#### 1700055N04Rik_ID227_5 --> 2 - 0 Original Alignment gaAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAG------ attgaggggcacttaacccatcatgtgcctttttattggtttttcttcaggaAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAATCCAATgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat Alignment from CESAR gaAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAG------ attgaggggcacttaacccatcatgtgcctttttattggtttttcttcaggaAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAATCCAATgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat Alignment from Spaln_aa2Genome GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAG------ attgaggggcacttaacccatcatgtgcctttttattggtttttcttcagGAAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAATCCAATgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat Alignment from Spaln_nt2Genome GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAG------ attgaggggcacttaacccatcatgtgcctttttattggtttttcttcagGAAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAATCCAATgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat Alignment from Pairagon GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCA---------------------------------G attgaggggcacttaacccatcatgtgcctttttattggtttttcttcagGAAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAATCCAATGTAATGTTATTTTATGTGGTTAATTTGgtaaatggcaaagagagctgaat Alignment from Exonerate_protein2genome GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAG attgaggggcacttaacccatcatgtgcctttttattggtttttcttcagGAAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAAtccaatgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat Alignment from Exonerate_coding2genome GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAG attgaggggcacttaacccatcatgtgcctttttattggtttttcttcagGAAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAAtccaatgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat Alignment from GeneWise GAAACTGTGTGGTGCTGAAGCCATCAGAAATTAGCAAGAACACAGAGAAGGTGCTGGCAGAGCTGCTACCCCAGTATCTGGACCAGAGC--- attgaggggcacttaacccatcatgtgcctttttattggtttttcttcagGAAACTGTGTGGTGCTTAAAAGATCTGAAATTAGCAGGAATACAGAGAAGGTGTTAGCAGAGCTTCCACCTCAGTATCTAGACCAATCCAATgtaatgttattttatgtggttaatttggtaaatggcaaagagagctgaat #### 2010012O05Rik_ID10003_2 --> 0 - 0 Original Alignment CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAA---gtaagaagatagctattatttcatcatatgcgtcaagattttcagatgtg Alignment from CESAR CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAA---gtaagaagatagctattatttcatcatatgcgtcaagattttcagat Alignment from Spaln_aa2Genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAA ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAAgtaagaagatagctattatttcatcatatgcgtcaagattttcagatgtg Alignment from Spaln_nt2Genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAA GAT ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAAgtaagaagatagctattatttcatcatatgcgtcaagattttcag-ATgt Alignment from Pairagon CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAA ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAAgtaagaagatagctattatttcatcatatgcgtcaagattttcagatgtg Alignment from Exonerate_protein2genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAA---gtaagaagatagctattatttcatcatatgcgtcaagattttcagat Alignment from Exonerate_coding2genome CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCTGAA---gtaagaagatagctattatttcatcatatgcgtcaagattttcagat Alignment from GeneWise CTGCTGGGGCAGGCAGCTCGAAACATGGTACTACAGGAAGATGCCATCTTACACTCGGAAGAT ccgtactatgtagaggcgggatcataacgttttccatatttttgttgcagCTGCTGGGTCAGGCAGCTCGTAACATGGTACTACAAGAAGATGCTATTTTGCGCTCT---GAAgtaagaagatagctattatttcatcatatgcgtcaagattttcagatgtg #### 9130011E15Rik_ID9675_6 --> 0 - 0 Original Alignment GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACAG aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTA---gtaattcttggttcaactgtcattcaaaattttgcaatacccagaagcaa Alignment from CESAR GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACAG aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTA---gtaattcttggttcaactgtcattcaaaattttgcaatacccagaag Alignment from Spaln_aa2Genome GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACAG aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTA gtaattcttggttcaactgtcattcaaaattttgcaatacccagaag Alignment from Spaln_nt2Genome GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACA-------G aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTAGTAATTCTTGgttcaactgtcattcaaaattttgcaatacccagaagcaa Alignment from Pairagon GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATT----------------------------------------------------- aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTAGTAATTCTTGGTTCAACTGTCATTCAAAATTTTGCAATACCCAGAAGCAA Alignment from Exonerate_protein2genome GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACAG aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTA---gtaattcttggttcaactgtcattcaaaattttgcaatacccagaag Alignment from Exonerate_coding2genome GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACAG aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTA---gtaattcttggttcaactgtcattcaaaattttgcaatacccagaag Alignment from GeneWise GTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGTATATTCGAAGCAATTTTACAGATA------------ aacatgttgctctgcattgtaaaagtggttatttgtgttttgcttcaaagGTCACAGATAATATCAGCCAGAACACTATCCTGGAATATGTAATGATCAACAGCATATTTGAAGCCATTTTAGTAATTCTTGGTTCAACTgtcattcaaaattttgcaatacccagaagcaa #### A630007B06Rik_ID12190_7 --> 0 - 0 Original Alignment GAATCTGAAGAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccag---------GAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from CESAR GAATCTGAAGAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG catgggtgtgttagatggcaaggtactccgtctcccccccccccccccag---------GAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from Spaln_aa2Genome GAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccagGAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from Spaln_nt2Genome GAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccagGAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from Pairagon GAATCTGAAGAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccag---------GAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from Exonerate_protein2genome GAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccagGAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from Exonerate_coding2genome GAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccagGAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct Alignment from GeneWise GAAATTAAGTCAAATGAGCTTGATGCAAAGCTCAGAGTTACAAAAGGAGAACTTGAAAAACAAATGCAAGAGAAATCTGACCAGCTGGAG gttagatggcaaggtacaaccatacctccgtctcccccccccccccccagGAAATCAAGTCAAATGAGCCTGATACGAAACTCAGAGTGACAAAAGGCGAACTTGAAAAACAAATGCGAGAAAAATCTGACCAGCTGGAAgtaggttataattgtcctacctagcataagacactccttctgatggggct #### Abcc2_ID8821_5 --> 0 - 0 Original Alignment GATAGCAAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC tacggttgtagctatgggcctcgggcttacgggctctcttttccttttag------AAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac Alignment from CESAR GATAGCAAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC aatcattacggttgtagctatgggccttacgggctctcttttccttttag------AAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac Alignment from Spaln_aa2Genome GATAGCAAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC tacggttgtagctatgggcctcgggcttacgggctctcttttccttttag------AAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac Alignment from Spaln_nt2Genome AAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC tacggttgtagctatgggcctcgggcttacgggctctcttttccttttagAAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac Alignment from Pairagon GATAGCAAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC tacggttgtagctatgggcctcgggcttacgggctctcttttccttttag------AAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac Alignment from Exonerate_protein2genome AAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC tacggttgtagctatgggcctcgggcttacgggctctcttttccttttagAAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AAGTCCAACATGACCTATTCCTGCCTGTTCTTCGTCTCCTATGGTTTCCAGATTGTCATTTTGATCCTTTCAGCCTTTTCAGAATCAAGCGACTCAACACAC tacggttgtagctatgggcctcgggcttacgggctctcttttccttttagAAGTCAAACATGACATACTCCTGTCTGTTCTTCATCTCCTCCAGTTTCCTGATTGTGGCTTTGATTCTTTCAGCATTTTCAGAATCAAGTGACTCTACACATgtatcaaagtcatgagtatttaaaaaagggtcattctagtgaatgtacac #### Acsl5_ID11603_8 --> 0 - 1 Original Alignment CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAg ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAagtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from CESAR CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAg tcacctctgtaacttgtattgttggttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAagtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from Spaln_aa2Genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAG ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAAgtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from Spaln_nt2Genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAG ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAAgtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from Pairagon CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAG ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAAgtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from Exonerate_protein2genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAG ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAAgtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from Exonerate_coding2genome CCTCCGAAGCCAGAGGATCTGAGCGTCATCTGTTTCACCAGTGGAACTACAG ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcag------AAGCCAGAAGATCTTGGCCTGATTTGCTTTGCTAGTGGGACTACAAgtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct Alignment from GeneWise ctgtaacttgtattgttggcttactttccttaccgtctcttttctttcagaagccagaagatcttggcctgatttgctttgctagtgggactacaagtacgtgctctgaaatcccacagtgctacagaaaaaatcacactccagct #### Acsl5_ID11610_15 --> 2 - 0 Original Alignment gt---CATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccaggcGGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from CESAR gt---CATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccaggcGGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from Spaln_aa2Genome GGTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccagGCGGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from Spaln_nt2Genome GGTCATGTTGGGAC--TCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccagGCGGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from Pairagon ---GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccagGCGGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from Exonerate_protein2genome GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccaggcgGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from Exonerate_coding2genome GTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccaggcgGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa Alignment from GeneWise --GGTCATGTTGGGACTCCAGTGGCTTGCAATTTTGTAAAGCTGGAAGATGTGGCTGACATGAACTACTTTTCAGTAAACAACGAAGGCGAG gatacaaatgggcttactctgcagttatggtgtgtttggatgtgttccagGCGGCCATGTTGGCACTCCAGTAGCCTCCAATTTTGTAAAGCTTGAAGACGTAGCGGAGATGAACTACTTTTCAGTAAACAATAAAGGTGAGgtgagtgagatatacagtaccaacttaggacagatgggagaactgtctaa #### Actn3_ID691_19 --> 0 - 0 Original Alignment TGACCGG ------AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGgtagaaggcttgacatgattaaacacaagcttgaccctaatagTCATATAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from CESAR TGACCGG ------AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGgtaatcggcttgacatgattaaacacaagcttgaccctaatagTCATATAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from Spaln_aa2Genome TGACCGG AAGCGGAATGGGATG------ATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGgtagaaggcttgacatgattaaacacaagcttgaccctaatagTCATATAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from Spaln_nt2Genome TGACCGG AAGCGGAATGGGA------TGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGgtagaaggcttgacatgattaaacacaagcttgaccctaatagTCATATAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from Pairagon TGACCGG-------------------------------------------------AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGGTAGAAGGCTTGACATGATTAAACACAAGCTTGACCCTAATAGTCATATAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from Exonerate_protein2genome TGACCGG AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGgtagaaggcttgacatgattaaacacaagcttgaccctaatagtcatatAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from Exonerate_coding2genome tgaccgggtagaaggcttgacatgattaaacacaagcttgaccctaatagtcatataagcggaacaggatgatggagcccgatgactttcgagcttgtctcatctccatgggttatgatctagtattcggattagagtcctatgacaccattagcttatttatgtctttgtc Alignment from GeneWise TGACCGG ------AAGCGGAATGGGATGATGGAGCCCGACGACTTCCGAGCTTGTCTCATCTCCATGGGTTACGATCTG TGACCGGgtagaaggcttgacatgattaaacacaagcttgaccctaatagTCATATAAGCGGAACAGGATGATGGAGCCCGATGACTTTCGAGCTTGTCTCATCTCCATGGGTTATGATCTAgtattcggattagagtcctatgacaccattagcttatttatgtctttgtc #### Actn3_ID692_18 --> 0 - 0 Original Alignment CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG AAGCGGA caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCAC---------gtacgtggcggagagtgcttgtattccttttttccacgctcagAAGCGGA Alignment from CESAR CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTGACCGG caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCAC---------gtacgtggcggagagtgcttatctttgttgttgtgttttgt Alignment from Spaln_aa2Genome CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCAC TTTGACC caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACgtacgtggcggagagtgcttgtattccttttttccacgctcag------- Alignment from Spaln_nt2Genome CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCAC TTTGACC caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACgtacgtggcggagagtgcttgtattccttttttccacgctcag------- Alignment from Pairagon CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCAC TTTGACC caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACgtacgtggcggagagtgcttgtattccttttttccacgctcag------- Alignment from Exonerate_protein2genome CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTTG ACCGGAAGCGGA caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACGTACgtggcggagagtgcttgtattccttttttccacgCTCAGAAGCGGA Alignment from Exonerate_coding2genome caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagcagattcgtgtgggctgggagcaactactgacctccattgcccacaccattaatgaagtggataaccaagtactcactagagatgctaagggcctaagccaggagcaactcaacgaattccgtgcctcattcaatcacgtacgtggcggagagtgcttgtattccttttttccacgctcagaagcgga Alignment from GeneWise CACATTCGTGTGGGCTGGGAGCAGTTGCTCACCTCCATTGCCCGCACCATCAATGAGGTCGAGAACCAGGTACTGACCCGAGATGCCAAGGGCCTGAGCCAGGAGCAGCTCAACGAATTCCGCGCCTCCTTCAACCACTTT-GAC---------------------------------CGGAAGCGGA caaaaccatttcgcgatggatatgtttttttctcgatctccccttaacagCAGATTCGTGTGGGCTGGGAGCAACTACTGACCTCCATTGCCCACACCATTAATGAAGTGGATAACCAAGTACTCACTAGAGATGCTAAGGGCCTAAGCCAGGAGCAACTCAACGAATTCCGTGCCTCATTCAATCACGTACGTGGCGGAGAGTGCTTGTATTCCTTTTTTCCACGCTCAGAAGCGGA #### Actn3_ID700_10 --> 0 - 0 Original Alignment CTGTTGGAGTGGATCCGCCGCACTGTCCCATGGCTAGAGAACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTTCG cctgttgcccattctgcccctaatgttgctgcccttactctctttttcag------GAGTGGAATTGCCGCACCTTA------------AACCATGTAGCTGAATCTAGCATG------------CAG---CTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAAC------TCAgtaaggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from CESAR CTGTTGGAGTGGATCCGCCGCACTGTCCCATGGCTAGAGAACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTTCG acgtcacctgttgcccattctgcccttgctgcccttactctctttttcag------GAGTGGAATTGCCGCACCTTA------------AACCATGTAGCTGAATCTAGCATG---------------CAGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAAC------TCAgtaaggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from Spaln_aa2Genome CTGTTGGAGTGGATCCGCCGCACTGTCCCATGGCTAGAGAACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTTCG cctgttgcccattctgcccctaatgttgctgcccttactctctttttcag------GAGTGGAATTGCCGCACCTTA------------AACCATGTAGCTGAATCTAGCATG---------------CAGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAAC------TCAgtaaggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from Spaln_nt2Genome GGAGTGGATCCGCCGCACTGTCCCATGGCTAGAGAACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTG cctgttgcccattctgcccctaatgttgctgcccttactctctttttcag-GAGTGGAATTGCCGCACCTT------------AAACCATGTAGCTGAATCTAGCATG---------------CAGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAACTCAgtaaggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from