGTGGATCCTGCTGTTCCTGTGGTGCCCATAG ctttgaaattgggaaaacagtgaaatgtgttgttttgtactttctttcagGA---GTTATGGTCAATGGACCTATCTCACCAATCCCAGTCAATGTGACGCCTAGTCCTGTAGATGCTGCTGTTCCAGCAGTCCCTATAGgtaaggtataatataccttctgagtgagaaggtgtgtcagagacagcatc #### Pcx_ID568_17 --> 0 - 0 Original Alignment GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG--------- tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGTTCCAACTTgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct Alignment from CESAR GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG--------- tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGTTCCAACTTgtgagttaggttgatgtggagtaaatcagtctttaaagctgcggctcttc Alignment from Spaln_aa2Genome GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG--------- tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGTTCCAACTTgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct Alignment from Spaln_nt2Genome GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAA tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAgttccaacttgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct Alignment from Pairagon GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG--------- tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGTTCCAACTTgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct Alignment from Exonerate_protein2genome GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGttccaacttgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct Alignment from Exonerate_coding2genome GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGttccaacttgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct Alignment from GeneWise GTGACACCATCCTCCAAGATTGTGGGGGACCTGGCCCAGTTCATGGTGCAGAATGGGTTGAGCCGGGCAGAGGCAGAAGCTCAGGCAGAAGAGCTGTCCTTCCCCCGCTCTGTGGTGGAGTTCCTGCAGGGCTACATTGGCATTCCCCATGGGGGTTTCCCTGAGCCCTTTCGCTCTAAG--------- tacttctctgctgcacttgcagaagcctctcttttttcctggcctcacagGTAAAGCCATCTTCCAAGATCTTGGCTGACCTAGCCCAGTTCAAGGTGCAGAATGGATCAAGTCGAACTGAAACGGAAGTTCAAGCAGAAGAGCTCTCCTTCCCCTGCTCCGTAGTGGAGTTCCTACAGGGACATATTGGTATCCCACAAGGAGGTTTCCCCAAGCCATTTCATTCTAAGTTCCAACTTgtgagttaggttgatgtggagtaaatcagtcttttgggcgtatcccctct #### Pdcd11_ID10116_10 --> 1 - 0 Original Alignment aTCAATTATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttaga------ATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from CESAR aTCAATTATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG tgttgggcctacatcaagaccactgtttaagtttgtccttatttctttaga------ATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from Spaln_aa2Genome -ATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttagAATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from Spaln_nt2Genome TATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttagAATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from Pairagon ATCAATTATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttagA------ATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from Exonerate_protein2genome ATCAATTATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttagA------ATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from Exonerate_coding2genome gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttagaatcgcagctccatttcttagatatcatgacatcaaaattggaacagtagtaaaggtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg Alignment from GeneWise ATCAATTATTGCAGCTCCATTCCTTAGATATCATGACATCAAAATAGGGACAGTAGTAAAG gcctacatcaagaccactgtagtcttttaagtttgtccttatttctttagA------ATCGCAGCTCCATTTCTTAGATATCATGACATCAAAATTGGAACAGTAGTAAAGgtatgtattcaattttcttttcagaaacagatttgcagttagtcttcatg #### Pdcd11_ID10126_20 --> 1 - 2 Original Alignment g---------------TTTCTCCCAATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAag tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagaGATTCTGAAAGGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAaggtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from CESAR g---------------TTTCTCCCAATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAag tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagaGATTCTGAAAGGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAaggtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from Spaln_aa2Genome GTTTCTCCCA---ATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAAG tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagagattctgaaagGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAAGgtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from Spaln_nt2Genome GTTTCTCCCAATAAG---TCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAAG tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagagattctgaaagGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAAGgtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from Pairagon ---------------GTTTCTCCCAATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAAG tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagAGATTCTGAAAGGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAAGgtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from Exonerate_protein2genome G---TTTCTCCCAATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAAG tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagagattctgaaagGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAAGgtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from Exonerate_coding2genome G---TTTCTCCCAATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAAG tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagagattctgaaagGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAAGgtgagagtctactcttgaggataagttgacagctgggatcaactctggct Alignment from GeneWise -AAGTTTCTCCCAATAAGTCACCCCAGATTTGTTCTGACCATCCTGGAGCTGAGTGTTCGGCCAAG tgtatgtgggtatacactatctagtaatcctttttatgttctttccccagagattctgaaagGGCCTTTCTTCCAATTAGCCACCCCAGATTTGTACTGACCATACTGGAGTTAAGTGTTCGTCCAAGgtgagagtctactcttgaggataagttgacagctgggatcaactctggct #### Pdcd11_ID10137_31 --> 0 - 2 Original Alignment ---AAGAAGAAGGGCAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCag gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagCTTAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCcggtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from CESAR ---AAGAAGAAGGGCAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCag gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagCTTAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCcggtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from Spaln_aa2Genome AAGAAGAAGGGC---AAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCAG gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagCTTAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCCGgtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from Spaln_nt2Genome AAGAAGAAGGG---CAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCAG gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagCTTAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCCGgtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from Pairagon ---AAGAAGAAGGGCAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCAG gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagCTTAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCCGgtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from Exonerate_protein2genome AAGAAGAAGGGCAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCAG gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagcttAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCCGgtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from Exonerate_coding2genome AAGAAGAAGGGCAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCAG gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagcttAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCCGgtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct Alignment from GeneWise ---AAGAAGAAGGGCAAGAAGGAGAGGGAGCTGGAGAAGCAGAAGGCAGAGAAGGAGCTGTCGCGCATTGAGGAGGCACTCATGGACCCTGGGCGACAGCCAGAGTCTGCGGATGACTTTGACCGGCTGGTGCTAAGCTCTCCCAACAGCTCCATCCTTTGGCTGCAGTACATGGCTTTCCACCTACAGGCCACGGAGATCGAGAAGGCCCGGGCTGTGGCTGAGAGGGCCCTGAAGACCATCTCATTCAG gcttttctgaataggtgccattatccaaacaccttcatgtttttgtctagCTTAAAAAGAAGGGCAAAAAAGAAAGGGCACTGGAGAAGCAAAAATTGAAGAAAGAGCTGTCGCGCATTGAAAAGGCACTAATGGACCCTTGGCGACAACCAGAGTCTGCTGACGTATCTGACCAGCTGGTGCTAAGTTTCCCTAACAGCTCCATCCTTTGGCTGCAGTACATGGCATTCCATCTGCAAACAACAGAGATTGAGCGGGCCCGGGCTGTCGCTGAGAGGGCTTTGAAGACCATCGCATTCCGgtaggaggtccaggccttctgcagtccaaaaggatgaggacttctcagct #### Pdcd11_ID10138_32 --> 1 - 0 Original Alignment aGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacaggGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATAC---------------------gtacgatgttggccacacatcccggtccaaccacaataacgcaatgcagt Alignment from CESAR aGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacaggGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATAC---------------------gtacgatgttggccacacatcccggtcca Alignment from Spaln_aa2Genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATAC---AAG tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacagGGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACGTACGATGTTGGCCACACATCCCGgtccaaccacaataacgcaatgcagt Alignment from Spaln_nt2Genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTAC tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacagGGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACgtacgatgttggccacacatcccggtccaaccacaataacgcaatgcagt Alignment from Pairagon AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTAC tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacagGGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACgtacgatgttggccacacatcccggtccaaccacaataacgcaatgcagt Alignment from Exonerate_protein2genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAGGAA tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacagGGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACGTACGATGTTGGCCACACATCCCGgtccaaccacaataacgcaatgcagt Alignment from Exonerate_coding2genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAGGAA tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacagGGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACGTACGATGTTGGCCACACATCCCGgtccaaccacaataacgcaatgcagt Alignment from GeneWise AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAGGAA tatgtgagtggctccaatgtaggtagatcactgtgggcttctctctacagGGAGGAACAAGAGAAGCTAAATATATGGGTAGCCCTGTTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACGTACGATGTTGGCCACACATCCCGgtccaaccacaataacgcaatgcagt #### Pde6c_ID7536_6 --> 0 - 2 Original Alignment GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTcc ctgactccgttgcattgcttaacgggagggtggtgttcctttcattccag------------------------GACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTccgtggctcatcaactgaaggctgtctaccctcccatgccatgataagacca Alignment from CESAR GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTcc ttcagtaaggtttccctcgactatcgagggtggtgttcctttcattccag------------------------GACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTccgtggctcatcaactgaaggctgtctaccctcccatgccatgataagacca Alignment from Spaln_aa2Genome -ATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCC ctgactccgttgcattgcttaacgggagGGTGGTGTTCCTTTCATTCCAGGACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTCCgtggctcatcaactgaaggctgtctaccctcccatgccatgataagacca Alignment from Spaln_nt2Genome GATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCC ctgactccgttgcattgcttaacgggagggtggtgttcctttcattccagGACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTCCgtggctcatcaactgaaggctgtctaccctcccatgccatgataagacca Alignment from Pairagon GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCCG------------------------------------------------- ctgactccgttgcattgcttaacgggagggtggtgttcctttcattccag------------------------GACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTCCGTGGCTCATCAACTGAAGGCTGTCTACCCTCCCATGCCATGATAAGACCA Alignment from Exonerate_protein2genome GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCC ctgactccgttgcattgcttaacgggAGGGTGGTGTTCCTTTCATTCCAGGACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTCCgtggctcatcaactgaaggctgtctaccctcccatgccatgataagacca Alignment from Exonerate_coding2genome ATCATCGATTACATTT ctgactccgttgcattgcttaacgggagggtggtgttcctttcattccaggactacactttgcatgggaaggaggaactcaatgtcattccgtggctcatcaactgaaggctgtctaccctcccaTGCCATGATAAGACCA Alignment from GeneWise -ATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCC ctgactccgttgcattgcttaacgggagGGTGGTGTTCCTTTCATTCCAGGACTACACTTTGCATGGGAAGGAGGAACTCAATGTCATTCCgtggctcatcaactgaaggctgtctaccctcccatgccatgataagacca #### Pde6c_ID7543_13 --> 0 - 0 Original Alignment GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from CESAR GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from Spaln_aa2Genome GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from Spaln_nt2Genome GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATGA ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAgtgcagtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from Pairagon GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from Exonerate_protein2genome GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from Exonerate_coding2genome GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa Alignment from GeneWise GTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATG------ ctctttaatgttggagtagttaccatgaacagtctgtgcttcatccatagATACTTACAAAGTGGATGTACACTGTCCGAAAGGGATACCGACCTGCTACATACCACAATTGGCGACATGGGTCAAATGTGGGGTATACAATATCTCCCCTGTTAATGAGTGCAgtaagcgctgtggaaagcttggatgctctcttcctactaaatgccagaaa #### Peo1_ID9266_3 --> 1 - 2 Original Alignment gTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGAC---ag accaccagttaaaattttatctatatgactgtcctccggcctctctgcaggTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGaggtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from CESAR gTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGAC---ag accaccagttaaaattttatctatatgactgtcctccggcctctctgcaggTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGaggtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from Spaln_aa2Genome GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAGG-- accaccagttaaaattttatctatatgactgtcctccggcctctctgcagGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGAGgtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from Spaln_nt2Genome GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAGGA- accaccagttaaaattttatctatatgactgtcctccggcctctctgcagGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGAGgtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from Pairagon GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGAC---AG accaccagttaaaattttatctatatgactgtcctccggcctctctgcagGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGAGgtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from Exonerate_protein2genome GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGAC---AG accaccagttaaaattttatctatatgactgtcctccggcctctctgcagGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGAGgtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from Exonerate_coding2genome GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGAC---AG accaccagttaaaattttatctatatgactgtcctccggcctctctgcagGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGAGgtgagtatcagagatgagattgagtggactggtaatggccccaagggttt Alignment from GeneWise GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAGG-- accaccagttaaaattttatctatatgactgtcctccggcctctctgcagGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACATGAGgtgagtatcagagatgagattgagtggactggtaatggccccaagggttt #### Pga5_ID2972_6 --> 1 - 2 Original Alignment c---------------------------------------AAGGATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATag tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagtGACCTCCCAGGTGTGACTGACACAGAGGAGGACAACTTTAAGGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATaggtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag Alignment from CESAR aatccttttttttgagccttggcataggagtgaactgatgctgcaggtcac Alignment from Spaln_aa2Genome GATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATAG tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagtgacctcccaggtgtgactgacacagaggaggacaactttaagGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATAGgtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag Alignment from Spaln_nt2Genome GATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATAG tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagtgacctcccaggtgtgactgacacagaggaggacaactttaagGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATAGgtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag Alignment from Pairagon ----------------------------CAAGGATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATAG tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagtgacctcccagGTGTGACTGACACAGAGGAGGACAACTTTAAGGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATAGgtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag Alignment from Exonerate_protein2genome CAAGGATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATAG tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagtgacctcccaggtgtgactgacacagaggaggacaacttTAAGGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATAGgtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag Alignment from Exonerate_coding2genome CAAGGATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATAG tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagtgacctcccaggtgtgactgacacagaggaggacaacttTAAGGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATAGgtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag Alignment from GeneWise -------------------------------------AGCAAGGATGAAAAGGGCAGCATGCTGATGCTAGGTGGAGTGGATCCCTCCTACTACCATGGAGAGCTTCACTGGGTACCAGTGTCCAAGCCCAGCTACTGGCAATTAGCTGTGGATAG tcatacagtttgaagtaccctggaaatttgaaaatattttttctctacagTGACCTCCCAGGTGTGACTGACACAGAGGAGGACAACTTTAAGGATGAAAAGGGCAGCATATTAATGTTAGGAGGAGTGGACCCCTCCTACTACCATGGAGAACTTCATTGGGTACCTGTCTCACAGCCGAGTTACTGGCGATTAGCTGCAGATAGgtaagtcataggcgcctattgccagtaggtactatcttagaagcatgcag #### Pik3ap1_ID8164_5 --> 2 - 0 Original Alignment acCTCTCCTCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagac------TCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatgta Alignment from CESAR acCTCTCCTCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG agtcatacctcataccctttcatagtttaaccggtgtctcgattgtccagac------TCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatttt Alignment from Spaln_aa2Genome ACCTCTCCTCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagAC------TCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatgta Alignment from Spaln_nt2Genome ACCTCTCCTCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagA------CTCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatgta Alignment from Pairagon ACCTCTCCTCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagA------CTCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatgta Alignment from Exonerate_protein2genome ACCTCTCCTCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagAC------TCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatgta Alignment from Exonerate_coding2genome TCGAGTGCTGCAAATCCT acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagactcagggaatgtctctctaaagctatattcaggggatctagtggtctgtgaaacaactgtcagttactatactgatatggaagaaatcgggaacttgctttcgagccctgccaatccagtggaattaatgtgtcaggtaagagcagaccaaaatcaatccaacccaacACCAACATCAGCAATGTA Alignment from GeneWise --TCGGGGAATGTTTCTCTGAAGGTCTATTCTGGGGACCTGGTGGTCTGCGAAACCACCGTCAGCTATTATACCGACATGGAGGAAATTGGGAACTTACTGTCGAGTGCTGCAAATCCTGTGGAGTTTATGTGTCAG acctcataccctttcatagggcaactttaaccggtgtctcgattgtccagACTCAGGGAATGTCTCTCTAAAGCTATATTCAGGGGATCTAGTGGTCTGTGAAACAACTGTCAGTTACTATACTGATATGGAAGAAATCGGGAACTTGCTTTCGAGCCCTGCCAATCCAGTGGAATTAATGTGTCAGgtaagagcagaccaaaatcaatccaacccaacaccaacatcagcaatgta #### Pitpnm1_ID306_3 --> 1 - 1 Original Alignment gTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTG---g ccatatactgcagaccctcaagcctgacacctcacctcatactctcttaggTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAggtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat Alignment from CESAR gTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTG---g ccatatactgcagaccctcaagcctgacacctcacctcatactctcttaggTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAggtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat Alignment from Spaln_aa2Genome GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTG---G ccatatactgcagaccctcaagcctgacacctcacctcatactctcttagGTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAGgtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat Alignment from Spaln_nt2Genome GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG--- ccatatactgcagaccctcaagcctgacacctcacctcatactctcttagGTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAGgtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat Alignment from Pairagon GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCG-------------------------------------------------------- ccatatactgcagaccctcaagcctgacacctcacctcatactctcttagGTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAGGTAGGCTCTTACATGCAATGTCTTATATGATTTAAGCTGAGGTCTTTCAT Alignment from Exonerate_protein2genome GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG ccatatactgcagaccctcaagcctgacacctcacctcatactctcttagGTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAACAGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAGgtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat Alignment from Exonerate_coding2genome GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG ccatatactgcagaccctcaagcctgacacctcacctcatactctcttagGTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAACAGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAGgtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat Alignment from GeneWise GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGGAT- ccatatactgcagaccctcaagcctgacacctcacctcatactctcttagGTACACCTGCCCCTTCATTGAGAAGTTCTCAATTGAAATCGAGGCCTACTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGCAGgtaggctcttacatgcaatgtcttatatgatttaagctgaggtctttcat #### Pitpnm1_ID319_16 --> 2 - 0 Original Alignment tcCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAG------------ gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagttCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGATTAAGAATCATgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from CESAR tcCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAG------------ gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagttCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGATTAAGAATCATgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from Spaln_aa2Genome TCCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAG gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagTTCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGattaagaatcatgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from Spaln_nt2Genome TCCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAGGTCA-------- gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagTTCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGATTAAGAATCATgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from Pairagon TCCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAG------------ gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagTTCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGATTAAGAATCATgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from Exonerate_protein2genome TCCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAG gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagTTCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGattaagaatcatgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from Exonerate_coding2genome gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagttctcgaccgctggtggggaaacaaacgcattgattattctctctactgcccagaagcacttacagcctttcccactgtcacactgccccacctctttcatgcaagctactgggagtcagcagatgtagttgccttcattctacgccagattaagaatcatgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc Alignment from GeneWise TCCTGGACCGCTGGTGGGGAAACAAGCGGATCGACTATTCACTGTACTGCCCCGAGGCACTCACGGCCTTCCCCACGGTCACGCTGCCCCACCTCTTCCACGCCAGCTACTGGGAATCAGCGGATGTAGTGGCCTTCATTCTGCGCCAGGTCATTGAGAAG gaacacagttgaagctgtgctgtcgctcgagaaatgtatgtgtgttttagTTCTCGACCGCTGGTGGGGAAACAAACGCATTGATTATTCTCTCTACTGCCCAGAAGCACTTACAGCCTTTCCCACTGTCACACTGCCCCACCTCTTTCATGCAAGCTACTGGGAGTCAGCAGATGTAGTTGCCTTCATTCTACGCCAGATTAAGAATCATgtatgtacaccccaggattggcctaacactgagtttagataacaggcgcc #### Pitpnm1_ID320_17 --> 0 - 0 Original Alignment GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACA---------------gtaaaaatcctagtttgattagctcagaattgttccttccttggctgttt Alignment from CESAR GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACA---GTAAAAATCCTAgtttgattagctcagaattgttccttccttggctg Alignment from Spaln_aa2Genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACA---GTAAAAATCCTAgtttgattagctcagaattgttccttccttggctg Alignment from Spaln_nt2Genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAA--GCAAACA-GTAAAAATCCTAgtttgattagctcagaattgttccttccttggctgtt Alignment from Pairagon GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACA ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACAgtaaaaatcctagtttgattagctcagaattgttccttccttggctgttt Alignment from Exonerate_protein2genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACA---GTAAAAATCCTAgtttgattagctcagaattgttccttccttggctg Alignment from Exonerate_coding2genome ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagattatggagaaagaatggccacaattgactgagtgtcaagaaccatccatctacagccctgccttccctaaggaaaagtggcagtgcaagcaaacagtaaaaatcctagtttgattagctcagaattgttccttccttggctgttt Alignment from GeneWise GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG ccattatagtatgggtgtgtcttgtatgtgacatctaaatattcttccagATTATGGAGAAAGAATGGCCACAATTGACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACA---GTAAAAATCCTAgtttgattagctcagaattgttccttccttggctg #### Pitpnm1_ID321_18 --> 0 - 0 Original Alignment ------------AACGTCACTTCCAACCACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAG GTGGATGTCTACGTCATGACACAGC ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCACCAGAGAAGAGgtaagactgacacacgcacccacagGTTGAGGTCTATGTCATGACACAGC Alignment from CESAR ------------AACGTCACTTCCAACCACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAG GTGGATGTCTACGTCATGACACAGC ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCACCAGAGAAGAGgtccccttttgccttatatttgcagGTTGAGGTCTATGTCATGACACAGC Alignment from Spaln_aa2Genome AACGTCACTTCCAAC------------CACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAG-------------------------GTGGATGTCTACGTCATGACACAGC ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCACCAGAGAAGAGGTAAGACTGACACACGCACCCACAgGTTGAGGTCTATGTCATGACACAGC Alignment from Spaln_nt2Genome ------------AACGTCACTTCCAACCACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAGGTGGAT-------------------------------GTCTACGTCATGACACAGC ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCAC--CAGAGAA----GAGGTAAGACTGACACACGCACCCACAGGTTGAGGTCTATGTCATGACACAGC Alignment from Pairagon ------------AACGTCACTTCCAACCACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAG-------------------------GTGGATGTCTACGTCATGACACAGC ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCACCAGAGAAGAGGTAAGACTGACACACGCACCCACAGGTTGAGGTCTATGTCATGACACAGC Alignment from Exonerate_protein2genome GTCAAGATCCGGAACGTCACTTCCAACCACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAG GTGGATGTCTACGTCATGA ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCACCAGAGAAGAGgtaagactgacacacgcacccacaggttgag------GTCTATGTCATGA Alignment from Exonerate_coding2genome ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcaggaagaacaaactaatgtcacttctaaccacaaagcaagtgacactgtgatatgtgagggccacccgcaagtactaaatggccatttcatgtatggaccactggatgtagttacactcaccagagaagaggtaagactgacacacgcacccacaggttgaggtctatgtcatgacacagc Alignment from GeneWise ------------AACGTCACTTCCAACCACCGAGCGAGTGACACCGTGGTATGTGAGGGCCGTCCCCAGGTGCTGAATGGGCGCTTCATGTATGGACCATTGGATGTGGTCACGCTCACTGGAGAGAAG GTGGATGTCTACGTCATGACACAGC ctttgctgtggatttttcatataattgtctctcgtttgttctctgggcagGAAGAACAAACTAATGTCACTTCTAACCACAAAGCAAGTGACACTGTGATATGTGAGGGCCACCCGCAAGTACTAAATGGCCATTTCATGTATGGACCACTGGATGTAGTTACACTCACCAGAGAAGAGgtaagactgacacacgcacccacagGTTGAGGTCTATGTCATGACACAGC #### Pitpnm1_ID323_20 --> 1 - 2 Original Alignment g---------------------GGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCag cattcctgttaaatactaacttagactgatatgttattattttattttaggCGCCTGAGGTTCAATGGCCAGGGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGaggtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from CESAR g---------------------GGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCag cattcctgttaaatactaacttagactgatatgttattattttattttaggCGCCTGAGGTTCAATGGCCAGGGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGaggtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from Spaln_aa2Genome G------------GGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCAG cattcctgttaaatactaacttagactgatatgttattattttattttaggcgcctgagGTTCAATGGCCAGGGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGAGgtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from Spaln_nt2Genome GGGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCAG cattcctgttaaatactaacttagactgatatgttattattttattttaggcgcctgaggttcaatggccag-GGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGAGgtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from Pairagon ---------------------GGGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCAG cattcctgttaaatactaacttagactgatatgttattattttattttagGCGCCTGAGGTTCAATGGCCAGGGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGAGgtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from Exonerate_protein2genome GGGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCAG cattcctgttaaatactaacttagactgatatgttattattttattttaggcgcctgaggttcaatggccaGGGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGAGgtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from Exonerate_coding2genome cattcctgttaaatactaacttagactgatatgttattattttattttaggcgcctgaggttcaatggccagggcgaccacacatatgctgaatgttgcttaaccattgtctccagaggtgctgaagcagtggttttcagcattgatggttcttttactgcgagtgtctcaatcatgggtagtgaccccaaggtgcgagctggggccgtagatgtggtgaggtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt Alignment from GeneWise ----------AGGGGAGACCACACCTATGCCGAGTGCTGTCTGACTGTGGTGTCCCGAGGCACAGAAGCTGTGGTCTTCAGCATCGATGGTTCTTTCACTGCCAGTGTCTCTATCATGGGCAGCGACCCCAAGGTGCGCGCTGGCGCAGTGGACGTGGTCAG cattcctgttaaatactaacttagactgatatgttattattttattttaggcgcctgagGTTCAATGGCCAGGGCGACCACACATATGCTGAATGTTGCTTAACCATTGTCTCCAGAGGTGCTGAAGCAGTGGTTTTCAGCATTGATGGTTCTTTTACTGCGAGTGTCTCAATCATGGGTAGTGACCCCAAGGTGCGAGCTGGGGCCGTAGATGTGGTGAGgtacggccagacttctgtgccatgtgatgatcttctgtctgtggggaggt #### Pkd2l1_ID8957_11 --> 0 - 2 Original Alignment AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG---ga ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGCgagtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from CESAR AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG---ga ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGCgagtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from Spaln_aa2Genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGAA-- ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGCGAgtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from Spaln_nt2Genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG---GA ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGCGAgtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from Pairagon AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG---GA ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGCGAgtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from Exonerate_protein2genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGA ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGcgagtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from Exonerate_coding2genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGA ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGcgagtaatgaattccctgcctgccagatgttctgatcacactgggctagggta Alignment from GeneWise AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGAA-- ttggtagcaacaccacatctatcacatttctggtattcatctacctacagAGCTACAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTCTCAGATGTACAAAAGGTCCTTAAGGGTGGAGAACCGGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAAGCGAgtaatgaattccctgcctgccagatgttctgatcacactgggctagggta #### Pkd2l1_ID8959_9 --> 1 - 0 Original Alignment tTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG------ atgagagacttgtacacacagagtgctccattatttcccccatcccacagtTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGGAATTTgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from CESAR tTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG------ atgagagacttgtacacacagagtgctccattatttcccccatcccacagtTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGGAATTTgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from Spaln_aa2Genome TTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG------ atgagagacttgtacacacagagtgctccattatttcccccatcccacagTTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGGAATTTgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from Spaln_nt2Genome TTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG------ atgagagacttgtacacacagagtgctccattatttcccccatcccacagTTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGGAATTTgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from Pairagon TTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG------ atgagagacttgtacacacagagtgctccattatttcccccatcccacagTTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGGAATTTgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from Exonerate_protein2genome TTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG atgagagacttgtacacacagagtgctccattatttcccccatcccacagTTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGgaatttgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from Exonerate_coding2genome TTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG atgagagacttgtacacacagagtgctccattatttcccccatcccacagTTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGgaatttgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat Alignment from GeneWise TTTCACTCAGTTCCGGATAATCCTTGGGGATTTTGACTACAATGCCATCGACAATGCCAACAGAATCCTGGGCCCTGTGTACTTTGTCACCTATGTCTTCTTCGTCTTCTTCGTGCTCCTG------ atgagagacttgtacacacagagtgctccattatttcccccatcccacagTTTCACTCAGTTCCGTATAATCCTTGGGGATTTTGACTACAATGCCATTGACAATGCTAACAGAATCCTTGGCCCTGTGTACTTTGTTACCTATGTCTTCTTCGTTTTTTTTGTGCTTCTGGAATTTgtaaagagaataacttaaagaccaatgggctatatttctgttggatatat #### Pkd2l1_ID8960_8 --> 0 - 2 Original Alignment ATATTCAAGTATATCAGCTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCat cttgtcgctccaactttctggaataccctctggactgtgataactttcag---------------AGTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCatgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from CESAR ATATTCAAGTATATCAGCTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCat cttgaacccattagccttgtcgctcccctctggactgtgataactttcag---------------AGTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCatgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from Spaln_aa2Genome CTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCAT cttgtcgctccaactttctggaataccctctggactgtgataactttcagagTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCATgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from Spaln_nt2Genome TCAGCTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCAT cttgtcgctccaactttctggaataccctctggactgtgataactttcag--AGTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCATgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from Pairagon ATATTCAAGTATATCAGCTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCAT cttgtcgctccaactttctggaataccctctggactgtgataactttcag---------------AGTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCATgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from Exonerate_protein2genome ATATTCAAGTATATCAGCTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCAT cttgtcgctccaactttctggaataccctctggacTGTGATAACTTTCAGAGTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCATgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from Exonerate_coding2genome ATATTCAAGTATATCAGCTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCAT cttgtcgctccaactttctggaataccctctggacTGTGATAACTTTCAGAGTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCATgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta Alignment from GeneWise CTTCAACAAGACCATGACACAGCTCTCCTCCACCCTGGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTCGCTTACGCCCAGCTTGGCTACCTGCTTTTTGGGACCCAAGTGGAAAACTTTAGCACTTTCGTCAAGTGCAT cttgtcgctccaactttctggaataccctctggactgtgataactttcagagTTTCAATAAGACCATGACACAGCTCTCATCCACCCTAGCTCGCTGTGCCAAGGACATCCTGGGCTTTGCCATCATGTTCTTCATTGTCTTCTTTGCTTATGCCCAGCTTGGCTACCTGCTTTTTGGGACTCAAGTGGAAAACTTCAGCACTTTTGTTAAGTGCATgtgagcacaaccattgtagacccttgggttttgagatcccagaatgttta #### Plcb3_ID1901_30 --> 0 - 0 Original Alignment CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAG---------gtaggtctcacggctttgtgtagggttgcatgttcacactaataggggaa Alignment from CESAR CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAG---------gtaggtctcacggctttgtgtagggttgcatgttcacacta Alignment from Spaln_aa2Genome CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGgtaggtctcacggctttgtgtagggttgcatgttcacactaataggggaa Alignment from Spaln_nt2Genome CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGG-----TAGgtctcacggctttgtgtagggttgcatgttcacactaatag Alignment from Pairagon CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGgtaggtctcacggctttgtgtagggttgcatgttcacactaataggggaa Alignment from Exonerate_protein2genome CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGgtaggtctcacggctttgtgtagggttgcatgttcacactaataggggaa Alignment from Exonerate_coding2genome tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagttaggagaggcccagaaacagcaacatgagcggttagtggcaggacaacagcaagtcctccagcaactagaggaagaggtaggtctcacggctttgtgtagggttgcatgttcacactaataggggaa Alignment from GeneWise CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG tctttgctcatcgctcagacttgcaaccactcttttcacgccttccccagTTAGGAGAGGCCCAGAAACAGCAACATGAGCGGTTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAA---------GAGgtaggtctcacggctttgtgtagggttgcatgttcacactaataggggaa #### Plcb3_ID1902_29 --> 1 - 0 Original Alignment --gt gGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG GGatgtaattaagcaggtcaatgtctgtcccccacccatgtgtgttacaga------ACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from CESAR gGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG ggatgtgagtacccagaagcaggtctgtcccccacccatgtgtgttacaga------ACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from Spaln_aa2Genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG ggatgtaattaagcaggtcaatgtctgtcccccacccatgtgtgttacagA------ACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from Spaln_nt2Genome A-CAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG ggatgtaattaagcaggtcaatgtctgtcccccacccatgtgtgttacagAACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from Pairagon GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG ggatgtaattaagcaggtcaatgtctgtcccccacccatgtgtgttacag------AACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from Exonerate_protein2genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG ggatgtaattaagcaggtcaatgtctgtcccccacccatgtgtgTTACAGAACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from Exonerate_coding2genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG ggatgtaattaagcaggtcaatgtctgtcccccacccatgtgtgTTACAGAACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac Alignment from GeneWise --CT GACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG GGATgtaattaagcaggtcaatgtctgtcccccacccatgtgtgttacagAACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCAACAGACAGgtgagaggtaatctcctttgtcaagaacttcctttgtcactaacagagac #### Plcb3_ID1903_28 --> 1 - 2 Original Alignment g---------GAGAAGAAGGAACTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAG---------------gt gGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctaggGGCCCACAGGAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAGTGTATGGTCACTGGatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagaGAA Alignment from CESAR g---------GAGAAGAAGGAACTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAGgt gGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctaggGGCCCACAGGAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAgtgtatggtcactggatgtgagtacccagaagcaggtcaatgtctgtcctgttctctctctagaGAA Alignment from Spaln_aa2Genome GGAGAAGAAGGAA---------CTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAGGT GGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctagGGGCCCACAGGAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAGTgtatggtcactggatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagAGAA Alignment from Spaln_nt2Genome GGAGAAGAAGGAACTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAGGT GGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctaggggcccacag-GAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAGTgtatggtcactggatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagAGAA Alignment from Pairagon GGAGAAGAAGGAACTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAGGT GGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctaggggcccacag-GAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAGTgtatggtcactggatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagAGAA Alignment from Exonerate_protein2genome GGAGAAGAAGGAACTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAGGT GGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctaggggcccacaGGAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAGTgtatggtcactggatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagAGAA Alignment from Exonerate_coding2genome tcggtataattcctcacatacaattcaacattcccccgtgtctctcctaggggcccacaggagaaaagagagcctcaaaagatcctggatagggagcgcaacaatagtatttcagaagccaagacaagggagaaacataagaaggaagtgtatggtcactggatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagagaa Alignment from GeneWise -------AGGGAGAAGAAGGAACTCCAGAAGATCCTGGACAGGAAGCGCAACAACAGCATCTCAGAGGCCAAGACAAGGGAGAAACACAAGAAGGAGGT GGAA tcggtataattcctcacatacaattcaacattcccccgtgtctctcctagGGGCCCACAGGAGAAAAGAGAGCCTCAAAAGATCCTGGATAGGGAGCGCAACAATAGTATTTCAGAAGCCAAGACAAGGGAGAAACATAAGAAGGAAGTgtatggtcactggatgtgagtacccagaagcaggtcaattatttggtgtaactctttatagAGAA #### Plcb3_ID1906_25 --> 2 - 2 Original Alignment ag---------GTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCct ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagaaCTTGTAAATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCctgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from CESAR ag---------GTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCct ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagaaCTTGTAAATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCctgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from Spaln_aa2Genome AG---------GTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCCT ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagAACTTGTAAATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCCTgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from Spaln_nt2Genome AG---------GTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCCT ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagAACTTGTAAATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCCTgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from Pairagon ---------AGGTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCCT ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagAACTTGTAAATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCCTgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from Exonerate_protein2genome AGGTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCCT ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagaacttgtaaATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCCTgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from Exonerate_coding2genome ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagaacttgtaaatgtaatccccacacccctagaagagctaagaagtcacaaggccatggtgaagctgcacagccgacagtgcgaccaagacctacaggaattacataagaagcaccagcataaggttatagcactcacccgacgtttgctcgatggcctggctcagacaagagcagaggggaagtgccagccatcttccagtgtcctgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca Alignment from GeneWise GGCAGCGAGATGATTTGATTGCCAGCATCCTCTCTGAGGTGACCCCTACACCTCTAGAGGAGCTCAGAAGCCACAAGGCTATGGTGAAGCTACGGAGCCGGCAG---GATCGAGACCTGCGGGAGTTGCATAAGAAGCACCAGCGCAAGGCTGTGGCCCTCACCCGCCGCCTTCTGGATGGCCTGGCCCAGGCCAGGGCTGAGGGGAAGTGCCGGCCCTCCCCCAGTGCCCT ccagccaggaagctagcataccaaccaatgttctgtgtgtgccctgccagAA---------------------------CTTGTAAATGTAATCCCCACACCCCTAGAAGAGCTAAGAAGTCACAAGGCCATGGTGAAGCTGCACAGCCGACAGTGCGACCAAGACCTACAGGAATTACATAAGAAGCACCAGCATAAGGTTATAGCACTCACCCGACGTTTGCTCGATGGCCTGGCTCAGACAAGAGCAGAGGGGAAGTGCCAGCCATCTTCCAGTGTCCTgtaagcataattgcaccatagcatggcagtatgtactggcttaacttaca #### Plcb3_ID1907_24 --> 2 - 1 Original Alignment gg---CAGCGAGATGATTTGATTGCCAGCATCCTCTCTg cactccacagatttgattgcttcactcctaatctagattacactttccagggACTCAGCCAGATGATTTGATTGCAAGCACCCTTTCAggtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata Alignment from CESAR gg---CAGCGAGATGATTTGATTGCCAGCATCCTCTCTg cactccacagatttgattgcttcactcctaatctagattacactttccagggACTCAGCCAGATGATTTGATTGCAAGCACCCTTTCAggtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata Alignment from Spaln_aa2Genome GG---CAGCGAGATGATTTGATTGCCAGCATCCTCTCTG cactccacagatttgattgcttcactcctaatctagattacactttccagGGACTCAGCCAGATGATTTGATTGCAAGCACCCTTTCAGgtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata Alignment from Spaln_nt2Genome GG---CAGCGAGATGATTTGATTGCCAGCATCCTCTCTG cactccacagatttgattgcttcactcctaatctagattacactttccagGGACTCAGCCAGATGATTTGATTGCAAGCACCCTTTCAGgtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata Alignment from Pairagon GG---CAGCGAGATGATTTGATTGCCAGCATCCTCTCTG cactccacagatttgattgcttcactcctaatctagattacactttccagGGACTCAGCCAGATGATTTGATTGCAAGCACCCTTTCAGgtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata Alignment from Exonerate_protein2genome GG---CAGCGAGATGATTTGATTGCCAGCATCCTCTCTG cactccacagatttgattgcttcactcctaatctagattacactttccagGGACTCAGCCAGATGATTTGATTGCAAGCACCCTTTCAGgtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise cactccacagatttgattgcttcactcctaatctagattacactttccagggactcagccagatgatttgattgcaagcaccctttcaggtgaggagtgtctatgggactaaggctaggtgagcctactctaaaccata #### Plcb3_ID1912_19 --> 0 - 0 Original Alignment GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------- acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGGGGCCCACCgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac Alignment from CESAR GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------- acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGGGGCCCACCgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac Alignment from Spaln_aa2Genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------- acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGGGGCCCACCgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac Alignment from Spaln_nt2Genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------- acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGGGGCCCACCgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac Alignment from Pairagon GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------- acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGGGGCCCACCgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac Alignment from Exonerate_protein2genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGgggcccaccgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------- acacgaaaattctctcatcaactttcaggtgtcctgcttccaacccctagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTATGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACCTCTCAGGGAAACTTGTTCAACCCTGTATGGGAAGAAGAACCGTTTGATTTCCCAAAGGGGCCCACCgtaagttccagcaattatgccctccatttcatgtaggacagcaagaccac #### Plcb3_ID1914_17 --> 1 - 1 Original Alignment aTACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTG---------g ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagaTACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGTCTACAATggtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg Alignment from CESAR aTACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTG---------g ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagaTACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGTCTACAATggtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg Alignment from Spaln_aa2Genome ATACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTG---------G ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagATACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGTCTACAATGgtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg Alignment from Spaln_nt2Genome ATACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTGG--------- ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagATACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGTCTACAATGgtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg Alignment from Pairagon ATACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTGG--------- ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagATACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGTCTACAATGgtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg Alignment from Exonerate_protein2genome ATACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTGG ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagATACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGtctacaatggtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ATACAACAAACAGCAGCTCAGCCGCATCTACCCTAAGGGCACACGAGTGGACTCCTCCAACTACATGCCTCAGCTCTTCTGGAACGTGGGTTGCCAGCTTGTTGCCCTCAACTTCCAGACCTTG---------G ggcctcctgactgctgtatccccatgacactaacatgtcattctctccagATACAACAGACAACAGCTTAGTCAGATATACTCCAGGAGCAAACAAGTG---TCCTCAAACTACATGCCTTATCTCTTTTGGAATGTAGGCTGCCAACTTGTTGCCTTCAACTTCCAGAGCCTGGTCTACAATGgtaagtatatgttcgcttttggcctccctaatcacctacctttaatttgg #### Plcb3_ID1926_5 --> 0 - 2 Original Alignment GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAgc tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTCTCA------ccgtcagcccagggctacaagcacacagggggtgggaaaatgtctcactgtg Alignment from CESAR GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAgc tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTCTCA------ccgtcagcccagggctacaagcacacagggggtgggaaaatgtctcactgtg Alignment from Spaln_aa2Genome GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAGC tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTC------TCACCgtcagcccagggctacaagcacacagggggtgggaaaatgtctcactgtg Alignment from Spaln_nt2Genome GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAGC tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTC------TCACCgtcagcccagggctacaagcacacagggggtgggaaaatgtctcactgtg Alignment from Pairagon GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAGC-------------------------------------------- tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTCTCACCGTCAGCCCAGGGCTACAAGCACACAGGGGGTGGGAAAATGTCTCACTGTG Alignment from Exonerate_protein2genome GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAGC tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTCTCACCGTCAGCccagggctacaagcacacagggggtgggaaaatgtctcactgtg Alignment from Exonerate_coding2genome tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtaggtatggtcagaggagttgtttagactagcaatgaacatattggcccagaatgcatcccaaaacacattctcaccgtcagcccagggctacaagcacacagggggtgggaaaatgtctcactgtg Alignment from GeneWise GTCTGGTCAGAGGAGTTGTTTAAACTGGCCATGAACATATTGGCTCAGAACGCCTCCCGGAACACCTTCCTGCGGAAAGC tcaatgggcctaatcctccattccataaagtcatctcacttgctctgtagGTATGGTCAGAGGAGTTGTTTAGACTAGCAATGAACATATTGGCCCAGAATGCATCCCAAAACACATTC------TCACCgtcagcccagggctacaagcacacagggggtgggaaaatgtctcactgtg #### Plekhs1_ID12098_3 --> 0 - 2 Original Alignment ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGAAATTGACgg cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATT---------aggtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from CESAR ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGAAATTGACgg cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATT---------aggtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from Spaln_aa2Genome ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGA cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATTAGgtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from Spaln_nt2Genome ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATC-G cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATTAGgtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from Pairagon ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGAAATTGACGG cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCAT---------TAGgtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from Exonerate_protein2genome ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGA cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATTAGgtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from Exonerate_coding2genome ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGA cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATTAGgtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt Alignment from GeneWise ACCTCCTGGAAAAAGCGTCTTTTTATTCTGTCCCAGAGTCGGGGAACGGGTCTCAGTCTTTCCTATTACAAAGACCATCAGCACAGAGGTTCCATCGA cattggctttactgacatcaactagtgcgttcatttttactgactgttagACCTCCTGGAAGAAGCGTTTGTTTATACTGTCCCAGAGCCGGGGATCCGGTCTTGGTCTTTCTTATTACAAAGATCATCAACACAGAGGCTCCATTAGgtaatgcatttcctccagtgggcaatgctcacactagaagcactagattt #### Pola2_ID1324_16 --> 1 - 2 Original Alignment cTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGAGA---------ag gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagcTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAGGACCGCCCTTaggtaatttaaacagcaaagtgaatcatacgtactagcaaggacatttaaac Alignment from CESAR cTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGAGA---------ag gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagcTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAGGACCGCCCTTaggtaatttaaacagcaaagtgaatcatacgtactagcaaggacatttaaac Alignment from Spaln_aa2Genome CTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGAGAAGT-------- gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagCTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAGGACCGCCCTTAGgtaatttaaacagcaaagtgaatcatacgtactagcaaggacatttaaac Alignment from Spaln_nt2Genome CTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGAGAA---------G gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagCTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAGGACCGCCCTTAGgtaatttaaacagcaaagtgaatcatacgtactagcaaggacatttaaac Alignment from Pairagon CTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGAGA------------------------------------------------------------- gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagCTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAGGACCGCCCTTAGGTAATTTAAACAGCAAAGTGAATCATACGTACTAGCAAGGACATTTAAAC Alignment from Exonerate_protein2genome CTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGA gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagCTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAggaccgcccttaggtaatttaaacagcaaagtgaatcatacgtactagcaaggacatttaaac Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTCTTCCGGGACGTCAGACAGATTCAGCCGAGTCCTTAAGCATATCCTGACGCAGAGA---------AG gatgaaatgatgaacttgccttattcccgtgctaatcttgtcacacccagCTCCTTGGGGACACCCGATAGATTCAGCAGAGTCCTCAAGCACATACTGACACAGAGGACCGCCCTTAGgtaatttaaacagcaaagtgaatcatacgtactagcaaggacatttaaac #### Pola2_ID1325_15 --> 0 - 2 Original Alignment ------CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTag agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATG---TACTCAACTACTGCAGATTTACTCTATCATGTTGGGGCTGAGGAACTGTTTaggtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag Alignment from CESAR ------CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTag agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTAC---TCAACTACTGCAGATTTACTCTATCATGTTGGGGCTGAGGAACTGTTTaggtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag Alignment from Spaln_aa2Genome CGAGTGCAGTTT------GTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCA---ACTACTGCAGATTTACTCTATCATGTTGGGGCTGAGGAACTGTTTAGgtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag Alignment from Spaln_nt2Genome GCGAGTGCAG-----TTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGT---ACTCAACTACTGCAGATTTACTCTATCATGTTGGGGCTGAGGAACTGTTTAGgtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag Alignment from Pairagon ------CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGT------------------------------TTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCAACTACTGCAGATTTACTCTATCATGTT---------------------------------GGGGCTGAGGAACTGTTTAGgtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag Alignment from Exonerate_protein2genome ------CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCA---ACTACTGCAGATTTACTCTATCATGTTGGGGCTGAGGAACTGTTTAGgtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ------CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG agctcactgtaggttttattgcaaggagacccctccttccccctgggcagAATATGCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCA---ACTACTGCAGATTTACTCTATCATGTTGGGGCTGAGGAACTGTTTAGgtaagtccatttgacccaataaatggtgttacttaacatagttcttgaag #### Pold4_ID437_2 --> 2 - 1 Original Alignment gg------GAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAg taggcagataagaagattagacagttcagatgtttttttgtcttaaacagggAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAggtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from CESAR gg------GAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAg taggcagataagaagattagacagttcagatgtttttttgtcttaaacagggAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAggtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from Spaln_aa2Genome GGGAAGACACCCAG------TCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG taggcagataagaagattagacagttcagatgtttttttgtcttaaacagGGAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from Spaln_nt2Genome GG------GAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG taggcagataagaagattagacagttcagatgtttttttgtcttaaacagGGAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from Pairagon GG------GAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG taggcagataagaagattagacagttcagatgtttttttgtcttaaacagGGAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from Exonerate_protein2genome GG------GAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG taggcagataagaagattagacagttcagatgtttttttgtcttaaacagGGAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from Exonerate_coding2genome GG------GAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG taggcagataagaagattagacagttcagatgtttttttgtcttaaacagGGAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc Alignment from GeneWise -----GGGGAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG taggcagataagaagattagacagttcagatgtttttttgtcttaaacagGGAACCCCGAAGACACACAGTCCCTCAGCCAGGAGGCGACTGCATTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtgaggaacccggcttcccggcttctgcatagcaaaaggcaactaccgtc #### Ppp1ca_ID411_5 --> 2 - 0 Original Alignment gcCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAG--- agctctcattctctagttatataaaaaacaggtctttcccatatctccaggcCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCgtagttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca Alignment from CESAR gcCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAG--- agctctcattctctagttatataaaaaacaggtctttcccatatctccaggcCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCgtagttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca Alignment from Spaln_aa2Genome GCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAGGTT agctctcattctctagttatataaaaaacaggtctttcccatatctccagGCCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCgtagttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca Alignment from Spaln_nt2Genome GCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAGGTT agctctcattctctagttatataaaaaacaggtctttcccatatctccagGCCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCgtagttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca Alignment from Pairagon GCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAGGTTGTAGAAGA------------------------------------------ agctctcattctctagttatataaaaaacaggtctttcccatatctccagGCCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCGTAGTTGAAAATGGTCTTCGGATTGGCGGGCAGTCCCGATGTATTGACCA Alignment from Exonerate_protein2genome GCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAGGTT agctctcattctctagttatataaaaaacaggtctttcccatatctccagGCCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCgtagttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca Alignment from Exonerate_coding2genome GCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAGGTT agctctcattctctagttatataaaaaacaggtctttcccatatctccagGCCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCgtagttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca Alignment from GeneWise GCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAGGCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGATTTGGACCTCATCTGCAGAGCACATCAGGTTGTA agctctcattctctagttatataaaaaacaggtctttcccatatctccagGCCTGTCACCAGGTTTACAATCCATGGAGCAGATCAGGCATATTATGCGGCCCACAGATGTTCCAGACCAAGGCCTGCTGTGTGATCTCCTGTGGTCTGATCCTGATAAGGATGTTCAAGGCTGGGCTGAGAATGACCGAGGTGTTTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTACATAAGCATGATTTGGACCTTATTTGCAGAGCTCATCAGTTCGTAgttgaaaatggtcttcggattggcgggcagtcccgatgtattgacca #### Ppp1r32_ID2840_11 --> 1 - 2 Original Alignment g------TACTTCGAGAATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAag aattaatgctctcaggcactaattaggaaatattacctattttaatgcagcCAGGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGGTCCA------CTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAaggtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from CESAR g------TACTTCGAGAATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAag aattaatgctctcaggcactaattaggaaatattacctattttaatgcagcCAGGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGGT------CCACTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAaggtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from Spaln_aa2Genome GTACTTCGAG------AATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAAG aattaatgctctcaggcactaattaggaaatattacctattttaatgcagCCAGGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGGT------CCACTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAAGgtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from Spaln_nt2Genome G--TACTTCGAGAATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAAG aattaatgctctcaggcactaattaggaaatattacctattttaatgcagccagGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGG------TCCACTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAAGgtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from Pairagon ------GTACTTCGAGAATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAAG aattaatgctctcaggcactaattaggaaatattacctattttaatgcagCCAGGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGG------TCCACTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAAGgtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from Exonerate_protein2genome GGGTACTTCGAGAATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAAG aattaatgctctcaggcactaattaggaaatattacctattttaatgcagccagGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGGT------CCACTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAAGgtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from Exonerate_coding2genome aattaatgctctcaggcactaattaggaaatattacctattttaatgcagccaggagtactttgagaatattcctgaggggttggatcgggaaggctggactcgaggtggcatacaaccccaaagagcaggtccacttagtgatctgaacaaccacactcttatggattccatgccaaatacagagaccctgacacatctgcatccccatgtaggaaggtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac Alignment from GeneWise ----GGGTACTTCGAGAATATCCCCAAGGGGCTGGATCGAGAAGGCTGGACTCGAGGTGGCATCCAGCCCCAGAAAGCAGGAGCCTACGCCCTCAGTGAGCTGAATAACCATACCCTCATGGACTCCACCCCAAATCCCACGGAGACCCTGAGGCACCTGCACCCCCATGTGGGAAG aattaatgctctcaggcactaattaggaaatattacctattttaatgcagCCAGGAGTACTTTGAGAATATTCCTGAGGGGTTGGATCGGGAAGGCTGGACTCGAGGTGGCATACAACCCCAAAGAGCAGGTCCA------CTTAGTGATCTGAACAACCACACTCTTATGGATTCCATGCCAAAT---ACAGAGACCCTGACACATCTGCATCCCCATGTAGGAAGgtgagttggttgattaggagaactgctctttgttgcaaaggaagatgaac #### Ppp1r32_ID2842_9 --> 0 - 0 Original Alignment GTGCCTACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcag------GCGTTGGCACGTCAGTCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from CESAR GTGCCTACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ccacctctcatagtgtccaattgtaccatctcctgtcctctccgccgcagGCG------TTGGCACGTCAGTCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from Spaln_aa2Genome ACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcagGCGTTGGCACGTCAGTCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from Spaln_nt2Genome ACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcagGCGTTGGCACGTCAGTCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from Pairagon GTGCCTACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcaggcgttggcacgtcag---------------------TCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from Exonerate_protein2genome ACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcagGCGTTGGCACGTCAGTCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from Exonerate_coding2genome ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcaggcgttggcacgtcagtctgccagcattagccatagattctaccgtgctccgcagcgaatgcaacaggctaatgttgccctgcttggaagggagactgtggggaataaagtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac Alignment from GeneWise ACTCCAGCCCCACAGTCTGCCAGCATGAGCCACAGGTCCTACCAGCCTCCCCAGCGGATGCAACAGACAAATGTTGCCCTGCTTGGCAGGGAGTCTGTGGGGAACAAG ctcatagtgtccaattgtacctccaccatctcctgtcctctccgccgcagGCGTTGGCACGTCAGTCTGCCAGCATTAGCCATAGATTCTACCGTGCTCCGCAGCGAATGCAACAGGCTAATGTTGCCCTGCTTGGAAGGGAGACTGTGGGGAATAAAgtgagacctcaaacacaagtcctatggtggcatcccagattatgggatac #### Ppp1r32_ID2843_8 --> 0 - 0 Original Alignment GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCTCTGAT------CGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAACCCCAGA attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAGCTA---gtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa Alignment from CESAR GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCTCT------GATCGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAACCCCAGA attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAGCTA---gtgagcagcattggggtaagacaacatatagctgtccctgtctagac Alignment from Spaln_aa2Genome GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCTCT------GATCGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAACCCC attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAGCTAgtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa Alignment from Spaln_nt2Genome GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCT------CTGATCGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAACCCCAGA attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAGC---TAgtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa Alignment from Pairagon GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCT------CTGATCGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAA attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAgctagtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa Alignment from Exonerate_protein2genome GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCTCT------GATCGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAACCCC attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAGCTAgtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa Alignment from Exonerate_coding2genome attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacaggggagtgatttcctgccagtgctgtccaggggatctgatcctgatcgagacacaggatttagccgagtgaacgaaagaacattaaagctagtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa Alignment from GeneWise GGAAGTGATTTCCTCCCTGTGCTGTCCAGAGGCTCTGAT------CGGGACACTGGATTCAGCCGAGTGAATGAAAGGACCTTGAACCCCAGA attttggatgctgttgtgtggtgtgacttgttgtgttttgtggttcacagGGGAGTGATTTCCTGCCAGTGCTGTCCAGGGGATCTGATCCTGATCGAGACACAGGATTTAGCCGAGTGAACGAAAGAACATTAAAG---CTAgtgagcagcattggggtaagacaacatatagctgtccctgtctagactaa #### Ppp1r32_ID2844_7 --> 0 - 0 Original Alignment ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from CESAR ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from Spaln_aa2Genome ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from Spaln_nt2Genome ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from Pairagon ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from Exonerate_protein2genome ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from Exonerate_coding2genome ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagctagttctgcatccaggtcgaagtatcagcaagtcatattacctacctctaacacaccctcaggtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat Alignment from GeneWise ---GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG ggtacaacacatgttcaccattaaatgttcctcctttttgacactttcagCTAGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATATTACCTACCTCTAACACACCCTCAGgtgagtattgtggtctgttggaacaatatgtttgacccaggtgctgagat #### Ppp1r32_ID2845_6 --> 2 - 0 Original Alignment at---CTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagatAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from CESAR at---CTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagatAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from Spaln_aa2Genome AT---CTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagATAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from Spaln_nt2Genome AT---CTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagATAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from Pairagon A---TCTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagATAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from Exonerate_protein2genome AT---CTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagATAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from Exonerate_coding2genome AT---CTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagATAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt Alignment from GeneWise --GATCTCTTGCTTAAGAAGACAATTGGTTCCAAAGAAGAGACTGGCTTCACGGAAGAGTCTACCAAGAATCCCATTGTCTTCCAGCCGCCCTCACAGGCCTTTCCTGGGGACCCT cccattggtttcacttagctgcctattgacattttatcttaaaattttagATAGTCTCTTGCTTAAGAAGACAATTGGATCTAAGAAGGAGATTGGGTTCTTAGAAGAGTCCACAAAAAATCCGCTTGTTTTTCAGCCTCCTTCACATACCTTCCCTGGGAAGTCTgtagggggtaatagtgtaacactcacaatgctccacatcaggggatgggt #### Prdx5_ID1854_3 --> 0 - 0 Original Alignment ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGG---------------------------gtgagcgatccttcagctagttgtgatcgaatgacgatgcgcctctgtct Alignment from CESAR ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGG---------------------------gtgagcgatccttcagctagttg Alignment from Spaln_aa2Genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGTG------------AGCGATCCTTCAgctagttgtgatcgaatgacgat Alignment from Spaln_nt2Genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGgtgagcgatccttcagctagttgtgatcgaatgacgatgcgcctctgtct Alignment from Pairagon ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGgtgagcgatccttcagctagttgtgatcgaatgacgatgcgcctctgtct Alignment from Exonerate_protein2genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGTGAGCGATCCTTCAGCTAGTTgtgatcgaatgacgatgcgcctctgtct Alignment from Exonerate_coding2genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAG gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGTGAGCGATCCTTCAGCTAGTTgtgatcgaatgacgatgcgcctctgtct Alignment from GeneWise ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAA- gctagccccagggcatgcactgatagtgtaaggtcccaccctgcccccagGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCCCGGAAAGCTAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGTGAGCGATCCTTCAGCTAGTTgtgatcgaatgacgatgcgcctctgtct #### Prpf19_ID3045_4 --> 0 - 1 Original Alignment CCTTGCAGGATGAGTGG GATGCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAg ctCTGGCTA CCTTACAAGATGAATGGgtcagtcttttcactctggtctcttgtcctcag---GCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAggtgagtctcattctactgtcctgtgattgtgacactcacagctTTGGCCA Alignment from CESAR CCTTGCAGGATGAGTGG GATGCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAg ctCTGGCTA CCTTACAAGATGAATGGgtaaggaatttcactctggtctcttgtcctcag---GCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAggtgagtctcattctactgtcagtgatgtcacctgtccccagctTTGGCCA Alignment from Spaln_aa2Genome CCTTGCAGGATGAGTGG GATGCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAG CTCTGGCTA CCTTACAAGATGAATGGgtcagtcttttcactctggtctcttgtcctcag---GCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAGgtgagtctcattctactgtcctgtgattgtgacactcacagCTTTGGCCA Alignment from Spaln_nt2Genome CCTTGCAGGATGAGTGG GATGCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAG CTCTGGCTA CCTTACAAGATGAATGGgtcagtcttttcactctggtctcttgtcctcag---GCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAGgtgagtctcattctactgtcctgtgattgtgacactcacagCTTTGGCCA Alignment from Pairagon CCTTGCAGGATGAGTGGG------------------------------ATGCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAG CTCTGGCTA CCTTACAAGATGAATGGGTCAGTCTTTTCACTCTGGTCTCTTGTCCTCAGGCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAGgtgagtctcattctactgtcctgtgattgtgacactcacagCTTTGGCCA Alignment from Exonerate_protein2genome TGCAGGATGAGTGGGAT GCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAG CTCTGGCTA TACAAGATGAATGG---gtcagtcttttcactctggtctcttgtcctcagGCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAGgtgagtctcattctactgtcctgtgattgtgacactcacagCTTTGGCCA Alignment from Exonerate_coding2genome ccttacaagatgaatgggtcagtcttttcactctggtctcttgtcctcaggcagtcatgctgcacagcttcactcttcgccaacaactgcaaactacccgccaggaactgtgccatgctctgtaccaacatgatgctgcctgccgagtcattgctcggctcaccaaagaggtcactgctgctcgagaaggtgagtctcattctactgtcctgtgattgtgacactcacagctttggcca Alignment from GeneWise CCTTGCAGGATGAGTGG------------------------------GATGCAGTCATGCTGCACAGCTTCACTCTTCGCCAGCAACTGCAGACAACCCGCCAGGAGCTGTCCCATGCTCTGTACCAACACGATGCTGCCTGCCGAGTCATTGCCCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAG CTCTGGCTA CCTTACAAGATGAATGGGTCAGTCTTTTCACTCTGGTCTCTTGTCCTCAGGCAGTCATGCTGCACAGCTTCACTCTTCGCCAACAACTGCAAACTACCCGCCAGGAACTGTGCCATGCTCTGTACCAACATGATGCTGCCTGCCGAGTCATTGCTCGGCTCACCAAAGAGGTCACTGCTGCTCGAGAAGgtgagtctcattctactgtcctgtgattgtgacactcacagCTTTGGCCA #### Prpf19_ID3046_5 --> 2 - 0 Original Alignment CTCGAGAAg ctCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAggtgagtattctactgtcaggctgttgttttctctctcaaagct---GCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta Alignment from CESAR CTCGAGAAg ctCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAggtgagtctcattctaccaggctgttgttttctctctcaaagct---GCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta Alignment from Spaln_aa2Genome CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAGgtgagtattctactgtcaggctgttgttttctctctcaaagCT---GCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta Alignment from Spaln_nt2Genome CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAGgtgagtattctactgtcaggctgttgttttctctctcaaagCT---GCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta Alignment from Pairagon CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAGgtgagtattctactgtcaggctgttgttttctctctcaaagCT---GCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta Alignment from Exonerate_protein2genome CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAGgtgagtattctactgtcaggctgttgttttctctctcaaagCT---GCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTCGAGAA--GCTCTG------------------------------------GCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG CTCGAGAAGGTGAGTATTCTACTGTCAGGCTGTTGTTTTCTCTCTCAAAGCTGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCTAGTTCACCACCCAGTGTAATAgtaggctatcacccccccactagcagtacctcatgggaactagagagtta #### Prpf19_ID3047_6 --> 0 - 0 Original Alignment GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATGACCCCTGAGATTATCCAGAAG ttgttatgggtgcctgtcatgtgacgctctctcttatatgctgttttcag------GGAGATGCAATGGAATTGGGTGAGCTTGCTGGAGAAATGGGCCCAGAGATTATCCAGAAAgtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from CESAR GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATGACCCCTGAGATTATCCAGAAG ttacttttgttatgggtgcctgtcagctctctcttatatgctgttttcag------GGAGATGCAATGGAATTGGGTGAGCTTGCTGGAGAAATGGGCCCAGAGATTATCCAGAAAgtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from Spaln_aa2Genome GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATGACCCCTGAGATTATCCAGAAG ttgttatgggtgcctgtcatgtgacgctctctcttatatgctgttttcag------GGAGATGCAATGGAATTGGGTGAGCTTGCTGGAGAAATGGGCCCAGAGATTATCCAGAAAgtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from Spaln_nt2Genome GGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATGACCCCTGAGATTATCCAGAAG ttgttatgggtgcctgtcatgtgacgctctctcttatatgctgttttcagGGAGATGCAATGGAATTGGGTGAGCTTGCTGGAGAAATGGGCCCAGAGATTATCCAGAAAgtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from Pairagon GTTGTGGGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGG---AATGACCCCTGAGATTATCCAGAAG ttgttatgggtgcctgtcatgtgacgctctctcttatatgctgttttcag------------GGAGATGCAATGGAATTGGGTGAGCTTGCTGGAGAAATGGGCCCAGAGATTATCCAGAAAgtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from Exonerate_protein2genome GGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATGACCCCTGAGATTATCCAGAAG ttgttatgggtgcctgtcatgtgacgctctctcttatatgctgttttcagGGAGATGCAATGGAATTGGGTGAGCTTGCTGGAGAAATGGGCCCAGAGATTATCCAGAAAgtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from Exonerate_coding2genome CAAGACAAGGCTACTGTGCT TTGTTATGGGTGCCTGTCATgtgacgctctctcttatatgctgttttcagggagatgcaatggaattgggtgagcttgctggagaaatgggcccagagattatccagaaagtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca Alignment from GeneWise CA TTgttatgggtgcctgtcatgtgacgctctctcttatatgctgttttcagggagatgcaatggaattgggtgagcttgctggagaaatgggcccagagattatccagaaagtgaggtgagatccatccactgtacaccgtgacctatcacattaaccaca #### Prpf19_ID3048_7 --> 0 - 0 Original Alignment CTTCAAGACAAGGCTACTGTGCTAACCACGGAG------CGTAAGAAG acctaactaatagtgatgccgatttcaggcccggctctctattttggtagCTTCAA---GAGGCTACTGTGTTG------------------------gtgagactagccaatgtgaaaaactggcgacttaatcatggacgcctttg Alignment from CESAR CTTCAAGACAAGGCTACTGTGCTAACCACGGAGCGTAAGAAG acctaactaatagtgatgccgatttcaggcccggctctctattttggtagCTTCAAGAG---GCTACTGTGTTG------------------gtgagactagccaatgtgaaaaactggcgact Alignment from Spaln_aa2Genome CTTCAAGACAAGGCTACTGT acctaactaatagtgatgccgatttcaggcccggctctctattttggtagCTTCAAGAG---GCTACTGTgttggtgagactagccaatgtgaaaaactggcgacttaatcatggacgcctttg Alignment from Spaln_nt2Genome CTTCAAGACAAGGCTACTGTGCTAACCACGGAGCGTAAG-AAG acctaactaatagtgatgccgatttcaggcccggctctctattttggtagCTTCAAG---AGGCTACTGTGTT----GGTGAGACTAGCCAATgtgaaaaactggcgacttaatcatggacgcctttg Alignment from Pairagon CTTCAAGACAAGGCTACTGTGCTAACCACGGAGCGTAAGAAG acctaactaatagtgatgccgatttcaggcccggctctctattttggtagCTTCAAG---AGGCTACTGTGTT------------------Ggtgagactagccaatgtgaaaaactggcgacttaatcatggacgcctttg Alignment from Exonerate_protein2genome acctaactaatagtgatgccgatttcaggcccggctctctattttggtagcttcaagaggctactgtgttggtgagactagccaatgtgaaaaactggcgacttaatcatggacgcctttg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise acctaactaatagtgatgccgatttcaggcccggctctctattttggtagcttcaagaggctactgtgttggtgagactagccaatgtgaaaaactggcgacttaatcatggacgcctttg #### Prpf19_ID3053_12 --> 0 - 1 Original Alignment TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAGATGAGACCTCCGGCTGCt acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGATGAG------------tgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from CESAR TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAGATGAGACCTCCGGCTGCt acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGATGAG------------tgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from Spaln_aa2Genome TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAGATGAGA acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGATGAGTgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from Spaln_nt2Genome TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAGATGAGA acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGATGAGTgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from Pairagon TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAGATGAGACCTCCGGCTGCT acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGATGAG------------Tgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from Exonerate_protein2genome TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAG acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGatgagtgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from Exonerate_coding2genome TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAG acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGatgagtgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat Alignment from GeneWise TACTGGGCCTTCTCTGACATCCAGACAGGGCGTGTGCTCACTAAGGTGACAGATGAGA acttaaagtgccagactgtgttcaaatgtgatagcctgggctctttatagTACTGGGCCTTCTTTGACATCCAGACAGGGCGTGTGCTCACTAAGGCAACAGATGAGTgtaaaggattacaaacaatttcaattaaccaccatccgctatcttattat #### Prpf19_ID3054_13 --> 2 - 0 Original Alignment ctCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGGGACTTGAAG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagccCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGG---------gtatgtcatggaacgtaacacaggcagaaacagcagctcacagtggggag Alignment from CESAR ctCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGGGACTTGAAG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagccCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGG---------gtatgtcatggaacgtaacacaggcagaaacagcagctcac Alignment from Spaln_aa2Genome CTCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagCCCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGGgtatgtcatggaacgtaacacaggcagaaacagcagctcacagtggggag Alignment from Spaln_nt2Genome CTCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagCCCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGGgtatgtcatggaacgtaacacaggcagaaacagcagctcacagtggggag Alignment from Pairagon CTCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagCCCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGGgtatgtcatggaacgtaacacaggcagaaacagcagctcacagtggggag Alignment from Exonerate_protein2genome CTCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGGGACTTGAAG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagCCCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGGGTATGTCATggaacgtaacacaggcagaaacagcagctcacagtggggag Alignment from Exonerate_coding2genome CTCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGGGACTTGAAG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagCCCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGGGTATGTCATggaacgtaacacaggcagaaacagcagctcacagtggggag Alignment from GeneWise CTCTTACCTGTGCACAGTTCCACCCTGATGGGCTCATCTTTGGAACAGGAACCATGGACTCCCAGATCAAGATCTGG gggagattgtgaaatatgaaccctacataactttccccttctgaattcagCCCTTACCTGTGCACAGTTCCACCCTGATGGTCTCACCTTTGGAAGTGGCACTATGGACTCCCAAATTAGAATTTGGgtatgtcatggaacgtaacacaggcagaaacagcagctcacagtggggag #### Prpf19_ID3055_14 --> 0 - 0 Original Alignment GAGCGTACCAATGTGGCCAACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGAC---TTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcag------------GTCGTAATCTTCCCT------GCTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from CESAR GAGCGTACCAATGTGGCCAACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGAC---TTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tagtattttctctcatagtcaattgtgatccgtgtggcccctgccctcag------------GTCGTAATCTTCCCT------GCTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from Spaln_aa2Genome GTGGCCAACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGAC---TTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcagGTCGTAATCTTCCCT------GCTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from Spaln_nt2Genome GTGGCCAACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGA---CTTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcagGTCGTAATCTTCCCTG------CTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from Pairagon GAGCGTACCAATGTGGCCAACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGG---ACTTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcag------------GTCGTAATCTTCCCTG------CTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from Exonerate_protein2genome AACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGAC---TTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcagGTCGTAATCTTCCCTGCTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from Exonerate_coding2genome AACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGAC---TTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcagGTCGTAATCTTCCCTGCTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc Alignment from GeneWise GTGGCCAACTTCCCTGGCCATTCTGGCCCCATTACCAGCATCGCCTTCTCTGAGAATGGGTACTACCTGGCCACAGCAGCTGATGATTCCTCAGTCAAGCTCTGGGAC---TTACGCAAGTTGAAGAACTTCAAGACATTGCAGCTGGACAACAACTTTGAG tcatagtcaattgacattctattaatgatccgtgtggcccctgccctcagGTCGTAATCTTCCCT------GCTGGGCCTATCACCACCATTGTATTCTCTGAAAATGGGTACTACTTGGCCACATCAACAGATGATCCTCCAGTCAAGCTTTGGGAAAACATACAGAAGCTGAAAAACTTTAAAATGTTGCAGTTGCACAATAACTTTGAGgtaagacacttgatcccttttcttctctttcgcagttcttgtgctacccc #### Pygm_ID1685_9 --> 0 - 0 Original Alignment GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTG---GCCATCCCAGAGCTGATGAGGATTCTGGTGGACCTGGAACGACTGGACTGGGACAAG gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCA------------------------------gtaagattttcctcaagaatcgacaggttctgcttggaatatcgtgtagt Alignment from CESAR GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTGGCC---ATCCCAGAGCTGATGAGGATTCTGGTGGACCTGGAACGACTGGACTGGGACAAG gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCA------------------------------gtaagattttcctcaagaat Alignment from Spaln_aa2Genome GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTGGCC---ATCCCAGAGCTGATGAGGATTCTGGTGGACCTG------------GAACGACTGGACTGGGAC---AAG gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCAGTAAGATTTTCCTCAAGAATCGACAGGTTCTGCTTGGAATATCGTgtagt Alignment from Spaln_nt2Genome GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTGGC---CATCCCAGAGCTGATGAGGATTCT- gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCAgtaagattttcctcaagaatcgacaggttctgcttggaatatcgtgtagt Alignment from Pairagon GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTGG---CCATCCCAGAGCTGATGAGGATTCTG gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCAgtaagattttcctcaagaatcgacaggttctgcttggaatatcgtgtagt Alignment from Exonerate_protein2genome GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTGGCC---ATCCCAGAGCTGATGAGGATTCTG gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCAgtaagattttcctcaagaatcgacaggttctgcttggaatatcgtgtagt Alignment from Exonerate_coding2genome gatggagtggtcacaaatattcccctgcttcaattattttgattttttaggtggtgatacaacttaatgacacacgtcattctttggctaccattcctgagctgatgaggatcccagtaagattttcctcaagaatcgacaggttctgcttggaatatcgtgtagt Alignment from GeneWise GTGGCCATCCAGCTCAATGACACCCACCCCTCTTTGGCC---ATCCCAGAGCTGATGAGGATT------------------CTGGTGGACCTGGAACGACTGGACTGGGACAAG gatggagtggtcacaaatattcccctgcttcaattattttgattttttagGTGGTGATACAACTTAATGACACACGTCATTCTTTGGCTACCATTCCTGAGCTGATGAGGATCCCAGTAAGATTTTCCTCAAGAATCGACAGGTTCTGCTTGGAATATCGTGTAgt #### Pygm_ID1686_10 --> 0 - 0 Original Alignment GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--- acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from CESAR GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--- acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from Spaln_aa2Genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from Spaln_nt2Genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from Pairagon GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from Exonerate_protein2genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from Exonerate_coding2genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat Alignment from GeneWise GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagacgaatggagggtgactaatgctccatttatttatttattttagGCCTGGGATGTTACAGTAAAGACCTGCATCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGACACCTGCAGATAATTTATGAGATTAATCAATGTTTCTTGAATCGAgtaaggacagaatgatgatgaggaacctgaggagctggagtatgatgtat #### Pygm_ID1687_11 --> 0 - 2 Original Alignment CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCat gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACAG---atgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from CESAR CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCat gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACAG---atgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from Spaln_aa2Genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAAC gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACAGATgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from Spaln_nt2Genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTC---AAACAGATgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from Pairagon CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACA---GATgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from Exonerate_protein2genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACAG---ATgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from Exonerate_coding2genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACAG---ATgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc Alignment from GeneWise CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAAC gaaagggaagagttatgaaccagggatgggctggggtttctttgccacagCAGGTGGCAGCTGCATCTCCAGGGGATGTAGACAGGCTGTGGCGCACGTCACTAGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGTTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAACAGATgtgagtagcattgggatcgaggtacgccacagggccacaagatagaaagc #### Pygm_ID1692_16 --> 0 - 1 Original Alignment GCTGCACCCGGGTACCACATGGCTAAGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAg tcaatgccttaagagctcgtttatcgataaattcctttccttctctccag------------------------GAGATGCTCATTAAAATTATCACTGCAATA---GATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGggtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from CESAR GCTGCACCCGGGTACCACATGGCTAAGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAg agaattaaaccctaagaagtgtcttgataaattcctttccttctctccag------------------------GAGATGCTCATTAAAATTATCACTGCAATA---GATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGggtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from Spaln_aa2Genome GCTGCACCCGGGTACCACATGGCTAAGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAG tcaatgccttaagagctcgtttatcgataaattcctttccttctctccag------------------------GAGATGCTCATTAAAATTATCACTGCAATA---GATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGGgtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from Spaln_nt2Genome -AGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAG tcaatgccttaagagctcgtttatcgataaattcctttccttctctccagGAGATGCTCATTAAAATTATCACTGCAAT---AGATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGGgtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from Pairagon GCTGCACCCGGGTACCACATGGCTAAGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAG tcaatgccttaagagctcgtttatcgataaattcctttccttctctccagG------------------------AGATGCTCATTAAAATTATCACTGCAAT---AGATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGGgtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from Exonerate_protein2genome GCTGCACCCGGGTACCACATGGCTAAGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAG tcaatgccttaagagctcgtttatcgATAAATTCCTTTCCTTCTCTCCAGGAGATGCTCATTAAAATTATCACTGCAATA---GATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGGgtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from Exonerate_coding2genome tcaatgccttaagagctcgtttatcgataaattcctttccttctctccaggagatgctcattaaaattatcactgcaatagatgtggtcaatcatgacccgacagtgggggatcgtctccaagtgctttttctggagaactatcaggtaacgcttgctgagaggggtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg Alignment from GeneWise GCTGCACCCGGGTACCACATGGCTAAGATGATCATCAAGCTTATCACTGCCATTGGGGATGTGGTCAACCACGACCCTGCGGTAGGAGACCGCCTCCGAGTGATCTTCCTGGAGAACTACCGAGTCTCCCTTGCTGAGAAAG tcaatgccttaagagctcgtttatcgataaattcctttccttctctccagGAG------------------------ATGCTCATTAAAATTATCACTGCAATA---GATGTGGTCAATCATGACCCGACAGTGGGGGATCGTCTCCAAGTGCTTTTTCTGGAGAACTATCAGGTAACGCTTGCTGAGAGGGgtaggccgcaccaatgctgatggactactgctgctggctaagaagctctg #### Rab1b_ID845_3 --> 0 - 0 Original Alignment GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT--------------------- gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGATTAACTGGGAAGCTTGTTCGGACgtgaggtctaatatgctcctgttttcttgttgctctctattttgttctca Alignment from CESAR GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT--------------------- gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGATTAACTGGGAAGCTTGTTCGGACgtgaggtctaatatgctcctgttttcttgttgctctgaggaccccttcct Alignment from Spaln_aa2Genome GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT--------- gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGATTAACTGGGAAgcttgttcggacgtgaggtctaatatgctcctgttttcttgttgctctctattttgttctca Alignment from Spaln_nt2Genome GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT--------- gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGATTAACTGGGAAgcttgttcggacgtgaggtctaatatgctcctgttttcttgttgctctctattttgttctca Alignment from Pairagon GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT----------------------------------------------------------------------- gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGATTAACTGGGAAGCTTGTTCGGACGTGAGGTCTAATATGCTCCTGTTTTCTTGTTGCTCTCTATTTTGTTCTCA Alignment from Exonerate_protein2genome GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGA gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGAttaactgggaagcttgttcggacgtgaggtctaatatgctcctgttttcttgttgctctctattttgttctca Alignment from Exonerate_coding2genome GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGA gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGAttaactgggaagcttgttcggacgtgaggtctaatatgctcctgttttcttgttgctctctattttgttctca Alignment from GeneWise GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT--------------------- gccaggtgttggcttgtttccatctcagctctgtgtgctttgacatttagGATGATACTCACACAGAGAGTTACATCAGCACCATTGGGGTTGATTTTAAGATACGGACAATTAAACTGGATGGCAAAATCATCAAACTACAGATTAACTGGGAAGCTTGTTCGGACgtgaggtctaatatgctcctgttttcttgttgctctctattttgttctca #### Rab3il1_ID2647_3 --> 0 - 0 Original Alignment GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTGAG------ gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTGTgttggtctgatcccctgggttaacaactcctggtgcttttacagctccct Alignment from CESAR GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTGAG------ gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTGTgttggtctgatcccctgggttaacaactcctggtgcttttacagctttct Alignment from Spaln_aa2Genome GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTGAGGAAG gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTgtgttggtctgatcccctgggttaacaactcctggtgcttttacagctccct Alignment from Spaln_nt2Genome GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTGAG------ gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTGTgttggtctgatcccctgggttaacaactcctggtgcttttacagctccct Alignment from Pairagon GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTG---------------------------------------------------------- gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTGTGTTGGTCTGATCCCCTGGGTTAACAACTCCTGGTGCTTTTACAGCTCCCT Alignment from Exonerate_protein2genome GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTGAG gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAAtactgtgttggtctgatcccctgggttaacaactcctggtgcttttacagctccct Alignment from Exonerate_coding2genome GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTTGAGGAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCA gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTGTGTTGGTCTGATCCCCTGGGTTAACAACTCCTGGTGCTTTTACAGCTCCCT Alignment from GeneWise GAGCTGAAGCTAAAGGATGAAGAGTGTGAACGGCTTTGCAAAGTACGTGCACAGCTGGAGCAGGAGCTTGAGGAGCTGACAGCCAGCCTGTTT----------------------------------------------------------- gctagtgacgactccaactgagggcccatctcccatctttctctctgcagGAGCTGAAGCTAAAGGATGAGGAGTGTAAACGACTTTGCAGAGTTCGTGTAGAACAAGAGCAGGAGATCGAAGAGCCAACAGCCAGTCTATTCAAATACTGTGTTGGTCTGATCCCCTGGGTTAACAACTCCTGGTGCTTTTACAGCTCCCT #### Rab3il1_ID2648_4 --> 0 - 0 Original Alignment GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAG------ gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAGCGTCCCgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc Alignment from CESAR GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAG------ gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAGCGTCCCgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc Alignment from Spaln_aa2Genome GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAG---ATC gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAGCGTCCCgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc Alignment from Spaln_nt2Genome GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAGATC gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAG--Cgtcccgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc Alignment from Pairagon GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAG------ gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAGCGTCCCgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc Alignment from Exonerate_protein2genome GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAGATCGAC gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAGCGTCCCgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAAGCTCACAAGATGGTTCGGGAAGCCAACATGAAGCAGGCGACATCGGAAAAGCAGTTGAAGGAGGCTTGGGGCAAGATCGAC gggttaacaactcctggtgcttttacagctttctctcatcttggtcctagGAAGCCCACAAAATGGTCCAGGAAGCAAACATGAAACAGGCAACATCAGAAAAACAGCTGAAGGAAGCATGGGGCAAGCGTCCCgttggttggagcaaaatgatcactaatgcagtctatccctttttccaagc #### Rasgrp2_ID1704_3 --> 1 - 2 Original Alignment cTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------ag gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagcTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGaggtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from CESAR cTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------ag gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagcTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGaggtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from Spaln_aa2Genome CTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTCAGG----- gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagCTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGAGgtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from Spaln_nt2Genome CTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------AG gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagCTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGAGgtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from Pairagon CTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------AG gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagCTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGAGgtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from Exonerate_protein2genome CTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------AG gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagCTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGAGgtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from Exonerate_coding2genome CTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------AG gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagCTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGAGgtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca Alignment from GeneWise