Pairagon CTGTTGGAGTGGATCCGCCGCACTGTCCCATGGCTAGAGAACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTTCG cctgttgcccattctgcccctaatgttgctgcccttactctctttttcaggagtggaattgccgcaccttaaaccatgtagctgaatctag--------------------------------------------------------------------CATGC------AGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAA------CTCAgtaaggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from Exonerate_protein2genome GAG---AACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTT cctgttgcccattctgcccctaatgttgctgcccttactctctttttcagGAGTGGAATTGCCGCACCTTAAACCATGTAGCTGAATCTAGCATGCAGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAACTCAGTAAggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from Exonerate_coding2genome GAG---AACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTT cctgttgcccattctgcccctaatgttgctgcccttactctctttttcagGAGTGGAATTGCCGCACCTTAAACCATGTAGCTGAATCTAGCATGCAGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAACTCAGTAAggaggtattctgcaagttccaactctgcctacatgcctacaaccct Alignment from GeneWise ---TGGATCCGCCGCACTGTCCCATGGCTAGAGAACCGCGTGGGCGAACCCAGCATGAGTGCCATGCAGCGCAAGCTGGAGGACTTCCGAGACTATCGACGCCTGCACAAGCCTCCCCGTGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGTTGCGCCTGAGCCACCGACCCGCTTTCATGCCCTCCGAGGGCAAGCTGGTTTCG cctgttgcccattctgcccctaatgttgctgcccttactctctttttcagGAGTGGAATTGCCGCACCTTA------------AACCATGTAGCTGAATCTAGCATG---------------CAGCTGGAGGACTTCCAAGACTATCAACACCTACGAAAGCCACCCTGTTTCCAAGAGACATGCCAGCTAGAGATCAACTTTAACATGCTGCAGGCTAAGTTGCGTCTGAGTCACCAACCTGCCTTCATGCCCTCTGAAGGCAAC------TCAgtaaggaggtattctgcaagttccaactctgcctacatgcctacaaccct #### Actn3_ID702_8 --> 2 - 0 Original Alignment atATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagat------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from CESAR atATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG tccatcagtgcccatggaatcctccgtttccataaccccacccccaccagat------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from Spaln_aa2Genome ATATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagAT------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from Spaln_nt2Genome ATATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagAT------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from Pairagon ATATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagAT------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from Exonerate_protein2genome ATATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagAT------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from Exonerate_coding2genome ATATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagAT------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg Alignment from GeneWise ATATCGTGAACACCCCCAAACCAGATGAGAAAGCCATCATGACCTATGTTTCCTGCTTCTACCATGCGTTTGCTGGGGCTGAGCAG agtgcccatggaatcctccatcatggtttccataaccccacccccaccagAT------AACACACCCAGACCAGATGAGAAAGCCATCATAACTTACCTTTCCTGTTTTTACGATGCATTTGCTGGGGCTGAGCAGgtgagagagctgttgtaaacatgacatcatacagtatgtcctggcagttg #### Actn3_ID705_5 --> 2 - 2 Original Alignment agACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATACC------ag atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagagGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCaggtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from CESAR agACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATACC------ag atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagagGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCaggtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from Spaln_aa2Genome AGACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATACCAGC----- atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagAGGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCAGgtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from Spaln_nt2Genome AGACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATAC------CAG atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagAGGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCAGgtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from Pairagon AGACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATA------CCAG atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagAGGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCAGgtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from Exonerate_protein2genome AGACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATACC------AG atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagAGGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCAGgtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from Exonerate_coding2genome AGACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATACC------AG atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagAGGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCAGgtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca Alignment from GeneWise AGACCTCAGCCAAAGAAGGCTTGCTTCTCTGGTGTCAGCGGAAAACAGCACCGTACCGCAATGTCAACGTACAGAACTTCCATACC------AG atgccagatgccgagccaagccatgtcagacactcatgttttctttgtagAGGCTGCCTCCAAACAGGCCTTGTTCCTCTGGTGCCAATGGAAAATAGCTCCATACCGTAATGTTAATGTACAGAACTTCCATACTCCACCCAGgtaaatatcctgcatatcgtagttaggatctataaaagtgaagggtgcca #### Actn3_ID706_4 --> 2 - 1 Original Alignment aa---------------ATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAg acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaaGAAATCATCTTCTATATAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAggtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt Alignment from CESAR aa---------------ATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAg acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaaGAAATCATCTTCTATATAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAggtaggttgatgccagatgccgagccaagccatgtcagacactcatgtttt Alignment from Spaln_aa2Genome AA------------ATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAG acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaagAAATCATCTTCTATATAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAGgtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt Alignment from Spaln_nt2Genome TTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAG acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaagaaatcatcttctatatagTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAGgtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt Alignment from Pairagon AA---------------ATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAG acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagAAGAAATCATCTTCTATATAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAGgtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt Alignment from Exonerate_protein2genome TGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAG acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaagaaatcatcttctatatAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAGgtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt Alignment from Exonerate_coding2genome TGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAG acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaagaaatcatcttctatatAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAGgtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt Alignment from GeneWise -----------GAAATTGTTGACGGGAACCTGAAGATGACCCTGGGCATGATCTGGACCATCATCCTCCGCTTTGCCATTCAGGACATCTCTGTAGAAG acataacgcgggggaaaaaatactctcatttcaccttccctgtcttctagaagAAATCATCTTCTATATAGTTGATGGCAACCTGAAGATGACCCTTGGCATGATTGGGACAATCATCCTCCGTTTTGCCATTCAGGACATCTCTGTAGAAGgtaggttgatgccagatgccgagccaagccatgtcaacttgtctgctgtt #### Acy3_ID250_4 --> 2 - 1 Original Alignment gtCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTGCGG---------GCCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAA------g ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcaggcCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAggtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt Alignment from CESAR gtCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTGCGG---------GCCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAA------g ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcaggcCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAggtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt Alignment from Spaln_aa2Genome GTCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTGCGG---------GCCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAAGGCATGG ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcagGCCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAGgtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt Alignment from Spaln_nt2Genome GTCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTGCGGGCCGACCTGT---------TCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAAGGCATGG ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcagGCCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAGgtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt Alignment from Pairagon GTCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTGCGGG---------CCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCA---------------------------------------------------------- ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcagGCCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAGGTGAGCCATTCCTAGTATTTTGTCAGGCAGGTCATGTTGATGGGAGTGTT Alignment from Exonerate_protein2genome GTCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTG---------CGGGCCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAAGGCATGG ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcagGCCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAGgtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt Alignment from Exonerate_coding2genome GTCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTG---------CGGGCCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAAGGCATGG ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcagGCCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAGgtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt Alignment from GeneWise GTCTGGAGATGGGCCCACAGCCTCAGGGCGTGCTG---------CGGGCCGACCTGTTCTCCCGGATGCGAGCTCTGGTGGCATCCATTCTGGACTTCATCGAGCTCTTCAACCAAGGCATGG ctggtagaagcaattttcaaggctagccctctctacgttggcctgttcagGCCTCGAGATGGGCCCACAGCCCCAAGGGGTTCTGTGGCCTGATCTATCTGATCTATTCTCACAGTTAAGAGCTTTAGTGGCATCAATTCTTGACTTCATTGAGCTCTTGAATCAATGGCTAGgtgagccattcctagtattttgtcaggcaggtcatgttgatgggagtgtt #### Adrbk1_ID479_16 --> 0 - 0 Original Alignment TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAGGAGGACACAAAAGGAATCAAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAG---------------------gtctggaacccatgtagcttgccaatcaaaagatactgtagaggaccccg Alignment from CESAR TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAGGAGGACACAAAAGGAATCAAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAG---------------------gtctggaacccatgtagcttgccaatcaa Alignment from Spaln_aa2Genome TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAGgtctggaacccatgtagcttgccaatcaaaagatactgtagaggaccccg Alignment from Spaln_nt2Genome TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAGgtctggaacccatgtagcttgccaatcaaaagatactgtagaggaccccg Alignment from Pairagon TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAGgtctggaacccatgtagcttgccaatcaaaagatactgtagaggaccccg Alignment from Exonerate_protein2genome TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAGGAGGACACAAAAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAGGTCTGGAACCCATgtagcttgccaatcaaaagatactgtagaggaccccg Alignment from Exonerate_coding2genome TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAGGAGGACACAAAAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGATGAGGTCTGGAACCCATgtagcttgccaatcaaaagatactgtagaggaccccg Alignment from GeneWise TACCCTCCTCCACTGATCCCCCCACGTGGGGAGGTGAATGCAGCTGACGCTTTCGACATTGGCTCCTTTGATGAGGAGGACACAAAAGGAATCAAG tgccccctgccactctcccctgcaatgaactctctatctcctatatccagTATCCTCCCCCATTGATCCCCCAACGTGGGGAGGTGAATGCAGCTGACGCTTTTGACATTGGCTCCTTTGAT---------------------GAGgtctggaacccatgtagcttgccaatcaaaagatactgtagaggaccccg #### Adrbk1_ID482_13 --> 1 - 0 Original Alignment aCACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTGACGATG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagcCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTT------gtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat Alignment from CESAR aCACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTGACGATG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagcCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTT------gtatgtctcgatctaatagaagcattgagaactatgtcaagctg Alignment from Spaln_aa2Genome ACACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagCCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTTgtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat Alignment from Spaln_nt2Genome ACACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagCCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTTgtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat Alignment from Pairagon ACACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagCCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTTgtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat Alignment from Exonerate_protein2genome ACACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagCCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTTgtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat Alignment from Exonerate_coding2genome ACACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagCCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACACTTgtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat Alignment from GeneWise ACACAGCCCCTTCCGGCAGCACAAGACCAAAGACAAGCATGAGATTGACCGCATGACGTTGACGATG ttctgatacacctccttttaacccaccttatgtgttctattctttcccagCCACAGTCACTTCCAGCAGCACAAGACAAAAGATACACATGACATCGACCGCATGACA------CTTgtatgtctcgatctaatagaagcattgagaactatgtcaagctgagtcat #### Adrbk1_ID484_11 --> 0 - 2 Original Alignment CCAGCCAACATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTgt gGGC accagcatgatgatgacatactctgtcactcatctctctttctgccttag---------ATTCTCCTAGAA---CATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGgtgtaggaacctacagactcacttcaatttcctatctttttgtccaaggGGC Alignment from CESAR CCAGCCAACATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTgt gGGC cacaaggcaaccagcatgatgatgatcactcatctctctttctgccttag---------ATTCTCCTA---GAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGgtgtaggaacctacagactcacttcaccttgcctgtcctctctttcaggGGC Alignment from Spaln_aa2Genome CCAGCCAACATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTGT GGGC accagcatgatgatgacatactctgtcactcatctctctttctgccttag---------ATTCTCCTA---GAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGGTgtaggaacctacagactcacttcaatttcctatctttttgtccaagGGGC Alignment from Spaln_nt2Genome CATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTGT GGGC accagcatgatgatgacatactctgtcactcatctctctttctgccttag-ATTCTCCT---AGAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGGTgtaggaacctacagactcacttcaatttcctatctttttgtccaagGGGC Alignment from Pairagon CCAGCCAACATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTGT GGGC accagcatgatgatgacatactctgtcactcatctctctttctgccttag---------ATTCTCCTA---GAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGGTgtaggaacctacagactcacttcaatttcctatctttttgtccaagGGGC Alignment from Exonerate_protein2genome CCAGCCAACATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTGT GGGC accagcatgatgatgacatactctgtcactcatctctctttctgCCTTAGATTCTCCTA------GAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGGTgtaggaacctacagactcacttcaatttcctatctttttgtccaagGGGC Alignment from Exonerate_coding2genome CCAGCCAACATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTGT GGGC accagcatgatgatgacatactctgtcactcatctctctttctgCCTTAGATTCTCCTA------GAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGGTgtaggaacctacagactcacttcaatttcctatctttttgtccaagGGGC Alignment from GeneWise ATTCTCCTGGATGAACATGGCCATGTGAGAATCTCGGACCTGGGCCTAGCCTGTGACTTCTCCAAGAAGAGGCCTCATGCCAGTGT GGGC accagcatgatgatgacatactctgtcactcatctctctttctgccttagATTCTCCTA---GAACATGGCCATGTGAGAATTTCTGATTTTAGCCTAGTATGTGACTTCTCCAAGAAGAGACCCCCTGCCGGGGTgtaggaacctacagactcacttcaatttcctatctttttgtccaagGGGC #### Adrbk1_ID486_9 --> 0 - 1 Original Alignment GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAAC------g gtGGGGAC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATggtgggtaagtctcgagactgccttccttttcatatttaccagggGTAGAG Alignment from CESAR GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAAC------g gtGGGGAC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATggtgggtaagtctcgagactgggtctctgcttgttcctctcagggGTAGAG Alignment from Spaln_aa2Genome GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACGGTGGGG AC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATGgtgggtaagtctcgagactgccttccttttcatatttaccaggggtagAG Alignment from Spaln_nt2Genome GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAA---CGGTGG-GG AC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATGGTGGgtaagtctcgagactgccttccttttcatatttaccaggggtagAG Alignment from Pairagon GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGA------ACGGTGGG------------------------------------------GAC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATGGTGGGTAAGTCTCGAGACTGCCTTCCTTTTCATATTTACCAGGGGTAGAG Alignment from Exonerate_protein2genome GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACGGTGGGG AC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATGgtgggtaagtctcgagactgccttccttttcatatttaccaggggtagAG Alignment from Exonerate_coding2genome GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACGGTGGGG AC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATGgtgggtaagtctcgagactgccttccttttcatatttaccaggggtagAG Alignment from GeneWise GACTGCCCCTTCATCGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTCAGCTTCATCCTGGACCTCATGAACGGTGGGG AC ccccactcagttcgccttctataagacagttccttcatatcttcttccagGACTGCTCCTTCACTGTGTGCATGTCATATGCATTCCACACACCAGACAAGCTAAGCTTTATCCTGGATCTTATGAATCTCTATGgtgggtaagtctcgagactgccttccttttcatatttaccaggggtagAG #### Adrbk1_ID488_7 --> 0 - 2 Original Alignment CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGat acacaataaaagtagcaactctacatagaacacacttttcttccctccag---CCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTA------atgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc Alignment from CESAR CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGat acacaataaaagtagcaactctacatagaacacacttttcttccctccag---CCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTA------atgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc Alignment from Spaln_aa2Genome ACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGG acacaataaaagtagcaactctacatagaacacacttttcttccctccagCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTAATgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc Alignment from Spaln_nt2Genome ACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGAT acacaataaaagtagcaactctacatagaacacacttttcttccctccagCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTA------ATgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc Alignment from Pairagon ACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCC acacaataaaagtagcaactctacatagaacacacttttcttccctccagCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCgccaggctgatgtaatgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc Alignment from Exonerate_protein2genome ACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGAT acacaataaaagtagcaactctacatagaacacacttttcttccctccagCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTA------ATgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc Alignment from Exonerate_coding2genome AGTTCACACGGTTCTGCCAGTGGAAGAATGTTGAGCTCAACATCCACCTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGGCAAGATGTACGCCATGAAGTGTCTGGA ACACAATAAAAGTAGCAACTCTACATAGAACACACTTTTCTTCCCTCCAGCCCATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTAATGTAAGTTCATCTTGTAGACAAGTAAAGgtgggtggtcaacaaagggcatc Alignment from GeneWise CTGACCATGAATGACTTCAGTGTGCATCGAATCATCGGGCGTGGGGGCTTCGGTGAGGTCTATGGGTGCCGGAAAGCAGACACAGG acacaataaaagtagcaactctacatagaacacacttttcttccctccagCCC---ATGAATGATTTTAGTGTACGTCAGATCATTGGACATGGTGGCTTTGGTGAGGTATATGGTTGCCGCCAGGCTGATGTAATgtaagttcatcttgtagacaagtaaaggtgggtggtcaacaaagggcatc #### Adrbk1_ID491_4 --> 0 - 0 Original Alignment CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATCTCTTCCAG--------------- acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAGAACTGGATCGGTACgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt Alignment from CESAR CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATCTCTTCCAG--------------- acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAGAACTGGATCGGTACgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt Alignment from Spaln_aa2Genome CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATCTCTTCCAG--------------- acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAGAACTGGATCGGTACgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt Alignment from Spaln_nt2Genome CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATCTCTTCCA-----------G acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAGAACTGGATCGgtacgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt Alignment from Pairagon CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATC------------------------------------------------------------------------- acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAGAACTGGATCGGTACGTAAAGTTAGGATGGTTATCACGGTATTAGACATTGGTAAGAGGTTGTTT Alignment from Exonerate_protein2genome CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATCTCTTCCAG acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAgaactggatcggtacgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt Alignment from Exonerate_coding2genome acattccattttgcttgttcttgttcatcacgagtgtctcctccttgcagcccttctcccaaaatgctgcagagcatgtgcaggctcaccttgtgaagaagcaggtccctccagatctgtttcaagaactggatcggtacgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt Alignment from GeneWise ----------------CCCTTTTCAAAGAATGCTACGGAGCATGTCCAGGGCCACCTGGTGAAGAAGCAGGTGCCTCCAGATCTCTTCCAG--------------- acattccattttgcttgttcttgttcatcacgagTGTCTCCTCCTTGCAGCCCTTCTCCCAAAATGCTGCAGAGCATGTGCAGGCTCACCTTGTGAAGAAGCAGGTCCCTCCAGATCTGTTTCAAGAACTGGATCGGTACgtaaagttaggatggttatcacggtattagacattggtaagaggttgttt #### Afap1l2_ID12244_19 --> 0 - 0 Original Alignment CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggcag---CAGCCCAAAGCTGCCACTCCTAATCCTCCACCA---GCTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from CESAR CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG tttatttagtacagacaagccagctcctctgccgtgccctgccctggcag---CAGCCCAAAGCTGCCACTCCTAATCCTCCACCA---GCTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from Spaln_aa2Genome CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggcag---CAGCCCAAAGCTGCCACTCCTAATCCTCCACCA---GCTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from Spaln_nt2Genome CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggcag---CAGCCCAAAGCTGCCACTCCTAATCCTCCACCAG---CTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from Pairagon CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggcag---CAGCCCAAAGCTGCCACTCCTAATCCTCCACCAG---CTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from Exonerate_protein2genome CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggCAGCAGCCCAAAGCTGCCACTCCTAATCCTCCACCA---GCTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from Exonerate_coding2genome CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggCAGCAGCCCAAAGCTGCCACTCCTAATCCTCCACCA---GCTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc Alignment from GeneWise CCACAGCCCAAAGCTGCCACCCCCAACCCCCCACCAGACTCCACGCCAGTCAACTCTGCATCTGTGCTCAAGAACAGGCCTCTTTCCGTCATGGTCACAGGCAAAGGCACTGTCCTGCAGAAAGCCAAG atttagtacagacaagccagctttgcctctgccgtgccctgccctggcagCAG---CCCAAAGCTGCCACTCCTAATCCTCCACCA---GCTACACCAGTTAATTCAGCATCTGTACTAAAAAATAGGCCGCTCTCTGTGATGGTTATTGGGAAAGGAACTGTCCTGCAGAAAGCTAAGgtgagttaccttattacaaactttgttgagccactaatccacaaaatgtc #### Aip_ID330_5 --> 0 - 1 Original Alignment GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATg ttcactgcagctgagactgaccccctcttgtttctgtttgaatatcttag------GCTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTggtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from CESAR GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATg gctgtcttcactgcagctgagactgtcttgtttctgtttgaatatcttag------GCTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTggtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from Spaln_aa2Genome GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ttcactgcagctgagactgaccccctcttgtttctgtttgaatatcttag------GCTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from Spaln_nt2Genome GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ttcactgcagctgagactgaccccctcttgtttctgtttgaatatcttagG------CTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from Pairagon GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ttcactgcagctgagactgaccccctcttgtttctgtttgaatatcttagG------CTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from Exonerate_protein2genome GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ttcactgcagctgagactgaccccctcttgtttctgtttgaataTCTTAGGCTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from Exonerate_coding2genome GAGCAGCCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ttcactgcagctgagactgaccccctcttgtttctgtttgaataTCTTAGGCTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc Alignment from GeneWise CCTGGCTCACCTGACTGGATCCAGTTGGACCTGCAGATCACACCACTGCTACTCAACTATTGCCAGTGCAAGCTGGTGGCTCAGGAGTATTATGAAGTGTTGGATCACTGCTCCTCCATCCTCAACAAGTATGATG ttcactgcagctgagactgaccccctcttgtttctgtttgaatatcttagGCTGGCTCATCAGACTGGGTCCAGTTAGACCTGCAGATCACACCACTGCTACCCAATTACTGCCAGTGCAAGCTTGTAGCTCCAGGGTATTATGAAGTACTGGATCACTGCTTGTCCATTCTCAACAAGTATGTTGgtgagtgtcatgcccaatacatgcccaatacaactcaactcagacttccc #### Aip_ID331_4 --> 0 - 0 Original Alignment GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG--- tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt Alignment from CESAR GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG--- tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt Alignment from Spaln_aa2Genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAGGAG tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt Alignment from Spaln_nt2Genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAG--- tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt Alignment from Pairagon GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGA------------------------------------------------------- tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAGTATGTCTCATAGATACAGTAGTAGGCAATAATGTACACATGGCTGTCTT Alignment from Exonerate_protein2genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAGGAG tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt Alignment from Exonerate_coding2genome GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAGGAG tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt Alignment from GeneWise GTAGAGAGTCCTGGCACCTATCAACAGGACCCATGGGCGATGACAGATGAGGAGAAAGCAAAGGCAGTACCAGTCATCCACCAAGAGGGCAACCGGTTGTACCGTGAGGGCCAGGTGAAAGAGGCTGCTGCCAAGTACTATGACGCCATCGCCTGCCTCAAGAATCTGCAGATGAAGGAG tggaagctatccatgggacatggcagagtctactatgatattttcactagGTAGAAAGTCCTGGTACCTATCAACATGACCCTTGGGCAATGACAGATGAGGAGAAAGCAAAGGAAGTACCTGTTATCCACCAGGAAGGCAACCGGTTGTACCGTGAAAGCCAGGTGAGGGAGGCTGCTCCAAAGTACTATGATGCCATTGCTTCCCTCAAGAATCTGCAAATGAAACGAgtatgtctcatagatacagtagtaggcaataatgtacacatggctgtctt #### Aldh3b2_ID237_3 --> 0 - 0 Original Alignment TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgtcttgccag---------GAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from CESAR TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG aatggtttgttagtaaactgagtcttgtgtcctcttgtctgtcttgccag---------GAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from Spaln_aa2Genome TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgtcttgccag---------GAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from Spaln_nt2Genome GAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgtcttgccagGAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from Pairagon TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgtcttgccag---------GAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from Exonerate_protein2genome TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgTCTTGCCAGGAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from Exonerate_coding2genome TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgTCTTGCCAGGAGTCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg Alignment from GeneWise TCAGGCTTCGAGTCAGACATGAGTGAGATCATCCTGTGCGAGAATGAGGTGGACCTGGCCCTCAAGAACCTGCAGACCTGGATGAAGGACGAGCCTGTGTCCACCAACTTG ttagtaaactgagtctgtcttttattgtgtcctcttgtctgtcttgccagGAG---------TCAGACATGAGTGAGGTTTTTCTGTGTGAAAATGAGGTGGACTTGGCCCTGAAGAATTTGCAGACGTGGATGAAGGATGAACCTGTACCCACAAATTTAgtgagacctgttggtgtactgtagctgcccccattcagaccctacccttg #### Aldh3b2_ID241_7 --> 2 - 1 Original Alignment ga---------AGTCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTg taaatggcttactaggtgagtaggtgccattttgttttactctcttacaggaATAGAAACTAGCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGTT------TTGCAAAATTCTATCACTCGTTTT------TACAATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTggtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from CESAR ga---------AGTCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTg taaatggcttactaggtgagtaggtgccattttgttttactctcttacaggaATAGAAACTAGCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGTT------TTGCAAAATTCTATCACTCGTTTTTAC------AATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTggtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from Spaln_aa2Genome TCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTG taaatggcttactaggtgagtaggtgccattttgttttactctcttacaggaatagaaactagCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGTT------TTGCAAAATTCTATCACTCGTTTTTAC------AATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTGgtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from Spaln_nt2Genome GAA---------GTCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTG taaatggcttactaggtgagtaggtgccattttgttttactctcttacagGAATAGAAACTAGCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGT------TTTGCAAAATTCTATCACTCGTTTTT------ACAATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTGgtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from Pairagon GA---------AGTCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTG taaatggcttactaggtgagtaggtgccattttgttttactctcttacagGAATAGAAACTAGCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGT------TTTGCAAAATTCTATCACTCGTTTTT------ACAATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTGgtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from Exonerate_protein2genome GA---------AGTCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTG taaatggcttactaggtgagtaggtgccattttgttttactctcttacagGAATAGAAACTAGCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGTT------TTGCAAAATTCTATCACTCGTTTTTAC------AATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTGgtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from Exonerate_coding2genome GA---------AGTCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTG taaatggcttactaggtgagtaggtgccattttgttttactctcttacagGAATAGAAACTAGCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGTT------TTGCAAAATTCTATCACTCGTTTTTAC------AATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTGgtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc Alignment from GeneWise TCCTCGGGTAGGCAAGATCGTCATGACTGCTGCTGCCAAACACCTGACACCCATCACCCTGGAGCTGGGGGGTAAGAACCCCTGCTATGTGGATGACAACTGCGACCCCCAGACAGTGGCCAACCGTGTGGCCTGGTTCCGCTATTTCAATGCCGGCCAGACCTGTGTGGCCCCCGATTATATCCTGTGTAGCCAGGAGATGCAGGAGCGGTTGGTGCCTGCCCTGCAGAATTCCATCACGCGTTTCTATGGAGATAACCCACAGACCTCCCCCAACCTGGGCAGAATCATCAACCAGAAGCATTTCAAGAGGCTCCAGGGATTGCTGGGCTGTGGCCGTGTGGCCATCGGTGGCCAGAGTGATGAGGGAGAGCGCTACATTG taaatggcttactaggtgagtaggtgccattttgttttactctcttacaggaatagaaactagCCCTCGAGTAGGCAAGATGGTGATGACAGCTATGGCCAACCACCTGACTCCCACTTCCCTGCAACTAGGAGGCAAGAACCCCTGCTAT---GATGATAACTGTGACCCACAGACAGTGACCAACAGAGTGGCCTGGTTCCACTATTTCAATGCTGGGCAAACCTGTGTTGCACCAGAATACATCTTATGTAGCCAAGAAATGCAGGAACAGTTGGTT------TTGCAAAATTCTATCACTCGTTTTTAC------AATCCACAGACCCCACCTAACCTAGGAAGGATGATTAATCAGAAGCATTTCAAGAGGCTTCCAGGACTGCTGGGGTGTGGCCGTGTGGCCATCGGTCTGCAGAGTGATGAGGGAGGGTGTTGCATTGgtaagaccttgctatttctgctggcccatcagagggaccatgccatctgc #### Ankrd13d_ID461_12 --> 2 - 1 Original Alignment agATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAg gtacaaaattacatgttactgggtacttattcctttctcctctgtaacagaaATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCT---ggtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from CESAR agATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAg gtacaaaattacatgttactgggtacttattcctttctcctctgtaacagaaATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCT---ggtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from