CTATCAGCAATCCCGGAAGGACAACTCCAATTCTCTACAGATGAAAACGTGTCACTTGGTC------AG gcagtaagtataaagcatatgcttaccttgtcccttttctataccttcagCTATCAACAATCCCAGAAGGATAACTCTAATTCCCTACAGATGAAAACATGTCACCTTGTCTGTCTGAGgtcagtctggtccctaaggtgaatcttggtcaaggcaggtgcaaggtcca #### Rasgrp2_ID1707_6 --> 0 - 0 Original Alignment ------TTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from CESAR ------TTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from Spaln_aa2Genome ATCCTGTTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from Spaln_nt2Genome ATCCTGTTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from Pairagon ATCCTGTTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from Exonerate_protein2genome ATCCTGTTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from Exonerate_coding2genome ATCCTGTTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt Alignment from GeneWise ------TTCCAAGACTACCACAGCTTTGTGACTCATGGCTGCACCGTAGACAACCCGGTCCTGGAGCGATTCATCTCCCTCTTCAACAGTGTCTCTCAGTGGGTCCAACTCATGATCCTCAGCAAGCCCACAGCCACGCAGCGGGCGCTGGTCATCACGCACTTCGTGCATGTGGCAGAG ctactcaacaatactaactgtcaacagtcctcaccattccctccctgtagATCCTTTTTCATGACTATCACAGTTTTGTCACACATGGATGCACTGTAGATAACCCAGTTCTGGAGCGATTCATCTCTCTCTTCAACAGTGTGCCCCAGTGGGTCCAGATAATGATCCTTAGCAAGCCAACAGCCACACAGCAGGCACTTGTCATTACTCACTTTGTACATGTAGCCGAGgtgagtacagtcctgtctcctttgttgaatgtacagatagatcacatttt #### Rasgrp2_ID1711_10 --> 0 - 0 Original Alignment CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCAGAGCACATTGAGAAGATGGTGGAG atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCAACCT---GTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGGCA------------------------gtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga Alignment from CESAR CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCAGAGCACATTGAGAAGATGGTGGAG atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCAA---CCTGTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGGCA------------------------gtgaggccatgctaatttctcagaaa Alignment from Spaln_aa2Genome CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTG atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCAA---CCTGTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGgcagtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga Alignment from Spaln_nt2Genome CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCA atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCC---TCAACCTGTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGGCAgtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga Alignment from Pairagon CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCA atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCAA---CCTGTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGGCAgtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga Alignment from Exonerate_protein2genome CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCA atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCAA---CCTGTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGGCAgtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga Alignment from Exonerate_coding2genome CCCACCAGCTGCACCCCGCCTCCCCGGCCCCCT ATATGCACTTCTACTATGACCCCTCGGGTACCAtgtccttgtgtgtccagcctaccagtccaacaagttgtatgtcacctcctcaacctgtgtttgaagagtggacttcagctgctaaacctaatcttgatcaagccctagtggcagtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga Alignment from GeneWise CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCA atatgcacttctactatgacccctcgggtaccatgtccttgtgtgtccagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCAACCT---GTGTTTGAAGAGTGGACTTCAGCTGCTAAACCTAATCTTGATCAAGCCCTAGTGGCAgtgaggccatgctaatttctcagaaaaaagctgtatgtttcacctgaaga #### Rbm20_ID11377_4 --> 1 - 1 Original Alignment t---------------------------GCTGGCCTCCGGAGTATACGTGCTTCA---GGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGg ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagtGTTGGTGACAACAAGAAGTTAATCGTAACTGGTCTCCAGAGTATCCGGGTATCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGggtgagcaaggtgaatggtagggctctgtgctagccattagttgtatgcaa Alignment from CESAR ccagttgtacattgtttccaaagaactaacactggtctcacaagaattgcc Alignment from Spaln_aa2Genome TGCTGGCCTCCGGAGTATACGTGCTTCAGGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGG ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagtgttggtgacaacaagaagttaatcgtaactggtctccagagTATCCGGGTA------------TCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGGgtgagcaaggtgaatggtagggctctgtgctagccattagttgtatgcaa Alignment from Spaln_nt2Genome AGTATACGTG---CTTCAGGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGG ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagtgttggtgacaacaagaagttaatcgtaactggtctccagAGTATCCGGGTATCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGGgtgagcaaggtgaatggtagggctctgtgctagccattagttgtatgcaa Alignment from Pairagon TG---------------------------CTGGCCTCCGGAGTATACGTG---CTTCAGGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGG ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagTGTTGGTGACAACAAGAAGTTAATCGTAACTGGTCTCCAGAGTATCCGGGTATCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGGgtgagcaaggtgaatggtagggctctgtgctagccattagttgtatgcaa Alignment from Exonerate_protein2genome TGCTGGCCTCCGGAGTATACGT---GCTTCAGGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGG ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagtgttggtgacaacaagaagttaatcgtAACTGGTCTCCAGAGTATCCGGGTATCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGGgtgagcaaggtgaatggtagggctctgtgctagccattagttgtatgcaa Alignment from Exonerate_coding2genome TGCTGGCCTCCGGAGTATACGT---GCTTCAGGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGGATTATACCTCAAATCTTGGAACATCATATGCAGCCATTCCAACGAGGGCC ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagtgttggtgacaacaagaagttaatcgtAACTGGTCTCCAGAGTATCCGGGTATCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGGGTGAGCAAGGTGAATGGTAGGGCTCTGTGCTAGCCATTAGTTGTATGCAA Alignment from GeneWise -------------------------AGTGCTGGCCTCCGGAGTATACGT---GCTTCAGGAGAGGGGACACTGTCTGCCTCTGCTAACAGCACAGCTGTTTATAACCCCACTGGAAACGAGG ctaatatgaaattaacaacgtaccattagtcgttgcctgtgtttctgtagTGTTGGTGACAACAAGAAGTTAATCGTAACTGGTCTCCAGAGTATCCGGGTATCATCAGGAGAGGGGACACACTCTGCCTCAGCTAATAGTACAGCCGTTTATAATCCAACAGGAAATGAGGgtgagcaaggtgaatggtagggctctgtgctagccattagttgtatgcaa #### Rbp4_ID7524_3 --> 0 - 2 Original Alignment TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATCGCT---GAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTG------ag caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGCA---AAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGCTGCaggtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from CESAR TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATC---GCTGAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTG------ag caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGCA---AAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGCTGCaggtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from Spaln_aa2Genome TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATC---GCTGAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAGC----- caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGCA---AAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGCTGCAGgtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from Spaln_nt2Genome TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATCGCTG---AGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAGC- caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGC---AAAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGCTgcaggtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from Pairagon TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCAT---CGCTGAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAG-- caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGC---AAAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGCTgcaggtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from Exonerate_protein2genome TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATC---GCTGAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAG caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGCA---AAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGctgcaggtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from Exonerate_coding2genome CGTTTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATC---GCTGAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAG caaatttagttggggggtgagcttaggcgtgacattcttcttgtttcCAGTTTTCAGACCTCCTGTATACTATTGCA---AAGGGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGctgcaggtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc Alignment from GeneWise TTCTCTGGGCTCTGGTATGCCATCGCCAAAAAGGACCCCGAGGGTCTCTTTTTGCAAGACAACATCATCGCT---GAGTTTTCTGTGGACGAGAAGGGTCATATGAGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAGC----- caaatttagttggggggtgagcttaggcgtgacattcttcttgtttccagTTTTCAGACCTCCTGTATACTATTGCAAAG---GGTCCGAAGGGGCTTTTTTTGCAAGACAATATCATTGCTGCTGAGTTTTCTGTAGACGAGAAGGGGCATATGAGTACTACTGCCAAGGGACAGGTACATCTCCTGAGCTGCAGgtgccggaacctgagtgcactactgtctctttagactaacaaagcccttc #### Rcor2_ID2099_10 --> 2 - 0 Original Alignment ctATTCGTAGATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA gccaactgttttgttcaaaaaaaaatataatgttctcttacacttgacagcc---------TATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaattttaacttctctgccttatagGTACAAA Alignment from CESAR ctATTCGTAGATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA agaggagtggccaactgttttgttctataatgttctcttacacttgacagcc---------TATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaagtatgctctctgtttcccacagGTACAAA Alignment from Spaln_aa2Genome GATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA gccaactgttttgttcaaaaaaaaatataatgttctcttacacttgacagCCTATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaattttaacttctctgccttatagGTACAAA Alignment from Spaln_nt2Genome CTATTCGTAGATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA gccaactgttttgttcaaaaaaaaatataatgttctcttacacttgacagC---------CTATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaattttaacttctctgccttatagGTACAAA Alignment from Pairagon CTATTCGTAGATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA gccaactgttttgttcaaaaaaaaatataatgttctcttacacttgacagCC---------TATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaattttaacttctctgccttatagGTACAAA Alignment from Exonerate_protein2genome CTATTCGTAGATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA gccaactgttttgttcaaaaaaaaatataatgttctcttacACTTGACAGCCTATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaattttaacttctctgccttatagGTACAAA Alignment from Exonerate_coding2genome CTATTCGTAGATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAGGTCCAGATTACATCTGTC gccaactgttttgttcaaaaaaaaatataatgttctcttacACTTGACAGCCTATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGGTGAGTGACCTCTCCGTGgaattttaacttctctgccttataggtacaaa Alignment from GeneWise GATACGGCAAAGACTTTGGGGCTATTGCAGAGGTGATTGGGAACAAGACTCTGACCCAAGTGAAGACCTTCTTTGTGAGCTATCGTCGCCGCTTCAACCTGGAAGAGGTGCTGCAGGAATGGGAGGCTGAGCAGGATGGGGCCCCCGCAGCTCCGGTCCCCACGGAAGAGGCCAGGCGAGGGGCTCCTGTACCAGCCACAGCCCTAGAAGAAGATGATGAG GTCCAGA gccaactgttttgttcaaaaaaaaatataatgttctcttacacttgacagCCTATGGGACAGACTTTGGGGCTATTGCAGAAGTGATCGGAAACAAGACCCTGACCCAAGTGAAGACATTCTTTGTGAGCTATCGCCGCCTCTTTAACCTGGAAGAGGTGCTGCAGGAATGGGAAGCTGAGCAAGATGGGGCCCCCACAGCCCTAGTCCCCACAGAAGAGGCCCGGCAAGGGGCTCCTGTTTCAACCACAGCCCTTGAAGAGGATGATAAGgtgagtgacctctccgtggaattttaacttctctgccttatagGTACAAA #### Rin1_ID807_2 --> 1 - 0 Original Alignment gCCATCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A tttagaacattggacagaggaagctgagaggttgacgtttctctccgtagg---GCAACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcagA Alignment from CESAR gCCATCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A gattttagaacattggacagaggaagagaggttgacgtttctctccgtagg---GCAACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaaaggttagcctttccttttatagA Alignment from Spaln_aa2Genome GCCATCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A tttagaacattggacagaggaagctgagaggttgacgtttctctccgtagG---GCAACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcagA Alignment from Spaln_nt2Genome GCCATCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A tttagaacattggacagaggaagctgagaggttgacgtttctctccgtagGGCA---ACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcagA Alignment from Pairagon GCCATCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A tttagaacattggacagaggaagctgagaggttgacgtttctctccgtagGGCA---ACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcagA Alignment from Exonerate_protein2genome ATCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A tttagaacattggacagaggaagctgagaggttgacgtttctctccgtagGGCAACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcagA Alignment from Exonerate_coding2genome tttagaacattggacagaggaagctgagaggttgacgtttctctccgtagggcaacagacccactgtatgacactcctgatacaagaggtgtccaggctggtgggtcacaccaaccggcatgcaaagtcagccttcacgagcgactgttgatcacatgtcttgtgtggcttcggctccgggccaatgcagctactgtactgcatgtactaagtacaaaacctccaggggtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcaga Alignment from GeneWise TCTACAGACCCACTGTATGACACACCTGATACCAGAGGGGTACAGGCAGGCGGGTCCCAACAGCCAGCACGTACTGTGAGCCTTCGGGAGCGGCTGCTGATCACCCGGCCTGTGTGGTTACAGCTGCGGGCCAACGCTGCAGCCGCGCTGCACGTGCTGAGGACAGAGCCTCCGGGG A tttagaacattggacagaggaagctgagaggttgacgtttctctccgtaggGCAACAGACCCACTGTATGACACTCCTGATACAAGAGGTGTCCAGGCTGGTGGGTCACACCAACCGGCATGCAAAGTCAGCCTTCACGAGCGACTGTTGATCACATGTCTTGTGTGGCTTCGGCTCCGGGCCAATGCAGCTACTGTACTGCATGTACTAAGTACAAAACCTCCAGGGgtaagcctcttagttacaagatcttaagtcttgtctgtctcctttgcagA #### Rin1_ID812_7 --> 2 - 1 Original Alignment aaTTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---g cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagaaTTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCggtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from CESAR aaTTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---g cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagaaTTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCggtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from Spaln_aa2Genome AATTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---G cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagAATTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCGgtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from Spaln_nt2Genome AATTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---G cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagAATTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCGgtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from Pairagon AATTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---G cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagAATTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCGgtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from Exonerate_protein2genome AATTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---G cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagAATTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCGgtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from Exonerate_coding2genome AATTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCA---G cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagAATTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCGgtgagttatcaccaacttccccagggctagtgcacatacacacctttaga Alignment from GeneWise AATTGGTCCTGGAGAAGTCCCTGCATCGCTCTGTTCTCAAGCCTCTTCGACCCATTCTGGCTGCCCGCCTGCGGCGCCGGCTTTCCGCAGATGGTTCCCTCGGCCGCCTAGCTGAGGGCTTCCGCCTGGCCCGGACCCAGGGGCCTGGAGCCTTCGGGTCCCACCTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTGCGCCAGAAGCTGCTGCAGCTCCTTCGTGCCTACTCACCTAGTGCCCAGGTCAAGTGGCTCCTGCAGGCCTGCAAGCTGCTATACACAGCCCTGAAGAGCCAGGCAGGA- cagtttggaaaggattccaacatcaaatcacaagaaaaattgtgtttcagAATTGGTGCTGGAGAAGTCCCAACATCGCTCAGTTCTCAAACCACTTCGACCCATCCTAGCTGCTCGTCTACGCCATCGCCTTTCTACTGATGGTTCTCTTGGGTGTCTAGCAGAGGGCTTTCTCCTCACCCAAACCCAGGGACCTGGGGCCTTTGGGCCCCACTTGACTCTTTCTTCCCCAGTGGAGACAGAACAGGTTTGTCAGAAACTTCTACAGCTCCTACGTGCATACTCGCCAAGCGCACAAGTTGAGTGGCTCCTACAGGCCTGCAAGCTACTGTATACAGCCCTAAAGAGCCAAGCATTCGgtgagttatcaccaacttccccagggctagtgcacatacacacctttaga #### Rnaseh2c_ID1103_2 --> 2 - 0 Original Alignment gg---------------------CTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC taggtcttgagaggcccatgggtttgacccacccacctgttcccctacaggaTCATTAATGCTCATGTCGAAATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTAGAGAGAGTCTTAgtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa Alignment from CESAR gg---------------------CTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC taggtcttgagaggcccatgggtttgacccacccacctgttcccctacaggaTCATTAATGCTCATGTCGAAATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTAGAGAGAGTCTTAgtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa Alignment from Spaln_aa2Genome GG---------------------CTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC taggtcttgagaggcccatgggtttgacccacccacctgttcccctacagGATCATTAATGCTCATGTCGAAATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTAGAGAGAGTCTTAgtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa Alignment from Spaln_nt2Genome GCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAG-GCGCAGGAGCCGCTGGAGCG taggtcttgagaggcccatgggtttgacccacccacctgttcccctacaggatcattaatgctcatgtcgaaattacagGTACCATTTCATGGCTGTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGAAGATGATGCCCAGGAACCATTAGAGAGAGT---CTT-AGTGAGTATTTAGAG-----AGTGTTCTAGTGGGCATGAAGTGATTATAC- Alignment from Pairagon ------------GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC taggtcttgagaggcccatgggtttgacccacccacctgttcccctacaggatcattaatgctcatgtcgaaattacagGTACCATTTCATGGCT--------------------GTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGA------------------------------------------------------------AGATGATGCCCAGGAACCATTAGAGAGAGTCTTAgtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa Alignment from Exonerate_protein2genome GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAG taggtcttgagaggcccatgggtttgacccacccacctgttcccctacaggatcattaatgctcatgtcgaAATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGAAGATGATGCCCAGgaaccattagagagagtcttagtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa Alignment from Exonerate_coding2genome taggtcttgagaggcccatgggtttgacccacccacctgttcccctacaggatcattaatgctcatgtcgaaattacaggtaccatttcatggctgtggcttgtggggtgaagagatagctgtcccccctgagtttgccggatttgtaatggttacagaagatgatgcccaggaaccattagagagagtcttagtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa Alignment from GeneWise --------------------GGGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC taggtcttgagaggcccatgggtttgacccacccacctgttcccctacagGATCATTAATGCTCATGTCGAAATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAAGAGATAGCTGTCCCCCCTGAGTTTGCCGGATTTGTAATGGTTACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTAGAGAGAGTCTTAgtgagtatttagagagtgttctagtgggcatgaagtgattatactagtaa #### Rps6ka4_ID1807_13 --> 0 - 0 Original Alignment CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG------ cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGCTTCTAgtaaggtgagcaaaggacatggagtttag Alignment from CESAR CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG------ cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGCTTCTAgtaaggtgagcaaaggacatggagtttag Alignment from Spaln_aa2Genome CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG------ cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGCTTCTAgtaaggtgagcaaaggacatggagtttag Alignment from Spaln_nt2Genome CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG------ cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGCTTCTAgtaaggtgagcaaaggacatggagtttag Alignment from Pairagon CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG------ cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGCTTCTAgtaaggtgagcaaaggacatggagtttag Alignment from Exonerate_protein2genome CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGcttctagtaaggtgagcaaaggacatggagtttag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG------ cataaggggaaaggtctaaattgtacaacccagtgagggcttgtatactttacatttacacttttcttcagCTACACACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTACTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCTTACGGAGTCTAGTTTCAGCCGTAAGCTTCATGTATGAGGAGGCTGGCGTAGTGCACCGTGACCTGAAACCTGAGCTTCTAgtaaggtgagcaaaggacatggagtttag #### Rps6ka4_ID1813_7 --> 0 - 2 Original Alignment ------------------------------GCTGTGGACTGGTGGAGCCTGGGTATCCTGCTCTTCGAGCTGCTGACAGGGGCCTCACCCTTCACACTGGAGGGAGAGAGGAACACTCAGGCTGAGGTGTCCcg GCAGAGCTGGGCGTGGTAAGgtgagttactttggtggactgagtgcgtgttccccaccgctctctgcctagTGTGAACATGGCTATGCCTCATCATTCCCCGCTGTGGACTGGTGGAGCCTTGGCATACTTCTCTTTGGGTTGCTTACTGGGGCTTCACCTTTCACCCTTGAGAGGGAGAGGAACACTCAGGCTGAAGTATCTcggtgagatcttattgagtgtaccagttgta Alignment from CESAR cgtcttctattttcaatctcttcactacattattgagcgctgggaaagtct Alignment from Spaln_aa2Genome AAG GCTGGACATGGC---------------AAGGCTGTGGACTGGTGGAGCCTGGGTATCCTGCTCTTCGAGCTGCTGACAGGGGCCTCACCCTTCACACTGGAGGGAGAGAGGAACACTCAGGCTGAGGTGTCCCG GCAGAgctgggcgtggtaaggtgagttactttggtggactgagtgcgtgttccccaccgctctctgcctagTGTGAACATGGCTATGCCTCATCATTCCCCGCTGTGGACTGGTGGAGCCTTGGCATACTTCTCTTTGGGTTGCTTACTGGGGCTTCACCTTTCACCCTTGAGAGGGAGAGGAACACTCAGGCTGAAGTATCTCGgtgagatcttattgagtgtaccagttgta Alignment from Spaln_nt2Genome GCAAG GCTGGACATGGCAAGGC---------------TGTGGACTGGTGGAGCCTGGGTATCCTGCTCTTCGAGCTGCTGACAGGGGCCTCACCCTTCACACTGGAGGGAGAGAGGAACACTCAGGCTGAGGTGTCCCG GCAGAgctgggcgtggtaaggtgagttactttggtggactgagtgcgtgttccccaccgctctctgcctagTGTGAACATGGCTATGCCTCATCATTCCCCGCTGTGGACTGGTGGAGCCTTGGCATACTTCTCTTTGGGTTGCTTACTGGGGCTTCACCTTTCACCCTTGAGAGGGAGAGGAACACTCAGGCTGAAGTATCTCGgtgagatcttattgagtgtaccagttgta Alignment from Pairagon GCAAGGCTGGACATGGCAAG---------------------------------------------------------------------------------GCTGTGGACTGGTGGAGCCTGGGTATCCTGCTCTTCGAGCTGCTGACAGGGGCCTCACCCTTCACACTGGAGGGAGAGAGGAACACTCAGGCTGAGGTGTCCCG GCAGAGCTGGGCGTGGTAAGGTGAGTTACTTTGGTGGACTGAGTGCGTGTTCCCCACCGCTCTCTGCCTAGTGTGAACATGGCTATGCCTCATCATTCCCCGCTGTGGACTGGTGGAGCCTTGGCATACTTCTCTTTGGGTTGCTTACTGGGGCTTCACCTTTCACCCTTGAGAGGGAGAGGAACACTCAGGCTGAAGTATCTCGgtgagatcttattgagtgtaccagttgta Alignment from Exonerate_protein2genome GCAAGGCTGGACATGGCAAG GCTGTGGACTGGTGGAGCCTGGGTATCCTGCTCTTCGAGCTGCTGACAGGGGCCTCACCCTTCACACTGGAGGGAGAGAGGAACACTCAGGCTGAGGTGTCCCG GCAGAGCTGGGCGTGGTAAGgtgagttactttggtggactgagtgcgtgttccccaccgctctctgcctagtgtgaacatggctatgcctcatcattccccGCTGTGGACTGGTGGAGCCTTGGCATACTTCTCTTTGGGTTGCTTACTGGGGCTTCACCTTTCACCCTTGAGAGGGAGAGGAACACTCAGGCTGAAGTATCTCGgtgagatcttattgagtgtaccagttgta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GCAAGGCTGGACATGGCAAG ------------------------------GCTGTGGACTGGTGGAGCCTGGGTATCCTGCTCTTCGAGCTGCTGACAGGGGCCTCACCCTTCACACTGGAGGGAGAGAGGAACACTCAGGCTGAGGTGTCCCG GCAGAGCTGGGCGTGGTAAGgtgagttactttggtggactgagtgcgtgttccccaccgctctctgcctagTGTGAACATGGCTATGCCTCATCATTCCCCGCTGTGGACTGGTGGAGCCTTGGCATACTTCTCTTTGGGTTGCTTACTGGGGCTTCACCTTTCACCCTTGAGAGGGAGAGGAACACTCAGGCTGAAGTATCTCGgtgagatcttattgagtgtaccagttgta #### Rps6ka4_ID1816_4 --> 2 - 0 Original Alignment GACGGATGCCAAGCTGCACCTCATCCTGg acTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTAcgtaaaagtttgcacttggcagtg---cctctgcccactttagatTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from CESAR ACTGCACTACGCCTTCCAGACGGATGCCAAGCTGCACCTCATC acTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG ACTGCACTATGCCTTTCAGACAGATACCAAGCTCCACCTCACTttggcagtgcctctgcccactttagatTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from Spaln_aa2Genome GACGGATGCCAAGCTGCACCTCATCCTGG ACTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTACgtaaaagtttgcacttggcagtgcctctgcccactttagATTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from Spaln_nt2Genome GACGGATGCCAAGCTGCACCTCATCCTGG ACTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTACgtaaaagtttgcacttggcagtgcctctgcccactttagATTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from Pairagon GACGGATGCCAAGCTGCACCT---------------------------------------CATCCTGGACTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTACGTAAAAGTTTGCACTTGGCAGTGCCTCTGCCCACTTTAGATTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from Exonerate_protein2genome GACGGATGCCAAGCTGCACCTCATCCTGG ACTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTACgtaaaagtttgcacttggcagtgcctctgcccactttagATTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from Exonerate_coding2genome GACGGATGCCAAGCTGCACCTCATCCTGG ACTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTACgtaaaagtttgcacttggcagtgcctctgcccactttagATTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca Alignment from GeneWise GACGGATGCCAAGCTGCACCTC---------------------------------------ATCCTGGACTACGTGAGCGGTGGTGAGATGTTCACTCACCTCTACCAGCGCCAGTACTTCAAGGAGGCTGAGGTTCGAGTGTATGGGGGCGAGATTGTGCTGGCCCTGGAACACCTGCACAAG GACAGATACCAAGCTCCACCTCACTTTACGTAAAAGTTTGCACTTGGCAGTGCCTCTGCCCACTTTAGATTATGTGTGCGGTGGTGAAATGTTTACTCACCTCTACCAGCGCCATTACTTCAAGGAGACTGAGGTACGAGTGTATGGGGGTGAGATTGTGCTAGCTTTAGAACACCTGCACAAGgtaactgacaacatggctattttgcaaca #### Rps6kb2_ID371_11 --> 0 - 0 Original Alignment TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG--- tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGGTCgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from CESAR TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGgtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from Spaln_aa2Genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGgtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from Spaln_nt2Genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGgtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from Pairagon TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGgtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from Exonerate_protein2genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGgtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from Exonerate_coding2genome tcttgaccacctacattcatttttgcccttttttttttttttttttttagttactgaagcgtaatccaacacaacaaattggggatgatttaggagatgctgctgatgtccaggtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa Alignment from GeneWise TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccacctacattcatttttgcccttttttttttttttttttttagTTACTGAAGCGTAATCCAACACAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCCAGgtcgtacatagatctgtcgctttacctgctggagaaaacagacatcaagaaaa #### Rps6kb2_ID372_10 --> 0 - 0 Original Alignment ------CCGCCCTTCACTGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagCCCCGACCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAAGTTA---CTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from CESAR ------CCGCCCTTCACTGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagCCCCGACCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAAGTTA---CTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from Spaln_aa2Genome CCGCCCTTC------ACTGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagCCCCGACCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAAG---TTACTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from Spaln_nt2Genome GCCGCCCTTCAC-----TGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagCCCCGACCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAA---GTTACTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from Pairagon -------------------------------------------------------GCCGCCCTTCACTGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG AGTGTAACTGCATTGAGCTCTTCCTTGCCTTGCCTTACCTTGCTGTCTAGCCCCGACCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAAGT---TACTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from Exonerate_protein2genome CCGCCCTTCACTGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagccccgaCCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAAGTTA---CTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from Exonerate_coding2genome agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagccccgaccgcctttcactgctgaaaaccagaagaaaccaactgataatataattaaaagtaagttactgcccccagatcttatgcctgacgctcgggaccttgctagaaaggtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc Alignment from GeneWise ------CCGCCCTTCACTGCAGAGAACCGGAAGAAAACTATGGATAAAATCATTAAAGGGAAGCTGGTGCTGCCCCCCTACCTCACCCCGGATGCCCGGGACCTTGCCAAAAAG agtgtaactgcattgagctcttccttgccttgccttaccttgctgtctagCCCCGACCGCCTTTCACTGCTGAAAACCAGAAGAAACCAACTGATAATATAATTAAAAGTAAGTTA---CTGCCCCCAGATCTTATGCCTGACGCTCGGGACCTTGCTAGAAAGgtgagttcctttctcagtcaaaaaaatacacacaccttcttcagatttcc #### Rps6kb2_ID374_8 --> 2 - 2 Original Alignment gcCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTAC------at aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagggCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAGTatgtgagttttgagagggataccccatgcgggactatgactgtgactctctc Alignment from CESAR gcCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTAC------at aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagggCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAGTatgtgagttttgagagggataccccatgcgggactatgactgcctctcctgt Alignment from Spaln_aa2Genome GCCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTACATG----- aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagGGCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAGTATgtgagttttgagagggataccccatgcgggactatgactgtgactctctc Alignment from Spaln_nt2Genome GCCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTACAT-- aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagGGCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAgtatgtgagttttgagagggataccccatgcgggactatgactgtgactctctc Alignment from Pairagon GCCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTACAT------ aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagGGCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAGTATgtgagttttgagagggataccccatgcgggactatgactgtgactctctc Alignment from Exonerate_protein2genome GCCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTAC------AT aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagGGCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAGTATgtgagttttgagagggataccccatgcgggactatgactgtgactctctc Alignment from Exonerate_coding2genome GCCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTG aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagggcacatcaaactaacatacttgggtctctgcaaggagtcaattcatgagggcactatcaatcacactttctgtGGTACCAAAGAGTACATCAGTATGTGAGTTTTGAGAGGGATACCCCATGCGGGACTATGACTGTGACTCTCTC Alignment from GeneWise GCCACATCAAACTGACAGACTTTGGACTTTGCAAGGAGTCCATTCATGAGGGTGCTATCACTCACACCTTCTGTGGCACCATTGAGTACATGGCC-- aaacttagttttcccagtgtcaattgacttctttcccttcttgtttctagGGCACATCAAACTAACATACTTGGGTCTCTGCAAGGAGTCAATTCATGAGGGCACTATCAATCACACTTTCTGTGGTACCAAAGAGTACATCAGTATgtgagttttgagagggataccccatgcgggactatgactgtgactctctc #### Rps6kb2_ID375_7 --> 1 - 1 Original Alignment cTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGg aggatacctactgtagcgagtaccttacttgttcaaatatggttacttagt------CTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAAA---ATGCTCACCAGTCAGggtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca Alignment from CESAR cTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGg gtctgcaggatacctactgtagcgatacttgttcaaatatggttacttagt------CTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAAA---ATGCTCACCAGTCAGggtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca Alignment from Spaln_aa2Genome CTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGG aggatacctactgtagcgagtaccttacttgttcaaatatggttacttagT------CTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAAA---ATGCTCACCAGTCAGGgtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca Alignment from Spaln_nt2Genome CCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGG aggatacctactgtagcgagtaccttacttgttcaaatatggttacttagTCTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAA---AATGCTCACCAGTCAGGgtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca Alignment from Pairagon ---------------------------------------------------CTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGG AGGATACCTACTGTAGCGAGTACCTTACTTGTTCAAATATGGTTACTTAGTCTT-------GCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAA---AATGCTCACCAGTCAGGgtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca Alignment from Exonerate_protein2genome CTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGG aggatacctactgtagcgagtaccttacttgttcaaatatggttacttagT------CTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAAA---ATGCTCACCAGTCAGGgtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca Alignment from Exonerate_coding2genome CTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGGGCCACATCAAACTGACA aggatacctactgtagcgagtaccttacttgttcaaatatggttacttagT------CTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAAA---ATGCTCACCAGTCAGGGTAAGATTCACATCACTgtatggtgataaaacttagttttcccagtgtca Alignment from GeneWise CTTCTACCTGGCAGAGATCACACTAGCCCTGGGCCATCTCCATTCCCACGGCATCATCTACCGGGACCTCAAGCCTGAGAACATCATGCTCAGCAGCCAGG aggatacctactgtagcgagtaccttacttgttcaaatatggttacttagT------CTTGCGGAGATCACATTGGCATTAGGCCATCTCCATTTCCATAGCATCATTTACCGTGATCACAAGCCAGGGAAA---ATGCTCACCAGTCAGGgtaagattcacatcactgtatggtgataaaacttagttttcccagtgtca #### Rrp12_ID8295_28 --> 1 - 1 Original Alignment c---------------ATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTg gtaggttagggcagggttgcctcctatttatccttgactaatctccctagcGTTACCATACATAAGATCGAGGAAGTTTCAGCTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGCAG------TTGGTC------AGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCGAAAGTAGCACATCGTATCCAGggtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from CESAR c---------------ATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTg gtaggttagggcagggttgcctcctatttatccttgactaatctccctagcGTTACCATACATAAGATCGAGGAAGTTTCAGCTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGCAG------TTGGTC------AGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCGAAAGTAGCACATCGTATCCAGggtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from Spaln_aa2Genome C---------------ATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaggttagggcagggttgcctcctatttatccttgactaatctccctagCGTTACCATACATAAGATCGAGGAAGTTTCAGCTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGCAG------TTGGTC------AGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCGAAAGTAGCACATCGTATCCAGGgtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from Spaln_nt2Genome CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaggttagggcagggttgcctcctatttatccttgactaatctccctagcgttaccatacataag-ATCGAGGAAGTTTCAGCTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGC------AGTTGG------TCAGGAGCCGATCATG---GAAGGATGGAGGTGG---TGCACCTCTCAATTTC------CCGAAAGTAGCACATCGTATCCAGGgtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from Pairagon CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaggttagggcagggttgcctcctatttatccttgactaatctccctagcgttaccatacataagatcgaggaagtttcag-----------------CTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGCAG-------------------------------------------------------------------------------------------------TTGgtcaggagccgatcatggaaggatggaggtggtgcacctctcaatttcccgaaagtagcacatcgtatccagggtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from Exonerate_protein2genome CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaggttagggcagggttgcctcctatttatccttgactaatctccctagcgttaccatacataaGATCGAGGAAGTTTCAGCTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGCAG------------TTGGTCAGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCGAAAGTAGCACATCGTATCCAGGgtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from Exonerate_coding2genome gtaggttagggcagggttgcctcctatttatccttgactaatctccctagcgttaccatacataagatcgaggaagtttcagctgactcaaaagatgagtttgaggaagaacagagaggccgaggcaaagagcagttggtcaggagccgatcatggaaggatggaggtggtgcacctctcaatttcccgaaagtagcacatcgtatccagggtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg Alignment from GeneWise -------------AGCATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaggttagggcagggttgcctcctatttatccttgactaatctccctagCGTTACCATACATAAGATCGAGGAAGTTTCAGCTGACTCAAAAGATGAGTTTGAGGAAGAACAGAGAGGCCGAGGCAAAGAGCAGTTG------------GTCAGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCGAAAGTAGCACATCGTATCCAGGgtaggtatgggtgaggatgcccttcatggctcggggggtcaagggttagg #### Rrp12_ID8301_22 --> 0 - 0 Original Alignment CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGAG--------- ggggcatataggattgactattcaatgctcttcacttccttttaaaatagCCC---CTGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAGCCAATAGATgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga Alignment from CESAR CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGAG--------- ggggcatataggattgactattcaatgctcttcacttccttttaaaatagCCC---CTGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAGCCAATAGATgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga Alignment from Spaln_aa2Genome CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGAG--------- ggggcatataggattgactattcaatgctcttcacttccttttaaaatagCCC---CTGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAGCCAATAGATgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga Alignment from Spaln_nt2Genome CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGA ggggcatataggattgactattcaatgctcttcacttccttttaaaatagCCCC---TGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAgccaatagatgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga Alignment from Pairagon CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGAG--------------------- ggggcatataggattgactattcaatgctcttcacttccttttaaaatagCCCC---TGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAGCCAATAGATGTTTGATTGCAGgtcagactctggactcctgaagccagacctaaggagga Alignment from Exonerate_protein2genome CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGAG ggggcatataggattgactattcaatgctcttcacttccttttaaaaTAGCCCCTGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAGccaatagatgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga Alignment from Exonerate_coding2genome ggggcatataggattgactattcaatgctcttcacttccttttaaaatagcccctgaaatgtctcatacatattgtgaaaacactgttagctgaacatgaagaattcacagctgcattgatccctgagccaatagatgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga Alignment from GeneWise CCCCGTTTGAAGTGCCTCATACATATTGTGAAGACGCTGTCGGCTGAGCATGAGGAGTTCATAGCTGCCCTCATCCCAGAG--------- ggggcatataggattgactattcaatgctcttcacttccttttaaaatagCCC---CTGAAATGTCTCATACATATTGTGAAAACACTGTTAGCTGAACATGAAGAATTCACAGCTGCATTGATCCCTGAGCCAATAGATgtttgattgcaggtcagactctggactcctgaagccagacctaaggagga #### Rrp12_ID8304_19 --> 0 - 2 Original Alignment TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACC---------ag gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCTTTGTGCGCaggtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from CESAR TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACC---------ag gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCTTTGTGCGCaggtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from Spaln_aa2Genome TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTCTGT gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCTTTGTGCGCAGgtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from Spaln_nt2Genome TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTCTGTCC gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACC--TTTGTGCGCAGgtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from Pairagon TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCAC---------CAG gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCTTTGTGCGCAGgtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from Exonerate_protein2genome TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTCTGT gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCTTTGTGCGCAGgtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from Exonerate_coding2genome gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagctggttaatagcttcctagagaaagccattgaaaaggttcttgacccccccagttcagatttcacctttgtgcgcaggtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca Alignment from GeneWise TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTCTGT gctcagagttaatggatgggccttttagccaagccctgcttttcctgcagCTGGTTAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCTTTGTGCGCAGgtaagcctgagcttttcaggtgcctggtgtacaatgcatggaacctgaca #### Rrp12_ID8305_18 --> 2 - 0 Original Alignment ag------------------GCTGACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGG---CAGCCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagACCTTGAACGATCAGAGTGCAGACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGGGGCGACAGCT---CCCCATCGTACA---GTCGAG---ATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from CESAR ag------------------GCTGACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGGCAG---CCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagACCTTGAACGATCAGAGTGCAGACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGGG---GCGACAGCTCCCCATCGTACAGTC---GAG---ATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from Spaln_aa2Genome ACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGGCAGCCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagaccttgaacgatcagagtgcagACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGGGGCGACAGCTCCCCATCGTACAGTC------GAGATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from Spaln_nt2Genome AG-GCTGACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGGCAGCCT---GTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagaccttgaacgatcagAGTGCAGACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGG---GGCGACAGCTCCCCATCGTACAGTCGAG------ATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from Pairagon AG------------------GCTGACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGG---CAGCCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATC--------------AAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagAGACCTTGAACGATCAGAGTGCAGACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGG---GGCGACAGCTCC--------------------CCATCGTACAGTCGAGATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from Exonerate_protein2genome AG-GCTGACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGGCAGCCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagaccttgaacgatcagAGTGCAGACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGGGGCGACAGCTCCCCATCGTACAGTC------GAGATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from Exonerate_coding2genome AG-GCTGACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGGCAGCCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagaccttgaacgatcagAGTGCAGACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGGGGCGACAGCTCCCCATCGTACAGTC------GAGATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt Alignment from GeneWise ACCGAGCTGAAGTGAGCCGCTTTGCCAAAAACTTCCTGCCAATCCTCTTCAACCTGTATGGGCAGCCTGTTGCAGCTGGAGAGGCGGCAGCCCCTCGCCGTGCTGTGCTGGAAACCATCAAAACTTACCTCACCATAACTGAGGCTCAG gatccgctatatgactttcccacctgacgctttatttctttcgttttcagagaccttgaacgatcagagtgcagACCGGGCTGATGTGAGTTGTTTTGCTACAAACTCATTGCCAATCCTCTTTAACTTATATGGGCAACAACAAGTTGCAGCTGGGGCGACAGCTCCCCATCGTACAGTC------GAGATTAAGAGCTACCTCAGTGTAACTGAATCACAGgttagtaatgcgtactgtggagaacttttaggaatatatctatatcaatt #### Rrp12_ID8306_17 --> 0 - 1 Original Alignment ATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGGCAg tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAG---ggtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from CESAR ATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGGCAg tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAG---ggtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from Spaln_aa2Genome ATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGGCAG tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAG---Ggtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from Spaln_nt2Genome ATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGGC------AG tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAGGGTATGAAAGgtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from Pairagon ATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGG tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAGGgtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from Exonerate_protein2genome ATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGG tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAGGgtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from Exonerate_coding2genome tgagggctgagcacatttgtgaagtattctgtcttctcatttctccacagatctggactcttcagccagggttctgtactagacctacagaagtggctgcctcttttaaagggctggcatgtgcattggggacagctattaatgaaagtcctgacttgaaagttagtgtatgccaaggtctacgcactctcatcacaaagggctatgagggtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg Alignment from GeneWise -----------------------------------------------CAGATCTGGACCCTCCTGCCTGGGTTCTGCACAAGGCCCACAGATGTGGCTGCCTCCTTCAAAGGCCTGGCACGGACTCTGGGCACAGCTATCAATGAACGCCCAGACCTGAGGGTCACTGTGTGCCAGGCCCTACGTACCCTCATCACTAAGGGCTGTGAGG TGAGGGCTGAGCACATTTGTGAAGTATTCTGTCTTCTCATTTCTCCACAGATCTGGACTCTTCAGCCAGGGTTCTGTACTAGACCTACAGAAGTGGCTGCCTCTTTTAAAGGGCTGGCATGTGCATTGGGGACAGCTATTAATGAAAGTCCTGACTTGAAAGTTAGTGTATGCCAAGGTCTACGCACTCTCATCACAAAGGGCTATGAGGgtatgaaaggtgactcctcctgatgtggtaacctgagttgatttacgtgg #### Rrp12_ID8308_15 --> 1 - 1 Original Alignment g---------GAGACTCTGGATTTCCCACGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAg aactgaaacattgactgagctaactacagcacgctccttttccctaccaggTTCAAGCTTGAAAATCTGGATTTT---CAGAGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAggtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from CESAR g---------GAGACTCTGGATTTCCCACGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAg aactgaaacattgactgagctaactacagcacgctccttttccctaccaggTTCAAGCTTGAAAATCTGGATTTT---CAGAGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAggtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from Spaln_aa2Genome G---------GAGACTCTGGATTTCCCACGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAG aactgaaacattgactgagctaactacagcacgctccttttccctaccagGTTCAAGCTTGAAAATCTGGATTTT---CAGAGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAGgtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from Spaln_nt2Genome G---------GAGACTCTGGATTTCCCACGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAG aactgaaacattgactgagctaactacagcacgctccttttccctaccagGTTCAAGCTTGAAAATCTGGATTT---TCAGAGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAGgtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from Pairagon GGAGACTCTGGATTTCCCACGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAG aactgaaacattgactgagctaactacagcacgctccttttccctaccaggttcaagcttgaaaatctggattttcag----------------------AGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAGgtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from Exonerate_protein2genome GGAGACTCTGGATTTCCCA------CGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAG aactgaaacattgactgagctaactacagcacgctccttttccctaccagGTTCAAGCTTGAAAATCTGGATTTTCAGAGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAGgtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from Exonerate_coding2genome aactgaaacattgactgagctaactacagcacgctccttttccctaccaggttcaagcttgaaaatctggattttcagagctggttgttgtctgtcatccgggattatgtccaggaaaccaggcttggcttcttcactacctatttcttgcccctagctacaacccttaagagaaaaggtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc Alignment from GeneWise -------GAGGAGACTCTGGATTTCCCACGGAGCTGGCTGCTGCCTGTCATCCGGGATCATGTTCGGGAAACCAGGCTTGGTTTCTTCACCACTTACTTCTTGCCCTTGGCCACCACTCTTAAGAGAAAAG aactgaaacattgactgagctaactacagcacgctccttttccctaccagGTTCAAGCTTGAAAATCTGGATTTT---CAGAGCTGGTTGTTGTCTGTCATCCGGGATTATGTCCAGGAAACCAGGCTTGGCTTCTTCACTACCTATTTCTTGCCCCTAGCTACAACCCTTAAGAGAAAAGgtagagaggtcttatccttataagatacaggtcacagaagaaatatcagc #### Sart1_ID960_15 --> 0 - 1 Original Alignment TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAA---g tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGggtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from CESAR TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAA---g tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGggtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from Spaln_aa2Genome TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAA---G tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGGgtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from Spaln_nt2Genome TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAA tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAgtgggtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from Pairagon TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAAG--- tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGGgtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from Exonerate_protein2genome TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAA---G tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGGgtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from Exonerate_coding2genome TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAA---G tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGGgtgagcttttggggtgggtcttattgcggttggatactttattcatcatg Alignment from GeneWise TTCTCTGCTTCCTCTACCACCATCCTGGATGAGGAGCCCATCGTGAACAGAGGGCTGGCTGCTGCCCTGCTCCTGTGTCAGAACAAAGGA- tgaaggtgatcgggggtggccacctttccggtattgttgcatttttctagTTCTCTGCTTCTTCTACCACTATCTTGGATGAGGAACCCATAGTAAACCGGGGGCTAGCAGCTGCCCTGCTCCTCTGTCAGAACAGAGTGGgtgagcttttggggtgggtcttattgcggttggatactttattcatcatg #### Sart1_ID963_12 --> 2 - 0 Original Alignment agGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGTGAGAAG ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagaaGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGGG------gtaagctctgtgcactaaagcagttacaatgagaggactgtgcactgttg Alignment from CESAR agGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGTGAGAAG ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagaaGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGGG------gtaagctctgtgcactaaagcagttacaatgagaggactgtgca Alignment from Spaln_aa2Genome AGGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGT ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagAAGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGGGgtaagctctgtgcactaaagcagttacaatgagaggactgtgcactgttg Alignment from Spaln_nt2Genome AGGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGTGAGAAG ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagAAGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGG------Ggtaagctctgtgcactaaagcagttacaatgagaggactgtgcactgttg Alignment from Pairagon AGGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGTGAGAAG ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagAAGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGG------Ggtaagctctgtgcactaaagcagttacaatgagaggactgtgcactgttg Alignment from Exonerate_protein2genome AGGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGT ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagAAGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGGGgtaagctctgtgcactaaagcagttacaatgagaggactgtgcactgttg Alignment from Exonerate_coding2genome AGGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGT ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagAAGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGGGgtaagctctgtgcactaaagcagttacaatgagaggactgtgcactgttg Alignment from GeneWise AGGATGGGGGAGCTCTTCCGCCAGGGTCCCCAGAGGGGCTGGAGGAAGACGAGGCAGAGCTGGAGCTGCAGAAGCAGCTGGAGAAGGGGCGCCGGCTGCGGCAGCTGCAGCAACTGCAGCAGCTCCGAGACAGTGGTGAGAAGGTG ggtctaacacatgcttgagtatcacgaaaccttctcttttgtctatgcagAAGATGGTGGGGCTCTTCCACCAGGAGCACCAGATGGACTGGACGAAGATGAGGCAGAACTGGAATTACAAAAGCAGCTAGAAAAGGGCCGTCGGCTGCGGCAGCTCCAGCAGTTACAGCAGCTAAGGGACAGTGGGGTAAGCTCTgtgcactaaagcagttacaatgagaggactgtgcactgttg #### Sart1_ID966_9 --> 0 - 0 Original Alignment ACAG ------CAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagCCGTACCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from CESAR ACAG ------CAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtatgcgtaatcagtctgtgagaatgtatcgtctttccccctccagCCGTACCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from Spaln_aa2Genome GCACAGCAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG acaggtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagCCGTACCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from Spaln_nt2Genome ACAG CAAAA------ACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagCCGTACCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from Pairagon ACAG CAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagccgtaccggag-----ACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from Exonerate_protein2genome ACAG CAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagccgtacCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from Exonerate_coding2genome ACAG CAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagccgtacCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc Alignment from GeneWise ACAG ------CAAAAACCTCGTTCTATCCTGGCCAAATATGATGAGGAACTGGAGGGCGAGCGACCACATTCCTTCCGTCTGGAGCAGGGTGGGATGGCCGATGGCCTGAGGGAACGAGAGTTAGAAGAAATCCGCACCAAGCTACGGCTGCAGGCTCAGTCTCTGAGCTCCGTAGGGCCCCGGCTTGCCTCTGAGTACCTCAGTCCCGAGGAGATG ACAGgtgagtgtaatcagtctgtgagaatgtatcgtctttccccctccagCCGTACCGGAGACCTTGTTCTATTCTAGCTAAGTATGATGAGGAATTAGGCAGTGAGCGTCCACATTCCTGCCGTCTTAAGCATGGTGGTATGGCTGATGGTCTACGGGAGAAAGAGTTAGAAGAAATTCGCACTAAGCTTCGACTACCAGCCCAATCACTAAGTTTAATGGGTCCCAGACTTAGTACCCAGTATCTTAGTCCTGAAGAGATGgtgagtcggtaggttatggtcatcaatacagtcctgtttacacttacacc #### Sart1_ID967_8 --> 2 - 0 Original Alignment ggGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGATTTGGCACAG CAAA agtgaagtgctgctttcactgccagctagttttgttttgttttgttttaggtGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGAC---------gtgagcgtaggatttgaaatcagtcctctgctctgctttctcacagCGGA Alignment from CESAR ggGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGATTTGGCACAG C agtgaagtgctgctttcactgccagctagttttgttttgttttgttttaggtGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGC---gtaggatttgaaatcgaacactctccccctttcttcctagC Alignment from Spaln_aa2Genome GGGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGATTTGGCA CAGC agtgaagtgctgctttcactgccagctagttttgttttgttttgttttagGTGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGCgtaggatttgaaatcagtcctctgctctgctttctcacag---C Alignment from Spaln_nt2Genome GGGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGATTTGGCA CAGC agtgaagtgctgctttcactgccagctagttttgttttgttttgttttagGTGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGCgtaggatttgaaatcagtcctctgctctgctttctcacagCGG- Alignment from Pairagon GGGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGA-------------------------------------TTTGGCACAGCAAA agtgaagtgctgctttcactgccagctagttttgttttgttttgttttagGTGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGCGTAGGATTTGAAATCAGTCCTCTGCTCTGCTTTCTCACAGCGGA Alignment from Exonerate_protein2genome GGGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGATTTGGCACAG CAAA agtgaagtgctgctttcactgccagctagttttgttttgttttgttttagGTGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGCGTAggatttgaaatcagtcctctgctctgctttctcacagCGGA Alignment from Exonerate_coding2genome GGGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGATTTGGCACAG CAAA agtgaagtgctgctttcactgccagctagttttgttttgttttgttttagGTGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGCGTAggatttgaaatcagtcctctgctctgctttctcacagCGGA Alignment from GeneWise GGGTACTGCAGGACGGGGAGGACGTGCTGGTGAATGTGAACATGGTGGACAAGGAGCGGGCGGACAAGAACGTGGAGCTTCGGAAAAAGAAGCCTGACTACCTGCCCTATGCGGAAGATGAGAGTGTGGACGAT---------------------------------------TTGGCACAGCA agtgaagtgctgctttcactgccagctagttttgttttgttttgttttagGTGTACTCCAGGATGGAGAAGATGTGCTGGTGAATGTGAATATGGTGGACAAAGAACACGCTGATCGAAATGTGGAGCTTCGGAAAGAGAAGGCAGACTACCTAAGCTATGTTGAGGATGAGGGTGTGGATGACGTGAGCGTAGGATTTGAAATCAGTCCTCTGCTCTGCTTTCTCA--CAGCG #### Sart1_ID969_6 --> 0 - 0 Original Alignment ---------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagCACTTTACTGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from CESAR ---------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagCACTTTACTGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from Spaln_aa2Genome -------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagCACTTTACTGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from Spaln_nt2Genome ---------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagCACTTTACTGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from Pairagon ---------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagCACTTTACTGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from Exonerate_protein2genome GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagcactttactGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from Exonerate_coding2genome GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagcactttactGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt Alignment from GeneWise ---------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG atctatctattaagtcccaaaccttttcttacacttgacttgtgttatagCACTTTACTGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTATGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAAAAGCGACAGgtatcaatccaatttcaggaatgacaattcccaagttgagtatcacaatt #### Sart1_ID970_5 --> 1 - 0 Original Alignment gAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagtAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCAAAA------gtatgtatgggtacaaatgggtatttaaaatctatctattaagtcccaaa Alignment from CESAR gAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagtAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCA------AAAgtatgtatgggtacaaatgggtatttaaaatctatctattaagtcccatt Alignment from Spaln_aa2Genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCA------AAAgtatgtatgggtacaaatgggtatttaaaatctatctattaagtcccaaa Alignment from Spaln_nt2Genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGCC------TACAGAAAGAGAAGGATTTGGC--AAAAGTATgtatgggtacaaatgggtatttaaaatctatctattaagtcccaaa Alignment from Pairagon GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCAAAAgtatgtatgggtacaaatgggtatttaaaatctatctattaagtcccaaa Alignment from Exonerate_protein2genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCAAAAGTATGTatgggtacaaatgggtatttaaaatctatctattaagtcccaaa Alignment from Exonerate_coding2genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacatgcccacagttctggaagacgccactttcatttgttctctagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCAAAAGTATGTatgggtacaaatgggtatttaaaatctatctattaagtcccaaa Alignment from GeneWise ---------------------------------------------------AAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG TCTTCACATGCCCACAGTTCTGGAAGACGCCACTTTCATTTGTTCTCTAGTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTACAGAAAGAGAAGGATTTGGCA------AAAgtatgtatgggtacaaatgggtatttaaaatctatctattaagtcccaaa #### Sec31b_ID9030_22 --> 0 - 0 Original Alignment CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAG--- aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from CESAR CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAG--- aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from Spaln_aa2Genome CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAG--- aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from Spaln_nt2Genome CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCA---G aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from Pairagon CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCA---G aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from Exonerate_protein2genome CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAGCAA aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from Exonerate_coding2genome aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagctgcctgaagcattcatgacgcctgcaccgactacagccccactccgtagtcctggaccggattcacaacaagccttgcttccaaaaccattagtctccagtgcaatcttaccccctcctggagcccccagagagtgtagcttgcaacgggtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta Alignment from GeneWise CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAGCAA aagctgaggcgctatgactacttagaaaaccctctctctgcctgtgtcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTCCGTAGTCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCTGGAGCCCCCAGAGAGTGTAGCTTGCAACGGgtgagtcaaagtctgcacttgccctaatcaaggcgatccgatatctctta #### Sec31b_ID9031_21 --> 2 - 0 Original Alignment ga---------------------------CCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagggTGGAAAATGGAGTCCATACGCTGGCTGCCTCAGGACTCATGGAAAGTTACACCAGGCTCTGAGGGCAATCTTCAAAGGAAGAAAgtgccagcctttccataaccatcagcctagtccatccctatgttcttact Alignment from CESAR ctgatctaaatgatcagatgccctcacatgtgttctcatccattggtttca Alignment from Spaln_aa2Genome GA------CCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagggtggaaaatggagtccatacGCTGGCTGCCTCAGGACTCATGGAAAGTTACACCAGGCTCTGAGGGCAATCTTCAAAGGAAGAAAgtgccagcctttccataaccatcagcctagtccatccctatgttcttact Alignment from Spaln_nt2Genome GACCCCAGGACTC-------------CTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagggtggaaaatggagTCCATACGCTGGCTGCCTCAGGACTCATGGAAAGTTACACCAGGCTCTGAGGGCAATCTTCAAAGGAAGAAAgtgccagcctttccataaccatcagcctagtccatccctatgttcttact Alignment from Pairagon G---------------------------ACCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagGGTGGAAAATGGAGTCCATACGCTGGCTGCCTCAGGACTCATGGAAAGTTACACCAGGCTCTGAGGGCAATCTTCAAAGGAAGAAAgtgccagcctttccataaccatcagcctagtccatccctatgttcttact Alignment from Exonerate_protein2genome GACCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagggtggaaaatggagtccatacgctggcTGCCTCAGGACTCATGGAAAGTTACACCAGGCTCTGAGGGCAATCTTCAAAGGAAGAAAgtgccagcctttccataaccatcagcctagtccatccctatgttcttact Alignment from Exonerate_coding2genome cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagggtggaaaatggagtccatacgctggctgcctcaggactcatggaaagttacaccaggctctgagggcaatcttcaaaggaagaaagtgccagcctttccataaccatcagcctagtccatccctatgttcttact Alignment from GeneWise --------------------------GGACCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG cattaaagttgtcggtgatgagcaaccaagaaggttgcaatatgtttcagGGTGGAAAATGGAGTCCATACGCTGGCTGCCTCAGGACTCATGGAAAGTTACACCAGGCTCTGAGGGCAATCTTCAAAGGAAGAAAgtgccagcctttccataaccatcagcctagtccatccctatgttcttact #### Sec31b_ID9037_15 --> 0 - 1 Original Alignment ---CTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTg cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAG---AGGAAGGACCTTGTGTGTGCTTTTTGCCTG---AACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTggtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from CESAR ---CTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTg cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAG---AGGAAGGACCTTGTGTGTGCTTTTTGCCTG---AACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTggtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from Spaln_aa2Genome CTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTG cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAG---AGGAAGGACCTTGTGTGTGCTTTTTGCCTG---AACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTGgtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from Spaln_nt2Genome --GCTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTG cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAGA---GGAAGGACCTTGTGTGTGCTTTTTGCCT---GAACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTGgtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from Pairagon ---CTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTG cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAGA---GGAAGGACCTTGTGTGTGCTTTTTGCCT---GAACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTGgtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from Exonerate_protein2genome CTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTG cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAGAGGAAGGACCTTGTGTGTGCTTTTTGCCTG---AACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTGgtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from Exonerate_coding2genome cactcttctaatggatcagtccataggtctctcccgccctcatctctcaggtgttcctagcctgcattataaaaaagaggaaggaccttgtgtgtgctttttgcctgaactggagagacacacttgctttgctactaacacattcaggtcctaaaaagtttccagaactttgtggtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc Alignment from GeneWise ---CTTCTAGCCTGTGTTGTAAAGAAGAATTGGAAGGACCTAGTATGTGCCTGTAGGCTGAAGAACTGGAGAGAGGCGCTGGCCTTGCTACTGACGTATTCAGGGCCAGAGAAGTTCCCTGAGCTCTGTG cactcttctaatggatcagtccataggtctctcccgccctcatctctcagGTGTTCCTAGCCTGCATTATAAAAAAGAGG---AAGGACCTTGTGTGTGCTTTTTGCCTG---AACTGGAGAGACACACTTGCTTTGCTACTAACACATTCAGGTCCTAAAAAGTTTCCAGAACTTTGTGgtacagatgagattaatatgattcattgtatttatgccaagcaaggcagc #### Sec31b_ID9038_14 --> 2 - 0 Original Alignment acACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagat---GATGGGCTACTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from CESAR acACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG atacagtaaagtattcactgagcaaaccttagtctctttgctggttacagat---GATGGGCTACTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Spaln_aa2Genome ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagAT---GATGGGCTACTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Spaln_nt2Genome CTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagATGATGGGCTACTAAGCC---CTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCA---TGGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Pairagon ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagA---TGATGGGCTACTAAGCC---CTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCA---TGGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Exonerate_protein2genome ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagAT---GATGGGCTACTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Exonerate_coding2genome ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCGCTTCTAGCCTGTGTT cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagAT---GATGGGCTACTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTGTAAGGACTGTTGTCcataattgtgttgctcacagccatgtcattcaaca Alignment from GeneWise ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG cagtaaagtattcactgagcaagtgaccttagtctctttgctggttacagAT---GATGGGCTACTAAGCCCT---TTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAAGAGCGGTTTTCAGATGCTGTTATTTTAGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaaggactgttgtccataattgtgttgctcacagccatgtcattcaaca #### Sec31b_ID9039_13 --> 0 - 1 Original Alignment GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCAGCC---TTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCACAGAAg ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCACA------ggtgaggctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from CESAR GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCA---GCCTTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCACAGAAg ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCACA------ggtgaggctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from Spaln_aa2Genome GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCA---GCCTTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACC- ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCACAGgtgaggctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from Spaln_nt2Genome GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCAGCC---TTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCACAGAAG ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCAC------AGgtgaggctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from Pairagon GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCT---CAGCCTTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCACAGAAG ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCAC------AGgtgaggctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from Exonerate_protein2genome GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCA---GCCTTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCACAGAAG ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCACAGGTGAGGctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from Exonerate_coding2genome GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCA---GCCTTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCACAGAAG ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCACAGGTGAGGctggcgtgttcctgcaaggggatatcactatataggcatcattg Alignment from GeneWise GCCTCCAAACACACTGCCAAGGAAGCCTCTGAGTCCTCAGCC---TTCTTTGATGAGCTGATACCTCAGAACATGACTCCCTGGGAGATCCCCACCA ggctaaatagatacacttcacacatggtgatctttgtgctctctctgtagGCCACCAAACACGCTGCAAGAGAAACTTCTGAGTCCTCAGCAGCTTTCTTTGATGAGTTAATACCTGAGAACATGACCCCCTGGGTGATCCCCACAGgtgaggctggcgtgttcctgcaaggggatatcactatataggcatcattg #### Sec31b_ID9044_8 --> 0 - 0 Original Alignment GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAGGCTGACAAG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCA---------gtaagtattgatgtcccaggttgtattcataggtaggaaacttgccggaa Alignment from CESAR GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAGGCTGACAAG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCA---------gtaagtattgatgtcccaggttgtattcataggtaggaaac Alignment from Spaln_aa2Genome GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAGGCTGAC---AAG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCAGTAAGTATTGATgtcccaggttgtattcataggtaggaaacttgccggaa Alignment from Spaln_nt2Genome GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCAgtaagtattgatgtcccaggttgtattcataggtaggaaacttgccggaa Alignment from Pairagon GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAG---- ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCAgtaagtattgatgtcccaggttgtattcataggtaggaaacttgccggaa Alignment from Exonerate_protein2genome GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAGGCTGACAAGGTG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCAGTAAGTATTGATgtcccaggttgtattcataggtaggaaacttgccggaa Alignment from Exonerate_coding2genome GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAGGCTGACAAGGTG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCAGTAAGTATTGATgtcccaggttgtattcataggtaggaaacttgccggaa Alignment from GeneWise GTGGTCTACAAGCTGCCCACACAGAGCAGCTGGTGCTTTGATGTTCAGTGGTGCCCTCAGAGCCCTCCCGTGTTCTCTGCTGTCTCCTTCGATGGCTGGATCAGTTTGTGCTCTGTGATGGGTAGGAGCTGGGAAGCCCAGCACATGAGGCAGGCTGACAAGGTG ccaggtttagttccactggtaagtgttctatgacttttgtctccttttagATAATCTACAAGTTGCCCACACAGAGCAGCTGGTGCTTTGATGTCCAGTGGTGCCCTCCCAGCCCTCCGGTACTTTCTGCAGTCTCTTTTGATGGTTGGATCAGTCTATGTTCCGTAACCGGAAGGAGCTGGGAAGTGCAGCATATGAGATCAGTAAGTATTGATgtcccaggttgtattcataggtaggaaacttgccggaa #### Sema4g_ID9244_2 --> 2 - 0 Original Alignment agCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagaaGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTC------------------------------------gtgaggtgctgttactggatttacaggaccgcagaagaggggcatctcca Alignment from CESAR agCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagaaGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTC------------------------------------gtgaggtgctgtta Alignment from Spaln_aa2Genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGC cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagAAGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTCGTGAGgtgctgttactggatttacaggaccgcagaagaggggcatctcca Alignment from Spaln_nt2Genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTC cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagAAGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTCgtgaggtgctgttactggatttacaggaccgcagaagaggggcatctcca Alignment from Pairagon GGCACTTCAAGGGCCAAACCCAGAACT-----------------------------------------------------------------ATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTC -----------------------AACTAGTTTCCTGTCTCTTTGTGGTAGAAGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTCgtgaggtgctgttactggatttacaggaccgcagaagaggggcatctcca Alignment from Exonerate_protein2genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGC cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagAAGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTCGTGAGgtgctgttactggatttacaggaccgcagaagaggggcatctcca Alignment from Exonerate_coding2genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGC cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagAAGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTCGTGAGgtgctgttactggatttacaggaccgcagaagaggggcatctcca Alignment from GeneWise AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGC cttgctcgtgccttattcctcagaactagtttcctgtctctttgtggtagAAGTTTCACAAGTACAACGCTTTAGGGAGGAGGCCCAAATTCATTCAACATTGCTGTTGGAGGAGGCTTCTGAAAGGTTGTCAGCAGGTGCGCGGGGTCCATTGTTCTCCCTCGTGAGgtgctgttactggatttacaggaccgcagaagaggggcatctcca #### Sema4g_ID9247_5 --> 0 - 1 Original Alignment GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTg agcaaacctgctctcatctaagctggttgttttcttcctctgtgctgtag---TCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTggtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from CESAR GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTg tcctataaacctgctctcatctaaggttgttttcttcctctgtgctgtag---TCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTggtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from Spaln_aa2Genome GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG agcaaacctgctctcatctaagctggttgttttcttcctctgtgctgtag---TCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from Spaln_nt2Genome GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG agcaaacctgctctcatctaagctggttgttttcttcctctgtgctgtag---TCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from Pairagon ------------------------------------------------ATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG AGCAAACCTGCTCTCATCTAAGCTGGTTGTTTTCTTCCTCTGTGCTGTAGTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from Exonerate_protein2genome GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG agcaaacctgctctcatctaagctggttgttttcttcctctgtgctgTAGTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from Exonerate_coding2genome GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG agcaaacctgctctcatctaagctggttgttttcttcctctgtgctgTAGTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt Alignment from GeneWise GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG agcaaacctgctctcatctaagctggttgttttcttcctctgtgctgtagTCT---GAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtttggaaaatgtaactgatccatcacaattctaagccatgaacattgtt #### Sema4g_ID9248_6 --> 2 - 1 Original Alignment atGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAAT------------------g tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagatGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATATGAAGTCGGTGGAACATggtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from CESAR atGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAAT------------------g tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagatGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATATGAAGTCGGTGGAACATggtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from Spaln_aa2Genome ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAAT------------------G tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagATGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATATGAAGTCGGTGGAACATGgtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from Spaln_nt2Genome ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG---- tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagATGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATATGAAgtcggtggaacatggtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from Pairagon ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCA------------------ATG tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagATGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATATGAAGTCGGTGGAACATGgtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from Exonerate_protein2genome ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagATGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATAtgaagtcggtggaacatggtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from Exonerate_coding2genome ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagATGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATAtgaagtcggtggaacatggtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg Alignment from GeneWise ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAAT----- tactagtagggcagcatgtcctgtctattctctgctgctatctcccacagATGGTGGCCTTTACACAGCCACCTGGTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGCGAACTGAGGAAGCACCAATGCACTGGCTCAATATGAAgtcggtggaacatggtatttatcaggtgctttgaaggtgttggttaaaggggacagctctagtg #### Sema4g_ID9249_7 --> 2 - 0 Original Alignment at------GCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagatGGGGGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from CESAR at------GCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagatGGGGGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from Spaln_aa2Genome AT------GCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagATGGGGGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from Spaln_nt2Genome ATG------CTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagATGGGGGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from Pairagon A------TGCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagATGGGGGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from Exonerate_protein2genome ATGCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagatggggGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from Exonerate_coding2genome ATGCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagatggggGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc Alignment from GeneWise -----GATGCTGAGTTTGTGTTCTCTGTGCTGGTGCGGGAGAGCAAGACAAGCGCAGTGGGTGATGATGACAAGATTTATTTCTTCTTCATGGAGCGTGAGGAAGGCTCCAGCAGCTTCACACAGAGTCGCAGCAGCCACCGTGTGGCTAGAGTAGCCCGTGTGTGCAAG gcatagtctgtgagtctgtgaaccaagaatgcttcctttttattttttagATGGGGGTGCAGAAGTTGTATTCTCTGTACTGGTGCGACAGAGTGAAACAAGTACTGTTGGTGGCGAGGACAGGATTTATTTTTTCTTCAAGGAACATGAGGAAGGTTCTAGTAATTTCACACAGAGTTGCAGCAGCCACAGGGTAGCTAGAGCACCTCGTGTTTGCAAGgtgccactgatgtacttctagaccagtgtaattcaagaagacgttcactc #### Sf1_ID1664_5 --> 1 - 2 Original Alignment gCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCag cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctaggCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGGC---aggtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from CESAR gCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCag cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctaggCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGGC---aggtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from Spaln_aa2Genome GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACC cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctagGCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGGCAGgtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from Spaln_nt2Genome GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAG cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctagGCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGG---CAGgtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from Pairagon GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAG cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctagGCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGG---CAGgtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from Exonerate_protein2genome GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAG cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctagGCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGGC---AGgtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from Exonerate_coding2genome GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAG cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctagGCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGGC---AGgtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt Alignment from GeneWise GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACC cctagaaaaagctggatacaagtgaggtcatatgtgttcgtttcccctagGCCTCCAGCAAAGCGTGTGAGTGATAAAGTCATGATACCACAATATGAATATCCAGAAATTAACTTTGTGAGCCTTCTCATTGGCAGgtaagctgtagtggttagcagacgatcgtttcccttgttgatcaagattt #### Sf1_ID1669_10 --> 0 - 1 Original Alignment ---TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGg ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGggtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from CESAR ---TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGg ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGggtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from Spaln_aa2Genome TCTCTCATGTCTACA---ACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGGgtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from Spaln_nt2Genome GTCTCTCATG--TCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGGgtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from Pairagon ---TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGGgtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from Exonerate_protein2genome ---TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGGgtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from Exonerate_coding2genome ---TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGGgtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg Alignment from GeneWise ---TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG ggctcggacattgtctatgctaaactagtgaccctgcatctgtttttcagGAATCTCTCATGTCTACAACTCAGAGCCACCCACCCTGTATGAATTCTGGTCCATCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCCGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAATGGgtatgaaaccaagagcatttgcttgggcaaatgtcagacatcccaaggtg #### Sf1_ID1670_11 --> 2 - 1 Original Alignment atCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAA---g tagtcttagatgccctcccattgatttctttctctcctgatgttttccagacCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCggtgagtctataacttttgatggtgtctctcatgattggggccaattggca Alignment from CESAR atCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAA---g tagtcttagatgccctcccattgatttctttctctcctgatgttttccagacCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCggtgagtctataacttttgatggtgtctctcatgattggggccaattggca Alignment from Spaln_aa2Genome ATCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAA---G tagtcttagatgccctcccattgatttctttctctcctgatgttttccagACCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCGgtgagtctataacttttgatggtgtctctcatgattggggccaattggca Alignment from Spaln_nt2Genome ATCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAA---G tagtcttagatgccctcccattgatttctttctctcctgatgttttccagACCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCGgtgagtctataacttttgatggtgtctctcatgattggggccaattggca Alignment from Pairagon ATCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAA------------------------------------------------------- tagtcttagatgccctcccattgatttctttctctcctgatgttttccagACCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCGGTGAGTCTATAACTTTTGATGGTGTCTCTCATGATTGGGGCCAATTGGCA Alignment from Exonerate_protein2genome tagtcttagatgccctcccattgatttctttctctcctgatgttttccagaccagtatcaagggagtacacccgtggcctcgggagtttatcatttgcatcaaggaaagcccggtgagtctataacttttgatggtgtctctcatgattggggccaattggca Alignment from Exonerate_coding2genome ATCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAA---G tagtcttagatgccctcccattgatttctttctctcctgatgttttccagACCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCGgtgagtctataacttttgatggtgtctctcatgattggggccaattggca Alignment from GeneWise ATCAGTACCTGGGAAGTACGCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAAGGT- tagtcttagatgccctcccattgatttctttctctcctgatgttttccagACCAGTATCAAGGGAGTACACCCGTGGCCTCGGGAGTTTATCATTTGCATCAAGGAAAGCCCGgtgagtctataacttttgatggtgtctctcatgattggggccaattggca #### Sf3b2_ID898_20 --> 0 - 0 Original Alignment GTTATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcag---ATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAA------CAAGTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from CESAR GTTATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG caggtggggtcattgatctataagatcacacaccccgctctgcaatgcag---ATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAA------CAAGTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from Spaln_aa2Genome GTTATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcag---ATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAA------CAAGTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from Spaln_nt2Genome ATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGACATG---GTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcagATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAACAAGT------AGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from Pairagon ATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcagATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAA------ACAAGTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from Exonerate_protein2genome ATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcagATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAA------CAAGTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from Exonerate_coding2genome ATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcagATGAGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAA------CAAGTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat Alignment from GeneWise GTTATGAGCCGGAAGGGCCCAGCCCCTGAATTGCAAGGTGTGGAAGTAGCGCTGGCGCCTGAGGAATTGGAGTTGGACCCCATGGCCATGACGCAGAAGTACGAGGAGCACGTTCGGGAGCAGCAGGCACAAGTAGAGAAGGAAGACTTCAGCGAC---ATGGTGGCTGAGCATGCTGCTAAGCAGAAG gtggggtcattgatctataagattttcacacaccccgctctgcaatgcagATG---AGCCAAAAGAGTGCTGCCTCTGAATTACAAGGTGTTGAGGTTGCATTGGCACCTGAAGAATTAGAGTTGGATTCTATGGCTACAATGCAGAAGTACAAAGAACATGTTCAGGAGAAACAA------GTAGAGAAGGGAGATTTCAGTGATATGATGGTGGCTGAGCATGCTGCAAAGCATAAGgtacagatggtttatgtatacagcatgggggttattctctctagtgagat #### Sf3b2_ID909_9 --> 0 - 0 Original Alignment AAAAACCGAAAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTGGAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG acattctcaacacaaacccgcctatgtaccttttctcctccgtattgcag---------CAACATCAAAACCAGAAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATCTGAAGGGTCAGGGCCGCCAACAGGA---ATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt Alignment from CESAR AAAAACCGAAAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTGGAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG gagcttctcacattctcaacacaaagtaccttttctcctccgtattgcagCAA---------CATCAAAACCAGAAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATCTGAAGGGTCAGGGCCGCCAACAGGA---ATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgctcctgcc Alignment from Spaln_aa2Genome AAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTGGAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG acattctcaacacaaacccgcctatgtaccttttctcctccgtattgcagCAACATCAAAACCAGAAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATCTGAAGGGTCAGGGCCGCCAACAGGA---ATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt Alignment from Spaln_nt2Genome AAAAACCGAAAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTGGAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG acattctcaacacaaacccgcctatgtaccttttctcctccgtattgcagCAA---------CATCAAAACCAGAAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATCTGAAGGGTCAGGGCCGCCAACAG--GA-ATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt Alignment from Pairagon AAAAACCGAAAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTG--------------------------GAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG acattctcaacacaaacccgcctatgtaccttttctcctccgtattgcagcaacatcaaaaccag------------------------AAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATC-----------------------------TGAAGGGTCAGGGCCGCCAACAGGAATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt Alignment from Exonerate_protein2genome ACCGAAAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTGGAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG acattctcaacacaaacccgcctatgtaccttttctcctccgtatTGCAGCAACATCAAAACCAGAAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATCTGAAGGGTCAGGGCCGCCAACAGGA---ATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt Alignment from Exonerate_coding2genome acattctcaacacaaacccgcctatgtaccttttctcctccgtattgcagcaacatcaaaaccagaagaagaaaaaaaaaccaaagcaggtgagggcagcctcatcaaagagctctggcgatcaagaaaaagactctagtcaatctgaagggtcagggccgccaacaggaatagagattaagtatgtgagtgaggaccctgggatccatgagcccaatttcatcttcttcaagagggtgtatgaggcttttaaggtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt Alignment from GeneWise CGAAAGCGTCGGAACCGAAAGAAGAAGAAAAAGCCACAGCGGGTGCGGGCAGCCTCATCAGAGAGCTCTGGGGACCGAGAGAAGGACTCCGGTCGGTCCCGCGGCTCGGACCCCCCTGCTGCTGACGTGGAGATTGAGTATGTGACCGAGGAGCCTGAGATCTACGAGCCCAATTTCATCTTCTTCAAGAGGATTTTTGAGGCTTTCAAG acattctcaacacaaacccgcctatgtaccttttctcctccgtattgcagCAA---CATCAAAACCAGAAGAAGAAAAAAAAACCAAAGCAGGTGAGGGCAGCCTCATCAAAGAGCTCTGGCGATCAAGAAAAAGACTCTAGTCAATCTGAAGGGTCAGGGCCGCCAACAGGA---ATAGAGATTAAGTATGTGAGTGAGGACCCTGGGATCCATGAGCCCAATTTCATCTTCTTCAAGAGGGTGTATGAGGCTTTTAAGgtaaggtctttacaggttgaggcagagactgtattatgcctgaaaagatt #### Sf3b2_ID911_7 --> 0 - 1 Original Alignment ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAGCAG---------g ttttttcaacaggataagttttagaccacttctaacattgttttcattagATT---GATCCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAG---AAACTTAAAggtaatattaacagataaacacacattagctgggagctgtcatcactactc Alignment from CESAR ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAGCAG------g ttttttcaacaggataagttttagaccacttctaacattgttttcattagATT---GATCCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAGAAACTTAAAggtaatattaacagataaacacacattagctgggagctgtcatcactactc Alignment from Spaln_aa2Genome ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAGCAGGAGGAGG ttttttcaacaggataagttttagaccacttctaacattgttttcattagATT---GATCCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAGAAACTTAAAGgtaatattaacagataaacacacattagctgggagctgtcatcactactc Alignment from Spaln_nt2Genome ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAGCAG------G ttttttcaacaggataagttttagaccacttctaacattgttttcattagAT---TGATCCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAGAAACTTAAAGgtaatattaacagataaacacacattagctgggagctgtcatcactactc Alignment from Pairagon ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAG------------------------------------------------------------ ttttttcaacaggataagttttagaccacttctaacattgttttcattagAT---TGATCCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAGAAACTTAAAGGTAATATTAACAGATAAACACACATTAGCTGGGAGCTGTCATCACTACTC Alignment from Exonerate_protein2genome ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAGCAGG ttttttcaacaggataagttttagaccacttctaacattgttttcattagATT---GATCCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAGAAACttaaaggtaatattaacagataaacacacattagctgggagctgtcatcactactc Alignment from Exonerate_coding2genome ttttttcaacaggataagttttagaccacttctaacattgttttcattagattgatccctcagtgggccccaaaattcctcaggctgtggaaaaaatccttcagttgaaggagagtcagcagcaagagatgaactctcagaaacttaaaggtaatattaacagataaacacacattagctgggagctgtcatcactactc Alignment from GeneWise ATGGATGATCCTTCTGTGGGCCCCAAGATCCCCCAGGCTTTGGAAAAGATTCTTCAGCTGAAGGAGAGCCGGCAGGAAGAGATGAACTCTCAGCAGGAGGAGG ttttttcaacaggataagttttagaccacttctaacattgttttcattagATTGAT---CCCTCAGTGGGCCCCAAAATTCCTCAGGCTGTGGAAAAAATCCTTCAGTTGAAGGAGAGTCAGCAGCAAGAGATGAACTCTCAGAAACTTAAAGgtaatattaacagataaacacacattagctgggagctgtcatcactactc #### Sf3b2_ID916_2 --> 2 - 0 Original Alignment gg------AGTCGCGAGGAGTTAGTAGAGCGGCTGCAGACCTACACCCGTCAG tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagggAGGCTGAGTCGTGAAGAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from CESAR gg------AGTCGCGAGGAGTTAGTAGAGCGGCTGCAGACCTACACCCGTCAG tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagggAGGCTGAGTCGTGAAGAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from Spaln_aa2Genome AGTTAGTAGAGCGGCTGCAGACCTACACCCGTCAG tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagggaggctgagtcgtgaagAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from Spaln_nt2Genome GGAGTCGCGAGGAGTTAGTAGA------GCGGCTGCAGACCTACACCCGTCAG tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagGGAGGCTGAGTCGTGAAGAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from Pairagon ---------------------------------------------------------GAGTCGCGAGGAGTTAGTAGAGCGGCTGCAGACCTACACCCGTCAG TGCAGTCTTATCTACTCCAGGACAAGGGCTCCTTCTCTCCGTCCCTGCAGGGAGGCTGAGTCGTGAAGAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from Exonerate_protein2genome GG------AGTCGCGAGGAGTTAGTAGAGCGGCTGCAGACCTACACCCGTCAG tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagGGAGGCTGAGTCGTGAAGAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from Exonerate_coding2genome tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagggaggctgagtcgtgaagaattagttgagaagctgcagacctatacccgtcaggtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac Alignment from GeneWise ----GAGGAGTTAGTAGAGCGGCTGCAGACCTACACCCGTCAG tgcagtcttatctactccaggacaagggctccttctctccgtccctgcagggaggctgagTCGTGAAGAATTAGTTGAGAAGCTGCAGACCTATACCCGTCAGgtgcgcgttactagtagactatctgatgatacgtctggaataacaaagac #### Sfxn3_ID9291_9 --> 1 - 2 Original Alignment c------TTGGTATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAag actgtttaggaggccatgctttcacaaacttttctttttctttaaactagcGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAgcgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from CESAR c------TTGGTATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAag actgtttaggaggccatgctttcacaaacttttctttttctttaaactagcGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAgcgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from Spaln_aa2Genome C-------TTGGTATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAAG actgtttaggaggccatgctttcacaaacttttctttttctttaaactagCGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAGCgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from Spaln_nt2Genome CTTGG------TATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAAG actgtttaggaggccatgctttcacaaacttttctttttctttaaactagCGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAGCgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from Pairagon ----------------------------------------------------------TGGTATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAAG ACTGTTTAGGAGGCCATGCTTTCACAAACTTTTCTTTTTCTTTAAACTAGCGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAGCgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from Exonerate_protein2genome GTAGGCTTCTGCTTGGTATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAAG actgtttaggaggccatgctttcacaaacttttctttttctttaaACTAGCGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAGCgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from Exonerate_coding2genome actgtttaggaggccatgctttcacaaacttttctttttctttaaactagcgtggctctggtattcgccaaccccctgtgttgtgccttgtttccacagagagcgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt Alignment from GeneWise ----TGCTTGGTATTTGCCACACCCCTGTGCTGCGCTCTGTTCCCTCAGAGAAG actgtttaggaggccatgctttcacaaacttttctttttctttaaactagCGTGGCTCTGGTATTCGCCAACCCCCTGTGTTGTGCCTTGTTTCCACAGAGAGCgtgagtgagtgatacctaacattgtcattttggggcccatagtaccattt #### Shoc2_ID11420_6 --> 0 - 0 Original Alignment GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAGGATCTGCAG acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAA---------gtaactggaccctactcggcaggccaggataagaacctggcatctgatta Alignment from CESAR GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAGGATCTGCAG acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAA---------gtaactggaccctactcggcaggccaggataagaacctggc Alignment from Spaln_aa2Genome GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAG acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAAgtaactggaccctactcggcaggccaggataagaacctggcatctgatta Alignment from Spaln_nt2Genome GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAG acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAAgtaactggaccctactcggcaggccaggataagaacctggcatctgatta Alignment from Pairagon GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAGGATCTGCAGAAA acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTC------------AAAgtaactggaccctactcggcaggccaggataagaacctggcatctgatta Alignment from Exonerate_protein2genome GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAGGATC acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAAGTAActggaccctactcggcaggccaggataagaacctggcatctgatta Alignment from Exonerate_coding2genome GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAGGATC acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAAGTAActggaccctactcggcaggccaggataagaacctggcatctgatta Alignment from GeneWise GTTCTGATCTTATCGAACAACCTTCTAAAGAAGCTGCCCCACGGCCTTGGGAACCTCAGAAAGCTACGAGAGCTGGACCTGGAGGAGAACAAGCTGGAGTCCTTGCCCAATGAGATCGCGTATCTCAAG acgagtgtctccattttgcatcacaaatcacatctatgttttctacgcagGTCCTGATCCTATCAAACAATCTCCTAAAGAAGCTCCCCTATGGCCTTGGGAATCTCAGGAAGTTATGGGAGTTGGATCTAGAAGAGAATAAATTGGAGTCCCTACCCAATGAGATCACCTATCTCAAAgtaactggaccctactcggcaggccaggataagaacctggcatctgatta #### Sipa1_ID1141_11 --> 0 - 1 Original Alignment GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAAG---------------a gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAAAGCCCCAGGAATTCTAagtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from CESAR GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAAG---------------a gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAAAGCCCCAGGAATTCTAagtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from Spaln_aa2Genome GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATC- gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAgtaaagccccaggaattctaagtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from Spaln_nt2Genome GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAAGA gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAA-Agccccaggaattctaagtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from Pairagon GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAA---------------GA gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAAAGCCCCAGGAATTCTAAgtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from Exonerate_protein2genome GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAAGA gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAAAGccccaggaattctaagtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from Exonerate_coding2genome --GCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAGGACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAAGA GTCTAATAACCCATAGCCCACTAACAATTTCCTTCTGGAATCCCTTCCAGGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAAAGccccaggaattctaagtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct Alignment from GeneWise GACCAGTCAGGAAGCCCCAGTAGCCATGAAGACACCAGTGACTCAGGCCCAGAACTGAGGGCCTCCATCCTGCCCAGAACCTTGTCTCTGCGGAATTCCATCAGTAAG---------------A gtctaataacccatagcccactaacaatttccttctggaatcccttccagGATCAATCAGGAAGCCCTAGTAGTCATGGGGATACCAGTGACTCTGGTCCAGAATTAAGGGCCCCAATCTTGCCTAGAACCTTATCAGTACGAAATACCATCAGTAAAGCCCCAGGAATTCTAAgtacgtcaggtgacacaggtaaggaacagcctcctattcatgccctgcct #### Sipa1_ID1142_10 --> 1 - 0 Original Alignment c------TCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagcCTAAAGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatctttat Alignment from CESAR c------TCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagcCTAAAGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatttcctt Alignment from Spaln_aa2Genome C------TCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagCCTAAAGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatctttat Alignment from Spaln_nt2Genome CTCCCTGTCCGATG------AGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagCCTAAAGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatctttat Alignment from Pairagon C------TCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagCCTAAAGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatctttat Alignment from Exonerate_protein2genome CTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagcctaaaGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatctttat Alignment from Exonerate_coding2genome aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagcctaaagtccctgactgatgaggtccctgtcctacccaagattacaccggacctcctactgattacaacagctaacacttccgctcctgatactgatagagaaacaccaccttcccaggtgggtaacaagtagggtctaataacccatagcccactaacaatctttat Alignment from GeneWise ----AGCTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG aactacgtgattgtaattaagaatagtctcagtctctctgttttctgcagCCTAAAGTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCGGACCTCCTACTGATTACAACAGCTAACACTTCCGCTCCTGATACTGATAGAGAAACACCACCTTCCCAGgtgggtaacaagtagggtctaataacccatagcccactaacaatctttat #### Sipa1_ID1146_6 --> 0 - 2 Original Alignment ---------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACag cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagAAGACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACaggtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from CESAR ---------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACag cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagAAGACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACaggtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from Spaln_aa2Genome ------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACAG cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagaagACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACAGgtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from Spaln_nt2Genome CTGAG GAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACAG cttgagccactgaagCTCAGgtatttttacattgctctctgcttgtacagaagacattactattaagGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACAGgtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from Pairagon ---------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACAG cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagAAGACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACAGgtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from Exonerate_protein2genome ---------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACAG cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagAAGACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACAGgtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from Exonerate_coding2genome ---------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACAG cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagAAGACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACAGgtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt Alignment from GeneWise ------CTCCTGAGGAAGCGTCATATCGGCAACGATATTGTGACCATCGTGTTCCAGGAGCCCGGTAGCAAGCCCTTCTGCCCTACGACAATCCGCTCTCACTTCCAGCACGTTTTCTTGGTGGTGCGTGCGCATGCTCCCTGCACCCCACACACCTCATACAG cttgagccactgaagctcaggtatttttacattgctctctgcttgtacagaagACATTACTATTAAGGAAATGTCACATCAGTAACTACATTGTGACTATTGTTTTTCAAGAGCCTGGCAGCAAACCATTCTGTCCTAAGACAGTATGCTCTCACTTCCCACATGTTTTCTTGGTGGTGCGAGCATTTGCTTCTTGCACTCCCCACACATCATACAGgtaagtacttggttaagctgggatctcagggatgggtaaattgtcatggt #### Slc18a2_ID12936_4 --> 2 - 1 Original Alignment tg---------TTTGCCTTCTCCAGCAGCTATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTg ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagtgATTCTCCTATTTGCATAT------GGTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTggtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from CESAR tgTTTGCC---TTCTCCAGCAGCTATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTg ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagtgATTCTCCTATTTGCATATGGTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTggtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from Spaln_aa2Genome TG---TTTGCCTTCTCCAGCAGCTATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTG ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagTGATTCTCCTATTTGCATATGGTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTGgtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from Spaln_nt2Genome TGTTTG-CCT-TCTCCAGCAGCT-ATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTG ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagTGATTCTCCTATTTGCATATGGTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTGgtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from Pairagon -------------------TGTTTGCCTTCTCCAGCAGCTATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTG ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagTGATTCTCCTATTTGCATATG----------------GTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTGgtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from Exonerate_protein2genome GTTATGTTTGCCTTCTCCAGCAGCTATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTG ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaaGTGATTCTCCTATTTGCATATGGTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTGgtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from Exonerate_coding2genome ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagtgattctcctatttgcatatggttatgccttactcctgattgccaagtccttgcaaggaataggttcatcttgctcatctgttgctggtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg Alignment from GeneWise --ATGTTTGCCTTCTCCAGCAGCTATGCCTTCCTGCTGATCGCCAGGTCCCTGCAGGGAATCGGCTCCTCTTGCTCATCTGTGGCTG ctggcatatgtagggaaccaggaaggcatgtctgtctgcccccctcaaagTGATTCTCCTATTTGCATATGGTTATGCCTTACTCCTGATTGCCAAGTCCTTGCAAGGAATAGGTTCATCTTGCTCATCTGTTGCTGgtacgttataactaaagtatcaccatgaactcataggtattgagtcaggg #### Slc22a12_ID1788_9 --> 1 - 2 Original Alignment g---------ATGACTGCAGTGGGCCTCTGCCAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAAca cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagaATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTTATTG---------------------------ATACCCTTGCTGGTTTATGGA------CCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAAcagtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from CESAR g---------ATGACTGCAGTGGGCCTCTGCCAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAAca cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagaATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTTATTG---------------------------ATACCCTTGCTGGTTTATGGA------CCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAAcagtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from Spaln_aa2Genome GATGACTGCAGTGGGCCTCTGC---------CAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAACA cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagAATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTTATTG---------------------------ATACCCTTGCTGGTTTATGGA------CCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAACAgtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from Spaln_nt2Genome GATGACTGCAGT---------GGGCCTCTGCCAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAACA cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagAATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTT---------------------------ATTGATACCCTTGCTGGTTTATGGA------CCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAACAgtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from Pairagon ---------GATGACTGCAGTGGGCCTCTGCCAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAACA cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagAATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTTA---------------------------TTGATACCCTTGCTGGTTTATGGA------CCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAACAgtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from Exonerate_protein2genome CCAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAACA cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgCAGAATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTTATTGATACCCTTGCTGGTTTATGGACCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAACAgtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from Exonerate_coding2genome cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagaatcggtgcgatgacttcagtttgtgtctgccatgtggtggctcgagggggagctactttggggcctttattgatacccttgctggtttatggaccagttctaagtggctttgcagcattactactgcctgagactaaaatattacctcttcctactattcaggatatacagaaacagtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg Alignment from GeneWise -------AGGATGACTGCAGTGGGCCTCTGCCAGGTGGCAGCCCGAGGGGGAGCCATGCTAGGGCCTTTGGTACGGCTGCTGGGTGTCTATGGCTCCTGGATGCCCCTGCTGGTGTATGGAGTGGTGCCAGTGTTAAGTGGCCTAGCTGCACTGCTGCTGCCTGAGACCAAGAACTTACCACTGCCTGACACCATCCAAGACATCCAGAAACA cactgagtaatgaatacaacagaaactgtctccctgtcccctctctgcagAATCGGTGCGATGACTTCAGTTTGTGTCTGCCATGTGGTGGCTCGAGGGGGAGCTACTTTGGGGCCTTTATTG---------------------------ATACCCTTGCTGGTTTATGGA------CCAGTTCTAAGTGGCTTTGCAGCATTACTACTGCCTGAGACTAAAATATTACCTCTTCCT---ACTATTCAGGATATACAGAAACAgtgcgattaaacagactgtttaaaaatgccatttgattccctccatcttg #### Slc22a12_ID1790_7 --> 1 - 1 Original Alignment g---------TTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATg ggtcaaggtcagggctattttaagtatttactaactcctgttctccctaggACTCGGCTGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGAC---------CTTGGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGGTT---CCTGGACTATGTATACTTTCCAATGTATTG------GATggtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from CESAR g---------TTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATg ggtcaaggtcagggctattttaagtatttactaactcctgttctccctaggACTCGGCTGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGAC---------CTTGGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGGTT---CCTGGACTATGTATACTTTCCAATGTATTG------GATggtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from Spaln_aa2Genome G----------TTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATG ggtcaaggtcagggctattttaagtatttactaactcctgttctccctagGACTCGGCTGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGAC---------CTTGGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGGTT---CCTGGACTATGTATACTTTCCAATGTATTG------GATGgtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from Spaln_nt2Genome G--------GTTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATG ggtcaaggtcagggctattttaagtatttactaactcctgttctccctagGACTCGGCTGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGA---------CCTTGGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGG---TTCCTGGACTATGTATACTTTCCAATGTATTGG------ATGgtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from Pairagon ---------GTTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATG ggtcaaggtcagggctattttaagtatttactaactcctgttctccctagGACTCGGCTGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGA---------CCTTGGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGG---TTCCTGGACTATGTATACTTTCCAATGTATTGG------ATGgtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from Exonerate_protein2genome GTTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATG ggtcaaggtcagggctattttaagtatttactaactcctgttctccctaggactcggctGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGAC---------CTTGGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGGTT---CCTGGACTATGTATACTTTCCAATGTATTG------GATGgtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from Exonerate_coding2genome ggtcaaggtcagggctattttaagtatttactaactcctgttctccctaggactcggctgttttccataggcttcaccttttatggactagctattgaccttgggagcaacatattcctcctccaatcgatcattgggattgtggatttcccagtaaagacaggtagtttgctcctgattacacatttgggccaacacctctgtcaggtcagttttttggttcctggactatgtatactttccaatgtattggatggtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg Alignment from GeneWise -------TGGTTTGCCTTTGGCTTCACCTTCTACGGCCTGGCCCTTGACCTGCAAGCCCTAGGAAGCAATATCTTCCTGCTCCAGGCACTCATCGGGATTGTGGACTTCCCGGTGAAGACAGGCAGCCTGCTGCTGATCAGCCGCTTGGGCCGGCGCCTCTGCCAGGTCAGCTTCCTGGTGCTCCCCGGACTCTGCATCCTGTCCAACATACTGGTGCCCCATG ggtcaaggtcagggctattttaagtatttactaactcctgttctccctagGACTCGGCTGTTTTCCATAGGCTTCACCTTTTATGGACTAGCTATTGACCTT---------GGGAGCAACATATTCCTCCTCCAATCGATCATTGGGATTGTGGATTTCCCAGTAAAGACAGGTAGTTTGCTCCTGATTACACATTTGGGCCAACACCTCTGTCAGGTCAGTTTTTTGGTT---CCTGGACTATGTATACTTTCCAATGTATTG------GATGgtatgtctataatcgcttactgagtaaaaatgtttgacagaaaagagagg #### Slc22a12_ID1791_6 --> 0 - 2 Original Alignment ---GTGCTGCGGTCAGCTATGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCtg tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCctgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from CESAR ---GTGCTGCGGTCAGCTATGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCtg tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCctgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from Spaln_aa2Genome GTGCTGCGGTCAGCTATGGAG---GAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCTG tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCCTgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from Spaln_nt2Genome GTGCTGCGGTCAGCTA---TGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCTG tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCCTgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from Pairagon ---GTGCTGCGGTCAGCTATGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCTG tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCCTgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from Exonerate_protein2genome ---GTGCTGCGGTCAGCTATGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCTG tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCCTgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from Exonerate_coding2genome ---GTGCTGCGGTCAGCTATGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCTGGTTT tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCCTGTACggtcatcaatacaatggtttgcaggcaagagcagttccccagttat Alignment from GeneWise ---GTGCTGCGGTCAGCTATGGAGGAGGAACCAAGCAGGGACAAAGCTGGTGCCAGTCTGGGCACTCTACTCCACACACCTGGGCTGCGCCACCGAACCATCATCTCCATGCTGTGCTG tggggcagaagcttgaagtgaaaattgattttttttttttccccttacagTCCGTCCTATGGTCAGCTATGGACAAAGAACCAAGCAGAGACCAGGCTTGTGCCAGTATTAGCACTTTACTCCACACACCTGGTCTACGTCACCGTAGTATTATCTCTATGCTGTGCCTgtacggtcatcaatacaatggtttgcaggcaagagcagttccccagttat #### Slc22a20_ID1344_9 --> 1 - 2 Original Alignment gCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGA---cg gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctaggCAAATGGGTATGGAGTTGACTTCTGTCAATGCT---ATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAACC---ACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTcggtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from CESAR gCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGA---cg gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctaggCAAATGGGTATGGAGTTGACTTCTGTCAATGCT---ATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAACC---ACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTcggtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from Spaln_aa2Genome GCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGACGA-- gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctagGCAAATGGGTATGGAGTTGACTTCTGTCAATGCT---ATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAACC---ACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTCGgtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from Spaln_nt2Genome GCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGAC---G gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctagGCAAATGGGTATGGAGTTGACTTCTGTCAATGC---TATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAAC---CACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTCGgtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from Pairagon GCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGA---CG gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctagGCAAATGGGTATGGAGTTGACTTCTGTCAATGC---TATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAACC---ACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTCGgtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from Exonerate_protein2genome GATCAGGCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGA---CG gactcaatcatctctagaccaggtcctttcttttctgttgcttgCTCTAGGCAAATGGGTATGGAGTTGACTTCTGTCAATGCT---ATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAACC---ACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTCGgtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from Exonerate_coding2genome gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctaggcaaatgggtatggagttgacttctgtcaatgctattggaggtttggtgctcccattgatcacatcattaggcgaaatcagcccagtattaccacctgtattttctggtgctacatctgttctagctggcatggctgtagcttgcttcctaaccactcgtaatgtaccactagtcgaagttatcactgctatggagagacctcggtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat Alignment from GeneWise GCAGATGGGGATGGGATTTGCTTCTGTCAATGCCCGCCTCGGAGGCTTGGTGGCACCCCTGATCACCACACTTGGCGAGATCAGTCCAGTTCTGCCACCTGTATCCTTTGGTGCCACTTCAGTCTTGGCTGGAATGGCTGTCGCCTGCTTCCTGACTGAGACCCGCAATGTGCCACTGGTAGAAACTATTGCTGCAATGGAGAGACGA-- gactcaatcatctctagaccaggtcctttcttttctgttgcttgctctagGCAAATGGGTATGGAGTTGACTTCTGTCAATGCT---ATTGGAGGTTTGGTGCTCCCATTGATCACATCATTAGGCGAAATCAGCCCAGTATTACCACCTGTATTTTCTGGTGCTACATCTGTTCTAGCTGGCATGGCTGTAGCTTGCTTCCTAACC---ACTCGTAATGTACCACTAGTCGAAGTTATCACTGCTATGGAGAGACCTCGgtttgtacattctgatgatgaccagcaacgcttatgtcatgtggacgtat #### Slc22a20_ID1351_2 --> 0 - 2 Original Alignment TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGAC------------------------------ag gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACCAATTTTGTTTGCACACAGATGGAGCCAGCaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from CESAR TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGACag gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACcaattttgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from Spaln_aa2Genome TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGACAGGTTGG gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACCAATTTTgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from Spaln_nt2Genome TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGACAGGTTGG gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACCAATTTTgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from Pairagon TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGT gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTgtagcagaccaattttgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from Exonerate_protein2genome TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGACAG gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACCAattttgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from Exonerate_coding2genome TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGACAG gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACCAattttgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt Alignment from GeneWise TGGGACCTGGTGTGTGAGGCCCGCACCCTTCGTGACCTGGCTCAGTCCATCTACATGTCCGGGGTGTTGGTGGGAGCCGCCTTGTTTGGTGGTCTTGCTGACAGGTTGG gcctaaccacacaaccatagtgcagtgcaaccttgtcacatttcttgcagTGGGATCTGGTTTGTGAAACCCGCACTCTACATGACCTGGCCCCATCTATCTATATGTCTGGAATATCAGTAGGCGCTGCCTTGTTTGGTTGTGTAGCAGACCAATTTTgtttgcacacagatggagccagcaggtaattgacttggatgaggaactctattcccttactcttaattgtaagtt #### Slc22a6_ID2284_5 --> 1 - 0 Original Alignment g---------TTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcaggCTAGACCGTTTCTACATTGAGTCAACACGGTGGTAC---TCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from CESAR g---------TTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcaggCTAGACCGTTTCTACATTGAGTCAACACGGTGGTAC---TCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from Spaln_aa2Genome G---------TTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcagGCTAGACCGTTTCTACATTGAGTCAACACGGTGGTAC---TCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from Spaln_nt2Genome GTTCTTCATTGAG---------TCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcagGCTAGACCGTTTCTACATTGAGTCAACACGGTGGTA---CTCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from Pairagon G---------TTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcagGCTAGACCGTTTCTACATTGAGTCAACACGGTGGTA---CTCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from Exonerate_protein2genome G---------TTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcagGCTAGACCGTTTCTACATTGAGTCAACACGGTGGTAC---TCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from Exonerate_coding2genome G---------TTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAGGTG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcagGCTAGACCGTTTCTACATTGAGTCAACACGGTGGTAC---TCATCTGGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGGTAaggtctagccttatcatgctcagatgggatctgcattactcctagac Alignment from GeneWise -------TGGTTCTTCATTGAGTCAGCCCGCTGGTACTCCTCCTCTGGAAGGCTGGACCTCACCCTCCGAGCCCTGCAGAGAGTGGCCCGCATCAACGGGAAACAAGAAGAGGGGGCTAAGCTGAGTATAGAG aaactcaataacttactatgctgatttctaaccctgctctgtccctgcagGCTAGACCGTTTCTACATTGAGTCAACACGGTGGTACTCATCT---GGTAGGTTAGACTTTACCCTCCGAGCTTTGCAGAGAGTGGCTTGTATCAATGCAAAACAGGAAGAAGGGCCCAAACTGTGCATTGAGgtaaggtctagccttatcatgctcagatgggatctgcattactcctagac #### Slc22a8_ID2275_8 --> 2 - 2 Original Alignment aaATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCTCag tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagaaATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCC---------aggtgcttgttaggtgcaaactttgggttagcagaccactaaaagagtggta Alignment from CESAR aaATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCTCag tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagaaATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCC---------aggtgcttgttaggtgcaaactttgggttagcagaccactaaaagagtggta Alignment from Spaln_aa2Genome AAATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCT tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagAAATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCCAGGTGCTTgttaggtgcaaactttgggttagcagaccactaaaagagtggta Alignment from Spaln_nt2Genome AAATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCTC--AG tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagAAATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCCAGGTGCTTGTTAGgtgcaaactttgggttagcagaccactaaaagagtggta Alignment from Pairagon AAATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCTCAG tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagAAATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCC---------CAGgtgcttgttaggtgcaaactttgggttagcagaccactaaaagagtggta Alignment from Exonerate_protein2genome AAATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCTC tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagAAATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCCAGGTGCTTGttaggtgcaaactttgggttagcagaccactaaaagagtggta Alignment from Exonerate_coding2genome AAATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCTACAGTCCTC tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagAAATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCCAGGTGCTTGttaggtgcaaactttgggttagcagaccactaaaagagtggta Alignment from GeneWise AAATGCAGCTCTTGAGAACAGCACTGGCTGTATTTGGGAAGGGATGCCTGTCTGGCTCCTTCAGCTGCCTCTTCCTCTACACAAGTGAGCTCTACCCT-- tcttccttagcaaattcacatgcaaaagtctcaaccgtttgtgtccccagAAATGGAGATCGTGAGGACAGCACTAGCTGTGTTTGGCATGGGATGCTTATCTGGTGCCTTTAGCTGCCTCTTCTTTTACACTAGTGAGCTCTACCCCAGgtgcttgttaggtgcaaactttgggttagcagaccactaaaagagtggta #### Slc22a8_ID2276_9 --> 1 - 2 Original Alignment gCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCCCTTACCAGAAACTATCGAGGACATACAAGACtg aattcagtatgagtgagccagactctcttggttctgctttctttccaaaggCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGA---------------------------------tggtaaggtcccttagccccttgacttttgtcacaattaacacagactttgg Alignment from CESAR gCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCCCTTACCAGAAACTATCGAGGACATACAAGACtg aattcagtatgagtgagccagactctcttggttctgctttctttccaaaggCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGA---------------------------------tggtaaggtcccttagccccttgacttttgtcacaattaacacagactttgg Alignment from Spaln_aa2Genome GCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCC CTTACCA aattcagtatgagtgagccagactctcttggttctgctttctttccaaagGCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGATGgtaaggtcccttagccccttgacttttgtcacaattaacacagACTTTGG Alignment from Spaln_nt2Genome GCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGG---------CCCTTA--CCAGAAACTATCGAGGACAT--ACA-AGACT--G aattcagtatgagtgagccagactctcttggttctgctttctttccaaagGCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGATGGTAAGGTCCCTTAGCCCCTTGACTTTTGTCACAATTAACACAGACTTTGg Alignment from Pairagon GCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCCCTTACCAGAAACTATCGAGGACATACAAGACTG aattcagtatgagtgagccagactctcttggttctgctttctttccaaagGCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGA---------------------------------TGgtaaggtcccttagccccttgacttttgtcacaattaacacagactttgg Alignment from Exonerate_protein2genome GCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCC CTTACCA aattcagtatgagtgagccagactctcttggttctgctttctttccaaagGCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGATGgtaaggtcccttagccccttgacttttgtcacaattaacacagACTTTGG Alignment from Exonerate_coding2genome GCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCC CTTACCA aattcagtatgagtgagccagactctcttggttctgctttctttccaaagGCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGATGgtaaggtcccttagccccttgacttttgtcacaattaacacagACTTTGG Alignment from GeneWise GCAAACAGGTATGGGTATCAGTAACATATGGGCTCGAGTGGGAAGTATGATAGCCCCACTGGTGAAAATCACGGGAGAACTGCAGCCCTTCATCCCTAATGTCATCTTTGGGACCATGACTCTACTGGGAGGCAGTGCTGCCTTCTTTCTGCTTGAGACCCTCAATCGGCC CTTACCA aattcagtatgagtgagccagactctcttggttctgctttctttccaaagGCAAACGGGCATGGGTATCAGTAATATATGGGCTCGGGTAGGAAGTATGATAGCCCCCCTGGTCAAAGTCACTGGTGAACTGCAGCTTTTCACTCCTAATGTTATCTTCGGTACCATG---CTACTTGGAGGCAGTGCTGCTTTCTTTCTACTTGAAACCTTAAATAGATGgtaaggtcccttagccccttgacttttgtcacaattaacacagACTTTGG #### Slc25a45_ID1291_2 --> 2 - 0 Original Alignment ga------GCTGTGGGCCTGGTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagggCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from CESAR ga------GCTGTGGGCCTGGTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagggCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from Spaln_aa2Genome GAGCTGTGGGCCTG------GTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagGGCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from Spaln_nt2Genome GAGCTGTGGG-CCTGGTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagggcagGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from Pairagon G------AGCTGTGGGCCTGGTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagGGCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from Exonerate_protein2genome GA------GCTGTGGGCCTGGTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagGGCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from Exonerate_coding2genome GA------GCTGTGGGCCTGGTCCTGGGGCACCCATTCGACACTGTAAAG gaatcatgtccagggggtctggctagacgtttttttactctcgcctatagGGCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat Alignment from GeneWise CCCGTGGAAGAGTTTGTGGCTGGCTGGATCTCTGGA---GCTGTGGGCCTGGTCCTGGGGCACCCATTCGACACTGTAAAG tcatgtccagggggtctgg---CTAGACGTTTTTTTACTCTCGCCTATAGGGCAGGAAGCTGTGGGACTGGTTCTGGGGCACCCATTTGATACTGTAAAGgtaagtacctgctgggatgaaggcaaatacactgtgatgaaggcaaatat #### Slc25a45_ID1293_4 --> 0 - 0 Original Alignment GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTC------GGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tacaggattccactgccaaagtttgttaacccctgtttcttcttccccag---CTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from CESAR GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTC------CTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tggtacaggattccactgccaaagtttaacccctgtttcttcttccccag---CTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from Spaln_aa2Genome GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTC------CTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tacaggattccactgccaaagtttgttaacccctgtttcttcttccccagCTAGGATTCTTT---AAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from Spaln_nt2Genome GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTC------GGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tacaggattccactgccaaagtttgttaacccctgtttcttcttccccag---CTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from Pairagon GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTC------CTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tacaggattccactgccaaagtttgttaacccctgtttcttcttccccag---CTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from Exonerate_protein2genome CTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTC------CTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tacaggattccactgccaaagtttgttaacccctgtttcttcttccccagCTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from Exonerate_coding2genome ACCAGGGCATTGTGGACTGCGTAGTCAAGACTTACCGCCATGAGTCAGTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTC------CTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG TACAGGATTCCACTGCCAAAGTTTGTTAACCCCTGTTTCTTCTTCCCCAGCTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa Alignment from GeneWise CTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTC------GGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG tacaggattccactgccaaagtttgttaacccctgtttcttcttccccagCTAGGATTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAACTCTGGTTAATTCGGTCTTGTTTTTGTTTGGAGTGTATAGCAACACACTTGTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGTCACACAAATACCTTTATAGCAGGTTGTACAAGAGGTCTCCGGCAGgtcagtaggtcatggacaaaggataacttacatacacttaggttggagaa #### Slc25a45_ID1294_5 --> 0 - 1 Original Alignment ---------------------GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCa actggtagagttgagttcaggacatcactctctattttgttctcactcagCTCCCTCCACACCCCTCTAAAGCCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGagtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from CESAR ---------------------GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCa actggtagagttgagttcaggacatcactctctattttgttctcactcagCTCCCTCCACACCCCTCTAAAGCCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGagtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from Spaln_aa2Genome ---------------------GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCA actggtagagttgagttcaggacatcactctctattttgttctcactcagCTCCCTCCACACCCCTCTAAAGCCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGAgtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from Spaln_nt2Genome GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCA actggtagagttgagttcaggacatcactctctattttgttctcactcagctccctccacacccctctaaag-CCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGAgtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from Pairagon GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCA actggtagagttgagttcaggacatcactctctattttgttctcactcagctccctccacacccctctaaag-CCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGAgtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from Exonerate_protein2genome GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCA actggtagagttgagttcaggacatcactctctattttgttctcactcagctccctccacacccctctaaaGCCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGAgtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from Exonerate_coding2genome GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCA actggtagagttgagttcaggacatcactctctattttgttctcactcagctccctccacacccctctaaaGCCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGAgtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt Alignment from GeneWise ---------------------GCCTACTGCCTGGCTCCTTTTGACCTCATCAAAGTCCGTCTACAAAACCAGACAGAGCCAAGGATGCAGATATCGAGTTCTATGCCCCGGTACCGGGGGCCTGTGCACTGTGCAGCCTCCATCTTGAGAGAAGAAGGACCCCAGGGACTGTTCAGAGGATCCTGGGCCCTGGTGTTGAGAGACACTCCTACGTTAGGAATGTACTTTGTCACCTATGAAGGGCTATGTCGCCAGTACACACCAGAAGGCCAGAATCCCA actggtagagttgagttcaggacatcactctctattttgttctcactcagCTCCCTCCACACCCCTCTAAAGCCTACTGTCTTGCACCCTTTGATCTCATACGGGTGCATCTACAAAATCAGACAGAGTCGAGGCTTCAGATATCTAGCTCAATGCCCCGGTATCGAGGTCCAGTCCACTGTGCAGCTTCAGTCCTGAGGGAGGAAGGACCCCAAGGACTGCTCAGGGGATCTTGGGCTTTGGTCTTGAGAGACACCCTTACATTGGGAATGTACTTTGTAGCCTATAAAGGGCTATGCCGCCAGTATACCCTAGGGGGACAAAACCCGAgtagaatagttgtaacccaagatcttcggctgcattgctgtcgttccctt #### Slc29a2_ID788_2 --> 1 - 0 Original Alignment cTACCACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctggcagctactcgagccttaattttctctttcagc---CACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from CESAR cTACCACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG gcgacatctgatggatggctggcagctcgagccttaattttctctttcagc---CACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from Spaln_aa2Genome CTACCACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctggcagctactcgagccttaattttctctttcagC---CACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from Spaln_nt2Genome CCACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctggcagctactcgagccttaattttctctttcagCCACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from Pairagon CTACCACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctggcagctactcgagccttaattttctctttcag---CCACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from Exonerate_protein2genome CTACCACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctggcagctactcgagccttaattttctctttcagC---CACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from Exonerate_coding2genome CACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctggcagctactcgagccttaattttctctttcagcCACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga Alignment from GeneWise GCGCGGGGAAACGCCCCTCGGGACAGCTAC---CACCTGGTTGGGATCAGCTTCTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAACTTCTTCATTACCGCCATCCCG acatctgatggatggctgGCAGCTACTCGAGCCTTAATTTTCTCTTTCAGCCACCTTGCTGGCATCAGCTTTTTCATTCTGGGACTGGGCACCCTTCTCCCCTGGAATTTCTTCATTACGGCAATCCCAgtgggttagtgcaatatggccaccttttcacaggctaagccttcttgaga #### Slc29a2_ID793_7 --> 0 - 1 Original Alignment AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTg agcccaggaactgtattgcacacaggccctgctgcttctcttccccccag---TTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAggtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from CESAR AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTg aagagcccaggaactgtattgcacagccctgctgcttctcttccccccag---TTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAggtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from Spaln_aa2Genome AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTG agcccaggaactgtattgcacacaggccctgctgcttctcttccccccag---TTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAGgtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from Spaln_nt2Genome AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTG agcccaggaactgtattgcacacaggccctgctgcttctcttccccccag---TTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAGgtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from Pairagon AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTG agcccaggaactgtattgcacacaggccctgctgcttctcttccccccag---TTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAGgtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from Exonerate_protein2genome AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTG agcccaggaactgtattgcacacaggccctgctgcttctcttcccccCAGTTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAGgtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from Exonerate_coding2genome AAGTTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTG agcccaggaactgtattgcacacaggccctgctgcttctcttcccccCAGTTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAGgtaagggcttggctgcaacttactctttcttttttagagggatgatgact Alignment from GeneWise TTTGCCCGTTACTACCTGACCGAGAAGCTGTCTCAGGCTCCAACTCAGGAGCTGGAGACTAAAGCTGAGCTCCTCCAAGCTG agcccaggaactgtattgcacacaggccctgctgcttctcttccccccagTTTCCACGCTACTACCTAACTAAGAAGCTATCTCAAGCTCCAACTCAGGAGCTTGAGAATAAGGCAGAACTCCTTCAAGCAGgtaagggcttggctgcaacttactctttcttttttagagggatgatgact #### Slit1_ID8232_7 --> 1 - 2 Original Alignment gACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCtt gtgtgattagctctcttggtccattgcttctgtactcctccccacttcagt---TTCAATAATAATAACATCAGTGCTATCCCC------CGTTTCAATCATATCCCTAAGCTCCACACTttgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from CESAR gACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCtt caggtgtgattagctctcttggtccgcttctgtactcctccccacttcagt---TTCAATAATAATAACATCAGTGCTATCCCC------CGTTTCAATCATATCCCTAAGCTCCACACTttgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from Spaln_aa2Genome GACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCTT gtgtgattagctctcttggtccattgcttctgtactcctccccacttcagT---TTCAATAATAATAACATCAGTGCTATCCCC------CGTTTCAATCATATCCCTAAGCTCCACACTTTgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from Spaln_nt2Genome GACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCTT gtgtgattagctctcttggtccattgcttctgtactcctccccacttcag---TTTCAATAATAATAACATCAGTGCTATCC------CCCGTTTCAATCATATCCCTAAGCTCCACACTTTgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from Pairagon GACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCTT gtgtgattagctctcttggtccattgcttctgtactcctccccacttcag---TTTCAATAATAATAACATCAGTGCTATCC------CCCGTTTCAATCATATCCCTAAGCTCCACACTTTgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from Exonerate_protein2genome GACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCTT gtgtgattagctctcttggtccattgcttctgtactcctccccacttCAGTTTCAATAATAATAACATCAGTGCTATCCCC------CGTTTCAATCATATCCCTAAGCTCCACACTTTgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from Exonerate_coding2genome gtgtgattagctctcttggtccattgcttctgtactcctccccacttcagtttcaataataataacatcagtgctatcccccgtttcaatcatatccctaagctccacactttgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat Alignment from GeneWise GACCCTGAACAACAACAACATCACCACCATCCCTGTGTCCAGTTTCAACCATATGCCCAAGCTTCGGACCTT gtgtgattagctctcttggtccattgcttctgtactcctccccacttcagT---TTCAATAATAATAACATCAGTGCTATCCCC------CGTTTCAATCATATCCCTAAGCTCCACACTTTgtcagtttgcaactgctggtgtatcacctacactatggataaggtgccat #### Slit1_ID8233_6 --> 1 - 2 Original Alignment aCAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTct tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagaCAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGAT---ctgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from CESAR aCAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTct tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagaCAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGAT---ctgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from Spaln_aa2Genome ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGT tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATCTgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from Spaln_nt2Genome ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCT tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGA---TCTgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from Pairagon ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCT tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGA---TCTgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from Exonerate_protein2genome ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCT tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGAT---CTgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from Exonerate_coding2genome tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagacagctggacaagaaccgcattagctgcatcaaggaaggggccctccgtgccctacgtggattggatctgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca Alignment from GeneWise ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGT tgccaaaactattcttgtggtcactttcgaaactcatttacttccaacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATCTgtgagtagaggagtatgaagatgaaattagtgcatcaacattgttatcca #### Slk_ID10264_16 --> 0 - 0 Original Alignment GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAACAG aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAA---gtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt Alignment from CESAR GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAACAG aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAA---gtgagcagtctggatagttcaatttctttacctcaatatgagatgta Alignment from Spaln_aa2Genome GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAA aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAAgtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt Alignment from Spaln_nt2Genome GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAA aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAAgtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt Alignment from Pairagon GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAA aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAAgtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt Alignment from Exonerate_protein2genome GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAA aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAAgtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt Alignment from Exonerate_coding2genome GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAA aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATAAAAgtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt Alignment from GeneWise GAAACAGAACAAATGCAGCGCTACAATCAACGACTTATTGAAGAACTGAAAAACAGACAGACTCAGGAACGAGCGAGACTGCCCAAGATTCAAAGAAGTGAAGCCAAGACACGAATGGCCATGTTTAAAAAAAGTTTGAGGATCAACTCAACAGCCACACCAGACCAGGACCGTGAAAAAATTAAACAG aatcccctaaaacagtcgttagttccgggctgtttccatctgtgttccagGAGACTGAACAAATGCAACGTTACAATCAACGACTCATTGAAGAGTTGAAAAATAGAGAGACTCAGGAGAGAGTGCGACTCGCCAAAATTCAAAGGAGCGAATCAAAAATAAGAATGGCTATGTTTAAGAAAAGTTTGCGGATCAATTCAACAGCCACACCTGATCAAGATCATGAAAAAATA---AAAgtgagcagtctggatagttcaatttctttacctcaatatgagatgtatgt #### Smc3_ID11336_24 --> 2 - 0 Original Alignment atTTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAAGCGTTTGAGAAGTACCAGACACTGAGCCTGAAGCAG gacagggtaagcagactcctctggtcctatagccttttcctccccaacagac---------------------------GCA---------GAGTTGCAACAAAGT------ACCTGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAA---AAGCAA---------AAA------------------ACCCTCCCTTGGGAAGTG------GAGGATCAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from CESAR atTTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAAGCGTTTGAGAAGTACCAGACACTGAGCCTGAAGCAG aatttgttaagcagactcctctggtcctatagccTTTTCCTCCCCAACAGAC------------------GCAGAGTTGCAACAAAGTACC------TGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCAAAAA------------------------------ACCCTCCCTTGGGAAGTG---GAGGAT---CAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from Spaln_aa2Genome ATTTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAAGCGT gacagggtaagcagACTCCTCTGGTCCTATAGCCTTTTCCTCCCCAACAGACGCAGAGTTGCAACAAAGTACC------TGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCAAAAAACCCTCCCTTGGGAAGTGGAGGATCAGACACTCCTGTTAAAGGAGGTAAgtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from Spaln_nt2Genome AGCTGG AATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAAGCGTTTGAGAAGTACCAGACACTGAGCCTGAAGCAG --CAGGgtaagcagactcctctggtcctatagccttttcctccccaacagA--CGCAGAGTTGCAACAAAGTA------CCTGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCA-------------AAAAA-----------------CCCTCCCTTGGGAA------GTGGAGGATCAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from Pairagon ATTTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAG---------------------------------------------AAGGAG gacagggtaagcagactcctctggtcctatagccttttcctccccaacagacgcag------------------------------------------AGTTGCAACAAAGTAC------CTGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCAAAAAACCCTCCCTTGGGAAGTGGAGGATCAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from Exonerate_protein2genome AT---TTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAA gacagGGTAAGCAGACTCCTCTGGTCCTATAGCCTTTTCCTCCCCAACAGACGCAGAGTTGCAACAAAGTACCTGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCAAAAAACCCTCCCTTGGGAAGTGGAGGATCAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from Exonerate_coding2genome AT---TTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAA gacagGGTAAGCAGACTCCTCTGGTCCTATAGCCTTTTCCTCCCCAACAGACGCAGAGTTGCAACAAAGTACCTGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCAAAAAACCCTCCCTTGGGAAGTGGAGGATCAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc Alignment from GeneWise --GATTTGGACAATTCCATTGACAAAACAGAAGCTGGAATTAAAGAGCTCCAGAAAAGTATGGAGCGCTGGAAAAATATGGAGAAAGAACACATGGATGCCATAAATCATGATACTAAAGAGCTGGAGAAGATGACCAACCGGCAAGGCATGCTGTTGAAGAAGAAGGAGGAGTGTATGAAGAAGATCCGGGAGCTGGGGTCCCTCCCCCAGGAAGCGTTTGAGAAGTACCAGACACTGAGCCTGAAGCAG gacagggtaagCAGACTCCTCTGGTCCTATAGCCTTTTCCTCCCCAACAGACGCAGAGTTGCAACAAAGTACC------TGGCAAAATACAGAGAAAGAGCACATGGATGCCATAAATCATGATATGAAAGAGTTAGATAAGATG---AACCAACAAGGCATGCTTCTTAAAAAGCAAAAA------------------------------ACCCTCCCTTGGGAAGTGGAGGAT------CAGACACTCCTGTTAAAGGAGgtaagtctctttgcaataagtgctcagcccccctatacatcttgttaatc #### Smc3_ID11338_26 --> 0 - 0 Original Alignment GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG------------------------------ tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAGTCTATTGCTGCCTCCCATCCTAGGTGACGACgtgaggacttattatacttagtttctcatgtacctttttactttaaaaac Alignment from CESAR GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATC--Agtctattgctgcctcccatcctaggtgacgacgtgaggacttattatacttagtttctcatgtacctttttactttaaaaac Alignment from Spaln_aa2Genome GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATC- ------AG tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAgtctattgctgcctcccatcctaggtgacgacgtgaggacttattatacttagTTTCTCATgtacctttttactttaaaaac Alignment from Spaln_nt2Genome GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCA tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAgtctattgctgcctcccatcctaggtgacgacgtgaggacttattatacttagtttctcatgtacctttttactttaaaaac Alignment from Pairagon GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAG--------------------------------------------------------------------------------- tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAGTCTATTGCTGCCTCCCATCCTAGGTGACGACGTGAGGACTTATTATACTTAGTTTCTCATGTACCTTTTTACTTTAAAAAC Alignment from Exonerate_protein2genome GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAGTctattgctgcctcccatcctaggtgacgacgtgaggacttattatacttagtttctcatgtacctttttactttaaaaac Alignment from Exonerate_coding2genome GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAGTctattgctgcctcccatcctaggtgacgacgtgaggacttattatacttagtttctcatgtacctttttactttaaaaac Alignment from GeneWise GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG------------------------------ tcatttaaaaaagaggcatgccacctagctgacccacacatcctctgcagGTCTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAGTCTAAGGACAAAGGGGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCGTCAGTTGACCAATTCACAGGAATTGGGATCAGTCTATTGCTGCCTCCCATCCTAGGTGACGACgtgaggacttattatacttagtttctcatgtacctttttactttaaaaac #### Smc5_ID5113_20 --> 0 - 0 Original Alignment GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTCACAGGACTGAATCCTTCG tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTC------------------gtaagtctccatattgtttagcggaagactacttactttgttcaccctat Alignment from CESAR GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTCACAGGACTGAATCCTTCG tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTC------------------gtaagtctccatattgtttagcggaagactac Alignment from Spaln_aa2Genome GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTCACAGGACTGAATCCTTCG tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTCGTAAGTCTCCAT---ATTgtttagcggaagactacttactttgttcaccc Alignment from Spaln_nt2Genome GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTC tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTCgtaagtctccatattgtttagcggaagactacttactttgttcaccctat Alignment from Pairagon GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTC tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTCgtaagtctccatattgtttagcggaagactacttactttgttcaccctat Alignment from Exonerate_protein2genome GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTCACAGGACTGAATCCTT tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTCGTAAGTCTCCATATTGtttagcggaagactacttactttgttcaccctat Alignment from Exonerate_coding2genome ATGGCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTCACAGGACTGAATCCTT tcagcatactggtatgctcattatttacgcctgttttctttcttttgTAGGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTCGTAAGTCTCCATATTGtttagcggaagactacttactttgttcaccctat Alignment from GeneWise GCTTTTCAAGATCTCCCAAACACATTGGATGAAATCGATGCATTATTAACTGAAGAAAGGTCAAGAGCTTCGTGCTTCACAGGACTGAATCCTTCG tcagcatactggtatgctcattatttacgcctgttttctttcttttgtagGCATTTGAAGATCTTCTAAACACATTGGATGAAACTGATGCATTATTAACTGCAGAAAGATCAAGGGCTTCATGCTTCGTAAGTCTCCAT---ATTgtttagcggaagactacttactttgttcaccc #### Snx15_ID1465_7 --> 2 - 1 Original Alignment aaAGTACAGGCCCCAGCCCTACCCACACAGGTGAGCTGGCAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCT------GCCCCAGCTTACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAg ttctacttcaggtccccaccccaggaagtctgaactttctctttaaccagca---------------------------------------GCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAggtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from CESAR aAGTACAGGCCCCAGCCCTACCCACACAGGTGAGCTG------------GCAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCCCCA------GCTTACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAg t---------CCCCACCCCAGGAAGTCT---GAACTTTCTCTTTAACCAGCAGCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAggtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from Spaln_aa2Genome CCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCC------CCAGCTTACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAG ttctacttcaggtccccaccccaggaagtctgaactttctctttaaccagcagCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAGgtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from Spaln_nt2Genome GTACAGGCCCCAGCC---CTACCCACACAGGTGAGCTGGCAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCCCCAGC------TTACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAG ttctacttcagGTCCCCACCCCAGGAAGTCTGAACTTTCTCTTTAACCAGCAGCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAGgtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from Pairagon GAGGAAAGTACAGGCCCCAGCCCTACCCACACAGGTGAGCTGGCAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCCCCAG------CTTACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAG ttctacttcaggtccccaccccaggaagtctgaactttctctttaaccag-------------------------------------------CAGCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAGgtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from Exonerate_protein2genome CAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCCCCAGCT------TACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAG ttctacttcaggtccccaccccaggaagtctgaactttctctttaaccagCAGCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAGgtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from Exonerate_coding2genome CAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCCCCAGCT------TACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAG ttctacttcaggtccccaccccaggaagtctgaactttctctttaaccagCAGCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAGgtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat Alignment from GeneWise CAGCCATTGAGGTAGAGTCCAAAAGGCTGGACCAGGAACCCTGGGAGCCAGGAGGACAGGAGGAGGAAGAAGCTGAGGATGGAGAGCCTGCCCCAGCT------TACCTTGGCCAGGCCACAGAGCTCATCACTCAAGCCCTGCGGAATGAAAAGGCTGGCGCCTACGCTGCTGCTCTCCAAGGCTACCAAGATGGGGTGCACATTCTTCTGCAGGGTGTCTCAG ttctacttcaggtccccaccccaggaagtctgaactttctctttaaccagCAGCAATTGAAGTTGGGGCTAAAAAACTGGATCATGAACCCTGGGAACCAGGTGGACAACAGCAGGAGGAAGCTGAGGATGGGGAACCTGCTCCAGGTCCCCCTTATCTTGGTCAAGCAGCAGAGCTTATCACTCAAACTGTTAGAAATAAAAAGGCAGGGACCTACACTGCTGCTCTTCAAGGATACCAAGATGGTGTTCACATCCTTTTGCAGGGTGTTTCAGgtaagcagtaaggtagtcctaaccctgttatttgaaagagggaggtcaat #### Snx15_ID1469_3 --> 0 - 1 Original Alignment ------GTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTg agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagTCCCTCGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTggtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from CESAR ------GTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTg agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagTCCCTCGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTggtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from Spaln_aa2Genome TAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTG agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagtccctcgtagTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTGgtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from Spaln_nt2Genome ------GTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTG agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagTCCCTCGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTGgtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from Pairagon ------GTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTG agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagTCCCTCGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTGgtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from Exonerate_protein2genome GTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTG agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagtccctcGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTGgtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from Exonerate_coding2genome AAAGAGGTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTG agtgtacccagcccttgctagggtctgcgacacttaccctgctctcccagTCCCTCGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTGgtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg Alignment from GeneWise --ATCTCAAAGAAGGACCCAGAGGATATCAAAGAGGTAGTAGTCTGGAAGCGGTACAGCGACTTCCGTAAGCTCCACGGGGACTTGGCCTATACTCACCGAAACCTCTTCCGTCGCCTAGAGGAGTTTCCGGCCTTCCCCCGTGCCCAGGTGTTTG agtgtacccagcccttgctagGGTCTGCGACACTTACCCTGCTCTCCCAGTCCCTCGTAGTAGTCTGGAAGCAGTACAGTGATTTCCGTAAGCTTCATGGTGAATTAGCCTACACCCACCGGAATCTCTTCCAGGATCTCGAGGAGTTCTCAGCATTCCCACAAGCCCAGGTGTTTGgtgaggtttagacaacatctccaggtgatgacatctagtatctctaaatg #### Snx32_ID1066_12 --> 2 - 0 Original Alignment AACAAg agCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAggtgagttggtcccacgggtaagttgcatgtttacttccatacagaa---------------------------TCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from CESAR AACAAg agCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAggtaagtcccacaggagtgtaagttgcatgtttacttccatacagaa---------------------------TCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from Spaln_aa2Genome AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagttggtcccacgggtaagttgcatgtttacttccatacagAA---------------------------TCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from Spaln_nt2Genome AACAAG---AGCT-----CATGG---ACTT-CAAGTCT-----CGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGGTGAGTTGGTCCCACGGGTAAGTTGCATGTTTACTTCCATACAGAATCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from Pairagon AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagttggtcccacgggtaagttgcatgtttacttccatacagAA---------------------------TCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from Exonerate_protein2genome AACAA AACAAggtgagttggtcccacgggtaagttgcatgtttacttccatacagaatcctctttccgtaagaacctcatcgagttgactgagctggagctcaagcaggccaaggtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from Exonerate_coding2genome aacaaggtgagttggtcccacgggtaagttgcatgtttacttccatacagaatcctctttccgtaagaacctcatcgagttgactgagctggagctcaagcaggccaaggtagcctggtattcaagttacatcaaaaagaactcaatctgctcattcta Alignment from GeneWise AACAA---GAGCTCATGGAC---------------TTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAGGCCAGC AACAAGGTGAGTTGGTCCCACGGGTAAGTTGCATGTTTACTTCCATACAGAA-TCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGGTAGCCtggtattcaagttacatcaaaaagaactcaatctgctcattcta #### Snx32_ID1067_11 --> 0 - 1 Original Alignment GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGC---CAGCGCTTCGAGCGCCTCTCTGACTCCGCCAAACAAg agCTCA acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAGCAACAGTTTGACTGTCTT------------------ggtaagacccacaggagtgtccgtccacccatctctgtccctcagaaCTTA Alignment from CESAR GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGCCAG---CGCTTCGAGCGCCTCTCTGACTCCGCCAAACAAg agCTCA acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAGCAACAGTTTGACTGTCTT------------------ggtaagacccacaggagtgtaagggctgaccaccatgtcccacagaaCTTA Alignment from Spaln_aa2Genome GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGC---CAGCGCTTCGAGCGCCTC- TCTGACT acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAGCAACAGTTTGACTGTCTTGgtaagacccacaggagtgtccgtccacccatctctgtccctca Alignment from Spaln_nt2Genome GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGCCAGCGCTTCGAGCGCCTCTCTGACTCC GCCAAA acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAG-----CAACAGTTTGACTGTCTTGgtaagacccacaggagtgtccgtccacccatctctgtccctcag------ Alignment from Pairagon GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGCCAGCGCTTCGAGCGCCTCTCTGACTCCGCCAAACA--------------------------------------------------------AGAGCTCA acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAGC---------------------------AACAGTTTGACTGTCTTGGTAAGACCCACAGGAGTGTCCGTCCACCCATCTCTGTCCCTCAGAACTTA Alignment from Exonerate_protein2genome GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGCCAGCGC acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAGCAAcagtttgactgtcttggtaagacccacaggagtgtccgtccacccatctctgtccctcagaactta Alignment from Exonerate_coding2genome acacttctgctatctattccataaatgctctgtatctcttcctcttctaggatctactctactgccgcctccgggcatcagctgagtatgagaatgctaacaaagctcttgataaagcccggacaaggaaccatgaagtatggccagcagagagacaccagcaactgtgttgccagcaacagtttgactgtcttggtaagacccacaggagtgtccgtccacccatctctgtccctcagaactta Alignment from GeneWise GACCTGTTGTACCGGCGGCTTCGGGCACTGGCTGACTACGAGAATGCTAACAAGGCACTGGACAAAGCTCGGACTAGGAACCGAGAAGTACGGCCAGCAGAGAGCCGCCAACAGCTGTGCTGCCAGCGC---TTCGAGCGCCTC--TCTGACTCCGCCAAA------------------------CAAGAGCTCA acacttctgctatctattccataaatgctctgtatctcttcctcttctagGATCTACTCTACTGCCGCCTCCGGGCATCAGCTGAGTATGAGAATGCTAACAAAGCTCTTGATAAAGCCCGGACAAGGAACCATGAAGTATGGCCAGCAGAGAGACACCAGCAACTGTGTTGCCAGCAACAGTTTGACTGTCTTGGTAAGACCCACAGGAGTGTCCGTCCACCCATCTCTGTCCCTCAGAACTTA #### Snx32_ID1070_8 --> 2 - 2 Original Alignment gc---------CTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGag atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggcCACAGTGGCCTGGCAGACAACTATATTCCCATTTCAGCT---GTGAGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAaggtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from CESAR gc---------CTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGag atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggcCACAGTGGCCTGGCAGACAACTATATTCCCATTTCAGCTGTG---AGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAaggtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from Spaln_aa2Genome GC---------CTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGAG atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaagGCCACAGTGGCCTGGCAGACAACTATATTCCCATTTCA---GCTGTGAGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAAGgtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from Spaln_nt2Genome --GCCTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGAG atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggccacagTGGCCTGGCAGACAACTATATTCCCATTTCAGCTG---TGAGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAAGgtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from Pairagon --GCCTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGAG atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggccacagTGGCCTGGCAGACAACTATATTCCCATTTCAGCTG---TGAGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAAGgtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from Exonerate_protein2genome GCCTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGAG atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggccacagtgGCCTGGCAGACAACTATATTCCCATTTCA---GCTGTGAGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAAGgtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from Exonerate_coding2genome atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggccacagtggcctggcagacaactatattcccatttcagctgtgagcagtcttgaaacccaagaagtgaaccaacttaaaaggtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt Alignment from GeneWise ----CTGGCAGACAACTATATCCCTATCTCTGCTGCACTGAGCAGTCTCGGAACCCAGGAAGTCAACCAACTCAAGAG atgtgcacatagcttgaattgcaataactctgtttttttccttgttaaaggccacagTGGCCTGGCAGACAACTATATTCCCATTTCAGCT---GTGAGCAGTCTTGAAACCCAAGAAGTGAACCAACTTAAAAGgtgagtgtcatgtgacatagcattgcccacccatgaaccattgttggggt #### Snx32_ID1072_6 --> 0 - 0 Original Alignment CTGAGTGTTCGAGAGAAGAACAGGAAGGAGGTCTTGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCACC---GGCATATCAGGGCTCAAG ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacag------GTCCATGAGAAGAACAGAAAGGAGGTTTCCGGG------CTGCGAGGT---GTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from CESAR CTGAGTGTTCGAGAGAAGAACAGGAAGGAGGTCTTGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCACC---GGCATATCAGGGCTCAAG acaacattattaagagtatccaagtcaggttgtttcctgttttcacacag------GTCCATGAGAAGAACAGAAAGGAGGTTTCCGGG------CTGCGAGGT---GTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from Spaln_aa2Genome CTGAGTGTTCGAGAGAAGAACAGGAAGGAGGTCTTGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCACCGGCATATCAGGGCTCAAG ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacag------GTCCATGAGAAGAACAGAAAGGAGGTTTCCGGG------CTGCGAGGTGTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from Spaln_nt2Genome GTGTTCGAGAGAAGAACAGGAAGGAGGTCTTGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCACCGG---CATATCAGGGCTCAAG ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacag--GTCCATGAGAAGAACAGAAAGGAGGTTT---CCGGGCTGC-GAGG-----TGTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from Pairagon CTGAGTGTTCGAGAGAAGAACAGGAAGGAGGTCT------TGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCAC---CGGCATATCAGGGCTCAAG ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacag------GTCCATGAGAAGAACAGAAAGGAGGTTTCCGGGCTGCGAGG---------------TGTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from Exonerate_protein2genome GTGTTCGAGAGAAGAACAGGAAGGAGGTCTTGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCACCGGCATATCAGGGCTCAAG ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacAGGTCCATGAGAAGAACAGAAAGGAGGTTTCCGGG------CTGCGAGGTGTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from Exonerate_coding2genome ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacaggtccatgagaagaacagaaaggaggtttccgggctgcgaggtgttaggtatgcagatgaaagcatcatcactggtggcatctcagggctcaaagtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt Alignment from GeneWise CTGAGTGTTCGAGAGAAGAACAGGAAGGAGGTCTTGGGAGGGCTCCTGAGGAGCATCGTCAGGTCTGCAGATGAAGTCCTCATCACCGGC---ATATCAGGGCTCAAG ttattaagagtatccaagtctcacgcaggttgtttcctgttttcacacagGTC------CATGAGAAGAACAGAAAGGAGGTTTCCGGG------CTGCGAGGT---GTTAGGTATGCAGATGAAAGCATCATCACTGGTGGCATCTCAGGGCTCAAAgtaagtgtagcgtctgttgtgctgggggcatcctgccaatccctccaggt #### Snx32_ID1074_4 --> 0 - 2 Original Alignment ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAgc tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtag------CCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAgcgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from CESAR ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAgc tcaagctggaaatgttgtgttaattggttgttttcccttttctgacgtag------CCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAgcgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from Spaln_aa2Genome CCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGC tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtagCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGCgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from Spaln_nt2Genome CCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGC tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtagCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGCgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from Pairagon GTACGCCGGCCTCATCATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGC tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtag----------------------CCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGCgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from Exonerate_protein2genome CCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGC tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtagCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGCgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from Exonerate_coding2genome CCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGC tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtagCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGCgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc Alignment from GeneWise CCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGC tggaaatgttgtgttaattaggcaaggttgttttcccttttctgacgtagCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAGAAACTGCAGAGGTTAGGTGAAGGCAATAGTTCAATCACTCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGCgtgaggatttcccgccatctcggtgattctagtagagctttcacagtctc #### Snx32_ID1075_3 --> 0 - 0 Original Alignment AGTGGCCTCCCTCACTTTGCCCAGTCTGAGTTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAA------GAGTACGCCGGCCTCATC ctgcgtcaacatagctataaaagaaattaccttctgctcctgctccttag------------------------------TTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from CESAR AGTGGCCTCCCTCACTTTGCCCAGTCTGAGTTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAAGAGTAC------GCCGGCCTCATC gagaagtaacttgaggtaacaagaaattaccttctgctcctgctccttag------------------------------TTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from Spaln_aa2Genome TCTGAGTTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAA------GAGTACGCCGGCCTCATC ctgcgtcaacatagctataaaagaaattaccttctgctcctgctccttag------TTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from Spaln_nt2Genome TTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAAGAGTACGC------CGGCCTCATC ctgcgtcaacatagctataaaagaaattaccttctgctcctgctccttagTTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from Pairagon AGTGGCCTCCCTCACTTTGCCCAGTCTGAGTTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAAGA ctgcgtcaacatagctataaaagaaattaccttctgctcctgctccttag------------------------------TTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAgtatgaatataacagccttgttgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from Exonerate_protein2genome AGTGGCCTCCCTCACTTTGCCCAGTCTGAGTTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAAGAGTACGCC------GGCCTCATC ctgcgtcaacatagctataaAAGAAATTACCTTCTGCTCCTGCTCCTTAGTTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from Exonerate_coding2genome AGTGGCCTCCCTCACTTTGCCCAGTCTGAGTTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAAGAGTACGCC------GGCCTCATC ctgcgtcaacatagctataaAAGAAATTACCTTCTGCTCCTGCTCCTTAGTTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg Alignment from GeneWise TTCTCAGTGGTTCGCCAGCACGAAGAGTTCATCTGGCTACATGACACCTATGTGGAAAACGAAGAGTACGCC------GGCCTCATC ctgcgtcaacatagctataaaagaaattaccttctgctcctgctccttagTTCTCAGTCGTTTGCCAGCATAAAGAGTTCATCTGGCTGCACGACACTTATGTAGAGAATGAAGAGTATGAATATAACAGCCTTGTTgtaaggtacaatagagcatggttgcagtgaaaaaagaccagggaaaggtg #### Sptbn2_ID611_6 --> 1 - 1 Original Alignment gCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGGATCCTGAAg cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagtCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAATGTAATGTCCACTACAATCTACAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTG---------ggtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from CESAR gCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGGATCCTGAAg cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagtCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAATGTAATGTCCACTACAATCTACAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTG---------ggtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from Spaln_aa2Genome GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTG- cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAATGTAATGTCCACTACAATCTACAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from Spaln_nt2Genome GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGG cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAATGTAATGTCCACTACAATCTACAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from Pairagon GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGG cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAATGTAATGTCCACTACAATCTACAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from Exonerate_protein2genome cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagtccagatctgttggattttgagtccctaaaaaaatgtaatgtccactacaatctacagaatgctttcaatcttgctgaaaaggaacttggccttagaagaatcctgggtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from Exonerate_coding2genome cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagtccagatctgttggattttgagtccctaaaaaaatgtaatgtccactacaatctacagaatgctttcaatcttgctgaaaaggaacttggccttagaagaatcctgggtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac Alignment from GeneWise GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGG cagtcaaagtggcgatggcacaacaggaaggtgtctgtctctttttgtagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAATGTAATGTCCACTACAATCTACAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtatcttggagaacctgcgttaagccagctggaagcaagatagagggtac #### Sptbn2_ID628_23 --> 0 - 2 Original Alignment ------GATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGag cAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGaggtaagcccatatagttatctattactgtgattttgattctttataagcAC Alignment from CESAR ------GATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGag cAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGaggtaagcccatatagttatctattactgctgacccttggttccctcagcAC Alignment from Spaln_aa2Genome GCCAAGGATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGAG CAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGAGgtaagcccatatagttatctattactgtgattttgattctttataagCAC Alignment from Spaln_nt2Genome GCCAAGGATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGAG CAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGAGgtaagcccatatagttatctattactgtgattttgattctttataagCAC Alignment from Pairagon AGTTACACATGATGGGCCAGGAAAAGGCCAAGGATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGAG CAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagggtccag---------------------------------ATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGAGgtaagcccatatagttatctattactgtgattttgattctttataagCAC Alignment from Exonerate_protein2genome GCCAAGGATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGAG CAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGAGgtaagcccatatagttatctattactgtgattttgattctttataagCAC Alignment from Exonerate_coding2genome GCCAAGGATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGAG CAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGAGgtaagcccatatagttatctattactgtgattttgattctttataagCAC Alignment from GeneWise ------GATGAGCTGAGCGCCCAGGCAGAAGTGAAGAAGCATCAGGTATTGGAACAAGCCCTTGCTGACTATGCCCAGACCATCAAACAACTAGCAGCCAGCAGTCAAGATATGATTGACCATGAACATCCAGAGAG CAC ctgttactcaagcaaacctgaattcatgtcttttacctttctgtcttcagGGTCCAGATGAGCTGAGTGCCCAGGCAGAGGTAAGGAAGCATCAGGTGCTAGAACAAGCGCTAGCTGACTATGCCCAAACCATTAAACAACTATCTGCCAGTAGTCAAGATATGATTGACCATGAGCATCCAGAGAGgtaagcccatatagttatctattactgtgattttgattctttataagCAC #### Sptbn2_ID631_26 --> 0 - 2 Original Alignment ---------GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCcg tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagAGTATGGACGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCcggtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from CESAR ---------GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCcg tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagAGTATGGACGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCcggtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from Spaln_aa2Genome -------GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCCG tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagAGTATGGACGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCCGgtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from Spaln_nt2Genome AG-------GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCCG tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagAGTATGGACGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCCGgtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from Pairagon ---------GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCCG tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagAGTATGGACGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCCGgtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from Exonerate_protein2genome GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCCG tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagagtatggacGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCCGgtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from Exonerate_coding2genome GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCCG tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagagtatggacGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCCGgtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg Alignment from GeneWise ---------GTCCAGCAAGTTCAAGATGATGGCCAAAGGCTACAGAAGGCCTATGCTGGAGACAAGGCTGAGGAAATTGGCCGTCACATGCAGGCAGTGGCTGAGGCCTGGGCCCAGCTCCAGGGAAGTTCTGCTGCCCGCCGACAGCTGTTACTGGATACCACGGACAAATTCCGATTCTTTAAGGCTGTCCGAGAGTTGATGCTGTGGATGGATGGGATTAACCTGCAGATGGATGCCCAGGAGCGGCCCCG tctgggatctaccatgtcttccaattctatcctgtttgttttgaccacagAGTATGGACGTCCAACAAGTTCATGATGATGGTCCACGGCTACAAAAGGCCTATGCTGGAGACAAGGCTGAGGCAATTGGTCGTCATATGCAGGCAGTTGCTGAGGCCTGGGCCCAGCTCCAAGGAAGTTCTGCTGCCCGCCGACAGCTGCTACTAGACACAACGGATAAATTTCGGTTCTTTAAGGCTGTCCGAGAGTTGATGCTATGGATGGATGGGATTAACCTGCAGATGGATGCTCAGGAGCAACCCCGgtatttcttgtggtggatggtttcacccgactgctactatgttgggttgg #### Sptbn2_ID636_31 --> 1 - 0 Original Alignment gACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCACAG gtgttgctaatactggcagatgaccctactgttccctctctccccaacagcAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCTTCC---gtatgtcgttatcgtgacagatgtctgttaactcagctaacatttaagta Alignment from CESAR gACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCACAG gtgttgctaatactggcagatgaccctactgttccctctctccccaacagcAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCTTCC---gtatgtcgttatcgtgacagatgtctgttaactcagctaacataatt Alignment from Spaln_aa2Genome GACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCA gtgttgctaatactggcagatgaccctactgttccctctctccccaacagCAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCTTCCgtatgtcgttatcgtgacagatgtctgttaactcagctaacatttaagta Alignment from Spaln_nt2Genome GACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCAC-AG gtgttgctaatactggcagatgaccctactgttccctctctccccaacagCAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCTTCCGTATgtcgttatcgtgacagatgtctgttaactcagctaacatttaagta Alignment from Pairagon GACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCA-------------------------------------------------- gtgttgctaatactggcagatgaccctactgttccctctctccccaacagCAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCTTCCGTATGTCGTTATCGTGACAGATGTCTGTTAACTCAGCTAACATTTAAGTA Alignment from Exonerate_protein2genome GACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCACAG gtgttgctaatactggcagatgaccctactgttccctctctccccaacagCAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCTTCC---gtatgtcgttatcgtgacagatgtctgttaactcagctaacatttaa Alignment from Exonerate_coding2genome gtgttgctaatactggcagatgaccctactgttccctctctccccaacagcaatcaatcaaaacttcccccattgtcccaagcaccatgtgttaatgtggtttgtacaggcactgactcttccgtatgtcgttatcgtgacagatgtctgttaactcagctaacatttaagta Alignment from GeneWise GACTCAGTCAAAATTGCCACCATCCACACAAGCACCCAGTGTTAATGGGGTCTGCACGGACACCGACTCCTCACAG gtgttgctaatactggcagatgaccctactgttccctctctccccaacagCAATCAATCAAAACTTCCCCCATTGTCCCAAGCACCATGTGTTAATGTGGTTTGTACAGGCACTGACTCT---TCCgtatgtcgttatcgtgacagatgtctgttaactcagctaacatttaagta #### Sptbn2_ID638_33 --> 0 - 2 Original Alignment GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACCCTG---CCCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCAAC------ag gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGaggtttgtataatacatacggatgccttttcctcactccccctagcttctaa Alignment from CESAR GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACCCTG---CCCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCAAC------ag gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGaggtttgtataatacatacggatgccttttcctcactccccctagcttctaa Alignment from Spaln_aa2Genome GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACC---CTGCCCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCAACAGG----- gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGAGgtttgtataatacatacggatgccttttcctcactccccctagcttctaa Alignment from Spaln_nt2Genome GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACCCTGC---CCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCAAC------AG gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGAGgtttgtataatacatacggatgccttttcctcactccccctagcttctaa Alignment from Pairagon GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACC---CTGCCCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCA------------------------------------------------------------ gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGAGGTTTGTATAATACATACGGATGCCTTTTCCTCACTCCCCCTAGCTTCTAA Alignment from Exonerate_protein2genome GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACC---CTGCCCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCAAC------AG gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGAGgtttgtataatacatacggatgccttttcctcactccccctagcttctaa Alignment from Exonerate_coding2genome gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagggctctggtatgggggatgagccccgtgggcctcagggtgagagacagactctgctgccccgtggagctgctccttctccaatgtcccaaagtaaatcattggaagcagcccatggtgccaccttacctatgcaaggtccggagctctcagctcaggaacagatggatgggatcctgggccgagaacaagacatggaagcgttgaacaagaaggctgcaaattacccgaggtttgtataatacatacggatgccttttcctcactccccctagcttctaa Alignment from GeneWise GGATCTGGCACAGGAGACGAGTCCAGTGGGCCCCGGGGAGAGAGGCAGACCCTG---CCCCGGGGCCCTGCTCCTTCTCCAATGCCCCAGAGCAGATCATCTGAAGCAGCTCATGGTGCCACCCTGCCCACACGAGGACCTGAGCTCTCTGCTCAGGAACAGATGGAAGGGATGCTGTGCCGCAAACAAGAGATGGAAGCCTTCAACAAGAAAGCTGCCAAC------AG gacagacaccccacagcaatgcagtagtcttttctgtgtgctccttcgagGGCTCTGGTATGGGGGATGAGCCCCGTGGGCCTCAGGGTGAGAGACAGACTCTGCTGCCCCGTGGAGCTGCTCCTTCTCCAATGTCCCAAAGTAAATCATTGGAAGCAGCCCATGGTGCCACCTTACCTATGCAAGGTCCGGAGCTCTCAGCTCAGGAACAGATGGATGGGATCCTGGGCCGAGAACAAGACATGGAAGCGTTGAACAAGAAGGCTGCAAATTACCCGAGgtttgtataatacatacggatgccttttcctcactccccctagcttctaa #### Sptbn2_ID639_34 --> 1 - 2 Original Alignment gTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAAACATGTTTTCAAGCTGgg cactccccctagcttctaacattgatagataactcttgctttcatttcaggTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATAT------GAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGC------------------gggtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc Alignment from CESAR gTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAAACATGTTTTCAAGCTGgg cactccccctagcttctaacattgatagataactcttgctttcatttcaggTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATAT------GAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGC------------------gggtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc Alignment from Spaln_aa2Genome GTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAA cactccccctagcttctaacattgatagataactcttgctttcatttcagGTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATAT------GAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGCGGgtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc Alignment from Spaln_nt2Genome GTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAA cactccccctagcttctaacattgatagataactcttgctttcatttcagGTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATA------TGAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGCGGgtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc Alignment from Pairagon GTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAAACATGTTTTCAAGCTGGG cactccccctagcttctaacattgatagataactcttgctttcatttcagGTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATAT------GAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGC------------------GGgtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc Alignment from Exonerate_protein2genome GTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAAACATGTTTTCAAGCTGGG cactccccctagcttctaacattgatagataactcttgctttcatttcagGTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATAT------GAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGCGGGTAAATTTGTAGGCTTAAggatctgctgtcgcgacccttagtgggcacgc Alignment from Exonerate_coding2genome cactccccctagcttctaacattgatagataactcttgctttcatttcaggtcatggcaaaatgtgtattgcgtacttaggtgtggaagccttggtttctacaaggatgcaaaggccgccagtgctggggtaccatatgaactgcccgtcagcctggctagggcccaaggtagtgtggcgtttgattatagaaagcgcgggtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc Alignment from GeneWise GTCATGGCAGAATGTGTACTGTGTACTTCGGCGTGGGAGCCTCGGCTTTTACAAGGATGCCAGGGCAGCTAGTGCAGGAGTGCCCTACCATGGAGAAGTGCCTGTCAGCCTGGCCAGGGCCCAGGGAAGTGTGGCCTTTGATTATCGGAAACGCAA cactccccctagcttctaacattgatagataactcttgctttcatttcagGTCATGGCAAAATGTGTATTGCGTACTTAGGTGTGGAAGCCTTGGTTTCTACAAGGATGCAAAGGCCGCCAGTGCTGGGGTACCATAT------GAACTGCCCGTCAGCCTGGCTAGGGCCCAAGGTAGTGTGGCGTTTGATTATAGAAAGCGCGGgtaaatttgtaggcttaaggatctgctgtcgcgacccttagtgggcacgc #### Ssh3_ID447_9 --> 0 - 0 Original Alignment ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTAT---gtgtgtatgagtcttctattcattctcaccatccccactccccgcagGGC Alignment from CESAR ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTAT---gtgtgtatgagtcttctattcattccatgtaataatttctcttctag Alignment from Spaln_aa2Genome ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTAC TTG taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTATgtgtgtatgagtcttctattcattctcaccatccccactccccgcag--- Alignment from Spaln_nt2Genome ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG- GGC taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTT------ATATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTATGTGTgtatgagtcttctattcattctcaccatccccactccccgcagGGC Alignment from Pairagon ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTT--------------------------------------------GGGC taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTT------ATATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTATGTGTGTATGAGTCTTCTATTCATTCTCACCATCCCCACTCCCCGCAGGGC Alignment from Exonerate_protein2genome ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTAC TTGGGC taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTATgtgtgtatgagtcttctattcattctcaccatccccactccccgCAGGGC Alignment from Exonerate_coding2genome ATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTAC TTGGGC taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagcttcatcgggcattagaactactccttggatgtcctttatatcgtgtctttattgataaccagATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTATgtgtgtatgagtcttctattcattctcaccatccccactccccgCAGGGC Alignment from GeneWise ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG---------------------------------------------GG taggccttcagaccgcttagacattaagtgatccaaaaatctcttttaagCTTCATCGGGCATTAGAACTACTCCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGCTGCTTCTCATGGCCCATCAGGATCAGACATCCCGAATCTACCCATACCTCTATGTGTGTATGAGTCTTCTATTCATTCTCACCATCCCCACTCC-CCGCAGGG #### Ssh3_ID450_6 --> 1 - 2 Original Alignment gGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGtg ttaccttctctcaaagtctacctgttacaacttcctgtggtctcctccagt---------GTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGtggtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from CESAR gGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGtg gcctattgattaccttctctcaaagtacaacttcctgtggtctcctccagt---------GTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGtggtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from Spaln_aa2Genome GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG ttaccttctctcaaagtctacctgttacaacttcctgtggtctcctccagT---------GTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGTGgtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from Spaln_nt2Genome TGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG ttaccttctctcaaagtctacctgttacaacttcctgtggtctcctccagTGTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGTGgtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from Pairagon GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG ttaccttctctcaaagtctacctgttacaacttcctgtggtctcctccag---------TGTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGTGgtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from Exonerate_protein2genome GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG ttaccttctctcaaagtctacctgttacaacttcctgtggtCTCCTCCAGTGTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGTGgtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from Exonerate_coding2genome CCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGGG-GGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG TTACCTTCTCTCAAAGTCTACCTGTTACAACTTCCTGTGGTCTCCTCCAGTGTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGTGgtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa Alignment from GeneWise GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG ttaccttctctcaaagtctacctgttacaacttcctgtggtctcctccagT---------GTGACACCCGGCGGCAAAAGCCGGATCTTCAAGCCTCTCTCTATTCAGACCATGTGgtaagtggtccaaattataagtttccaaggatacttggttgaccttctaa #### Ssh3_ID451_5 --> 1 - 2 Original Alignment tTCCCAC---------AGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATgg acattatagaggtagacagattggagaaacccccagcccttgctttgtagt------AGCTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATgggtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from CESAR tTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATgg ctgctattgacattatagaggtagacagacccccagcccttgctttgtagtagcTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATgggtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from Spaln_aa2Genome TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGG acattatagaggtagacagattggagaaacccccagcccttgctttgtagtagCTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATGGgtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from Spaln_nt2Genome TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGG acattatagaggtagacagattggagaaacccccagcccttgctttgtagtagCTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATGGgtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from Pairagon TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGG acattatagaggtagacagattggagaaacccccagcccttgctttgtagtagCTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATGGgtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from Exonerate_protein2genome TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGG acattatagaggtagacagattggagaaacccccagcccttgctttgtagtagCTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATGGgtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from Exonerate_coding2genome acattatagaggtagacagattggagaaacccccagcccttgctttgtagtagctgcacaagttgcacacttggactggttgtgcccctttggagtgttactcatgtatacctatatggagatgggtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc Alignment from GeneWise TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGG acattatagaggtagacagattggagaaacccccagcccttgctttgtagtagCTGCACAAGTTGCACACTTGGACTGGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATATGGAGATGGgtaagtggctctccgtcagggaaacaagatagggctgagaaaattgggcc #### Stambpl1_ID6902_9 --> 1 - 0 Original Alignment cACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagcACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from CESAR cACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagcACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from Spaln_aa2Genome CACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagCACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from Spaln_nt2Genome CACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagCACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from Pairagon CACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagCACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from Exonerate_protein2genome CACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagCACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from Exonerate_coding2genome tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagcactggtatcttcaggctgaccaacgctggcatgcttgaggtttctacttgtaaaaagaaaggcttccatcctcacaccaaggaccccaagctcttcagtccgctcgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa Alignment from GeneWise CACCGGCATTTTCAGGCTCACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAGGGCTTCCATCCTCACACCAAGGACCCCAAGCTGTTCAGT------ tgttcctgactggttccttctgatgtgctcaatattctaaattctcccagCACTGGTATCTTCAGGCTGACCAACGCTGGCATGCTTGAGGTTTCTACTTGTAAAAAGAAAGGCTTCCATCCTCACACCAAGGACCCCAAGCTCTTCAGTCCGCTCgtgagcagaataggaatggaaagttattcaactatataaagaggaatcaa #### Stip1_ID1988_13 --> 0 - 2 Original Alignment GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCT------------GAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGC---------------------ga caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACA------------------CTTGACGTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCC---------AGTGCATTCCTGGTCTATGCTGCTgagtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from CESAR GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGAT------------AGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTG------------AGCga caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACA------------------CTTGACGTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCAGTGCATTCCTGGTCTATGCTGCTgagtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from Spaln_aa2Genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTG------------AGCGA caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACACTTGAC------GTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCAGTGCATTCCTGGTCTATGCTGCTGAgtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from Spaln_nt2Genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCC caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGA----CAGCCCTGAGGAA--GTTACACTTGACGTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCAgtgcattcctggtctatgctgctgagtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from Pairagon GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAG------------ACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGCGA caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGT------------------TACACTTGACGTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCC-------------Agtgcattcctggtctatgctgctgagtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from Exonerate_protein2genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGCGA caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACACTTGAC------GTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCAGTGCATTCCTGGTctatgctgctgagtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from Exonerate_coding2genome caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagcaagcagcagacaaataccagcgatgcatgatggcacagtacaacagacatgacaggtcacatgacagccctgaggaagttacacttgacgttcagcaaataatgagtgttccatccatgagactcatactggagcaaatgcaaaaagaccccagtgcattcctggtctatgctgctgagtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg Alignment from GeneWise GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTG------------AGCGA caaacacaaatcagggctaaagtcttccggctccttcctccttccccaagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACACTTGAC------GTTCAGCAAATAATGAGTGTTCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCAGTGCATTCCTGGTCTATGCTGCTGAgtaagctaaataacaatggagaggaaggatggaatagaaatatttgtttg #### Stip1_ID1994_7 --> 2 - 2 Original Alignment ctGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATCGCC---------aa ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagctGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTGCTCCATGGACAaagtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from CESAR ctGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATCGCC---------aa ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagctGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTGCTCCATGGACAaagtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from Spaln_aa2Genome CTGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATC ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagCTGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTgctccatggacaaagtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from Spaln_nt2Genome CTGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATCGC--------CAAA ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagCTGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTGCTCCATGGACAAAgtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from Pairagon CTGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATCGCC---------AA ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagCTGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTGCTCCATGGACAAAgtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from Exonerate_protein2genome CTGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATCGCCAA ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagCTGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTGCTCCatggacaaagtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from Exonerate_coding2genome ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagctgttcactttgacaagggtgattataacgaatgtcgggatctctgcgaaaaggctatagaggttggaagagagaatcgtgaggattaccgtcaaattgctccatggacaaagtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact Alignment from GeneWise CTGTGCACTTTGAGAAGGGCGACTATAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTGGGCAGAGAGAACCGAGAGGACTACCGGCAGATCGCC---------AA ttgttcgtttatctagcttttttatctagaagctcgctttcttcccacagCTGTTCACTTTGACAAGGGTGATTATAACGAATGTCGGGATCTCTGCGAAAAGGCTATAGAGGTTGGAAGAGAGAATCGTGAGGATTACCGTCAAATTGCTCCATGGACAAAgtgaggcatcaaatgctgaacgaggcaaggcacctttcttagtgcctact #### Stip1_ID1997_4 --> 2 - 2 Original Alignment agAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGC---ac tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagagAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAacgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc Alignment from CESAR agAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGC---ac tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagagAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAacgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc Alignment from Spaln_aa2Genome AGAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGCACG-- tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagAGAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAACgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc Alignment from Spaln_nt2Genome AGAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGCA---C tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagAGAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAACgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc Alignment from Pairagon AGAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGC---AC tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagAGAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAACgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc Alignment from Exonerate_protein2genome AGAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGC---AC tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagAGAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAACgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AGAGGAAATTCATGAATCCATTCAACTTGCCTAATCTATACCAAAAGTTGGAAAACGACCCCAGGACAAGGTCGCTGCTCAGTGACCCCACCTACAGGGAGCTCATAGAACAGCTGCAGAACAAGCCGTCAGACCTGGGCACG-- tttaccaaccagccccatgactcatatcttcctacctcctgaattttcagAGAGGAAATTCATGAATCCATTTAACCTTCCAAACCTATATCAAAAGTTGGAAAATGACCCAGGTGCAAGGTCATTGCTAAGTGACCCTGCCTACCGGGAGCTCATAGAACAGCTGCAAAACAAGCCATCTGACTTGGGCATAACgtaagccaatgatgcaccttaggagaactatctgcagtatctgagatctc #### Stx3_ID3300_6 --> 0 - 1 Original Alignment CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTa tacaccaatatagtttgataggctcacccccctgactatgtggtccccag------ATCCTCTTGCAGAAA---GTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCagtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from CESAR CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTa taagactacaccaatatagtttgatacccccctgactatgtggtccccag------ATCCTCTTGCAGAAA---GTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCagtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from Spaln_aa2Genome CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA tacaccaatatagtttgataggctcacccccctgactatgtggtccccag------ATCCTCTTGCAGAAA---GTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCAgtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from Spaln_nt2Genome GTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA tacaccaatatagtttgataggctcacccccctgactatgtggtccccagATCCTCTTGCAGAA---AGTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCAgtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from Pairagon AAAGTCCCAGCACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA tacaccaatatagtttgataggctcacccccctgactatgtggtccccagatcctcttgcagAAA-------------------------------GTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCAgtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from Exonerate_protein2genome GTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA tacaccaatatagtttgataggctcacccccctgactatgtggtccccagatcctcttgcagaaaGTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCAgtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from Exonerate_coding2genome CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA tacaccaatatagtttgataggctcacccccctgactatgtGGTCCCCAGATCCTCTTGCAGAAAGTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCAgtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa Alignment from GeneWise GTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA tacaccaatatagtttgataggctcacccccctgactatgtggtccccagATCCTCTTGCAGAAA---GTGGAGGTGATGACCAAGTACAACGACACCCAGTTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATCAgtaggattcaagtaccagtggatatcttgccatgtagccactacccttaa #### Suv420h1_ID146_8 --> 0 - 2 Original Alignment ---------TTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAag ttatttggactagttaagtcaatggttggtaaactgctccccttccttagAGCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAaggtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from CESAR ---------TTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAag ttatttggactagttaagtcaatggttggtaaactgctccccttccttagAGCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAaggtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from Spaln_aa2Genome ---------TTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAAG ttatttggactagttaagtcaatggttggtaaactgctccccttccttagAGCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAAGgtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from Spaln_nt2Genome GTTTGTGTCA--------ACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAAG ttatttggactagttaagtcaatggttggtaaactgctccccttccttagAGCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAAGgtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from Pairagon ---------TTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAAG ttatttggactagttaagtcaatggttggtaaactgctccccttccttagAGCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAAGgtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from Exonerate_protein2genome TTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAAG ttatttggactagttaagtcaatggttggtaaactgctccccttccttagagcccactgTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAAGgtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from Exonerate_coding2genome AACTGTAAGTTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAAG ttatttggactagttaagtcaatggttggtaaactgctccccttccttagAGCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAAGgtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt Alignment from GeneWise CTGTAAGTTTGTGTCAACTGGTCGAGATACAGCATGCGTTAAGGCTCTGAGAGATATTGAACCTGGAGAAGAAATTTCTTGTTACTATGGAGATGGCTTTTTTGGAGAAAATAATGAGTTCTGCGAATGTTATACTTGTGAAAG ttatttggactagttaagtcaatggttggtaaactgctccccttccttagagCCCACTGTTTGTGTCAACTGGACGAGATACAGTATGTGTGAAGGCTCTGAGAGATATTGAGCCTGGAGAAGAGATCTCTTGTTATTATGGAGATGGGTTTTTTGGAGAAAATAATGAGTTCTGTGAGTGTTATACTTGTGAAAGgtaattacctatgtcctggacctaagtcctagacccaacctcagaggagt #### Syvn1_ID1385_4 --> 0 - 1 Original Alignment ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACTGCCGCATCGTCt gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTGTAGG------tgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from CESAR ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACTGCCGCATCGTCt gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTGTAGG------tgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from Spaln_aa2Genome ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACTGCCGCA gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTGTAGGTgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from Spaln_nt2Genome ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACT gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTgtaggtgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from Pairagon ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACT gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTgtaggtgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from Exonerate_protein2genome ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACTGCCGCA gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTGTAGGTgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from Exonerate_coding2genome gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagatggagcgtagtcccaacattccctggctcttccattgtaggtgtgcggccttccgttgcttcatacaccaaaggaattttgttaacgggcga Alignment from GeneWise ATGGAACGCAGCCCCAACATCTCCTGGCTCTTCCACTGCCGCATCGTCTCTCTC- gacctacatgtgaggcttagttgaccattaaagaaggctcctctgcctagATGGAGCGTAGTCCCAACATTCCCTGGCTCTTCCATTGTAGGTGTGCGGCCTTCCgttgcttcatacaccaaaggaattttgttaacgggcga #### Syvn1_ID1386_5 --> 2 - 0 Original Alignment ctCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTGAG tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagttCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTT---------gtgagcgcagcgttccagggcaagaggtaacaagtcagctcttctacaag Alignment from CESAR ctCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTGAG tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagttCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTT---------gtgagcgcagcgttccagggcaagaggtaacaagtcagctc Alignment from Spaln_aa2Genome CTCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTGAG tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagTTCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTTGTGAGCGCAgcgttccagggcaagaggtaacaagtcagctcttctacaag Alignment from Spaln_nt2Genome CTCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTGAG- tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagTTCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTTG----TGAGCgcagcgttccagggcaagaggtaacaagtcagctcttcta Alignment from Pairagon CTCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTT tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagTTCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTTgtgagcgcagcgttccagggcaagaggtaacaagtcagctcttctacaag Alignment from Exonerate_protein2genome CTCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTG tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagTTCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTTGTGAGCGcagcgttccagggcaagaggtaacaagtcagctcttctacaag Alignment from Exonerate_coding2genome CTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTG tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagttCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTATTTGTGAGCGcagcgttccagggcaagaggtaacaagtcagctcttctacaag Alignment from GeneWise CTCTCATGTTTCTCCTGGGTATCCTGGACTTCCTCTTCGTCAGCCACGCTTATCACAGCATCCTGACCCGTGGGGCTTCTGTGCAGCTGGTATTTGGCTTTGAGTAC tcaaacataaggtcgagaagccttatcacttctctctcttctgcccccagTTCTCATGTTTCTCCTGGGCATCCTGGATTTCCTTTTTGTCAGCCACACTTATCACAGGGTTGTGACTCGTGGTACTTCAGTGCAGTTGGTA------------TTTgtgagcgcagcgttccagggcaagaggtaacaagtcagctcttctacaag #### Tbc1d10c_ID401_3 --> 0 - 0 Original Alignment GTAAAGATCCAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG agacataaaggttggggactggtcctttaccctttcttttcacccctcag---------CAATGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgccctgttgaacttggtgccttttagGAGCTGG Alignment from CESAR GTAAAGATCCAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG tcctggacaagacataaaggttgggtttaccctttcttttcacccctcag---------CAATGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgcccatgaatgcaatgtcattcccagGAGCTGG Alignment from Spaln_aa2Genome GTAAAGATCCAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG agacataaaggttggggactggtcctttaccctttcttttcacccctcag---------CAATGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgccctgttgaacttggtgccttttagGAGCTGG Alignment from Spaln_nt2Genome CAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG agacataaaggttggggactggtcctttaccctttcttttcacccctcagCAATGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgccctgttgaacttggtgccttttagGAGCTGG Alignment from Pairagon CATGTCCCGACGATACAAGAAGGTAAAGATCCAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG agacataaaggttggggactggtcctttaccctttcttttcacccctcag-------------------------------CAATGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgccctgttgaacttggtgccttttagGAGCTGG Alignment from Exonerate_protein2genome AAGGTAAAGATCCAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG agacataaaggttggggactggtcctttaccctttcttTTCACCCCTCAGCAATGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgccctgttgaacttggtgccttttagGAGCTGG Alignment from Exonerate_coding2genome agacataaaggttggggactggtcctttaccctttcttttcacccctcagcaatgtcataagggcattcccactgtcttgtgtgcacggtgttggcccctcctatgtggggcccggatgtgtcagaagaataatcccggtacatatcaggtaagaaggccaggaatgccctgttgaacttggtgccttttaggagctgg Alignment from GeneWise GTAAAGATCCAGTGCCGCAAGGGCATCCCCTCAGCCCTGCGTGCCCGGTGTTGGCCCCTCCTGTGTGGGGCCCGGATGTGTCAGAAGAACAACCCTGGCACCTACCAG GAGCTGG agacataaaggttggggactggtcctttaccctttcttttcacccctcagCAA---------TGTCATAAGGGCATTCCCACTGTCTTGTGTGCACGGTGTTGGCCCCTCCTATGTGGGGCCCGGATGTGTCAGAAGAATAATCCCGGTACATATCAGgtaagaaggccaggaatgccctgttgaacttggtgccttttagGAGCTGG #### Tcirg1_ID172_15 --> 0 - 0 Original Alignment GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTATCCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAGCAG--- GATGAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCTT---ACCCCC------CTCCTACATGAGCACCAGCATAGAAGAAACTCCCAAACACGG---GCAGGCCAACAATCCgtgaggacatagtgttgagctgctcttcttttgggtttcagGATGAGGAC Alignment from CESAR GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTATCCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAGCAG--- GATGAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCTT---ACCCCC------CTCCTACATGAGCACCAGCATAGAAGAAACTCCCAAACACGG---GCAGGCCAACAATCCgtgaggacatagtgttgaggatggtttttattctatttcagGATGAGGAC Alignment from Spaln_aa2Genome GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTATCCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAGCAG GATGAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCTT---ACCCCC------CTCCTACATGAGCACCAGCATAGAAGAAACTCCCAAACACGGGCAGGCCAACAATCCgtgaggacatagtgttgagctgctcttcttttgggtttcagGATGAGGAC Alignment from Spaln_nt2Genome GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTATCCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAGCAG--- GATGAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCT-----TACCC----CCCTCCTACATGAGCACCAGCATAGAAGAAACTCCCAAACACGG---GCAGGCCAACAATCCgtgaggacatagtgttgagctgctcttcttttgggtttcagGATGAGGAC Alignment from Pairagon GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTAT----------------------CCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAG--------------------------------------------CAGGATGAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCTTACCCCCCTCCTACATG-------------------------------AGCACCAGCATAGAAGAAACTCCCAAACACGG---GCAGGCCAACAATCCGTGAGGACATAGTGTTGAGCTGCTCTTCTTTTGGGTTTCAGGATGAGGAC Alignment from Exonerate_protein2genome GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTATCCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAGCAG GATGAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCTT---ACCCCC------CTCCTACATGAGCACCAGCATAGAAGAAACTCCCAAACACGGGCAGGCCAACAATCCgtgaggacatagtgttgagctgctcttcttttgggtttcagGATGAGGAC Alignment from Exonerate_coding2genome gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaaggaagtggtccagtatatcctagtcatcttggcactagctactgtccccattttgcttcttacccccctcctacatgagcaccagcatagaagaaactcccaaacacgggcaggccaacaatccgtgaggacatagtgttgagctgctcttcttttgggtttcaggatgaggac Alignment from GeneWise GAAGTGGTACAGTACGTGCTGGTGGTCCTGGCTTTGGCTACCGTTCCTATCCTGTTGCTGGGCACACCCTTGTACCTGCTGCGCCAGCACCGCCACAGAAGAAACACTCAGAGAAGGCCAGCAGGCCAGCAGGAT ---GAGGAC gtaacaattcaataactatgaccccactctcttgttttgtgttttgtaagGAAGTGGTCCAGTATATCCTAGTCATCTTGGCACTAGCTACTGTCCCCATTTTGCTTCTT---ACCCCCCTC------CTACATGAGCACCAGCATAGAAGAAACTCCCAAACACGG---GCAGGCCAACAATCCgtgaggacatagtgttgagctgctcttcttttgggtttcagGATGAGGAC #### Tcirg1_ID180_7 --> 1 - 0 Original Alignment cTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAA------ GTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagcTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGGACATGgtaggatgttcatcacagatggctttctttctggtatttacagGTCTTAG Alignment from CESAR cTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAA------ GTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagcTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGGACATGgtaggatgttcatcacagatggacgtctccttttgtttttcagGTCTTAG Alignment from Spaln_aa2Genome CTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAA------ GTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagCTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGGACATGgtaggatgttcatcacagatggctttctttctggtatttacagGTCTTAG Alignment from Spaln_nt2Genome CTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAAGTCCTG G------ tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagCTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGGACATGgtaggatgttcatcacagatggctttctttctggtatttacagGTCTTAG Alignment from Pairagon CTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGG-------------------------------------------------AAGTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagCTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGGACATGGTAGGATGTTCATCACAGATGGCTTTCTTTCTGGTATTTACAGGTCTTAG Alignment from Exonerate_protein2genome CTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAA GTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagCTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGgacatggtaggatgttcatcacagatggctttctttctggtatttacagGTCTTAG Alignment from Exonerate_coding2genome CTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAA GTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagCTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGgacatggtaggatgttcatcacagatggctttctttctggtatttacagGTCTTAG Alignment from GeneWise CTTCCACTGTCATGTCTTCCCATACCTGGAGCAGGAGGAAGCCCGGTTCAGGACCTTGCAGCAGCTGCAGCAGCAAAGCCAGGAGCTTCAGGAA------ GTCCTGG tgccaagattcctaagttcaggactcgatttgccccggggctgcctgcagCTTTCACTGCCATGTCTTCTCATTTCTGGAACAGGAGGAAGCCCGGTTTAGGACCTCAAAGCAGTTACAGCAGCAGAGTCAGGAACTCCAAGAGGACATGgtaggatgttcatcacagatggctttctttctggtatttacagGTCTTAG #### Tcirg1_ID185_2 --> 0 - 1 Original Alignment CCTCGTGGAGTTCAGAGAC ------CTCAACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACGTTTa GCCTGTGGATTTGAGAGATgtaaagagtaatcctgagtttccctttctagCTGGTGTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAG---ATTagtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from CESAR CCTCGTGGAGTTCAGAGAC CTC------AACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACGTTTa GCCTGTGGATTTGAGAGATgtgagtagtaatcctgagtttccctttctagCTGGTGTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAG---ATTagtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from Spaln_aa2Genome CCTCGTGGAGTTCAGAGAC CTC------AACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACG- GCCTGTGGATTTGAGAGATgtaaagagtaatcctgagtttccctttctagCTGGTGTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAGATTAgtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from Spaln_nt2Genome CCTCGTGGAGTTCAGAGAC-------------------------------CT------CAACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACGTTTA GCCTGTGGATTTGAGAGATGTAAAGAGTAATCCTGAGTTTCCCTTTCTAGCTGGTGTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAGA---TTAgtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from Pairagon CCTCGTGGAGTTCAGAGAC-------------------------------------CTCAACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACGTTTA GCCTGTGGATTTGAGAGATGTAAAGAGTAATCCTGAGTTTCCCTTTCTAGCTGGTGTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAGA---TTAgtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from Exonerate_protein2genome CCTCGTGGAGTTCAGAGAC CTCAACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACGTTTA GCCTGTGGATTTGAGAGATgtaaagagtaatcctgagtttccctttctagctggtgTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAG---ATTAgtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from Exonerate_coding2genome gcctgtggatttgagagatgtaaagagtaatcctgagtttccctttctagctggtgttcaatgagttggtgagtgctgtccagagacgctttgtagtagatgtgcagcactgtgaggagctggacaagattagtgagtacttgcttggcttactgagatgacaggatgtactttttatttac Alignment from GeneWise CCTCGTGGAGTTCAGAGAC CTC------AACGAATCCGTGAGCGCCTTCCAGAGACGCTTCGTGGTAGACGTCCGGCGCTGCGAGGAACTGGAGAAGACGTTTA GCCTGTGGATTTGAGAGATgtaaagagtaatcctgagtttccctttctagCTGGTGTTCAATGAGTTGGTGAGTGCTGTCCAGAGACGCTTTGTAGTAGATGTGCAGCACTGTGAGGAGCTGGACAAG---ATTAgtgagtacttgcttggcttactgagatgacaggatgtactttttatttac #### Tctn3_ID7995_6 --> 2 - 0 Original Alignment GTGCCGAGAGCAACCCTGCAg gtTTCCTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTCTTGAAG GTGCAGAGAGCAACCCAGCAggtgagttagttttctcttggggaatgtaggaTTTCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTC------gtaccttttgaaaatagccgggtttctgcagcttctgatttctaaatggt Alignment from CESAR GTGCCGAGAGCAACCCTGCAg gtTTCCTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTCTTGAAG GTGCAGAGAGCAACCCAGCAggttgtgtagttttctcttggggaatgtaggaTTTCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTC------gtaccttttgaaaatagccgggtttctgcagcttctgatttcta Alignment from Spaln_aa2Genome GTGCCGAGAGCAACCCTGCAGGTTTC-----------------------------CTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTC GTGCAGAGAGCAACCCAGCAGGTGAGTTAGTTTTCTCTTGGGGAATGTAGGATttCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTCgtaccttttgaaaatagccgggtttctgcagcttctgatttctaaatggt Alignment from Spaln_nt2Genome GTGCCGAGAGCAACCCTGCAGGT-----------------------------TTCCTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTC GTGCAGAGAGCAACCCAGCAGGTGAGTTAGTTTTCTCTTGGGGAATGTAGGATTTCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTCgtaccttttgaaaatagccgggtttctgcagcttctgatttctaaatggt Alignment from Pairagon GTGCCGAGAGCAACCCTGCAGGT-----------------------------TTCCTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTC GTGCAGAGAGCAACCCAGCAGGTGAGTTAGTTTTCTCTTGGGGAATGTAGGATTTCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTCgtaccttttgaaaatagccgggtttctgcagcttctgatttctaaatggt Alignment from Exonerate_protein2genome CCGAGA GCAACCCTGCAGGTTTCCTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTCTTGAAG CAGAGAgcaacccagcaggtgagttagttttctcttggGGAAT---GTAGGATTTCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTCGTACCTtttgaaaatagccgggtttctgcagcttctgatttctaaatggt Alignment from Exonerate_coding2genome gtgcagagagcaacccagcaggtgagttagttttctcttggggaatgtaggatttctagagactaagagcatgacctcttcccgtttcctaaaggacctatctggtagctatagctctgagccagctctggatgcagtttcggactacaactttagagtcgtaccttttgaaaatagccgggtttctgcagcttctgatttctaaatggt Alignment from GeneWise GTGCCGAGAGCAACCCTGCAG GTTTCCTAGAGAGTAAAAGCACAACGTGTCCTCGTTTCTTCAGGGACCTGGCCAGTAGCTGCACCTCGGAGCCAGCCCTGGATGCTGCCTCTTACTATAACTTCAGAGTCTTGAAGGTTCCAAGAGGTGTGACTGATCTTCAGAATATGAAG GTGCAGAGAGCAACCCAGCAGgtgagttagttttctcttggggaatgtagGATTTCTAGAGACTAAGAGCATGACCTCTTCCCGTTTCCTAAAGGACCTATCTGGTAGCTATAGCTCTGAGCCAGCTCTGGATGCAGTTTCGGACTACAACTTTAGAGTC------GTACCT---------------TTTGAAAATAGCCGGgtttctgc #### Tdrd1_ID12218_19 --> 2 - 1 Original Alignment ccAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTCA---g tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagcaAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAggtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from CESAR ccAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTCA---g tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagcaAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAggtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from Spaln_aa2Genome CCAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTCA---G tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagCAAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAGgtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from Spaln_nt2Genome CCAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTC---AG tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagCAAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAGgtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from Pairagon CCAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTC---AG tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagCAAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAGgtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from Exonerate_protein2genome CCAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTCA---G tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagCAAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAGgtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from Exonerate_coding2genome CCAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTCA---G tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagCAAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAGgtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa Alignment from GeneWise CCAGCCCTTCAGCAGAGCAGTGGAAGACAATGGAATTGCCAGTTAACAAGACTATAGCAGCAAATGTACTAGAGATCATAAGCCCAGCCTTGTTCTACGCCATCCCCAGTGAAATGTCAGAA- tggaagcagtgtttggtgtatgaggacaacatttattctcttttctgcagCAAGACCTTCAGCAGAACAGTGGAAAACAATGGAGTTACCAGTGAATGAGAACATAGCAGCAACTGTGCTAGAAAGCATAAGCCCAGCCTTATTGTATGCTATCGCTAGTGAAATGGCCAAAGgtgagttaagagcttactgcacccatactgccctcttggtgaaaatgcaa #### Tectb_ID11563_6 --> 1 - 2 Original Alignment gTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAG---------gg aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtaggTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGTATCGACATgggtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca Alignment from CESAR gTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAG---------gg aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtaggTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGTATCGACATgggtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca Alignment from Spaln_aa2Genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAA aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtagGTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAgtatcgacatgggtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca Alignment from Spaln_nt2Genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAA aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtagGTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAgtatcgacatgggtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca Alignment from Pairagon GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAG---------GG aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtagGTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGTATCGACATGGgtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca Alignment from Exonerate_protein2genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAA aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtagGTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAgtatcgacatgggtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAG---------GG aaattcaattttgtaatggtattgttttagtgatctgatttgccttgtagGTTCAAAGTGGTCTTGAATAGCTGCTGGGCTACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGTATCGACATGGgtaagaaccaatgacaactacatgatgctggtatgtttcttggaccccca #### Tjp2_ID5274_13 --> 2 - 2 Original Alignment tgTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCag tacttagccttcttgatggtagagccctcactcacgtccccggcccgcagct---AGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCaggtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt Alignment from CESAR tgTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCag tattacttagccttcttgatggtagcctcactcacgtccccggcccgcagct---AGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCaggtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt Alignment from Spaln_aa2Genome TGTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCAG tacttagccttcttgatggtagagccctcactcacgtccccggcccgcagCT---AGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCAGgtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt Alignment from Spaln_nt2Genome TGTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCAG tacttagccttcttgatggtagagccctcactcacgtccccggcccgcag---CTAGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCAGgtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt Alignment from Pairagon TGTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCAG tacttagccttcttgatggtagagccctcactcacgtccccggcccgcag---CTAGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCAGgtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt Alignment from Exonerate_protein2genome TGTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCAG tacttagccttcttgatggtagagccctcactcacgtccccggcccgCAGCTAGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCAGgtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TGTACAGAGATATCCTGGCTTGTGGCAGGGGAGATTCGTTTTTCATAAGAAGCCACTTTGAATGTGAGAAGGAAACTCCCCAGAGCCTGGCCTTCACCAGGGGAGAGGTCTTCCGAGTGGTAGACACGCTGTACGATGGCAAGCTGGGCCACTGGCTGGCCGTGAGGATCGGGAATGAGCTGGAGAAAGGCTTGATCCCTAACAAAAGCAG tacttagccttcttgatggtagagccctcactcacgtccccggcccgcagCT---AGAGACATCTTGGCTTGTGGCAGGGGGGATTTGTTTTTCATAAGAAGTCACTTTGAATGTGAGAAGGAAACTCCCCAGAGTTTGGCCTTCACTAGGGGTGAGGTCTTTCGAGTGATAGACACTCTCTATGAAGACAAGTTGGGTCACTGGCTAGCTGTGAGGATCGGGAATGAGCTAGAGCAAGGACTAATCCCCAACAAAAGCAGgtaagaaccccattttgtcagactccaccacgcctattacacctcaaagt #### Tjp2_ID5278_9 --> 1 - 1 Original Alignment cTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATG---GGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCA---------------g ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagcACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCA---AATCAACAAAAAGGCCCAGATCCTTTTCCAATAggtaggttgttatgctaatcttttttctaacctaaaatgtagacagggtgg Alignment from CESAR cTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATG---GGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCA---------------g ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagcACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAAT---CAACAAAAAGGCCCAGATCCTTTTCCAATAggtaggttgttatgctaatcttttttctaacctaaaatgtagacagggtgg Alignment from Spaln_aa2Genome CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATG---GGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAG ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagCACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAAT---CAACAAAAAGGCCCAGatccttttccaataggtaggttgttatgctaatcttttttctaacctaaaatgtagacagggtgg Alignment from Spaln_nt2Genome CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTG---CCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAG AAGGCCCAG ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagCACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTA---TGGCCAGTAAGGAGCCAAATCAACAAAAAGgcccagatccttttccaataggtaggttgttatgctaatcttttttctaacctaaaatgtagACAGGGTGG Alignment from Pairagon CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGT---GCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAG--------------- ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagCACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTAT---GGCCAGTAAGGAGCCAA---ATCAACAAAAAGGCCCAGATCCTTTTCCAATAGgtaggttgttatgctaatcttttttctaacctaaaatgtagacagggtgg Alignment from Exonerate_protein2genome CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATG---GGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAG ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagCACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAAT---CAACAAAAAGGCCCAGatccttttccaataggtaggttgttatgctaatcttttttctaacctaaaatgtagacagggtgg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGT---GCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAG---------GAAGAAGGCCCAGTT- ttgttgttcaatgaagcattgaccactgcttctcacgtttgtgattgcagCACTAAAGAAGAAATATCCGGCAAACTGTCAAGGATGGGGGGAGCCATGCCCACATCCTTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAATCAACAAAAAGGCCCAGATCCTTTTCCAATAGgtaggttgttatgctaatcttttttctaacctaaaatgtagacagggtgg #### Tle4_ID3619_18 --> 0 - 1 Original Alignment ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCAAGTTTGCCCACTGTg tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTC---------------agtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg Alignment from CESAR ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCAAGTTTGCCCACTGTg tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTC---------------agtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg Alignment from Spaln_aa2Genome ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCAAGTTTGCCCACTGTG tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTCAGTGAGTATACACTCAgctgaaccacgctgcacatctggcattgcttgctg Alignment from Spaln_nt2Genome ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCA tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTCAgtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg Alignment from Pairagon ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCA tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTCAgtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg Alignment from Exonerate_protein2genome ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCA tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTCAgtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg Alignment from Exonerate_coding2genome ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGTGTGCTGTCACTCA tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTGTCTTGTCCCTCAgtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg Alignment from GeneWise ATCTTTTCATTGGGCTATTGCCCAACTGGAGAGTGGCTTGCAGTGGGGATGGAGAATAGCAATGTGGAAGTATTGCATGTCACCAAACCAGACAAATACCAGTTGCATCTTCATGAGAGCTGT tttgcttcacagcaaggtgttgtcaaccttttctgttctttactacttagACTTTTTCATTGGGATATTGCCCTACTGGAAAGTGGCTTGCAGTGGGCATGGAAAATAGCAACGTGGATGTATTGCATGTCACCAAACCAGACAAATGTCAGTTGCATCTTCATGAGAGCTGTgtcttgtccctcagtgagtatacactcagctgaaccacgctgcacatctggcattgcttgctg #### Tm7sf2_ID1413_7 --> 0 - 1 Original Alignment GAGTCTGTCCTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGg cttgctgttgtcaagggagcctcttctgatatttcaactctttccttcag---------CTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCC---TTCATCTGCCTGCTCCAGggtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from CESAR GAGTCTGTCCTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGg aacatccagcttgctgttgtcaaggctgatatttcaactctttccttcag---------CTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCC---TTCATCTGCCTGCTCCAGggtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from Spaln_aa2Genome GAGTCTGTCCTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGG cttgctgttgtcaagggagcctcttctgatatttcaactctttccttcag---------CTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCC---TTCATCTGCCTGCTCCAGGgtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from Spaln_nt2Genome GAGTCTGTC CTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGG CTTGCTGTTgtcaagggagcctcttctgatatttcaactctttccttcagCTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCCT---TCATCTGCCTGCTCCAGGgtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from Pairagon GAGTCTGTCCTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGG cttgctgttgtcaagggagcctcttctgatatttcaactctttccttcag---------CTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCCT---TCATCTGCCTGCTCCAGGgtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from Exonerate_protein2genome GAGTCTGTCCTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGG cttgctgttgtcaagggagcctcttctgatatttcaactctttccttcag---------CTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCC---TTCATCTGCCTGCTCCAGGgtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from Exonerate_coding2genome GAGTCTGTCCTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGG cttgctgttgtcaagggagcctcttctgatatttcaactctttccttcag---------CTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCC---TTCATCTGCCTGCTCCAGGgtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc Alignment from GeneWise CTCACCACCATGGACATAATACATGATGGTTTTGGCTTCATGCTGGTCTTTGGAGATCTAGCTTGGGTACCATTCACCTACAGCCTGCAGGCCCAGTTCCTGTTGTACCATCCACAGCCTCTGGGGTTGCCCATGGCCTTGCTCATCTGCCTCCTTAAGG cttgctgttgtcaagggagcctcttctgatatttcaactctttccttcagCTCACCACTATGGACATTATACATGATGGGTTTAGCTTCATGCTTGTCTTTGGGGATTTAGCTTGGATACCACTGATCTACAGTCTGCAGGCCCAGTTCCTTTTATACCACCCCCAACCACTAGGATACCCAATGGCCTTC---ATCTGCCTGCTCCAGGgtaagtcccaaaatgctcaaccatgcaccaccaatcatgtagttgggacc #### Tm7sf2_ID1418_2 --> 2 - 0 Original Alignment gc---GTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccaggtGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtccttccatctctg Alignment from CESAR gc---GTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccaggtGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtctaaaagcgttgg Alignment from Spaln_aa2Genome GC---GTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccagGTGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtccttccatctctg Alignment from Spaln_nt2Genome GCG---TCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccagGTGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtccttccatctctg Alignment from Pairagon GCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccaggtgaagttgcag---------CTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtccttccatctctg Alignment from Exonerate_protein2genome GC---GTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccagGTGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtccttccatctctg Alignment from Exonerate_coding2genome GC---GTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG cgagggcattactcacactttaatccaagtagtgccacatctgtcaccagGTGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgtgcgacctcccccttgatatgacctattttgtgtccttccatctctg Alignment from GeneWise --GGCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAGGTG----------------------------------------------- cgagggcattactcacactttaatccaagtagtgccacatctgtcaccagGTGAAGTTGCAGCTTTGTTAATACTGCTACCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACTTGCCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTATTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGGTGTGCGACCTCCCCCTTGATATGACCTATTTTGTGTCCTTCCATCTCTG #### Tmem179b_ID2371_2 --> 0 - 2 Original Alignment GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCAC---ag ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCATA---GATTCCCACCCGaggcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from CESAR GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCAC---ag ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCATA---GATTCCCACCCGaggcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from Spaln_aa2Genome GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCACAG ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCATAGATTCCCACCCGAGgcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from Spaln_nt2Genome GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCACAG ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCATAGATTCCCACCCGAGgcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from Pairagon GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCAC---AG ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCAT---AGATTCCCACCCGAGgcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from Exonerate_protein2genome GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCACAG ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCATAGATTCCCACCCGAGgcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from Exonerate_coding2genome GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCAGCTGCATCGAAGACTCCCACAG ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAGTTGCATAGATTCCCACCCGAGgcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt Alignment from GeneWise GGCTCCTTTGGTGGTAACTGTCCCTTGTATGGTGTGGCTGCACTCAATGGCTCCTCTCTGGCCTTGTTAGGTCCCTCAGCCCCTTCCCTCTGCTACTTCGTGGCTGGGGCTTCAGGCATCTTGGCACTCTACTGCCTTCTGCTTCTCTTCTTCTGGGTCTACAGCA ttaccataagacagacacttcatctaccactcctttgatttgtctttcagGGCTCTTATGGTGGCAACTGTCCATTGTATGGTGCTGTTGCTCTCAATGGCCCCTCACTAGCTTTGCTCAGTCCAGCAGCTCCTTCCCTATGCTATTTTGTTGCTGGGGGTTCAGGAATCTTGGTTCTCTACTGTCTCCTATTTCTGTTTTTCTGGGTCTACAGTAgttgcatagattcccacccgaggcaagccctcctcctggaatgaggggtaactgggggggattatcaatatt #### Tmem180_ID9861_3 --> 1 - 2 Original Alignment gTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTgg atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagg---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTgggtaagacactacttcagctcaagctcccatggccaatacaactatgattg Alignment from CESAR gTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTgg ggtatgcctagtgtgtaggagtcccctctcacaacaacttccttctgcagg---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTgggtaagacactacttcagctcaagctcccatggccaatacaactatgatcc Alignment from Spaln_aa2Genome GTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTGG atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagG---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTGGgtaagacactacttcagctcaagctcccatggccaatacaactatgattg Alignment from Spaln_nt2Genome GTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTGG atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagG---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTGGgtaagacactacttcagctcaagctcccatggccaatacaactatgattg Alignment from Pairagon GTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTGG atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagG---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTGGgtaagacactacttcagctcaagctcccatggccaatacaactatgattg Alignment from Exonerate_protein2genome GTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTGG atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagG---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTGGgtaagacactacttcagctcaagctcccatggccaatacaactatgattg Alignment from Exonerate_coding2genome GTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTGG atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagG---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTGGgtaagacactacttcagctcaagctcccatggccaatacaactatgattg Alignment from GeneWise GTCAGGAGCAGGGCTCTCCTCCAGAGACGTGGTGCTGACCCGGGTCCGGGCTCTGGGCTGGCATGGGCCGCTGCTGGCACTGTCCTTCCTGGCATTCTGGGTGCCCTGGGCCCCTGCTGGCTTGCAATTCTTACTGTGCCTGTGCCTTTATGATGGCTTCCTGACGCTCGTGGACCTCCACCACCATGCCTTGCTGGCCGACCTGGCGCTCTCATCCCACGACCGCACCCACCTCAACTTTTACTGCTCCCTCTTCAGTGCAGCTGGCTCCTTGTCAGTCTTCGCCTCCTACGCCTTTTGGAACAAGGAGGACTTCTCCTCCTTCCGTGCCTTCTGTGTGGTACTAGCTGCTGGCTCTGGGCTGGGCTTTCTGGGAACCACACAATTATTGAAGCGGCAGATTGAAGCGACCAGAAGGGACAGGGGTTGCCCGGGCCTGGACCTGGATGGTGG atgcctagtgtgtaggagtcccttactctcacaacaacttccttctgcagG---GGAGCAGGGCTCTCCTCTAGGGATGTGGTGCTAACTCGTGTGCGGTCCCTAGGCTGGCATGGTCAACTGTGGGCATTGGCATTCCTTGCGTATTGGGTATCTTGGGCACCTGCTGGACTACAATTCTTCTTGTGCCTTTGCCTCTATGATAGCCTCCTGACCCTGGTGGACCTCCACCATCACACTTTGCTAGCTGACCTGGCACTGTCATCCCGTGATCACACTCACCTCAATTTCGATTGCTCCCTTTTCAGTGCAGCTGGTTCGTTATCTGTCTTTGCCTCTCATGCCTTTTGGAACAAGGAGGATTTCACCTCATTCCTGGCATTTTGTGTAGTGCTTGCCGCTGGATCTGGACTGGGCTTCCTTGGCACCACACAATTATTAAAGTGGCAGATTGAACCATCCAGAAGGGACAGGGGTTGCCCAGGTTTGGATCTAGATGGTGGgtaagacactacttcagctcaagctcccatggccaatacaactatgattg #### Trpt1_ID1982_5 --> 2 - 1 Original Alignment gcATTCGTCCAAATTGTGAGGTGGCGGTGTTCATCGATGGACCCCTAGCCCTCACA---------g ttgatagaagacacctcacttcagatgtgtattttttttttcaattttaggtGTTTGTCCAAAT------GTAACTGTATTGATTGATGGACCACTAGCTCTCACAAGAACCTTAggtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc Alignment from CESAR gcATTCGTCCAAATTGTGAGGTGGCGGTGTTCATCGATGGACCCCTAGCCCTCACA---------g ttgatagaagacacctcacttcagatgtgtattttttttttcaattttaggtGTTTGTCCAAAT------GTAACTGTATTGATTGATGGACCACTAGCTCTCACAAGAACCTTAggtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc Alignment from Spaln_aa2Genome GCATTCGTCCAAATTGTGAGGTGGCGGTGTTCATCGATGGACCCCTAGCCCTCACA---------G ttgatagaagacacctcacttcagatgtgtattttttttttcaattttagGTGTTTGTCCAAAT------GTAACTGTATTGATTGATGGACCACTAGCTCTCACAAGAACCTTAGgtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc Alignment from Spaln_nt2Genome GCATTCGTCCAAATTGTGAGGTGGCGGTGTTCATCGATGGACCCCTAGCCCTCACA---------G ttgatagaagacacctcacttcagatgtgtattttttttttcaattttagGTGTTTGTCCAAAT------GTAACTGTATTGATTGATGGACCACTAGCTCTCACAAGAACCTTAGgtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc Alignment from Pairagon GCATTCGTCCAAATTGTGAGGTGGCGGTGTTCATCGATGGACCCCTAGCCCTCAC---------AG ttgatagaagacacctcacttcagatgtgtattttttttttcaattttagGTGTTTGTCCAAAT------GTAACTGTATTGATTGATGGACCACTAGCTCTCACAAGAACCTTAGgtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc Alignment from Exonerate_protein2genome GCATTCGTCCAAATTGTGAGGTGGCGGTGTTCATCGATGGACCCCTAGCCCTCACAG ttgatagaagacacctcacttcagatgtgtattttttttttcaattttagGTGTTTGTCCAAAT------GTAACTGTATTGATTGATGGACCACTAGCTCTCACAAgaaccttaggtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ttgatagaagacacctcacttcagatgtgtattttttttttcaattttaggtgtttgtccaaatgtaactgtattgattgatggaccactagctctcacaagaaccttaggtaagtatcgccccttaaggaggctattgtgtaaggcagtctccaaaatc #### Tsga10ip_ID978_2 --> 0 - 2 Original Alignment ACCAACGCCAGACTCACTGCAAATCGGCGCTTCTCCCAGGTGCTGTCAGCACTGGGGGTAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCCCGGAAGCACag aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagACTAATGCCTGTCTTACAGGAAATTGGCAA------CAGGTTTTATCTGGACTAGGTCTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCCC---------aggtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca Alignment from CESAR ACCAACGCCAGACTCACTGCAAATCGGCGCTTCTCCCAGGTGCTGTCAGCACTGGGGGTAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCCCGGAAGCACag aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagACTAATGCCTGTCTTACAGGAAATTGGCAA------CAGGTTTTATCTGGACTAGGTCTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCCC---------aggtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca Alignment from Spaln_aa2Genome ACCAACGCCAGACTCACTGCAAATCGGCGCTTCTCCCAGGTGCTGTCAGCACTGGGGGTAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCCCG aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagACTAATGCCTGTCTTACAGGAAATTGGCAA------CAGGTTTTATCTGGACTAGGTCTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCCCAGgtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca Alignment from Spaln_nt2Genome ACCAACGCCAGACTCACTGCAAATCGGCGCTTCTCCCAGGTGCTGTCAGCACTGGGGGTAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCCCG GAAGCACA aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagACTAATGCCTGTCTTACAGGAAATTGGC------AACAGGTTTTATCTGGACTAGGTCTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCCCAGgtaagcaatcgcgagcatgttaggcatggtgtgctaaatcagGTTATACA Alignment from Pairagon TAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCCCGGAAGCACAG aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagactaatgcctgtcttacaggaaattggcaacaggttttatctggactaggtcTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCC---------CAGgtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca Alignment from Exonerate_protein2genome ACCAACGCCAGACTCACTGCAAATCGGCGCTTCTCCCAGGTGCTGTCAGCACTGGGGGTAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCCCGGAAGCACAG aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagACTAATGCCTGTCTTACAGGAAAT------TGGCAACAGGTTTTATCTGGACTAGGTCTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCCC---------AGgtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca Alignment from Exonerate_coding2genome aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctagactaatgcctgtcttacaggaaattggcaacaggttttatctggactaggtctagatgatgatcagctattagctgaggcaggtattgctgaaagcactcccaggtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca Alignment from GeneWise CAGACCAACGCCAGACTCACTGCAAATCGGCGCTTCTCCCAGGTGCTGTCAGCACTGGGGGTAGACGAGGACCAGCTGCTGGCCGAGGCAGGCAATGCTGAGAGCACCCCC-- aacaagccttatgtcatgtgtcttagtttacttcttttcttctcccctag---ACTAATGCCTGTCTTACAGGAAAT------TGGCAACAGGTTTTATCTGGACTAGGTCTAGATGATGATCAGCTATTAGCTGAGGCAGGTATTGCTGAAAGCACTCCCAGgtaagcaatcgcgagcatgttaggcatggtgtgctaaatcaggttataca #### Tut1_ID2551_4 --> 2 - 0 Original Alignment gcTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcaggcTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from CESAR gcTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcaggcTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from Spaln_aa2Genome GCTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcagGCTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from Spaln_nt2Genome GCTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcagGCTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from Pairagon GCTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcagGCTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from Exonerate_protein2genome GCTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcagGCTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from Exonerate_coding2genome GCTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAG--- gactctctctatccatgacacctttccttaaggtgtgtttctcctttcagGCTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt Alignment from GeneWise GCTGTGTGGTCCATCCTTTTGGCTCTACTGTAAATAGCTTTGATGTTCATGGCTGTGATCTCGACCTCTTCTTGGACATGGGTGATATGGAAGAGACCGAGCCA gactctctctatccatgacacctttccttaaggtgtgtttctcctttcagGCTGTGTGGTCCATCCTTTTGGATCTACTGTGAACAGCTTTGATGTTCATGGTTGTGATCTAGACCTCTTTTTGGACATGGGAGATATGGAAGAGACTGAGCAGgtatgagggtagacagtctctgccatggaatctcagataagtaaagtatt #### Ubxn1_ID2442_6 --> 1 - 0 Original Alignment aCAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAG--- atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagaCAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGATCgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from CESAR aCAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAG--- atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagaCAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGATCgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from Spaln_aa2Genome ACAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAG--- atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagACAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGATCgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from Spaln_nt2Genome ACAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAG--- atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagACAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGATCgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from Pairagon ACAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAG--- atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagACAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGATCgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from Exonerate_protein2genome ACAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAG atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagACAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGatcgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from Exonerate_coding2genome atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagacagagaactcgagaaatgattgaaagagacagagccgaaaggactaaaaagatcgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga Alignment from GeneWise ACAAAGGGTTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAGTAT atttgttttatgtctatgttgttttctaaaccaattgaacactgtcttagACAGAGAACTCGAGAAATGATTGAAAGAGACAGAGCCGAAAGGACTAAAAAGATCgtgagtgatcccaaaatttgtacttgtaattggtagcatgcagtcaagga #### Ubxn1_ID2443_7 --> 0 - 0 Original Alignment TATGGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG ttcaagcacacacctcaatatggtactgctgcgcttctctttcctttcag---GGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from CESAR TATGGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG acgttcaagcacacacctcaatatgctgctgcgcttctctttcctttcag---GGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from Spaln_aa2Genome TATGGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG ttcaagcacacacctcaatatggtactgctgcgcttctctttcctttcag---GGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from Spaln_nt2Genome GGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG ttcaagcacacacctcaatatggtactgctgcgcttctctttcctttcagGGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from Pairagon TATGGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG ttcaagcacacacctcaatatggtactgctgcgcttctctttcctttcag---GGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from Exonerate_protein2genome GGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG ttcaagcacacacctcaatatggtactgctgcgcttctctttcctttcagGGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from Exonerate_coding2genome TTCGAGAAAAAATTGAAAGGGACAAAGCAGAGAGAGCCAAGAAGTATGGTGGT---AGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG TTCAAGCACACACCTCAATATGGTACTGCTGCGCTTCTCTTTCCTTTCAGGGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta Alignment from GeneWise GGTGGTAGTGTGGGTTCTCGGTCATCCCCACCAGCAACAGACCCAGGTCCTGTTCCTTCTTCTCCCAGCCAGGAGCCCCCTACTAAGCGGGAGTATGACCAGTGTCGTATACAG ttcaagcacacacctcaatatggtactgctgcgcttctctttcctttcagGGTGGCAGTGTGGGTTCTCGAACGTCTCCACCAGCAATGGACCCCGGTCCTGTACCATCTCCTCCAAGCCAAGAGCCCCCTACTAAGCGGGAGTATGATCAGTGTCGTACACAAgtaacctctccaagtgaccatcctcctcaggactttcatgtaactctcta #### Vegfb_ID1955_5 --> 1 - 2 Original Alignment aCCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACag cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcaga---AAAAAGAAGGAGTCTACTGTTCGGCCTGACcggtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from CESAR aCCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACag gaccctagtctgaacctggtggtcttggctcactctcctttgtcccgcaga---AAAAAGAAGGAGTCTACTGTTCGGCCTGACcggtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from Spaln_aa2Genome ACCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACAG cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcagA---AAAAAGAAGGAGTCTACTGTTCGGCCTGACCGgtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from Spaln_nt2Genome AAAAAAAAAGGAGAGTGCTGTGAAGCCAGACAG cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcagAAAAAAGAAGGAGTCTACTGTTCGGCCTGACCGgtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from Pairagon ACCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACAG cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcag---AAAAAAGAAGGAGTCTACTGTTCGGCCTGACCGgtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from Exonerate_protein2genome ACCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACAG cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcagA---AAAAAGAAGGAGTCTACTGTTCGGCCTGACCGgtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from Exonerate_coding2genome ACCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACAG cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcagA---AAAAAGAAGGAGTCTACTGTTCGGCCTGACCGgtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac Alignment from GeneWise cctagtctgaacctggtggtctgactggctcactctcctttgtcccgcagaaaaaagaaggagtctactgttcggcctgaccggtgggtctgttcctgcatcttttcatgcattaggggagataaaaaagtac #### Vegfb_ID1957_3 --> 2 - 0 Original Alignment tgGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGT---GTGACTGTGCAGCGCTGTGGTGGCTGC---TGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagtg---------ATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from CESAR tgGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGCTGCTGC---CCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG agaaatgaaaaagtggaaactttttgtcttgcctgcctctcttaacccagtg---------ATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from Spaln_aa2Genome GGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagTGATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from Spaln_nt2Genome GGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagTGATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from Pairagon GGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGT---GACTGTGCAGCGCTGTGGTG---GCTGCTGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagTGATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from Exonerate_protein2genome GGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagTGATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from Exonerate_coding2genome GGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagTGATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac Alignment from GeneWise GGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGCTGCTGC---CCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG aaagtggaaacttttttggcacttggtcttgcctgcctctcttaacccagTGATTGATGTCTATGCACGTTCTGTATGCCAACCTAGGGAGGTGGCAGCTCCACTGAGTATGAAACTCATGGGTAATATTGTCAAACAGCTGGTCCCAAGCTGTGTTGGAACTGTGCAGTGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCTTGGAATGTGTGGCTGCAGAGCAACATCAAGTTCGAATGCAAgttaatgactaatatggatgtaagtacttggtagtatcaatctggttcac #### Vldlr_ID5814_13 --> 2 - 0 Original Alignment acCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagacCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from CESAR acCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagacCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from Spaln_aa2Genome CTCGACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- tatgcagtcaacatgcttgctctctgcctgaactgtcttgatccta gACCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from Spaln_nt2Genome ACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagACCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from Pairagon ACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagACCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from Exonerate_protein2genome ACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagACCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from Exonerate_coding2genome ACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG--- gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagACCTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg Alignment from GeneWise TCGACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAGGAT gtctatgcagtcaacatgcttgctctctgcctgaactgtcttgatcctagAC---CTGGTTAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTTGCTCATCCTCTTGCCCTCTCTATATTTGAGATGgtgagttataccatatgaccttgtataaatgaactttatagaaaaagtgg #### Vps13a_ID4053_70 --> 1 - 0 Original Alignment t------GGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagtTGTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGTAC---GAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from CESAR t------GGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagtTGTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGTAC---GAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from Spaln_aa2Genome T------GGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagTTGTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGTAC---GAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from Spaln_nt2Genome ACGT---GGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagTTGTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGT---ACGAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from Pairagon ACGTGGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagttgttctggggtactgtttgtcatag-----------------------AGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGT---ACGAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from Exonerate_protein2genome ACGTGGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagttgTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGTAC---GAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from Exonerate_coding2genome ACGTGGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagttgTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGTAC---GAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt Alignment from GeneWise ----CGTGGCGTGTTGTTCGTAACAAAGGGAACATTTGGACAGCTTACATGTGAGTGGCAGTACACTTTTGATGAATTCACCAAAGAGCCGTTCATTGTCCATGGGAGAAGACTGCGCATTGAAGCCAAG ttagaggtttgtttattcacaggccccaactagtccatttgttacaacagTTGTTCTGGGGTACTGTTTGTCATAGAGGGAGCATTCAGACAACTTACATGTGAGTGGCAATATACGTAC---GAATTTACTAAAGAGCCATTCATTGTCCGTGGGAGAAGACTGCGTATTGAGGCTAAAgtaagcgcacttagttccgtgtctcagttatagcacataaagccttgtgt #### Vps13a_ID4058_65 --> 2 - 0 Original Alignment gtGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT acaccagtgaggaaaaggttttatctgattaattttcttcctttttataggtGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGT---------gtaatacctgaccagtgccactgtgtcctgaattacatagaaggtctgtt Alignment from CESAR gtGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT acaccagtgaggaaaaggttttatctgattaattttcttcctttttataggtGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGT---------gtaatacctgaccagtgccactgtgtcctgaattacataga Alignment from Spaln_aa2Genome GTGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGC acaccagtgaggaaaaggttttatctgattaattttcttcctttttatagGTGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTgtaatacctgaccagtgccactgtgtcctgaattacatagaaggtctgtt Alignment from Spaln_nt2Genome GTGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGC acaccagtgaggaaaaggttttatctgattaattttcttcctttttatagGTGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTgtaatacctgaccagtgccactgtgtcctgaattacatagaaggtctgtt Alignment from Pairagon GTGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT acaccagtgaggaaaaggttttatctgattaattttcttcctttttatagGTGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGG---------Tgtaatacctgaccagtgccactgtgtcctgaattacatagaaggtctgtt Alignment from Exonerate_protein2genome GTGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT acaccagtgaggaaaaggttttatctgattaattttcttcctttttatagGTGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTGTAATACCTgaccagtgccactgtgtcctgaattacatagaaggtctgtt Alignment from Exonerate_coding2genome acaccagtgaggaaaaggttttatctgattaattttcttcctttttataggtgggctagctagtgctgcctctaaactgactagcgctatgtcgaaaggagtagcagccatgaccatggatgaagactaccagcaggaaagaaaagaagcaatgaataagcggccagctggactaagagagggcatcacccgaggagggaaaggtgtaatacctgaccagtgccactgtgtcctgaattacatagaaggtctgtt Alignment from GeneWise GTGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGC acaccagtgaggaaaaggttttatctgattaattttcttcctttttatagGTGGGCTAGCTAGTGCTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGGAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTgtaatacctgaccagtgccactgtgtcctgaattacatagaaggtctgtt #### Vps13a_ID4059_64 --> 0 - 1 Original Alignment GGGGCTATCCAGGGTCCTGAAGAGTTTGTGGAGGGAATGGCGCTAGGATTGAAAGCACTAGTTGGTGGAGCCGTT---------g tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagGGGGCTATCCAAGGTCCTGAGGAATTTGTAGCAGGAATGGCATTAGGATTAAAAGCACTGATTGGTGGAGCTGTTATGTGTTGGggtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga Alignment from CESAR GGGGCTATCCAGGGTCCTGAAGAGTTTGTGGAGGGAATGGCGCTAGGATTGAAAGCACTAGTTGGTGGAGCCGTT---g tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagGGGGCTATCCAAGGTCCTGAGGAATTTGTAGCAGGAATGGCATTAGGATTAAAAGCACTGATTGGTGGAGCTGTTATGtgttggggtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga Alignment from Spaln_aa2Genome GGGGCTATCCAGGGTCCTGAAGAGTTTGTGGAGGGAATGGCGCTAGGATTGAAAGCACTAGTTGGTGGAGCCGTT---------G tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagGGGGCTATCCAAGGTCCTGAGGAATTTGTAGCAGGAATGGCATTAGGATTAAAAGCACTGATTGGTGGAGCTGTTATGTGTTGGGgtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga Alignment from Spaln_nt2Genome GGGGCTATCCAGGGTCCTGAAGAGTTTGTGGAGGGAATGGCGCTAGGATTGAAAGCACTAGTTGGTGGAGCCGTTG- tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagGGGGCTATCCAAGGTCCTGAGGAATTTGTAGCAGGAATGGCATTAGGATTAAAAGCACTGATTGGTGGAGCTGTTATgtgttggggtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga Alignment from Pairagon GGGGCTATCCAGGGTCCTGAAGAGTTTGTGGAGGGAATGGCGCTAGGATTGAAAGCACTAGTTGGTGGAGCCGTT------------------------------------------------------------ tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagGGGGCTATCCAAGGTCCTGAGGAATTTGTAGCAGGAATGGCATTAGGATTAAAAGCACTGATTGGTGGAGCTGTTATGTGTTGGGGTGCCTATAACAGGACTAGTAATGCAAATATCATGTAACACCAGTGAGGA Alignment from Exonerate_protein2genome tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagggggctatccaaggtcctgaggaatttgtagcaggaatggcattaggattaaaagcactgattggtggagctgttatgtgttggggtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga Alignment from Exonerate_coding2genome tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagggggctatccaaggtcctgaggaatttgtagcaggaatggcattaggattaaaagcactgattggtggagctgttatgtgttggggtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga Alignment from GeneWise GGGGCTATCCAGGGTCCTGAAGAGTTTGTGGAGGGAATGGCGCTAGGATTGAAAGCACTAGTTGGTGGAGCCGTTGGT- tgacagtggtgtcaccccagattttcataactcggtgatcgtctctttagGGGGCTATCCAAGGTCCTGAGGAATTTGTAGCAGGAATGGCATTAGGATTAAAAGCACTGATTGGTGGAGCTGTTATGTgttggggtgcctataacaggactagtaatgcaaatatcatgtaacaccagtgagga #### Vps13a_ID4067_56 --> 0 - 0 Original Alignment ---GTT---------CGTTTAACACCTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagGGTGTTCATTTAACACATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from CESAR ---GTTCGTTTAACA---------CCTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagGGTGTTCATTTAACACATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from Spaln_aa2Genome GTTTAACACCTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagggtgttcatttaacacATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from Spaln_nt2Genome G---TTCGTTTAACAC---------CTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagGGTGTTCATTTAACACATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from Pairagon ---GTTCGTTTAACA---------CCTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagGGTGTTCATTTAACACATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from Exonerate_protein2genome GTTTAACACCTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagggtgttcatttaacacATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from Exonerate_coding2genome ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagggtgttcatttaacacatctaacccctagtggcaatgatatgaggattttgcaaactcgccttatacctgtgcgtagaaactatcttccagcactaaagatagcatacaatacagtagtacatcagtgggcatttcggattcagatttataggattcaggtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa Alignment from GeneWise ------------GTTCGTTTAACACCTAGTGGCAATGACATGAAAATTCTGCAACCACATGTGATACCTGTCCGGAGAAATTACCTGCCAGCACTAAAAGTAGAATATAACACATCTGCACATCAGTCGTCATTCAGAATTCAGATTTATAGAATACAG ttacaaaaacacactacaaccaaattgctttcctcccactgtttccaaagGGTGTTCATTTAACACATCTAACCCCTAGTGGCAATGATATGAGGATTTTGCAAACTCGCCTTATACCTGTGCGTAGAAACTATCTTCCAGCACTAAAGATAGCATACAATACAGTAGTACATCAGTGGGCATTTCGGATTCAGATTTATAGGATTCAGgtgaggttgaaaatcgaacgaggacaagattgacattaacgggtgccaaa #### Vps13a_ID4068_55 --> 1 - 0 Original Alignment t------------------------TCTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagtGAAAAGAAGCCAGAATGTCCTAAAACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATG---ATCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from CESAR tTCTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG gtgggaacctgagcttttcttttacacctgtcaggattttctgtgcacagtgaaaagaagccagaatgtcctaaaACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATG---ATCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from Spaln_aa2Genome GCATTACAAGTTCTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagtgaaaagaagccagAATGTCCTAAAACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATG---ATCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from Spaln_nt2Genome TT----------CTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagtgaaaagaagccagAATGTCCTAAAACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATGA---TCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from Pairagon TT------------------------CTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagTGAAAAGAAGCCAGAATGTCCTAAAACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATGA---TCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from Exonerate_protein2genome TTCTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagtgaaaagaagccagaatgtcctaaAACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATG---ATCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from Exonerate_coding2genome cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagtgaaaagaagccagaatgtcctaaaactgatgtggtctgggaggcaaagccaaaggagaagactaggtggaaacctatgatcaagcacacagtcaagttagagaaggggtttagggcatacatggaggcctcaccgttggaggacaaggtggtggagttggacaacatcccagtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt Alignment from GeneWise ----------------------AGTTCTGATGTGGTTTGGGAGGCAAAACCAAAGAAGAAGGCCAGGTGGAAGCCCATGAGTGTGAAGCACACAGAGAAGCTGGAGAAGGAGTTCAGGGAGTACACAGAGGCCTCGCCCTTGGAGGACAAAGTGGTCGAGTTGGACAACATTCCG cacctgtcaggattttctgtgcacatatcaggtcctggtctcgcacacagTGAAAAGAAGCCAGAATGTCCTAAAACTGATGTGGTCTGGGAGGCAAAGCCAAAGGAGAAGACTAGGTGGAAACCTATG---ATCAAGCACACAGTCAAGTTAGAGAAGGGGTTTAGGGCATACATGGAGGCCTCACCGTTGGAGGACAAGGTGGTGGAGTTGGACAACATCCCAgtgagttctatcttgtgatttatgtacaatacttaagtaatgatcttctt #### Vps13a_ID4069_54 --> 0 - 2 Original Alignment GATATGATGACGCCCATAAGTGTGGGGAAAAAAACCATTTATTTAGTGTCGTTCTTTGAAGGCCTGCAGCGTATTATTTTATTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCGGAGCTGGAAGTTGTGCTGGCGTTACAGGATGTCGGGATTTCACTTGTCAATAACTATACAAAGCAAGAAGTAGCCTACATAGGCATTACAag aagagtaggagaagaggttatgtagttggttctgttttgttttattccag---ATGATGACACCAATAAGTCTGGGTAAAGAGACAATTTATTTAGTGTCATTCTTTGAAGGCCTGCAGCACATTATTTTGTTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCAGAACTGGAAGTTGTGCTGGCATTACAGGATGTCGGAATTTCACTTGTCAATAATTATACAAAGCAAGAAGCAGCCTACATAGGCATTACAaggtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from CESAR GATATGATGACGCCCATAAGTGTGGGGAAAAAAACCATTTATTTAGTGTCGTTCTTTGAAGGCCTGCAGCGTATTATTTTATTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCGGAGCTGGAAGTTGTGCTGGCGTTACAGGATGTCGGGATTTCACTTGTCAATAACTATACAAAGCAAGAAGTAGCCTACATAGGCATTACAag attaagagtaggagaagaggttatgttggttctgttttgttttattccag---ATGATGACACCAATAAGTCTGGGTAAAGAGACAATTTATTTAGTGTCATTCTTTGAAGGCCTGCAGCACATTATTTTGTTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCAGAACTGGAAGTTGTGCTGGCATTACAGGATGTCGGAATTTCACTTGTCAATAATTATACAAAGCAAGAAGCAGCCTACATAGGCATTACAaggtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from Spaln_aa2Genome ATGATGACGCCCATAAGTGTGGGGAAAAAAACCATTTATTTAGTGTCGTTCTTTGAAGGCCTGCAGCGTATTATTTTATTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCGGAGCTGGAAGTTGTGCTGGCGTTACAGGATGTCGGGATTTCACTTGTCAATAACTATACAAAGCAAGAAGTAGCCTACATAGGCATTACAAG aagagtaggagaagaggttatgtagttggttctgttttgttttattccagATGATGACACCAATAAGTCTGGGTAAAGAGACAATTTATTTAGTGTCATTCTTTGAAGGCCTGCAGCACATTATTTTGTTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCAGAACTGGAAGTTGTGCTGGCATTACAGGATGTCGGAATTTCACTTGTCAATAATTATACAAAGCAAGAAGCAGCCTACATAGGCATTACAAGgtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from Spaln_nt2Genome ATGATGACGCCCATAAGTGTGGGGAAAAAAACCATTTATTTAGTGTCGTTCTTTGAAGGCCTGCAGCGTATTATTTTATTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCGGAGCTGGAAGTTGTGCTGGCGTTACAGGATGTCGGGATTTCACTTGTCAATAACTATACAAAGCAAGAAGTAGCCTACATAGGCATTACAAG aagagtaggagaagaggttatgtagttggttctgttttgttttattccagATGATGACACCAATAAGTCTGGGTAAAGAGACAATTTATTTAGTGTCATTCTTTGAAGGCCTGCAGCACATTATTTTGTTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCAGAACTGGAAGTTGTGCTGGCATTACAGGATGTCGGAATTTCACTTGTCAATAATTATACAAAGCAAGAAGCAGCCTACATAGGCATTACAAGgtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from Pairagon GATATGATGACGCCCATAAGTGTGGGGAAAAAAACCATTTATTTAGTGTCGTTCTTTGAAGGCCTGCAGCGTATTATTTTATTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCGGAGCTGGAAGTTGTGCTGGCGTTACAGGATGTCGGGATTTCACTTGTCAATAACTATACAAAGCAAGAAGTAGCCTACATAGGCATTACAAG aagagtaggagaagaggttatgtagttggttctgttttgttttattccag---ATGATGACACCAATAAGTCTGGGTAAAGAGACAATTTATTTAGTGTCATTCTTTGAAGGCCTGCAGCACATTATTTTGTTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCAGAACTGGAAGTTGTGCTGGCATTACAGGATGTCGGAATTTCACTTGTCAATAATTATACAAAGCAAGAAGCAGCCTACATAGGCATTACAAGgtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from Exonerate_protein2genome aagagtaggagaagaggttatgtagttggttctgttttgttttattccagatgatgacaccaataagtctgggtaaagagacaatttatttagtgtcattctttgaaggcctgcagcacattattttgttcactgaagatccaagagtgtttaaagtaacgtatgaaagtgaaaaggcagagttagcagaactggaagttgtgctggcattacaggatgtcggaatttcacttgtcaataattatacaaagcaagaagcagcctacataggcattacaaggtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from Exonerate_coding2genome aagagtaggagaagaggttatgtagttggttctgttttgttttattccagatgatgacaccaataagtctgggtaaagagacaatttatttagtgtcattctttgaaggcctgcagcacattattttgttcactgaagatccaagagtgtttaaagtaacgtatgaaagtgaaaaggcagagttagcagaactggaagttgtgctggcattacaggatgtcggaatttcacttgtcaataattatacaaagcaagaagcagcctacataggcattacaaggtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc Alignment from GeneWise ATGATGACGCCCATAAGTGTGGGGAAAAAAACCATTTATTTAGTGTCGTTCTTTGAAGGCCTGCAGCGTATTATTTTATTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCGGAGCTGGAAGTTGTGCTGGCGTTACAGGATGTCGGGATTTCACTTGTCAATAACTATACAAAGCAAGAAGTAGCCTACATAGGCATTACAAG aagagtaggagaagaggttatgtagttggttctgttttgttttattccagATGATGACACCAATAAGTCTGGGTAAAGAGACAATTTATTTAGTGTCATTCTTTGAAGGCCTGCAGCACATTATTTTGTTCACTGAAGATCCAAGAGTGTTTAAAGTAACGTATGAAAGTGAAAAGGCAGAGTTAGCAGAACTGGAAGTTGTGCTGGCATTACAGGATGTCGGAATTTCACTTGTCAATAATTATACAAAGCAAGAAGCAGCCTACATAGGCATTACAAGgtaatgaccaacttatctcaaaagctagaacttctcaattaggcctcctc #### Vps13a_ID4074_49 --> 0 - 0 Original Alignment GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTAGTCATGGAGCCATTAGATGCAAAGGTCTGAAAATGGAATACCAA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAGT------------------------------------------gtaaataagtccagtgctctaaagacctcttctgatatactgcgttggcc Alignment from CESAR GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTAGTCATGGAGCCATTAGATGCAAAGGTCTGAAAATGGAATACCAA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAGT------------------------------------------gtaaataa Alignment from Spaln_aa2Genome GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTAGTCATGGAGCCATTAGATGCAAAGGTCTGAAAATGGAATACCAA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAGT------GTAAATAAGTCCAGTGCTCTAAAGACCTCTTCTGATatactgcg Alignment from Spaln_nt2Genome GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTAGTC--ATGGAGCCATTAGATGCAAAGGTCTGAAAATGGAATACCAA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAGTGTAAATAAGTCCAGTGCTCTAAAGACCT-CTTCTGATATACTGCgttggc Alignment from Pairagon GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTAGT cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAGTgtaaataagtccagtgctctaaagacctcttctgatatactgcgttggcc Alignment from Exonerate_protein2genome GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAgtgtaaataagtccagtgctctaaagacctcttctgatatactgcgttggcc Alignment from Exonerate_coding2genome GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGTAgtgtaaataagtccagtgctctaaagacctcttctgatatactgcgttggcc Alignment from GeneWise GTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGATCAGTTTTCAATTGATACTGTTGGTAGTCATGGAGCCATTAGATGCAAAGGTCTGAAAATGGAATACCAA cttcaagtatctgtttcctcattgttagttttctttcctttctcttttagGTTCAGCTTATGGTAACTGATAGTGAGCTTTCAGACCAATTTTCAATTGATACTGTTGGT------------------------------------------AGTgtaaataagtccagtgctctaaagacctcttctgatatactgcgttggcc #### Vps13a_ID4093_30 --> 2 - 1 Original Alignment ctTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA---g aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagcaCTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTggtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from CESAR ctTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA---g aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagcaCTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTggtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from Spaln_aa2Genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA---G aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTGgtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from Spaln_nt2Genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAG--- aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTGgtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from Pairagon CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAG--- aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTGgtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from Exonerate_protein2genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA---G aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTGgtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from Exonerate_coding2genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA---G aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTGgtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc Alignment from GeneWise CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAGGG- aggtcgtgtgtaaatgatctctgagacccactttttggctttatttgcagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTGAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATTGAAGCTGgtaagtatatatatttcctgtttaaggatagacaaaattcaaaaggcagc #### Vps13a_ID4109_14 --> 0 - 0 Original Alignment GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCA---------gtgagttcaatgtgtacgccctgtcatttaaatggtcatgagccatttta Alignment from CESAR GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCA---------gtgagttcaatgtgtacgccctgtcatttaaatggtcatga Alignment from Spaln_aa2Genome GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCA taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAgtgagttcaatgtgtacgccctgtcatttaaatggtcatgagccatttta Alignment from Spaln_nt2Genome GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGA-AGTTGAG--- taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGTGAGTTCAATGTgtacgccctgtcatttaaatggtcatgagccatttta Alignment from Pairagon GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCA taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAgtgagttcaatgtgtacgccctgtcatttaaatggtcatgagccatttta Alignment from Exonerate_protein2genome GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGTGAGTTCAatgtgtacgccctgtcatttaaatggtcatgagccatttta Alignment from Exonerate_coding2genome taggagttaggagggtcatatttatagagaaacatcttttctctgtacaggaattggagaaaactttggatgttttgaacatgcctataagtagacagcaagcagtgagttcaatgtgtacgccctgtcatttaaatggtcatgagccatttta Alignment from GeneWise GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAA- taggagttaggagggtcatatttatagagaaacatcttttctctgtacagGAATTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGTGAgttcaatgtgtacgccctgtcatttaaatggtcatgagccatttta #### Vps13a_ID4119_4 --> 2 - 1 Original Alignment gtAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTa ttactgacaggaccaaccactccctcttgaccttttttgtttgtggataggt---------CTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTagtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from CESAR gtAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTa cattgctagttactgacaggaccaacttgaccttttttgtttgtggataggt---------CTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTagtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from Spaln_aa2Genome GTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTA ttactgacaggaccaaccactccctcttgaccttttttgtttgtggatagGT---------CTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTAgtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from Spaln_nt2Genome GTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTA ttactgacaggaccaaccactccctcttgaccttttttgtttgtggatagGT---------CTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTAgtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from Pairagon GTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTA ttactgacaggaccaaccactccctcttgaccttttttgtttgtggatagGT---------CTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTAgtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from Exonerate_protein2genome TCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTA ttactgacaggaccaaccactccctcttgaccttttttgtttgtgGATAGGTCTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTAgtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from Exonerate_coding2genome ttactgacaggaccaaccactccctcttgaccttttttgtttgtggataggtcttaaaatcccatggaaaaacctttatactcaacctgttggagccgttctggaagaaatctttttactcataataccttcttctagtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt Alignment from GeneWise GTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTA ttactgacaggaccaaccactccctcttgaccttttttgtttgtggatagGT---------CTTAAAATCCCATGGAAAAACCTTTATACTCAACCTGTTGGAGCCGTTCTGGAAGAAATCTTTTTACTCATAATACCTTCTTCTAgtgagctacttaaagtagctcaaagctttagcttttccccaggtctagtt #### Vps37c_ID2983_3 --> 2 - 0 Original Alignment agAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagagAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGAC------gtaggtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from CESAR agAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagagAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAG------GACgtaggtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from Spaln_aa2Genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGACgtaggtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from Spaln_nt2Genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGA--CGTAGgtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from Pairagon AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGACgtaggtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from Exonerate_protein2genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGACGTAGgtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from Exonerate_coding2genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGACGTAGgtccgtggcaagcattgctccttgatttggcttattccaaattgga Alignment from GeneWise AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAG caattgaaggattttgctgtcagatttagtacaataattctgtgttgcagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGGAGATTGAGGAGGACgtaggtccgtggcaagcattgctccttgatttggcttattccaaattgga #### Vwce_ID2948_3 --> 2 - 1 Original Alignment ccCTCTGCTCCTTTGGCTGTGGGAGTGGCATCTGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAg acatcacacgccagatccatccagacatacctttctctccttcgttccagcc------------------------------TGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAggtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga Alignment from CESAR ccCTCTGCTCCTTTGGCTGTGGGAGTGGCATCTGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAg atgcccatcgatatctgtaaccagacatacctttctctccttcgttccagcc------------------------------TGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAggtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga Alignment from Spaln_aa2Genome CCTCTGCTCCTTTGGCTGTGGGAGTGGCATCTGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAG acatcacacgccagatccatccagACATACCTTTCTCTCCTTCGTTCCAGCC---TGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAGgtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga Alignment from Spaln_nt2Genome CCTGCCCCTCTGCTCCTTTGGCTGTGGGAGTGGCATCTGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAG cacacgccagatccatccagACATACCTTTCTCTCCTT----CGTTCCAG-----CCTGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAGgtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga Alignment from Pairagon TGCCCCTCTGCTCCTTTGGCTGTGGGAGTGGCATCTGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAG acatcacacgccagatccatccagacatacctttctctccttcgttccag---------------------------------CCTGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAGgtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga Alignment from Exonerate_protein2genome TGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAG acatcacacgccagatccatccagacatacctttctctccttcgttccagccTGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAGgtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ----------------------------TCCTTTGGCTGTGGGAGTGGCATCTGCATCGCTCCCAATGTCTGTTCCTGCCAGGATGGAGAGCAAGGGGCCACTTGCCCAG ACATCACACGCCAGATCCATCCAGACATACCTTTCTCTCCTTCGTTCCAGCCTGCATAACTCCTAATGTTTGCTCATGCCAGGATGGAGAACAAGGTGCTACGTGCCCAGgtcagtggtgtgaaataaggaggtctgcataaaaagttcttgttctggga #### Vwce_ID2953_8 --> 2 - 0 Original Alignment ctTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAG--- agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagctTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGGGCgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat Alignment from CESAR ctTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAG--- agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagctTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGGGCgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat Alignment from Spaln_aa2Genome CTTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAG--- agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagCTTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGGGCgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat Alignment from Spaln_nt2Genome CTTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAG--- agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagCTTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGGGCgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat Alignment from Pairagon CTTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAG--- agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagCTTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGGGCgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat Alignment from Exonerate_protein2genome CTTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAG agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagCTTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGggcgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTTTCCCGAAGGCCGTTCTGGCCCCATCTGCCATCCTGCAGCCCCGACAGCATCCTGCTAAGATGTCCCTGCTCCTCCCTGAGGCAGGCCGGCCTGCCCTGTCCCCAGGACACAGCCCTCCTCCAGGGGCCCCAGGATACCCCACTGGAGTTAGAACAATCAGTCAGCCATCTACCACCCAGGTCCTACCCACATTCTTTCCCACACAGTTGATATCCACTCCAGTGCCAAGTTCCTCCCCACTGGGGACCCTTGGACCCCCCTCACTCCTCCAGGGGGCTGTAGGGACCCCTTCCTCACCTAGGGGTCCTGAAAGCCCAAAGCTGGGAGCAGGGTCCTCTTCCTGTTGGCACCTGGGAGCCACGTATGAATCAGGCAGCCGCTGGAACCAGCCCGGATGTTCTCAGTGCTTGTGCCAGGAT agtgcctgcaagctttccccactgcctttgtgtgtgtgtatcattttcagCTTTCCCAAAAGCTGTTCTGGCACCATCAGCAATCTTACAACCCCGATTGCATCCAGCCACAATGTCCTTGCTCCTTCCTGAAGCAGGGCAGCCTGCACTCTCCCCAGGACACAGTCCCCCACCAGGAGCACCAGGCTATCCTACTGGGGTTGGAACAATTAGCCAGCCATCTAATACACCTGTCCTACCTGCATACTTTCCAACCCAGCTGGTCTCTACCCCAGTGCCAAGTACATCCCCACTGGGGACCCTTGTACCCCCTTTACTTCTCCAGGGAACTGTTGGGACCCCATCATCACCCAGGGGTCCAGAAAGTCCAGAGCTGGGTGCAGGGTCCTCTTCCTGCTGGCACTTGGGTGTTACATACAAATCAGGCAGTCACTGGAACCAGCCTGGATGTTCTCAGTGCTTATGCCAGGGCgtgagttggtgtggaggtccaatgactccacaagtgaatattctagccat #### Wdr74_ID2315_5 --> 0 - 0 Original Alignment ---------CTCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from CESAR ---------CTCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from Spaln_aa2Genome CTCTTGGAACTG---------AAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from Spaln_nt2Genome C---------TCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from Pairagon CTCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagcgggatgaacttttag-------AACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from Exonerate_protein2genome ---------CTCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from Exonerate_coding2genome ---------CTCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta Alignment from GeneWise ---------CTCTTGGAACTGAAGGTGGGTCCTGGGGTGTGTAGGATGCGCCAAGATCCCACACATACACATGTGGTTGCCACATGTGGGAAAGAAAATGCTTTGAAAGTATGGGACCTACAGGGGTCTGAGGAGCCTGTATTCAGGGCCAAAAAT agtctataatagactacaagtctataataaaccgctgtctttccacacagCGGGATGAACTTTTAGAACTCAAAGCAGGTCTAGGGGTGGGTAGAATGCACCAAGACTGCACACATACACATGTTGTTATTACATGCGGGAAGGAGAATGCCCTGAAAGTATGGGACTTACAGGGATCTGAGGAGCCTGTGTTTAGGGCCAAAAATgtgaggctaggtaaagagaagtaatatatcatcaccaggtatctttatta #### Wdr74_ID2318_8 --> 1 - 1 Original Alignment tTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAg ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagtTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGAC---------ggtaagtttgactagtaacccattgtgttcttgagaatgaatgtagaggct Alignment from CESAR tTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAg ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagtTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGAC---------ggtaagtttgactagtaacccattgtgttcttgagaatgaatgaaatttcc Alignment from Spaln_aa2Genome TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGAT- ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagTTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGACGgtaagtttgactagtaacccattgtgttcttgagaatgaatgtagaggct Alignment from Spaln_nt2Genome TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagTTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTG---------ACGgtaagtttgactagtaacccattgtgttcttgagaatgaatgtagaggct Alignment from Pairagon TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagTTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGAC---------Ggtaagtttgactagtaacccattgtgttcttgagaatgaatgtagaggct Alignment from Exonerate_protein2genome TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATT ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagTTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGACGgtaagtttgactagtaacccattgtgttcttgagaatgaatgtagaggct Alignment from Exonerate_coding2genome TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATT ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagTTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGACGgtaagtttgactagtaacccattgtgttcttgagaatgaatgtagaggct Alignment from GeneWise TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAGGGCG ttaggcaattcaggagccacataaatcgactctgtgaactctgctttcagTTCTGTCATTGTGGGGAATACTCATGGTGAGCTGGCAGAGATTGACGGTAAGTTTGACTAgtaacccattgtgttcttgagaatgaatgtagaggct #### Wdr74_ID2319_9 --> 2 - 0 Original Alignment gg---------CGTCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagggTACAGGTTCAGGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTTG---TGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from CESAR gg---------CGTCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagggTACAGGTTCAGGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTTG---TGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from Spaln_aa2Genome TCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagggtacaggttcagGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTTG---TGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from Spaln_nt2Genome GGC---------GTCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagGGTACAGGTTCAGGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTT---GTGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from Pairagon GGCGTCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagggtacaggttcagG----CTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTT---GTGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from Exonerate_protein2genome GG---------CGTCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagGGTACAGGTTCAGGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTTG---TGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from Exonerate_coding2genome GG---------CGTCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagGGTACAGGTTCAGGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTTG---TGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt Alignment from GeneWise TCTACTGGGCTGTCTGAAGGGGCTTGCAGGTAGTGTTCGTGGGCTGCAGTGTCACCCTTCAAAGCCCCTATTAGCCTCATGTGGCTTGGACAGAGTCTTGAGGATACACAGGATCCGCAATCCACGTGGGCTAGAGCATAAG ttcttgagaatgaatgtagtctgccaaattgactgtcccttctgttccagggtacaggttcagGCTAGTTGGCTGTCTGAAGAGCCTCGCAGGTGGTGTTCGTGGGTTG---TGCCATCCTTCAAAGCCCCTAGTGGCTTCATGTGGCCTGGACAGAATACTGAGGATGCACAGGATACGCAACCTGTGTGGTGTGGAGCACAAGgtaaggttgagcaaacgtagcagctgtcctagtgatcaggttatggcagt #### Wdr74_ID2320_10 --> 0 - 0 Original Alignment GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAACTGGGAG tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAAT------gtaaccgagtcagaggaataaataaatataataaggaacagaatcatgtg Alignment from CESAR GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAACTGGGAG tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAAT------gtaaccgagtcagaggaataaataaatataataaggaacagaat Alignment from Spaln_aa2Genome GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAAC tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAATgtaaccgagtcagaggaataaataaatataataaggaacagaatcatgtg Alignment from Spaln_nt2Genome GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAACTGGGAGGAT tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAA-TGTAACCGAgtcagaggaataaataaatataataaggaacagaatcatgtg Alignment from Pairagon GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAAC-------------------------------------------------- tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAATGTAACCGAGTCAGAGGAATAAATAAATATAATAAGGAACAGAATCATGTG Alignment from Exonerate_protein2genome GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAACTGGGAGGAT tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAATGTAACCGAGtcagaggaataaataaatataataaggaacagaatcatgtg Alignment from Exonerate_coding2genome TCTCCTGTCA TAGTGATCAGgttatggcagtcttaagcaggtgtatatctgactttccaggtttatcttaagtgccaacttaactgtctgctcctgtctagccgggataatgtaaccgagtcagaggaataaataaatataataaggaacagaatcatgtg Alignment from GeneWise GTTTATCTCAAGTCTCAACTGAACTGCCTTCTCCTGTCAGGCCGGGATAAC tagtgatcaggttatggcagtcttaagcaggtgtatatctgactttccagGTTTATCTTAAGTGCCAACTTAACTGTCTGCTCCTGTCTAGCCGGGATAATgtaaccgagtcagaggaataaataaatataataaggaacagaatcatgtg #### Wdr96_ID10341_30 --> 0 - 0 Original Alignment ---------ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTAGTG---GCAGAGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacagGATTTCCTCACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from CESAR ---------ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTAGTGGCA---GAGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacagGATTTCCTCACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from Spaln_aa2Genome CAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTA---GTGGCAGAGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacaggatttcctcactgagacagCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from Spaln_nt2Genome ---------ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTAGTGGCAG---AGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacagGATTTCCTCACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from Pairagon ---------ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTAGTGGCAG---AGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacagGATTTCCTCACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from Exonerate_protein2genome ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTA---GTGGCAGAGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacaggatttcctcACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from Exonerate_coding2genome ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTA---GTGGCAGAGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacaggatttcctcACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata Alignment from GeneWise ---------ACCAAGACTGCAGAAGCCATCCAGAAGGCGAGAGAAGATCTGGACGTATTCAAGGAGCACCATGACATGTTAGTGGCA---GAGGACAAA tgactatgctggcttcatggcattttagattgttatctcttaaatcacagGATTTCCTCACTGAGACAGCAGAGGACATCCAGAAATCAAGAGAAGATCTCATTGTTTTCAATGAGCACCATGACATGTTGGTGGTAGTGAAGGATAAAgtaagttatcaccatcagaaaagggacacaagaggattcttattataata #### Wnt8b_ID9022_5 --> 2 - 0 Original Alignment gg---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagggACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from CESAR gg---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagggACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Spaln_aa2Genome GG---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagGGACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Spaln_nt2Genome GG---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagGGACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Pairagon GG---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagGGACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Exonerate_protein2genome GG---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagGGACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Exonerate_coding2genome GG---GGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagGGACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from GeneWise --GGGGGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggacttccatgccctatagaaccctcaccccaccccatgtagGGACCGGGCAAGGTTGGCTCTGGGGTGGATGCAGTGATAATGCAGGCTTTGGAGAGGCAATCTCCAAGCAATTTGTTGACGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCTATAAACTTGCACAACAATGAAGCCGGCCACAAGgtaggttcaatagtggttgatggcatgcatcatgagacctgtcattgtag #### Xpnpep1_ID11139_16 --> 2 - 1 Original Alignment gc---------CACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAG------------CCCTTGGAAGCGGGCATGATCGTCACTGATg agacctatggtttctcagcatctcaattatacctcgcccttcttccccaggaATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACA---------ATTACTGATggtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from CESAR gc---------CACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAGCCCTTGGAAGCGGGCATG---ATCGTCACTGATg agacctatggtttctcagcatctcaattatacctcgcccttcttccccaggaATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACAATTACTGATggtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from Spaln_aa2Genome GCCACCTTCTGGAC---------TCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAGCCCTTGGAAGCGGGCATG---ATCGTCACTGATG agacctatggtttctcagcatctcaattatacctcgcccttcttccccagGAATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACAATTACTGATGgtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from Spaln_nt2Genome GC---------CACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAGCCCTTGGAAGCGGGCATG---ATCGTCACTGATG agacctatggtttctcagcatctcaattatacctcgcccttcttccccagGAATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACAATTACTGATGgtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from Pairagon G---------CCACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCA---TCAGTTATAAAACATTCTCCGATGAGCCCTTGGAA agacctatggtttctcagcatctcaattatacctcgcccttcttccccagGAATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAgtaactttagaaacaattactgatggtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from Exonerate_protein2genome GC---------CACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAGCCCTTGGAAGCGGGCATG---ATCGTCACTGATG agacctatggtttctcagcatctcaattatacctcgcccttcttccccagGAATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACAATTACTGATGgtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from Exonerate_coding2genome GC---------CACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAGCCCTTGGAAGCGGGCATG---ATCGTCACTGATG agacctatggtttctcagcatctcaattatacctcgcccttcttccccagGAATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACAATTACTGATGgtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc Alignment from GeneWise --------GGCCACCTTCTGGACTCCTTTGCCCGGTCAGCCTTGTGGGATTCTGGTCTGGATTACCTGCATGGAACAGGACATGGCGTTGGGTCCTTTTTGAATGTTCACGAGGGGCCCTGTGGCATC---AGTTATAAAACATTCTCCGATGAGCCCTTGGAAGCGGGCATG---ATCGTCACTGATG agacctatggtttctcagcatctcaattatacctcgcccttcttccccagGAATTAATAATCATCTCCTGGACTCGTTTGCCTGGTCTGCCTTGTGGGACTCTGGACTTGACTTTCTACATGGTACAGGGCATGGAATTGGACCCTTCTTGAATGTTCATGAGGGGCCTTGTGGCATAGTTAGTTATAAAACTCTCTCAGACAAGCCTTTAGAAGTAACTTTAGAAACAATTACTGATGgtaagtcacagtatacttttgctgttgtgggtggacctttaattcttgcc #### Xpnpep1_ID11145_11 --> 0 - 2 Original Alignment ---GTTCCCAAAGGTGGCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAag taggccaagatttgaaaggaccacccacttaaattgttttttccatttagCATATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAaggtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from CESAR ---GTTCCCAAAGGTGGCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAag taggccaagatttgaaaggaccacccacttaaattgttttttccatttagCATATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAaggtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from Spaln_aa2Genome GTTCCCAAAGGT---GGCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAAG taggccaagatttgaaaggaccacccacttaaattgttttttccatttagCATATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAAGgtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from Spaln_nt2Genome GTTCCCAAAGGTG---GCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAAG taggccaagatttgaaaggaccacccacttaaattgttttttccatttagCATATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAAGgtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from Pairagon G--------------------------------------------------TTCCCAAAGGTGGCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAAG tagGCCAAGATTTGAAAGGACCACCCACTTAAATTGTTTTTTCCATTTAGCATATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAAGgtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from Exonerate_protein2genome GTTCCCAAAGGTGGCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAAG taggccaagatttgaaaggaccacccacttaaattgttttttccatttagcatATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAAGgtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from Exonerate_coding2genome taggccaagatttgaaaggaccacccacttaaattgttttttccatttagcatattcctaaaggtggtgtaactgagatctcagcggctgacaaatctgaggaattacgaaggtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg Alignment from GeneWise ---GTTCCCAAAGGTGGCGTTACGGAGATCTCTGCGGCTGACAAGGCCGAGGAATTTCGAAG taggccaagatttgaaaggaccacccacttaaattgttttttccatttagCATATTCCTAAAGGTGGTGTAACTGAGATCTCAGCGGCTGACAAATCTGAGGAATTACGAAGgtgtgactcagctctgtgttatgagtcaggcttgtacatgggtccgggtg #### Zdhhc16_ID8345_2 --> 0 - 0 Original Alignment GTGTTTGTGGTGCTGGTGATCGTGCTGACCGGGTCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG atgctggcatacaacttactctgacaactgtgtttccgctttgctgacag---------------------------------TCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg Alignment from CESAR GTGTTTGTGGTGCTGGTGATCGTGCTGACCGGGTCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG ttggactatggacccctactctgacaactgtgtttccgctttgctgacag---------------------------------TCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg Alignment from Spaln_aa2Genome TCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG atgctggcatacaacttactctgacaactgtgtttccgctttgctgacagTCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg Alignment from Spaln_nt2Genome TCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG atgctggcatacaacttactctgacaactgtgtttccgctttgctgacagTCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg Alignment from Pairagon GTGTTTGTGGTGCTGGTGATCGTGCTGACCGGGTCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG atgctggcatacaacttactctgacaactgtgtttccgctttgctgacag---------------------------------TCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg Alignment from Exonerate_protein2genome GTGTTTGTGGTGCTGGTGATCGTGCTGACC---GGGTCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG atgctggcatacaaCTTACTCTGACAACTGTGTTTCCGCTTTGCTGACAGTCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TCCATCGTGGCCATTGCTTATCTGTGTGTCCTGCCCCTCATCCTCCGAACCTACTCGGTACCACGGCTCTGCTGGCATTTCTTCTATAGTCACTGGAATCTGATCCTCATCGTCTTCCATTACTACCAGGCCATCACCACTCCTCCTGGATACCCACCCCAG atgctggcatacaacttactctgacaactgtgtttccgctttgctgacagTCAATTGTGGCCATTGCGTATCTATGTGTTCTACCGCTACTCCTTCGAACTTACTCAGTACCCCAACTCTGCTGGCAGTTTCTTTATAGCCACTGGAATCTCATTCTCATTGTCTCCCAGCATTATCAAGCCATCGCTACTCCTCACAAATATCCACCTCAGgtgagcgccccacagtgcaagtttcactaaagacaatgctttcttgctgg #### Zdhhc6_ID11621_8 --> 0 - 2 Original Alignment GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCTGcg gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTACA---GGGCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGGG---aggtaagtagaggagggggttctttatctgtaaactactgtcgtgtatcgtc Alignment from CESAR GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCTGcg gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTACA---GGGCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGGG---aggtaagtagaggagggggttctttatctgtaaaaaaccaatgcctctgttt Alignment from Spaln_aa2Genome GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCT gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTACA---GGGCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGGGAGgtaagtagaggagggggttctttatctgtaaactactgtcgtgtatcgtc Alignment from Spaln_nt2Genome GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCTGCG gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTAC--AGG-GCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGG---GAGgtaagtagaggagggggttctttatctgtaaactactgtcgtgtatcgtc Alignment from Pairagon GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGG---------------------------------------------------C gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTAC---AGGGCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGGGAGGTAAGTAGAGGAGGGGGTTCTTTATCTGTAAACTACTGTCGTGTATCGTC Alignment from Exonerate_protein2genome GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCTGCG gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTACA---GGGCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGGG---AGgtaagtagaggagggggttctttatctgtaaactactgtcgtgtatcgtc Alignment from Exonerate_coding2genome AGAAGTGTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCTG gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGT------TCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTAC---AGGGCCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAG-GGGGAGgtaagtagaggagggggttctttatctgtaaactactgtcgtgtatcgtc Alignment from GeneWise GTTCGCTATAAAGTCATAGAAGATTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACGAGCCCCTGCACTGAGGAGCCTCGGATCCGGCTGCAGAAAGGAGAGTTCATCTTAGCAACGAGAGGGCT gggatgtcaaaggggcaccacagtgcagtgcgactgttttctcttctcagGTTCACTACAAGTTTATAGAGGAGTACAACAGTGCTAGCTGCCCATTGAATATAGGAGTGAGAACCTTCTTTACAAGTCCATGTACAGGG---CCCCGAGTCCAACTGCAACAAGGTGAATTCATACTAGCAATGAGGGGGAGgtaagtagaggagggggttctttatctgtaaactactgtcgtgtatcgtc #### Zdhhc6_ID11622_7 --> 0 - 0 Original Alignment ---ATAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from CESAR ---ATAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from Spaln_aa2Genome ATAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from Spaln_nt2Genome A---TAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from Pairagon ---ATAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from Exonerate_protein2genome ---ATAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from Exonerate_coding2genome ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagggcgtagaacagccaaagcaaaaggtagataaaaaagtcagaactgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag Alignment from GeneWise ---ATAGAACAGTTGAAGCAAAAGGCAGACAAGAGAGTCAGAAGT ggaaaaccgctgagttatagctttctcccattatacatatgttgttaaagGGCGTAGAACAGCCAAAGCAAAAGGTAGATAAAAAAGTCAGAACTgtaaccactatgaaatggcagtaaaatgcaaagactgcatggagcctcag #### Zfp91_ID3462_4 --> 2 - 2 Original Alignment atGTTCCAGAAGAACATCAGTCTCCCGGTGGCATT---ag atagaagttgaattttgggcagtgaatgatataattattttcttttctagatGTTACTGAAGAGCAACGAACCCCTGGTGGGACCAAAaggtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from CESAR atGTTCCAGAAGAACATCAGTCTCCCGGTGGCATT---ag atagaagttgaattttgggcagtgaatgatataattattttcttttctagatGTTACTGAAGAGCAACGAACCCCTGGTGGGACCAAAaggtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from Spaln_aa2Genome ATGTTCCAGAAGAACATCAGTCTCCCGGTGGCATTAGTAG atagaagttgaattttgggcagtgaatgatataattattttcttttctagATGTTACTGAAGAGCAACGAACCCCTGGTGGGACCAAAAGgtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from Spaln_nt2Genome ATGTTCCAGAAGAACATCAGTCTCCCGGTGG---CATTAG atagaagttgaattttgggcagtgaatgatataattattttcttttctagATGTTACTGAAGAGCAACGAACCCCTGGTGGGACCAAAAGgtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from Pairagon atagaagttgaattttgggcagtgaatgatataattattttcttttctagatgttactgaagagcaacgaacccctggtgggaccaaaaggtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from Exonerate_protein2genome atagaagttgaattttgggcagtgaatgatataattattttcttttctagatgttactgaagagcaacgaacccctggtgggaccaaaaggtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from Exonerate_coding2genome atagaagttgaattttgggcagtgaatgatataattattttcttttctagatgttactgaagagcaacgaacccctggtgggaccaaaaggtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat Alignment from GeneWise atagaagttgaattttgggcagtgaatgatataattattttcttttctagatgttactgaagagcaacgaacccctggtgggaccaaaaggtgagcagctgcttgcttaacccaatgtttcatattactgagtgttacat ####