Spaln_aa2Genome AGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCT- gtacaaaattacatgttactgggtacttattcctttctcctctgtaacagAAATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCTGgtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from Spaln_nt2Genome AGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAG gtacaaaattacatgttactgggtacttattcctttctcctctgtaacagAAATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCT---Ggtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from Pairagon AGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTTCAG gtacaaaattacatgttactgggtacttattcctttctcctctgtaacagAAATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCT---Ggtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from Exonerate_protein2genome AGATTGAGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTT gtacaaaattacatgttactgggtacttattcctttctcctctgTAACAGAAATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCTGgtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from Exonerate_coding2genome AGATTGAGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTT gtacaaaattacatgttactgggtacttattcctttctcctctgTAACAGAAATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTG---TCAGTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCTGgtaagcagactatagccataccagctgtctgtagccataccagccatctg Alignment from GeneWise -------------------------------------------------GAGATTCCCCTCTTCCATGTGCTCAATGCCCGCATCACCTTCAGTAACCTTTGCGGCTGTGATGAGCCTGTGAGCTCGGTGTGCGTCCCCAACTCCAGTTCTGCCATTTCTGCTT GTACAAAATTACATGTTACTGGGTACTTATTCCTTTCTCCTCTGTAACAGAAATTGCCCTCTTCCATGTTCACAATGCCCACACCACCTTTAGTAACCTATGCAGCTGTGATGAACCTGTGTCA---GTGTGTGTCCCCAACTCCAGTCTGGCAATTTCTGCTGgtaagcagactatagccataccagctgtctgtagccataccagccatctg #### Ankrd13d_ID464_9 --> 2 - 0 Original Alignment ggGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacacataaacaggtcaagttaaaactttacattcctaggaGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---------gtgaggtactatttggataaactacagaccaggaaggctgggcaagtggg Alignment from CESAR ggGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacacataaacaggtcaagttaaaactttacattcctaggaGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC---------gtgaggtactatttggataaactacagaccaggaaggctgg Alignment from Spaln_aa2Genome GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCC gcctgcctacttacacataaacaggtcaagttaaaactttacattcctagGAGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCCgtgaggtactatttggataaactacagaccaggaaggctgggcaagtggg Alignment from Spaln_nt2Genome GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACACTTTG gcctgcctacttacacataaacaggtcaagttaaaactttacattcctagGAGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCC----GTGAGgtactatttggataaactacagaccaggaaggctgggcaag Alignment from Pairagon GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCC gcctgcctacttacacataaacaggtcaagttaaaactttacattcctagGAGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCCgtgaggtactatttggataaactacagaccaggaaggctgggcaagtggg Alignment from Exonerate_protein2genome GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACAC gcctgcctacttacacataaacaggtcaagttaaaactttacattcctagGAGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCCGTGAGgtactatttggataaactacagaccaggaaggctgggcaagtggg Alignment from Exonerate_coding2genome GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCCCACAC gcctgcctacttacacataaacaggtcaagttaaaactttacattcctagGAGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCCGTGAGgtactatttggataaactacagaccaggaaggctgggcaagtggg Alignment from GeneWise GGGGGAAGACTCCATTCCAGTCCTTCCTGGGCATGGCCCAGCAGCACTCCTCC gcctgcctacttacacataaacaggtcaagttaaaactttacattcctagGAGGAAAGACTCCATTCCAATCCTTCTTGGGTATGGCCCAGCAACATTCACCCgtgaggtactatttggataaactacagaccaggaaggctgggcaagtggg #### Ankrd1_ID7101_4 --> 0 - 0 Original Alignment ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGATGAG ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGTGAT---gtaagcaggagtagtactgtgccctgccactttctggcctgccatttgcc Alignment from CESAR ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGATGAG ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGTGAT---gtaagcaggagtagtactgtgccctgccactttctggcctgccattt Alignment from Spaln_aa2Genome ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGAT ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGTGATgtaagcaggagtagtactgtgccctgccactttctggcctgccatttgcc Alignment from Spaln_nt2Genome ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGATG-AG ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGTGATGTAAgcaggagtagtactgtgccctgccactttctggcctgccatttgcc Alignment from Pairagon ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGAT ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGTGATgtaagcaggagtagtactgtgccctgccactttctggcctgccatttgcc Alignment from Exonerate_protein2genome ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGAT ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGTGATgtaagcaggagtagtactgtgccctgccactttctggcctgccatttgcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ACTGAACCTGTGGATGTGCCGAGGTTTCTGAAAGCTGCGCTGGAGAACAAACTGCCAGTTGTAGAGAAATTCCTGTCAGACAAGAACAGCCCCGACGTCTGCGATGAG ggatggaaggataggaaaacaatcagtacattcggttgcattcccaacagAGTGAGCCTGTTGATGTACCTAGGTTTCTAAAAGCTGCACTGGATAACAAACTTCCAGTTGTAGAAAAGTTCCTCTCAGAGAAGAACAGTCCTGATGTCTGT---GATgtaagcaggagtagtactgtgccctgccactttctggcctgccatttgcc #### Apba1_ID5242_11 --> 0 - 0 Original Alignment ---------ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc Alignment from CESAR ---------ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc Alignment from Spaln_aa2Genome ATCTGCAGCCTCATG---------AGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc Alignment from Spaln_nt2Genome A---------TCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc Alignment from Pairagon ---------ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc Alignment from Exonerate_protein2genome AATGGAATTATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---------ATCTGCAGCCTCATGAGAGGGGGAATCGCTGAGAGAGGAGGCGTCCGCGTGGGACATCGGATCATCGAAATCAATGGCCAGAGTGTCGTAGCCACACCACACGAGAAGATCGTCCACATCCTCTCCAATGCTGTTGGGGAG tactaaaaacaaaatgcagtaggacagagctttattttttcccccctcagAATGACCTAATCTGCAGCCTTACAAGAGGGGGAATAGCTGAAAGAGGAGATGTCCGTGTTGGACATCGAATCATTGAAATTAATGGCCAAAGTATTGTAGCTATACCACATGAAGAGATTGTCCACATCCTGTCCAATGCTGTGGGGGAGgtaggttcagatcagttggtcaggctttatagtggtgtcttttccttctc #### Atg2a_ID1514_3 --> 2 - 1 Original Alignment ga---------CCAGGGGCTGCGGACTCTCAGAGTTGGGCCTCATGCATGACCACAAGCTTGCAGCTGGCTCAAGAGTGCCTTCGGGAAGGGTTGCCAGAACCCTCAGAACCACCACAGCCCCTGGAGGGGCTGGAAATGTTTGCACAGACCATTGAGACTg ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagggCCACTGGATCCTGGGGCTGCAGATGCACAGAGTTGGGCTTCTTGC---ACCACTAGCTTACATCTGGCCCAGGATTGTTTCCAAGAAGCACTCCCAGAACCCTCAGAACCTCCACAGCCCCTAGAGGGTCTTGCCATGTTTGCACAGACCATAGAGACTggtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from CESAR gaCCA---------GGGGCTGCGGACTCTCAGAGTTGGGCCTCATGCATGACCACAAGCTTGCAGCTGGCTCAAGAGTGCCTTCGGGAAGGGTTGCCAGAACCCTCAGAACCACCACAGCCCCTGGAGGGGCTGGAAATGTTTGCACAGACCATTGAGACTg ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagggCCACTGGATCCTGGGGCTGCAGATGCACAGAGTTGGGCTTCTTGC---ACCACTAGCTTACATCTGGCCCAGGATTGTTTCCAAGAAGCACTCCCAGAACCCTCAGAACCTCCACAGCCCCTAGAGGGTCTTGCCATGTTTGCACAGACCATAGAGACTggtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from Spaln_aa2Genome GA---------CCAGGGGCTGCGGACTCTCAGAGTTGGGCCTCATGCATGACCACAAGCTTGCAGCTGGCTCAAGAGTGCCTTCGGGAAGGGTTGCCAGAACCCTCAGAACCACCACAGCCCCTGGAGGGGCTGGAAATGTTTGCACAGACCATTGAGACTG ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagGGCCACTGGATCCTGGGGCTGCAGATGCACAGAGTTGGGCTTCTTGC---ACCACTAGCTTACATCTGGCCCAGGATTGTTTCCAAGAAGCACTCCCAGAACCCTCAGAACCTCCACAGCCCCTAGAGGGTCTTGCCATGTTTGCACAGACCATAGAGACTGgtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from Spaln_nt2Genome GACCA---------GGGGCTGCGGACTCTCAGAGTTGGGCCTCATGCATGACCACAAGCTTGCAGCTGGCTCAAGAGTGCCTTCGGGAAGGGTTGCCAGAACCCTCAGAACCACCACAGCCCCTGGAGGGGCTGGAAATGTTTGCACAGACCATTGAGACTG ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagGGCCACTGGATCCTGGGGCTGCAGATGCACAGAGTTGGGCTTCTTGC---ACCACTAGCTTACATCTGGCCCAGGATTGTTTCCAAGAAGCACTCCCAGAACCCTCAGAACCTCCACAGCCCCTAGAGGGTCTTGCCATGTTTGCACAGACCATAGAGACTGgtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from Pairagon GACCA---------GGGGCTGCGGACTCTCAGAGTTGGGCCTCATGCATGACCACAAGCTTGCAGCTGGCTCAAGAGTGCCTTCGGGAAGGGTTGCCAGAACCCTCAGAACCACCACAGCCCCTGGAGGGGCTGGAAATGTTTGCACAGACCATTGAGACTG ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagGGCCACTGGATCCTGGGGCTGCAGATGCACAGAGTTGGGCTTCTTGC---ACCACTAGCTTACATCTGGCCCAGGATTGTTTCCAAGAAGCACTCCCAGAACCCTCAGAACCTCCACAGCCCCTAGAGGGTCTTGCCATGTTTGCACAGACCATAGAGACTGgtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from Exonerate_protein2genome ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagggccactggatcctggggctgcagatgcacagagttgggcttcttgcaccactagcttacatctggcccaggattgtttccaagaagcactcccagaaccctcagaacctccacagcccctagagggtcttgccatgtttgcacagaccatagagactggtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from Exonerate_coding2genome ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagggccactggatcctggggctgcagatgcacagagttgggcttcttgcaccactagcttacatctggcccaggattgtttccaagaagcactcccagaaccctcagaacctccacagcccctagagggtcttgccatgtttgcacagaccatagagactggtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc Alignment from GeneWise --------GGACCAGGGGCTGCGGACTCTCAGAGTTGGGCCTCATGCATGACCACAAGCTTGCAGCTGGCTCAAGAGTGCCTTCGGGAAGGGTTGCCAGAACCCTCAGAACCACCACAGCCCCTGGAGGGGCTGGAAATGTTTGCACAGACCATTGAGACTG ttgcacggaaccgatctctttggcaccaatttatcttttggatttttcagGGCCACTGGATCCTGGGGCTGCAGATGCACAGAGTTGGGCTTCTTGC---ACCACTAGCTTACATCTGGCCCAGGATTGTTTCCAAGAAGCACTCCCAGAACCCTCAGAACCTCCACAGCCCCTAGAGGGTCTTGCCATGTTTGCACAGACCATAGAGACTGgtgagtaggtccctattgatgttctcctgctcaatcaccaggatagaacc #### Atg2a_ID1518_7 --> 2 - 1 Original Alignment acCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACG---g ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagatCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAGCTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCACGGCCAACCCCCTCAATTTGGACAGCACAGATggtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from CESAR acCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACG---g ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagatCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAGCTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCACGGCCAACCCCCTCAATTTGGACAGCACAGATggtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from Spaln_aa2Genome ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACG---G ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAGCTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCACGGCCAACCCCCTCAATTTGGACAGCACAGATGgtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from Spaln_nt2Genome ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGGA-- ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAGCTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCACGGCCAACCCCCTCAATTTGGACAGCACAGATGgtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from Pairagon ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGG--- ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAGCTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCACGGCCAACCCCCTCAATTTGGACAGCACAGATGgtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from Exonerate_protein2genome ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagatcctgctggactggctgacaagctgaacaagagctgccaactggggccagaagatctgtggctcattgagcaagacctgaatcagcagctgcaagcaggtgctgtggcagagtctctcagcttgtaccccacggccaaccccctcaatttggacagcacagatggtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from Exonerate_coding2genome ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagatcctgctggactggctgacaagctgaacaagagctgccaactggggccagaagatctgtggctcattgagcaagacctgaatcagcagctgcaagcaggtgctgtggcagagtctctcagcttgtaccccacggccaaccccctcaatttggacagcacagatggtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg Alignment from GeneWise ACCCTGCAGGCCTGGCCGACAAGCTGAACAAGAGCCGTCCACTGGGTGCTGAGGACTTGTGGCTCATTGAGCAAGATCTGAACCAGCAGCTGCAGGCGGGTGCTGTGGCTGAGTCCCTCAGCCTGTACCCCATCACCAACCCCCTCAATTTGGACAGCACGGAC- ctcatggaaagacagacatccaagcaggcctcacagcccttgtctcctagATCCTGCTGGACTGGCTGACAAGCTGAACAAGAGCTGCCAACTGGGGCCAGAAGATCTGTGGCTCATTGAGCAAGACCTGAATCAGCAGCTGCAAGCAGGTGCTGTGGCAGAGTCTCTCAGCTTGTACCCCACGGCCAACCCCCTCAATTTGGACAGCACAGATGgtaagggttgactgttggtttgcagtgggcaatgacacaagacaggctgg #### Atg2a_ID1521_10 --> 1 - 0 Original Alignment GGCCTGCCCTTGTAGC---CACGTCcg gTTAACTGGCACAGCCGTGCAGCTGTCCTGGGAGCTGCGCACGGGCAGCCACAGCCGGAGG---ACAAGCAGCACCGAAGTGCACTTTGGACAGCTGGAGGTGCTGGAGTGCCTATGGCCCAGGGCTGCCACAGAGCCAGAGTACACGGAG--------------------------- AGCCTGCCCTTGTAGCCACCACATAaggtaagccccggcaccccccacaggCTATCTGGAACTGCTGTACAGCTTTCCTGGGAGTTGCACACTGGCAGCCACAGCCGGAGGACAACAAGCAGCACTGAAGTGCACTTCAGCAAATTGGAAGTTTTGGAATGCCTGTGGCACAGAGCTGCAACACCACCCAAATACACAGAGTATCGGTCCCGGCGCTCCACTAACTGCgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag Alignment from CESAR ccaaggctaactcaggtcagatcaaaatcatgagggacaattggtgatgtc Alignment from Spaln_aa2Genome GGCCTGCCCTTGTAGCCAC--------------------------GTCCGGTTAACTGGCACAGCCGTGCAGCTGTCCTGGGAGCTGCGCACGGGCAGCCACAGCCGGAGG---ACAAGCAGCACCGAAGTGCACTTTGGACAGCTGGAGGTGCTGGAGTGCCTATGGCCCAGGGCTGCCACAGAGCCAGAGTACACGGAGATCCTGAG AGCCTGCCCTTGTAGCCACCACATAAGGTAAGCCCCGGCACCCccCACAGGCTATCTGGAACTGCTGTACAGCTTTCCTGGGAGTTGCACACTGGCAGCCACAGCCGGAGGACAACAAGCAGCACTGAAGTGCACTTCAGCAAATTGGAAGTTTTGGAATGCCTGTGGCACAGAGCTGCAACACCACCCAAATACACAGAG---TATCGgtcccggcgctccactaactgcgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag Alignment from Spaln_nt2Genome GGCCTGCCCTTGTA GCCACGTCCGGTTAACTGGCACAGCCGTGCAGCTGTCCTGGGAGCTGCGCACGGGCAGCCACAGCCGGAGGA---CAAGCAGCACCGAAGTGCACTTTGGACAGCTGGAGGTGCTGGAGTGCCTATGGCCCAGGGCTGCCACAGAGCCAGAGTACACGGA AGCCTGCCCTTGTAgccaccacataaggtaagccccggcaccccccacagGC----------TATCTGGAACTGCTGTACAGCTTTCCTGGGAGTTGCACACTGGCAGCCACAGCCGGAGGACAACAAGCAGCACTGAAGTGCACTTCAGCAAATTGGAAGTTTTGGAATGCCTGTGGCACAGAGCTGCAACACCACCCAAATACACAGAgtatcggtcccggcgctccactaactgcgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag Alignment from Pairagon GGCCTGCCCTTGTAGCCAC------------GTCC--------------GGTTAACTGGCACAGCCGTGCAGCTGTCCTGGGAGCTGCGCACGGGCAGCCACAGCCGGAGG---ACAAGCAGCACCGAAGTGCACTTTGGACAGCTGGAGGTGCTGGAGTGCCTATGGCCCAGGGCTGCCACAGAGCCAGAGTACACGGAG--------------------------- AGCCTGCCCTTGTAGCCACCACATAAGGTAAGCCCCGGCACCCCCCACAGGCTATCTGGAACTGCTGTACAGCTTTCCTGGGAGTTGCACACTGGCAGCCACAGCCGGAGGACAACAAGCAGCACTGAAGTGCACTTCAGCAAATTGGAAGTTTTGGAATGCCTGTGGCACAGAGCTGCAACACCACCCAAATACACAGAGTATCGGTCCCGGCGCTCCACTAACTGCgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag Alignment from Exonerate_protein2genome GGCCTGCCCTTGTAGCCACGTCCGGTT AACTGGCACAGCCGTGCAGCTGTCCTGGGAGCTGCGCACGGGCAGCCACAGCCGGAGGACAAGCAGCACCGAAGTGCACTTTGGACAGCTGGAGGTGCTGGAGTGCCTATGGCCCAGGGCTGCCACAGAGCCAGAGTACACGGAG AGCCTGCCCTTGTAGCCACCACATAAGgtaagccccggcaccccccacaggctatctggAACTGCTGTACAGCTTTCCTGGGAGTTGCACACTGGCAGCCACAGCCGGAGGACAACAAGCAGC---ACTGAAGTGCACTTCAGCAAATTGGAAGTTTTGGAATGCCTGTGGCACAGAGCTGCAACACCACCCAAATACACAGAGtatcggtcccggcgctccactaactgcgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag Alignment from Exonerate_coding2genome agcctgcccttgtagccaccacataaggtaagccccggcaccccccacaggctatctggaactgctgtacagctttcctgggagttgcacactggcagccacagccggaggacaacaagcagcactgaagtgcacttcagcaaattggaagttttggaatgcctgtggcacagagctgcaacaccacccaaatacacagagtatcggtcccggcgctccactaactgcgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag Alignment from GeneWise GGCCTGCCCTTGTAGCCAC--GTC------------------------CGGTTAACTGGCACAGCCGTGCAGCTGTCCTGGGAGCTGCGCACGGGCAGCCACAGCCGGAGGACA---AGCAGCACCGAAGTGCACTTTGGACAGCTGGAGGTGCTGGAGTGCCTATGGCCCAGGGCTGCCACAGAGCCAGAGTACACG-- AGCCTGCCCTTGTAGCCACCACATAAGGTAAGCCCCGGCACCCCCCACAGGCTATCTGGAACTGCTGTACAGCTTTCCTGGGAGTTGCACACTGGCAGCCACAGCCGGAGGACAACAAGCAGCACTGAAGTGCACTTCAGCAAATTGGAAGTTTTGGAATGCCTGTGGCACAGAGCTGCAACACCACCCAAATACACAGAgtatcggtcccggcgctccactaactgcgtaagtgtaattgtgctctaagcatgctgttctagtgaatgtttcagcag #### Atg2a_ID1524_13 --> 0 - 1 Original Alignment ACAGAGCCCCCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAg cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcag---------CCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGggtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from CESAR ACAGAGCCCCCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAg tgagcatttcctaagtcccaacctgcctgactctgcctcctcctttgcag---------CCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGggtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from Spaln_aa2Genome CCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAG cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcagCCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGGgtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from Spaln_nt2Genome CCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAG cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcagCCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGGgtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from Pairagon ACAGAGCCCCCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAG cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcag---------CCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGGgtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from Exonerate_protein2genome CCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAG cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcagCCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGGgtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from Exonerate_coding2genome cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcagcctcaggcaactgagttgcagacagtcttccgtctatcagcaccttgggctaccctcagattaccttttcctgtccctgacctgcggcctgatcgggacccttggtcaggccaaactgttcaggctaggcagttgcaactgagtgagttgactgaacctcagttctgttcagagctaaatagtgggcctggccccccagcgccaacgtgtttggagcttacttgctcagacctgcagggtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac Alignment from GeneWise CCACAGGCCACTGAGCTGCAGACAGTGTTTCGTCTCTCAGCACCCCGGGCCACCCTGAGGCTACGCTTCCCCATCCCAGACCTACGGCCTGACCGGGACCCCTGGGCTGGCCAGGCTGTGCGGGCTGAGCAGCTGCGACTG---GAGCTGAGTGAGCCCCAGTTCCGCTCAGAGCTCAACAGTGGGCCTGGCCCCCCAGCTCCTACCCGCCTGGAACTTACTTGCTCAGACCTGCAAG cctaagtcccaacctgatccaaccccctgactctgcctcctcctttgcagCCTCAGGCAACTGAGTTGCAGACAGTCTTCCGTCTATCAGCACCTTGGGCTACCCTCAGATTACCTTTTCCTGTCCCTGACCTGCGGCCTGATCGGGACCCTTGGTCAGGCCAAACTGTTCAGGCTAGGCAGTTGCAACTGAGTGAGTTGACTGAACCTCAGTTCTGTTCAGAGCTAAATAGTGGGCCTGGCCCCCCAGCGCCAACGTGTTTGGAGCTTACTTGCTCAGACCTGCAGGgtgtgtccttgctacatatggatggggtagtctgcttccatcttatgtac #### Atg2a_ID1532_21 --> 0 - 0 Original Alignment GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG gcttgcccagtcggatcaagctgttggatcagccccctctgtcgctgcag---------------------TCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAACAT---------TCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from CESAR GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tctttactctctttcgtgccagcttggatcagccccctctgtcgctgcag---------------------TCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from Spaln_aa2Genome GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tgcccagtcggatcaagctgttggatcagCCCCCTCTG---TCGCTGCAGTCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from Spaln_nt2Genome CTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG gcttgcccagtcggatcaagctgttggatcagccccctctgtcgctgcagTCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from Pairagon ---CACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG gcttgcccagtcggatcaagctgttggatcagccccctctgtcgctgcagTCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from Exonerate_protein2genome GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGG gcttgcccagtcggatcaagctgttggatCAGCCCCCTCTGTCGCTGCAGTCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAACATTCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from Exonerate_coding2genome gcttgcccagtcggatcaagctgttggatcagccccctctgtcgctgcagtcacacacggcaaccctttgccactacatggccccacctgaacattccaaggtatgttaagaccactgaagtcatggccttacatgacaattatatccttg Alignment from GeneWise GAATTTTTGGTGACAGTACGGCTGCACAAAGCCACTCTACGCCACTACATGGCCCCACCTGAACAGAGCTGGCACTCCCAG tgcccagtcggatcaagctgttggatcagCCCCCTCTG---TCGCTGCAGTCACACACGGCAACCCTTTGCCACTACATGGCCCCACCTGAA---------CATTCCAAGgtatgttaagaccactgaagtcatggccttacatgacaattatatccttg #### Atg2a_ID1534_23 --> 1 - 2 Original Alignment gCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTC------ag attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagaCCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACATTTTTACTAAAAGTCaagtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from CESAR gCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTC------ag attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagaCCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACATTTTTACTAAAAGTCaagtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from Spaln_aa2Genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTCAGG----- attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagACCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACATTTTTACTAAAAGTCAAgtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from Spaln_nt2Genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCT------CAG attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagACCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACATTTTTACTAAAAGTCAAgtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from Pairagon GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCAT attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagACCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATgtactcacctacatttttactaaaagtcaagtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from Exonerate_protein2genome GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTC------AG attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagACCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACATTTTTACTAAAAGTCAAgtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from Exonerate_coding2genome attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagaccactctacctccctgtgcaggtcctggtcactgcagagactttcactctctccagcaacattgttatgtactcacctacatttttactaaaagtcaagtgagttactctatatgctccattgtggaccattcaatacttgcatgatt Alignment from GeneWise GCCCCTCTACCTCCCTGTGCGTGTCCTGGTCACTGCTGAGACCTTCACCCTCTCCAGCAACATTGTCATGGACACGTCCACCTTCCTGCTCAGGTTC-- attgcacatggattttaggcaagtctatggtcatccttttatgcctgcagACCACTCTACCTCCCTGTGCAGGTCCTGGTCACTGCAGAGACTTTCACTCTCTCCAGCAACATTGTTATGTACTCACCTACATTTTTACTAAAAGTCAAgtgagttactctatatgctccattgtggaccattcaatacttgcatgatt #### Atg2a_ID1537_26 --> 0 - 0 Original Alignment AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACAGAGATCGCTGGCCAGAAG gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCCAGA------------------gtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac Alignment from CESAR AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACAGAGATCGCTGGCCAGAAG gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCC------------------AGAgtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac Alignment from Spaln_aa2Genome AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACAGAGATCGCTGGCCAGAAG gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCC------------------AGAgtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac Alignment from Spaln_nt2Genome AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACA gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCCAGAgtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac Alignment from Pairagon AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACA gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCCAGAgtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac Alignment from Exonerate_protein2genome AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACAGAGATCGCTGGCCAGAAG gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCCAGAGTGAGCAAATGAATGCTGacaagtcaatggtgacaagaggctcctgaaac Alignment from Exonerate_coding2genome gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagagccagccattgcttgagctgcactgctccaacaatgtggtatatgtgcatagctgtgctgactcttgtgccctaccattcaatctgctgcaatacttaacaagctcaggtgacctgcatcccccaccccgaccccctagccccagagtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac Alignment from GeneWise AGCCAGCCTCTGTTTGAGCTGCGCTGCTCCAACAACGTGGTGCACGTGCATAGCTGTGCTGACTCCTGCGCCCTGCTGGTCAACCTGCTCCAGTACCTAACCAGCTCGGGTGACCTGCACCCCCCACCCCGGCCCCCCAGCCCTACA gggaattgcaagtagtgacatttctgtgtgtagtttttgaaattttatagAGCCAGCCATTGCTTGAGCTGCACTGCTCCAACAATGTGGTATATGTGCATAGCTGTGCTGACTCTTGTGCCCTACCATTCAATCTGCTGCAATACTTAACAAGCTCAGGTGACCTGCATCCCCCACCCCGACCCCCTAGCCCCAGAgtgagcaaatgaatgctgacaagtcaatggtgacaagaggctcctgaaac #### Atg2a_ID1539_28 --> 2 - 0 Original Alignment gtGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATTGCG tcagaaactgaaagttggactttatactgactcggctgttgtctttccaggtGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGGT---AAGGCAAGGGAGCATGAA------GAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGGT------gtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt Alignment from CESAR gtGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATTGCG tcagaaactgaaagttggactttatactgactcggctgttgtctttccaggtGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGGT------gtatcccgattatgggaatggagtgcttggttagaactgctgct Alignment from Spaln_aa2Genome GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGC tcagaaactgaaagttggactttatactgactcggctgttgtctttccagGTGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGGTgtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt Alignment from Spaln_nt2Genome GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATT tcagaaactgaaagttggactttatactgactcggctgttgtctttccagGTGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGG---TAAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGG---Tgtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt Alignment from Pairagon GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAG tcagaaactgaaagttggactttatactgactcggctgttgtctttccagGTGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGG---TAAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGgtgtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt Alignment from Exonerate_protein2genome GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAG tcagaaactgaaagttggactttatactgactcggctgttgtctttccagGTGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGgtgtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt Alignment from Exonerate_coding2genome GGTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAG tcagaaactgaaagttggactttatactgactcggctgttgtctttccaGGTGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGCATAGgtgtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt Alignment from GeneWise GTGGCCCACTTCCTCAGGCCTCTCCCGTCTCCGTCTATCTGTTCCCAGGTGAACGGAGTGGGGCCCAGGCCCCTTTGCCTCCTCCTGGGGCCTCTTCTCATACCTTGGGTTCTAAGGCAAAGGAACATGAAAACGAAGAGGAAGGGGACGGAGACACCCTGGACAGTGATGAGTTCTGCATCCTTGACGCCCCTGGCCTAGGCATTGCG tcagaaactgaaagttggactttatactgactcggctgttgtctttccagGTGGCAGACTTACTCAGGCCTCCCCTAACTCAGCTTAT---TTCCCCGGTGGTCAGAGTGGAGTGCAGGCACCTTCACATCCTCCTGGAGCCTCCTCACATACCTTGGGT---AAGGCAAGGGAGCAT------GAAGAGGAAGGTGATGGGGACAGTCTGGATAGTGATGAATTCTGCATCCTCGATGCCCCTGGC------ATAGGTgtatcccgattatgggaatggagtgcttggttagaactgctgcttccatt #### Atg2a_ID1545_34 --> 2 - 2 Original Alignment ct---------CCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCT------GACCAGCAGCCTATCTACTTCag gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagccAGCCTGACTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAaggtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt Alignment from CESAR ct---------CCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCT------GACCAGCAGCCTATCTACTTCag gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagccAGCCTGACTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAaggtgagagcatccagacaggatgacacaaacctttctcccttttctcccct Alignment from Spaln_aa2Genome CT---------CCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCT------GACCAGCAGCCTATCTACTTCAG gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagCCAGCCTGACTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAAGgtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt Alignment from Spaln_nt2Genome C-----TCCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCTGACCA------GCAGCCTATCTACTTCAG gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagccagCCTGACTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAAGgtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt Alignment from Pairagon CTCCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCT------GACCAGCAGCCTATCTACTTCAG gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagccagcctgactcctcag--------GAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAAGgtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt Alignment from Exonerate_protein2genome CTCCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCT------GACCAGCAGCCTATCTACTTCAG gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagccagcctgaCTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAAGgtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt Alignment from Exonerate_coding2genome CTCCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCT------GACCAGCAGCCTATCTACTTCAG gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagccagcctgaCTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAAGgtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt Alignment from GeneWise --------GCTCCCCGAGAGACCCACAGCCGGCCCGGCAGCCCCCAGGAAGGGCAGTCTGAGGACACAGAGACAGCCAGCAACCCACCGGAAGCTCCAGGCAGTAGCCACAGCTCCTCTGACCAG------CAGCCTATCTACTTCAG gcaactcccctctgctaatcttaaacatttctgtctgacaaaacttacagCCAGCCTGACTCCTCAGGAGACCCACAGTTGGCCAGATAGCCCTCAAGGAGGACAGTCTGAGGACACAGAGACAGCAAGTAACCCCCTGGAATCTCCGGGAAGTAGCCACAGTTTTTCTGACCAAGACCAGCAACCCGTCTACTTAAGgtgagagcatccagacaggatgacacaaaccttttgtttgtttgtttgtt #### Bbs1_ID732_2 --> 1 - 1 Original Alignment cAACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTC---TCCTCCTGCCTG---------t cataccttttaaacccatctccccttcttcagaaacattgttctcccaaggAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTGCATGtgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg Alignment from CESAR cAACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTCTCCTCC------------TGCCTGt cataccttttaaacccatctccccttcttcagaaacattgttctcccaaggAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTGCATGtgtaagtcctgatgccttacttgcagcccaggatataacgagactgcctgt Alignment from Spaln_aa2Genome CAACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTC---TCCTCCTGCCTGTCAC cataccttttaaacccatctccccttcttcagaaacattgttctcccaagGAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTgcatgtgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg Alignment from Spaln_nt2Genome CAACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTCTCCTC------------CTGCCTGT cataccttttaaacccatctccccttcttcagaaacattgttctcccaagGAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTGCATGTgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg Alignment from Pairagon CAACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTCTCCT------------CCTGCCTGT cataccttttaaacccatctccccttcttcagaaacattgttctcccaagGAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTGCATGTgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg Alignment from Exonerate_protein2genome CAACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTC---TCCTCCTGCCTGTCAC cataccttttaaacccatctccccttcttcagaaacattgttctcccaagGAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTgcatgtgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg Alignment from Exonerate_coding2genome cataccttttaaacccatctccccttcttcagaaacattgttctcccaaggaacgaggtaaattccaagtggctggatgcacactatgaccctatggctaacaaccatactttctcgtcttcttgtctggcctgcatgtgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg Alignment from GeneWise AACGAAGCCAATTCTAAATGGCTGGACGCACACTACGACCCCATGGCCAACATCCACACCTTC---TCCTCCTGCCTGTCACTGGCAG cataccttttaaacccatctccccttcttcagaaacattgttctcccaaggAACGAGGTAAATTCCAAGTGGCTGGATGCACACTATGACCCTATGGCTAACAACCATACTTTCTCGTCTTCTTGTCTGGCCTGCATGTgtaagtcctgatgccttacttgcagcccaggatataacgagactgctttg #### Best1_ID2631_8 --> 0 - 2 Original Alignment GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCag cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCCT------ACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTACC---------aggtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from CESAR GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCag cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCCT------ACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTACC---------aggtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from Spaln_aa2Genome GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTT cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCCT------ACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTACCAGgtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from Spaln_nt2Genome GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCC------TACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTAC---------CAGgtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from Pairagon GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTTCAACATCAG cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCC------TACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTAC---------CAGgtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from Exonerate_protein2genome GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTT cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCCT------ACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTACCAGgtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from Exonerate_coding2genome GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTT cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCCT------ACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTACCAGgtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg Alignment from GeneWise GTGTCCCTGTTGTCCGTGGATGGGATGCACCAGAACTTGCCTCCCATGGAACGTGACATGTACTGGAACGAGGCAGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCAGGTCTCGCCGGCATTCCTTCATGGGCTCCACCTT cctctgtcttgggttaaatcatttaacatttcaaactctcctcccctcagGTGGCATTGTCATCTGTTGACCGAATGCACCAGAACCTGCCACCCATGGAGCGTGACATGTACTGGAATGAATCAGAGCCTCATCCT------ACGGCTGCCTCAGCCAGGTCTCGATGGCACTCATTCATGGGAACTACCAGgtgagttatgataaagctcccacaatgcatccaggagaacagttcatatg #### Best1_ID2637_2 --> 1 - 1 Original Alignment aATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGg tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagaATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTT------ggtaaggagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from CESAR aATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGg tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagaATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTT------ggtaaggagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from Spaln_aa2Genome AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTC- tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagAATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTTGgtaaggagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from Spaln_nt2Genome AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCG tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagAATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTTGgtaaggagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from Pairagon AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCG tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagAATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTTGgtaaggagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from Exonerate_protein2genome AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTG tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagAATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTTGGTAAGgagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from Exonerate_coding2genome AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTG tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagAATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTTGGTAAGgagagtagcttgttgtagctctagtactatcatactatctctacc Alignment from GeneWise AATGGTTCTCTCGAGTGATCAGCAGCTGTTGTTTGAGAAGCTGGCTCTGTACTGCGACAGCTACATTCAGCTCATCCCTATATCCTTCGTTCTGGGT- tcacagtgcaagtaaaagcttagagaatgtttgtgtctgtcaatccgcagAATGATTCTCTCAAGTGACCAGCAGCTTTTGTTCAAGAAGGTGGCTCTGTACTGTGCTAGCTACATTGAGCTCATCCCAATAGCGTTTGGTAAGGAGAgtagcttgttgtagctctagtactatcatactatctctacc #### Bscl2_ID2423_6 --> 0 - 2 Original Alignment TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCag tgtagccagaatcacatgtagacatctcttccatttggcttctctttcag------CCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGAGCCTACCTCTGGATCCATGCCCACTTTACAGGGCTCaggtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt Alignment from CESAR TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCag cctcaatgtagccagaatcacatgtctcttccatttggcttctctttcag------CCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGAGCCTACCTCTGGATCCATGCCCACTTTACAGGGCTCaggtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt Alignment from Spaln_aa2Genome TATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCAG tgtagccagaatcacatgtagacatctcttccatttggcttctctttcag------CCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGAGCCTACCTCTGGATCCATGCCCACTTTACAGGGCTCAGgtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt Alignment from Spaln_nt2Genome CCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCAG tgtagccagaatcacatgtagacatctcttccatttggcttctctttcagCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGAGCCTACCTCTGGATCCATGCCCACTTTACAGGGCTCAGgtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt Alignment from Pairagon TAGAACTCTACTCTGACTATAGGGAGAATTCGTATGTGCCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCAG tgtagccagaatcacatgtagacatctcttccatttggcttctctttcag--------------------------------------CCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGAGCCTACCTCTGGATCCATGCCCACTTTACAGGGCTCAGgtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt Alignment from Exonerate_protein2genome tgtagccagaatcacatgtagacatctcttccatttggcttctctttcagccaacaactggagcaattattgaaattcacagtaaacgcattgagatgtatggagcctacctctggatccatgcccactttacagggctcaggtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCAACAACTGGAGCAATTATTGAGATCCACAGCAAGCGCATCCAGATGTATGGAGCCTACCTCCGGATCCATGCCCACTTCACTGGGCTCAG tgtagccagaatcacatgtagacatctcttccatttggcttctctttcagCCAACAACTGGAGCAATTATTGAAATTCACAGTAAACGCATTGAGATGTATGGAGCCTACCTCTGGATCCATGCCCACTTTACAGGGCTCAGgtaagcaaagtgtagaagggacaacttttctacaatatggcccaaatagt #### Bscl2_ID2424_7 --> 1 - 0 Original Alignment gTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG------ ccaacttaactctaacagccatgtgtttctttttcccccctaccccacaggTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAgtaagtgttcttgggctcattttctctcactagacaaaggaacctatatc Alignment from CESAR gTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG------ ccaacttaactctaacagccatgtgtttctttttcccccctaccccacaggTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAgtaagtgttcttgggctcattttctctcactagacaaaggaacctatatc Alignment from Spaln_aa2Genome GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG------ ccaacttaactctaacagccatgtgtttctttttcccccctaccccacagGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAgtaagtgttcttgggctcattttctctcactagacaaaggaacctatatc Alignment from Spaln_nt2Genome GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCA ccaacttaactctaacagccatgtgtttctttttcccccctaccccacagGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAgtacctagtaagtgttcttgggctcattttctctcactagacaaaggaacctatatc Alignment from Pairagon GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG------ ccaacttaactctaacagccatgtgtttctttttcccccctaccccacagGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAgtaagtgttcttgggctcattttctctcactagacaaaggaacctatatc Alignment from Exonerate_protein2genome GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAGGTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCG ccaacttaactctaacagccatgtgtttctttttcccccctaccccacagGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAGTAAGTGTTCTTGGGCTCATTTTCTCTCACTAGACAAAGGAACCTATATC Alignment from Exonerate_coding2genome GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAGGTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCG ccaacttaactctaacagccatgtgtttctttttcccccctaccccacagGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAGTAAGTGTTCTTGGGCTCATTTTCTCTCACTAGACAAAGGAACCTATATC Alignment from GeneWise GTACCTGCTGTACAACTTCCCCATGACCTGCGCCTTCGTGGGTGTGGCCAGCAACTTCACGTTCCTCAGCGTCATCGTGCTCTTCAGCTATATGCAGTGGGTGTGGGGTGCTGTCTGGCCCCGCCACCGCTTCTCTCTGCAG------ ccaacttaactctaacagccatgtgtttctttttcccccctaccccacagGTACCTGCTTTACAATTTTCCTATGACTTGTGCCTTTGTGGGTGTAGCAAGCAACTTCACATTTCTCAGTGTCATTGTGCTTTTCAGTTATATGCAGTGGGCATGGGGTGCTGTCTGGCCTCATCACCACTCCTCCTTGCAGTACCTAgtaagtgttcttgggctcattttctctcactagacaaaggaacctatatc #### Bscl2_ID2425_8 --> 0 - 1 Original Alignment ------------GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAg ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttagGAACCTATGATGGTTAATACATGTCAAAGGGACAACTCACAGCACGGA------GACCATATTTCACACCACCAACCAggtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from CESAR ------------GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAg ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttagGAACCTATGATGGTTAATACATGTCAAAGGGACAACTCACAGCACGGAGAC------CATATTTCACACCACCAACCAggtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from Spaln_aa2Genome ------------GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAG ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttagGAACCTATGATGGTTAATACATGTCAAAGGGACAACTCACAGCACGGAGAC------CATATTTCACACCACCAACCAGgtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from Spaln_nt2Genome G------------TTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAG ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttagGAACCTATGATGGTTAATACATGTCAAAGGGACAACTCACAGCACGGAGAC------CATATTTCACACCACCAACCAGgtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from Pairagon ------------GTTAATATCCGACAAAGGGATAACTCACACCACGGGGCCCCGCGTCGGATCTCGCGCCATCAGCCAG ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttagGAACCTATGATGGTTAATACATGTCAAAGGGACAACTCACAGCACGGAGAC------CATATTTCACACCACCAACCAGgtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from Exonerate_protein2genome ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttaggaacctatgatggttaatacatgtcaaagggacaactcacagcacggagaccatatttcacaccaccaaccaggtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from Exonerate_coding2genome ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttaggaacctatgatggttaatacatgtcaaagggacaactcacagcacggagaccatatttcacaccaccaaccaggtaagcgaattaggcattaggaatttggaaatagaccagggattccttca Alignment from GeneWise ccagtataggatcacaactcattggttgtgtgtgttctttgttcccttaggaacctatgatggttaatacatgtcaaagggacaactcacagcacggagaccatatttcacaccaccaaccaggtaagcgaattaggcattaggaatttggaaatagaccagggattccttca #### Bscl2_ID2427_10 --> 2 - 1 Original Alignment ag---GGCCAGCTGTCTGAGGAAGAGAAACCAGAGAAGCGGCCCCTGAATGGAGAGGAGGAGCAAGAGCCAGAGGCTAGTGATg aatttctaatactcccacccccattgcaactcctctgccttgttccatagagCCAGGCCAA---CCAGAAGAGATGAAAGCAAAGAAGTGGCCGCTGAATAGGGAGGACAAGCGGGAACCGGATGCTGGTGCTggtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from CESAR ag---GGCCAGCTGTCTGAGGAAGAGAAACCAGAGAAGCGGCCCCTGAATGGAGAGGAGGAGCAAGAGCCAGAGGCTAGTGATg aatttctaatactcccacccccattgcaactcctctgccttgttccatagagCCAGGCCAA---CCAGAAGAGATGAAAGCAAAGAAGTGGCCGCTGAATAGGGAGGACAAGCGGGAACCGGATGCTGGTGCTggtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from Spaln_aa2Genome AGGGCCAGCTGTCTGAGGAAGAGAAACCAGAGAAGCGGCCCCTGAATGGAGAGGAGGAGCAAGAGCCAGAGGCTAGTGATG aatttctaatactcccacccccattgcaactcctctgccttgttccatagAGCCAGGCCAACCAGAAGAGATGAAAGCAAAGAAGTGGCCGCTGAATAGGGAGGACAAGCGGGAACCGGATGCTGGTGCTGgtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from Spaln_nt2Genome AG---GGCCAGCTGTCTGAGGAAGAGAAACCAGAGAAGCGGCCCCTGAATGGAGAGGAGGAGCAAGAGCCAGAGGCTAGTGATG aatttctaatactcccacccccattgcaactcctctgccttgttccatagAGCCAGGCCAAC---CAGAAGAGATGAAAGCAAAGAAGTGGCCGCTGAATAGGGAGGACAAGCGGGAACCGGATGCTGGTGCTGgtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from Pairagon AGGGCCAGCTGTCTGAGGAAGA---GAAACCAGAGAAGCGGCCCCTGAATGGAGAGGAGGAGCAAGAGCCAGAGGCTAGTGATG aatttctaatactcccacccccattgcaactcctctgccttgttccatagagccaggccaaccag------------------AAGAGATGAAAGCAAAGAAGTGGCCGCTGAATAGGGAGGACAAGCGGGAACCGGATGCTGGTGCTGgtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from Exonerate_protein2genome aatttctaatactcccacccccattgcaactcctctgccttgttccatagagccaggccaaccagaagagatgaaagcaaagaagtggccgctgaatagggaggacaagcgggaaccggatgctggtgctggtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from Exonerate_coding2genome aatttctaatactcccacccccattgcaactcctctgccttgttccatagagccaggccaaccagaagagatgaaagcaaagaagtggccgctgaatagggaggacaagcgggaaccggatgctggtgctggtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga Alignment from GeneWise --GAGGGCCAGCTGTCTGAGGAAGAGAAACCAGAGAAGCGGCCCCTGAATGGAGAGGAGGAGCAAGAGCCAGAGGCTAGTGATG aatttctaatactcccacccccattgcaactcctctgccttgttccatagAGCCAGGCCAA---CCAGAAGAGATGAAAGCAAAGAAGTGGCCGCTGAATAGGGAGGACAAGCGGGAACCGGATGCTGGTGCTGgtacagactgcttggggggtcgcttgcttaacataatgtagtcgagaaga #### Btaf1_ID7227_10 --> 0 - 0 Original Alignment ATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA--------------- tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAATTAATACTCTCTGGAgtgagggcaggttaaagctatggatgtacatacccactccatatcttccc Alignment from CESAR ATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA--------------- tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAATTAATACTCTCTGGAgtgagggcaggttaaagctatggatgtacatacccactccatatacttcc Alignment from Spaln_aa2Genome GATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA-------------- tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAATTAATACTCTCTGGAgtgagggcaggttaaagctatggatgtacatacccactccatatcttccc Alignment from Spaln_nt2Genome ATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA--------------- tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAATTAATACTCTCTGGAgtgagggcaggttaaagctatggatgtacatacccactccatatcttccc Alignment from Pairagon ATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA--------------- tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAATTAATACTCTCTGGAgtgagggcaggttaaagctatggatgtacatacccactccatatcttccc Alignment from Exonerate_protein2genome ATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAAttaatactctctggagtgagggcaggttaaagctatggatgtacatacccactccatatcttccc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ATGATTCAGCAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCGTTGGACAGATTTGGAGACTTCGTTTCTGATGAA--------------- tctttctctagtacagagttaacattggaacatcaatttgattccttcagATCATTCAACAGCATCAAGAGTGGTTGGAAGACTTAGTCATTAGACTCCTTTGTGTTTTTGCATTGGACAGATTTGGAGACTTTGTTTCTGATGAATTAATACTCTCTGGAgtgagggcaggttaaagctatggatgtacatacccactccatatcttccc #### Btaf1_ID7248_27 --> 0 - 2 Original Alignment GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGag cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGT---aggtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgaga Alignment from CESAR GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGag cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGT---aggtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaataacc Alignment from Spaln_aa2Genome GGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTC cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGTAGgtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgaga Alignment from Spaln_nt2Genome GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGAG cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGT---AGgtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgaga Alignment from Pairagon GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGAG cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGT---AGgtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgaga Alignment from Exonerate_protein2genome GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGAG cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGT---AGgtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgaga Alignment from Exonerate_coding2genome GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGTCAGAG cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGT---AGgtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgaga Alignment from GeneWise GATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTAGGAAAAACATTACAGTCCATCTGCATTCTAGCAGGAGATCACTGT-- - cattcttttcaatttctttgccttccccaatattttaattttctttatagGATGGTGTGAACTGGTTAGCCTTTCTCAATAAGTATAAGCTTCATGGAATTCTGTGTGATGACATGGGCTTGGGAAAAACATTACAGTCCATCTGTATTCTAGCAGGAGATCACTGTAGgtaagcagtgccttgcaatgcttgcttaaaacctgatcaatctaatgagA #### Btaf1_ID7253_32 --> 2 - 0 Original Alignment gt---------------------GTCCTGGCAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCAG gataatataatggcttcttgagtcctgaatcactatggtttgtttttcaggtTGCGGACTAACTGATGAATTCGTACTAGCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga Alignment from CESAR gt---------------------GTCCTGGCAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCAG gataatataatggcttcttgagtcctgaatcactatggtttgtttttcaggtTGCGGACTAACTGATGAATTCGTACTAGCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga Alignment from Spaln_aa2Genome GGT---------------------GTCCTGGCAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCA gataatataatggcttcttgagtcctgaatcactatggtttgtttttcagGTTGCGGACTAACTGATGAATTCGTACTAGCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga Alignment from Spaln_nt2Genome CAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCAG gataatataatggcttcttgagtcctgaatcactatggtttgtttttcaggttgcggactaactgatgaattcgtactagCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga Alignment from Pairagon GT---------------------GTCCTGGCAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCAG gataatataatggcttcttgagtcctgaatcactatggtttgtttttcagGTTGCGGACTAACTGATGAATTCGTACTAGCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga Alignment from Exonerate_protein2genome GTGTCCTGGCAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCAG gataatataatggcttcttgagtcctgaatcactatggtttgtttttcaggttgcggactaactgatgaatTCGTACTAGCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --------------------GGTGTCCTGGCAATGGACGCTCTGCACCGCCAAGTCCTGCCGTTCCTTCTCAGAAGAATGAAAGAAGATGTTTTGCAGGATCTTCCACCTAAAATTATTCAAGACTATTACTGTACTCTCAGCCCTCTCCAG gataatataatggcttcttgagtcctgaatcactatggtttgtttttcagGTTGCGGACTAACTGATGAATTCGTACTAGCAATGGATGCTCTACAGCACCAGGTCCTGCCACTACTTTTGAGAAGAATGAAAGAAGCTGTATTGCATGATCTTCCACCCAAAATTATACAAGACTACTATTGTACTCTCAGTCCTCTTCAAgtatttattgccttcatggctagtgtggtactatttgtattgaggactga #### Btrc_ID9458_8 --> 0 - 0 Original Alignment ---------ACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagCAACCTAACACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from CESAR ---------ACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagCAACCTAACACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from Spaln_aa2Genome AGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagcaacctaacacaatagAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from Spaln_nt2Genome CAT--TGAGACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagCAACCTAACACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from Pairagon ---------ACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagCAACCTAACACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from Exonerate_protein2genome ACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagcaacctaacACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from Exonerate_coding2genome ACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagcaacctaacACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag Alignment from GeneWise ---------ACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGAATCCACTGCCGGAGTGAAACAAGTAAAGGGGTTTACTGTTTACAGTACGACGACCAGAAGATAGTCAGCGGCCTTCGAGACAACACCATCAAG tgcgatgggtcgttaggatgtttcactgggcttctctttccttaacccagCAACCTAACACAATAGAGTCCAATTGGAGATGTGGGCGACATAGTTTACAGAGGATTTACTGCCGGAGTGAAACAAGCAAAGGGGTTTATTGTTTACAGTATGATGATCAGAAGATAGTCAGTGGTCTTCAAGACAACACCATCAAGgtatgctaagctgcttgtatcgccataagatttgacttttggggtcagag #### Btrc_ID9463_12 --> 1 - 2 Original Alignment gCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATgg ttgagaagtaacttacttttgcctttttaccaacttattttgttttacagg---------ATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATgggtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from CESAR gCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATgg acctagttgttgagaagtaacttactttaccaacttattttgttttacagg---------ATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATgggtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from Spaln_aa2Genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGG ttgagaagtaacttacttttgcctttttaccaacttattttgttttacagG---------ATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATGGgtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from Spaln_nt2Genome CATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGG ttgagaagtaacttacttttgcctttttaccaacttattttgttttacagGATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATGGgtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from Pairagon GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGG ttgagaagtaacttacttttgcctttttaccaacttattttgttttacagG---------ATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATGGgtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from Exonerate_protein2genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGG ttgagaagtaacttacttttgcctttttaccaacttattttGTTTTACAGGATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATGGgtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from Exonerate_coding2genome GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGG ttgagaagtaacttacttttgcctttttaccaacttattttGTTTTACAGGATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATGGgtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca Alignment from GeneWise GCTGTGGGACATAGAGTGTGGAGCATGCCTGCGAGTGTTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGATTTGATAACAAAAGGATAGTGAGCGGAGCCTATGATGG ttgagaagtaacttacttttgcctttttaccaacttattttgttttacagG---------ATAGAGTGTGGAGCATGCCTGCAGGTATTGGAGGGCCATGAGGAGTTGGTACGCTGCATTCGGTTTGATAACAAAAGGATTGTAAGCAGAACGTATGATGGgtgagtttactggtaatatcttttgatcagagaaagaggttgaagacaca #### C030046E11Rik_ID6307_21 --> 0 - 2 Original Alignment GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTCTGGGAAAag caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCG---------cggtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from CESAR GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTCTGGGAAAag caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCG---------cggtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from Spaln_aa2Genome GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTC caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCGCGgtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from Spaln_nt2Genome GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTCTGGG caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCC----GCGgtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from Pairagon GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTCTGGGAAAAG caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCGC---------Ggtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from Exonerate_protein2genome GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTC caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCGCGgtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from Exonerate_coding2genome GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTC caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCGCGgtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt Alignment from GeneWise GAGCCCAGTTCAAGTGGTGGGTTTGAGTTCTTCAGGAATCGGAGCATCAGTTTATCCCAGTCAGCTGAGAATGTTCCTCCTGGTAAATTCGGCTTACAGAAAACACTAAGTATGCCAACTGGTCCTTC caaagagctagcttctttggttgcacttctcagcctctgtcttccctcagGAGCCAAGCTCCAGTGGTGGTTTTGAGTTTTTCCGGAACCGGAGTATCAGCTTATCCCAGTCAGCTGAGAATGTTCCCCCTGGCAAATTCGGATTACAAAAAACATTAAGTATACCAACTGGTCCGCGgtgagtaactatagcggccagattttaagcagtaatgtaaaatatttatt #### Cabp2_ID289_4 --> 2 - 1 Original Alignment agCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCa ccttataacagctagggtggaatttttctagacctgtgcttcccttccagag------ATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTagtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from CESAR agCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCa tcacccccttataacagctagggtgttctagacctgtgcttcccttccagag------ATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTagtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from Spaln_aa2Genome ATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctagggtggaatttttctagacctgtgcttcccttccagagATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from Spaln_nt2Genome CTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAG ccttataacagctagggtggaatttttctagacctgtgcttcccttccag----AGATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGgttagtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from Pairagon GATCGAGAGCTGAGACCAGAAGAGATCGAAGAGCTGCAGATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctagggtggaatttttctagacctgtgcttcccttccag-------------------------------------AGATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from Exonerate_protein2genome ATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctagggtggaatttttctagacctgtgcttcccttccagagATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from Exonerate_coding2genome ATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctagggtggaatttttctagacctgtgcttcccttccagagATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg Alignment from GeneWise ATCGCCTTCCAGGAGTTTGACCGAGACCGGGACGGCTACATCGGCTACCGGGAGCTGGGTGCCTGCATGCGGACACTGGGCTACATGCCCACGGAGATGGAGCTCATTGAGATATCACAACAGATCA ccttataacagctagggtggaatttttctagacctgtgcttcccttccagagATAGGCTTCCAGGAGTTTGACCGAGACAGGGACGGCTACATCGGGTACCGAGAGCTGGGTGACTGCATGCAGACACTGGGATACATGCCCACAGAGATGGCGCTCATAGAGATATCACAACAGGTTAgtaattgtgattcttgtggccagtgcacatagccccctggcacatgggtg #### Cabp2_ID290_5 --> 2 - 0 Original Alignment gtGGTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caccctgcactaacctaagccctcaaagatgcattatgtattttttttaggt---GGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from CESAR gtGGTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caacaccctgcactaacctaagcccaagatgcattatgtattttttttaggt---GGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from Spaln_aa2Genome AGTGGTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG cctgcactaacctaagccctcaaagatgcattatgtatttttttta gGTGGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from Spaln_nt2Genome GTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caccctgcactaacctaagccctcaaagatgcattatgtattttttttagGTGGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from Pairagon ATCAGTGGTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caccctgcactaacctaagccctcaaagatgcattatgtattttttttag-------GTGGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from Exonerate_protein2genome GTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caccctgcactaacctaagccctcaaagatgcattatgtattttttttagGTGGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from Exonerate_coding2genome GTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caccctgcactaacctaagccctcaaagatgcattatgtattttttttagGTGGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca Alignment from GeneWise GTGGGAAGGTGGATTTTGAAGATTTTGTGGAGCTGATGGGTCCCAAGCTGCTGGCAGAGACGGCAGACATGATTGGCGTGAGGGAGCTTCGAGACGCCTTCCGGGAG caccctgcactaacctaagccctcaaagatgcattatgtattttttttagGTGGGAAGGTTCACTTTGAAATCTTCATAGAGCTGATGGGTCCCAAGCTACTAGTAGAGACAGTGGGCATGATTGGGGAAAGAGAACTTAAAGACACTTTTAGGGAGgtaagccttaggtgctgggtggcagtagcaattcagtgtgtttttggaca #### Cabp4_ID342_2 --> 0 - 1 Original Alignment ------GATCGTGAACTGGGCCCTGAGGAGTTGGAGg ccataatcaggctctgcatggatggcggcctgttttctccccctcttgagGCGCTAGATCGTGAGCTGGGGCCTGAGGAGTTGGAAggtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct Alignment from CESAR ------GATCGTGAACTGGGCCCTGAGGAGTTGGAGg ccataatcaggctctgcatggatggcggcctgttttctccccctcttgagGCGCTAGATCGTGAGCTGGGGCCTGAGGAGTTGGAAggtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct Alignment from Spaln_aa2Genome GATCGTGAACTG------GGCCCTGAGGAGTTGGAGG ccataatcaggctctgcatggatggcggcctgttttctccccctcttgagGCGCTAGATCGTGAGCTGGGGCCTGAGGAGTTGGAAGgtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct Alignment from Spaln_nt2Genome GATCGTGAACTGGGCCCTGAGGAGTTGGAGG ccataatcaggctctgcatggatggcggcctgttttctccccctcttgaggcgctagATCGTGAGCTG-GGGCCTGAGGAGTTGGAAGgtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct Alignment from Pairagon ATCGTGAACTGGGCCCTGAGGAGTTGGAGG ccataatcaggctctgcatggatggcggcctgttttctccccctcttgaggcgctagATCGTGAGCTGGGGCCTGAGGAGTTGGAAGgtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct Alignment from Exonerate_protein2genome GATCGTGAACTGGGCCCTGAGGAGTTGGAGG ccataatcaggctctgcatggatggcggcctgttttctccccctcttgaggcgctaGATCGTGAGCTGGGGCCTGAGGAGTTGGAAGgtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ccataatcaggctctgcatggatggcggcctgttttctccccctcttgaggcgctagatcgtgagctggggcctgaggagttggaaggtgagtgactcttcctctttatgagaagcctcggagttgataaaatatct #### Carns1_ID387_5 --> 0 - 1 Original Alignment GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACCA---------------g tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAATGGCACCAAGTGTTggtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat Alignment from CESAR GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTA---------CCAg tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAATGGCACCAagtgttggtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat Alignment from Spaln_aa2Genome GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACCA---------------G tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAATGGCACCAAGTGTTGgtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat Alignment from Spaln_nt2Genome GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACCA--G tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAATGgcaccaagtgttggtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat Alignment from Pairagon GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACC------------------------------------------------------------------- tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAATGGCACCAAGTGTTGGTGCGTTTTAATGTTGACTCGCAAGCCCAAACGGCCTTAATGAGATGCAT Alignment from Exonerate_protein2genome GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACCAG tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAAtggcaccaagtgttggtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat Alignment from Exonerate_coding2genome GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACCAG tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAAtggcaccaagtgttggtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat Alignment from GeneWise GTGGCTGTGAGGCTCAGTGGCTGTCGCTGGCGTGGACAGCAGGCATTGCCTCTGCACCTGCGGGTAGAGCCATCCACAGTGGTGAACACGGTGCTGGGATTGCTGGAGAAGCTGGAGGAGGAGGAGAGTGTCCTTGTGGAGGCCATGTGCCCACCTGTCCGGCTGCCCTTACCAGGCGGTCCT- tctaccatcgagtggtaattttgtaaagctccctttgtttctgcctgtagGTGGCAGCAAGACTCAGTGGCTGCCATTGGCATGGTCAGCAGGCATTGCCTTTACATCTGCAGGTAAAGCCATCCACAGTAGTGATGATGGTACTAGGATTATTGAAAAAACTGGAAGAGGAGGAGAGTGTCCTTGTAGAGCCAATTTGTCCACCTGTCCGCCTGCCCTTGCCAATGGCACCAAgtgttggtgcgttttaatgttgactcgcaagcccaaacggccttaatgagatgcat #### Carns1_ID389_3 --> 2 - 1 Original Alignment gcTGCCCTGGGGCAGAGGTGACCTTGTGCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTg ataggcagcagagattacattgatatgatactgtcttgctttgctggcaggc---------------------------GTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTggtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from CESAR gcTGCCCTGGGGCAGAGGTGACCTTGTGCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTg gcaaggagtaacaatatggaggatatgatactgtcttgctttgctggcaggc---------------------------GTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTggtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from Spaln_aa2Genome GCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTG ataggcagcagagattacattgatatgatactgtcttgctttgctggcagGCGTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTGgtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from Spaln_nt2Genome GCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTG ataggcagcagagattacattgatatgatactgtcttgctttgctggcagGCGTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTGgtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from Pairagon GCTGCCCTGGGGCAGAGGTGACCTTGTGCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTG ataggcagcagagattacattgatatgatactgtcttgctttgctggcag---------------------------GCGTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTGgtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from Exonerate_protein2genome GCTGCCCTGGGGCAGAGGTGACCTTGTGCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTG ggcagcagagattacattgatatGATACTGTCTTGCT---TTGCTGGCAGGCGTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTGgtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from Exonerate_coding2genome GCTGCCCTGGGGCAGAGGTGACCTTGTGCATTCTGGGTTCTCCCAGCACCTTCCTATCTCTGTTGCTGGAGGGTGGGGTCCAGAGCCCTG ggcagcagagattacattgatatGATACTGTCTTGCT---TTGCTGGCAGGCGTTCTAGGGTCACTCAGCACCTTCCTATCACTGTTGCTGGAGGGTGGGGTCCAAAGCCCTGgtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg Alignment from GeneWise ataggcagcagagattacattgatatgatactgtcttgctttgctggcaggcgttctagggtcactcagcaccttcctatcactgttgctggagggtggggtccaaagccctggtgtgatattgcttccaaatgcccccttgtcctacaaaattggaacatgg #### Catsper1_ID928_5 --> 1 - 1 Original Alignment c------------ATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCt ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagtTGGGACCTTGTGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACtgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from CESAR c------------ATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCt ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagtTGGGACCTTGTGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACtgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from Spaln_aa2Genome C------------ATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTC ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagTTGGGACCTTGTGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from Spaln_nt2Genome GCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagttgggaccttgtgattttgactag-AGTCCAGGAAGTAGCTG---CCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from Pairagon CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagttgggaccttgtgattttgactagag--------------TCCAGGAAGTAGCTG---CCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from Exonerate_protein2genome CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagttgggaccttgtGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from Exonerate_coding2genome CATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagttgggaccttgtGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg Alignment from GeneWise ----------AGCATCCTGACCAGCCTCCACGAAGTGGCCGGGACTCTGAGTGGATCTTTACCATCCATCACGGCCATCCTCACCCTCATGTTTACCTGCCTCT ccatttgcttcaatgataacttaacttttattcccatctctctccaaaagTTGGGACCTTGTGATTTTGACTAGAGTCCAGGAAGTAGCT---GCCCTTAGTGGATCTTTACCCTCAATCACAGCCATCCTCACCCTCATGTTTACCTGCCACTgtaagatgcacaatggaagttggatacaattattctaaataggttaggtg #### Catsper1_ID931_8 --> 1 - 0 Original Alignment cCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTGGAG------ atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagtCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGGAAAGCGAAgtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from CESAR cCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTGGAG------ atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagtCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGGAAAGCGAAgtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from Spaln_aa2Genome CCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTG------GAG atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagTCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGGAAAGCGAAgtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from Spaln_nt2Genome CCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTGGAG------ atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagTCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGGAAAGCGAAgtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from Pairagon CCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTGGAG------ atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagTCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGGAAAGCGAAgtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from Exonerate_protein2genome CCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTG atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagTCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGgaaagcgaagtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from Exonerate_coding2genome CCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTG atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagTCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGgaaagcgaagtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg Alignment from GeneWise CCTGGTGATTGCTGTCCTGGTAGATAACTTCCAGATGGCGTTGCTCAAAGGCCTAGAGAAAGTGAAGCTGGAG------ atcctcattcctaagccccatttatgcaattgtgttgcctgtcattacagTCTAGTAATTGCAGCTCTAGTAGACAACTTCCTAATGGTCCTGCTCAAAGGCCTGGAGAAAGTGAAGCTGGAAAGCGAAgtaggcacgatgtagaagggtagataatccagatgtgctgtgcaaaggtg #### Ccdc88b_ID1826_23 --> 1 - 2 Original Alignment gGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTACCaa gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccaggGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGGAT---ATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCAT---aagtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from CESAR gGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTACCaa gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccaggGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGGAT---ATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCAT---aagtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from Spaln_aa2Genome GGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTAC gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccagGGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGGAT---ATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCATAAgtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from Spaln_nt2Genome GGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTACCAA gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccagGGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGGAT---ATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCAT---AAgtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from Pairagon GGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTACCAA gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccagGGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGG---ATATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCAT---AAgtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from Exonerate_protein2genome GGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTAC gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccagGGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGGAT---ATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCATAAgtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from Exonerate_coding2genome gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccagggaccaactcaatgggttgcgccaacagaaacagaagctgttggatatcatggaccaataccgggtagtacagcctgggccactcccccataagtgtgcggttagcaccttatttttcatgttagtattttgctttattccac Alignment from GeneWise GGACCAGCTTAATGCCTTGCGCCGGGAGAAACAGAAGCTGGTGGAGAAAATCATGGACCAGTACCGTGTGCTAGAACCTGGGCCCCTACCCCGTAC gcccacttaaggtcagattgatgttacctatgtcttgttctgttttccagGGACCAACTCAATGGGTTGCGCCAACAGAAACAGAAGCTGTTGGAT---ATCATGGACCAATACCGGGTAGTACAGCCTGGGCCACTCCCCCATAAgtgtgcggttagcaccttatttttcatgttagtattttgctttattccac #### Ccdc88b_ID1827_22 --> 0 - 2 Original Alignment CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTAC---ct cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGAGT---GACCCTGTGCATTGTGAGCAGCCAGAATACGCCctgtcagaccacttaaggtcagattgatgttaccaccaaagccctttgcctt Alignment from CESAR CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTAC---ct cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGAGT---GACCCTGTGCATTGTGAGCAGCCAGAATACGCCctgtcagaccacttaaggtcagattgatgttacctatgtcttgttctgtttt Alignment from Spaln_aa2Genome CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTACCTG-- cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGAGT---GACCCTGTGCATTGTGAGCAGCCAGAATACGCCCTgtcagaccacttaaggtcagattgatgttaccaccaaagccctttgcctt Alignment from Spaln_nt2Genome CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTAC---CT cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGA---GTGACCCTGTGCATTGTGAGCAGCCAGAATACGCCCTgtcagaccacttaaggtcagattgatgttaccaccaaagccctttgcctt Alignment from Pairagon CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTA---CCT cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGA---GTGACCCTGTGCATTGTGAGCAGCCAGAATACGCCCTgtcagaccacttaaggtcagattgatgttaccaccaaagccctttgcctt Alignment from Exonerate_protein2genome CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTAC---CT cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGAGT---GACCCTGTGCATTGTGAGCAGCCAGAATACGCCCTgtcagaccacttaaggtcagattgatgttaccaccaaagccctttgcctt Alignment from Exonerate_coding2genome CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAG cttcaatggataggtctactaataaattcacccctcctcctcgcccccagctcttaacacagcttcatacagtacaaaaagaggagaataggcagcttttagtagagGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGAGTGACCCTGTGCATTGTGAGCAGCCAGAATACGCCCTGTCAGACCAC---TTAAGGTCAGATTGATGTTACCACCAAAGCCCTTTGC Alignment from GeneWise CTTCTGACCCAGCTTCGCAGCGCGCAGGAGGAGGAGAACAGGCAGCTGTTAGCCGAGGTCCAGGCCCTGAGCCGGGAGAACAGGGAGCTGCTGGAGCGCAGCCTGGAGAGCCGCGACCATCTGCATCGAGAGCAGCGAGAGTACCTG-- cttcaatggataggtctactaataaattcacccctcctcctcgcccccagCTCTTAACACAGCTTCATACAGTACAAAAAGAGGAGAATAGGCAGCTTTTAGTAGAGGTGAAGGCTTCAAGCCGTACAAACAGGGAGTTGCAGGAGCGTAGTTTGGAGAGT---GACCCTGTGCATTGTGAGCAGCCAGAATACGCCCTgtcagaccacttaaggtcagattgatgttaccaccaaagccctttgcctt #### Ccdc88b_ID1828_21 --> 1 - 0 Original Alignment aGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGTGAG cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagaGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGT---gtaaacgaggacaacaatgggtatataagccttcatacactaatagtcac Alignment from CESAR aGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGTGAG cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagaGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGT---gtaaacgaggacaacaatgggtatataagccttcatacactaatagt Alignment from Spaln_aa2Genome AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTG------CGTGAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGT cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagAGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGTgtaaacgaggacaacaatgggtatataagccttcatacactaatagtcac Alignment from Spaln_nt2Genome AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGTGA------GTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGT cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagAGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGTgtaaacgaggacaacaatgggtatataagccttcatacactaatagtcac Alignment from Pairagon AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGT cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagAGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGTgtaaacgaggacaacaatgggtatataagccttcatacactaatagtcac Alignment from Exonerate_protein2genome AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTG------CGTGAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGT cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagAGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGTgtaaacgaggacaacaatgggtatataagccttcatacactaatagtcac Alignment from Exonerate_coding2genome AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTG------CGTGAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGTGAGC cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagAGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGTGTAAacgaggacaacaatgggtatataagccttcatacactaatagtcac Alignment from GeneWise AGCTCAGATGCTACTGGCCGAGGTGTCCCGGGAGCGAGGGGAGCTCCAAGGTGAACGCGGGGAGCTGCGGAGCCGCCTGGCGAGGCTGGAGCTGGAGCGCGCACAACTTGAGATCCAGAGCCAGCAGCTGCGT------GAGTCCAACCAGCAGTTGGACCTGAGTGCCTGTCGTCTGACCACACAGTGT cttaatctcaggtgactgaatatctaagaggttgctactatctactgcagAGCCCAAATGTTACTGACTGAGGTGACACGAGGGTGTGGAGAGATCCAGGGAGAATGTGGGGAGCTGTGGGGATGTCTATCAAGAATAGAACTAGAGCGGGCACAACTTGAAATCCAGAGCCAGCAGCTGTGTGTGTGGGAGTCCAACCAGCAATTGGATTTGAGTGCATGTCACCTGACGCCACAATGTgtaaacgaggacaacaatgggtatataagccttcatacactaatagtcac #### Ccdc88b_ID1829_20 --> 1 - 2 Original Alignment gCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGag atgagccaatggtcaggaaaattgctctgtgtcctttgttcccgcaccagt------------CATGCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAAcggtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from CESAR gCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGag ctcaaaaagccaatgagccaatggttctgtgtcctttgttcccgcaccagtCAT------------GCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAAcggtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from Spaln_aa2Genome GCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGAG atgagccaatggtcaggaaaattgctctgtgtcctttgttcccgcaccagTCAT------------GCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAACGgtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from Spaln_nt2Genome GCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGAG atgagccaatggtcaggaaaattgctctgtgtcctttgttcccgcaccagTCATGCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGA---AGAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAACGgtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from Pairagon GCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGAG atgagccaatggtcaggaaaattgctctgtgtcctttgttcccgcaccagTCAT------------GCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAACGgtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from Exonerate_protein2genome GCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGAG atgagccaatggtcaggaaaattgctctgtgtcctttgTTCCCGCACCAGTCATGCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAACGgtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from Exonerate_coding2genome GCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGAG atgagccaatggtcaggaaaattgctctgtgtcctttgTTCCCGCACCAGTCATGCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAACGgtagtcttgttagctctggcttacctccccccctaccatagcattatcat Alignment from GeneWise GCATGAGCAGTTGCAGGCCCAACGGGCCAATGTGGAAGCACAAGAGGTAGCCCTACTGGCAGAGCGTGAGCGCCTGATGCAGGATGGACATCGGCAGCGCGGCCTGGAGGAGGAGCTGCGGAGACTTCAGAATGAGCACGAGAGA-- atgagccaatggtcaggaaaattgctctgtgtcctttgttcccgcaccagTCAT------------GCCCAGTGGGCAAATGTTGAGGCTCAAGATGTAGCACTGCTGGCAGAA---GAACAACTGATGCAGGATGGGCAGTGCCAGTGTGGGCTCGATGAGGAGCTGCGCAGGCTTCATAATGAACATCAACGGTAgtcttgttagctctggcttacctccccccctaccatagcattatcat #### Ccdc88b_ID1831_18 --> 0 - 0 Original Alignment AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- gagctaatagggctcacaacattaatatagaaataacatatcattttcagAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from CESAR AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- gagctaatagggctcacaacattaatatagaaataacatatcattttcagAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from Spaln_aa2Genome AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- gagctaatagggctcacaacattaatatagaaataacatatcattttcagAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from Spaln_nt2Genome AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- gagctaatagggctcacaacattaatatagaaataacatatcattttcagAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from Pairagon AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- gagctaatagggctcacaacattaatatagaaataacatatcattttcagAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from Exonerate_protein2genome GGACTGTGGAGACCCAGAATGGACGGCTC---ATCGAAGTGGAGCGAAATAATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- GAGCTAATAGGGCTCACAACATTAATATAGAAATAACATATCATTTTCAGAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from Exonerate_coding2genome GGACTGTGGAGACCCAGAATGGACGGCTC---ATCGAAGTGGAGCGAAATAATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAG--- GAGCTAATAGGGCTCACAACATTAATATAGAAATAACATATCATTTTCAGAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta Alignment from GeneWise --------------------------------------------------AATGCCACACTGGTGGCTGAGAAGGCGGCTCTGCAGGGGCAGCTGCAGCACCTGGAGGGGCAGCTGGGGAGCCTGCAGGGCCGTGCACAGGAGCTCCTGCTACAGAGTCAGCGGGCTCAGGAGCACAGCAGTCGCCTGCAGGCT GAGCTAATAGGGCTCACAACATTAATATAGAAATAACATATCATTTTCAGAATGCCACATTGGTGGCAGAGAAAGTGGCTCTGCAGGGACAATTGCAGCATCTCGAGGGCCAGCTGGGGAGCCTACATGGTCGTGCACAGGAATTGCTTCTACAGAGTCAACGGGCTCAAGAGCACAGTAGTTGCTTGCAGCCCgtgagtttgggtgattgaatgggttgggtcatgcaccttgaaacaatgta #### Ccdc88b_ID1836_13 --> 2 - 0 Original Alignment cc------------------------------------TCCCTACCCGGAGCAGCACCCTCACTGCAAGATGAGGTGAGGGAAGCAGAGGCTGGGAGGCTAAGGGCAGTGGAACGGGAGAACCGGGAGCTTCGAGGCCAACTACAGATGCTTCAGGCACAGCTTGGCAGCCAG ttgagtagggcaacatgaccagacagaatctgtcttgctctttcctgcagcgTCATTGGAGGATTGTCCTGTTGATTGCGATGAACAATCCCTTCCTGGCCCAGCACCCTCACTGCAGGATGAGGTGAGGAAAGTAGAGGGTGGCCGTCTTAGGGCAGTGGATCGGGAAAATCGGGAGCTTCGAGGTCAA---CATATG------GCACAGCTTGGGAGCCAGgtaattcctctgttgtttcatctctgagtaatccagttccttgtggatac Alignment from CESAR tgatgagagattaaccattagtctaagtaggctgtaatttgacacttgtac Alignment from Spaln_aa2Genome CCTCCCTACCCGGAGCAGCACCCTCACTGCAAGATGAGGTGAGGGAAGCAGAGGCTGGGAGGCTAAGGGCAGTGGAACGGGAGAACCGGGAGCTTCGAGGCCAACTACAGATGCTTCAGGCACAGCTTGGCAGCCAG ttgagtagggcaacatgaccagacagaatctgtcttgctctttcctgcagcgtcattggaggattgtcctgttgattgcgatgaacAATCCCTTCCTGGCCCAGCACCCTCACTGCAGGATGAGGTGAGGAAAGTAGAGGGTGGCCGTCTTAGGGCAGTGGATCGGGAAAATCGGGAGCTTCGAGGTCAA---CATATG------GCACAGCTTGGGAGCCAGgtaattcctctgttgtttcatctctgagtaatccagttccttgtggatac Alignment from Spaln_nt2Genome CCTCCCTACCCGGAGCAG- CACCCTCACTGCAAGATGAGGTGAGGGAAGCAGAGGCTGGGAGGCTAAGGGCAGTGGAACGGGAGAACCGGGAGCTTCGAGGCCAACTACAGATGCTTCAGGCACAGCTTGGCAGCCAG ttgagtagggcaacatgaccagacagaatctgtcttgctctttcctgcagCGTCATT----GGAGGATTgtcctgttgattgcgatgaacaatcccttcctggcccagCACCCTCACTGCAGGATGAGGTGAGGAAAGTAGAGGGTGGCCGTCTTAGGGCAGTGGATCGGGAAAATCGGGAGCTTCGAGGTCA---ACATAT------GGCACAGCTTGGGAGCCAGgtaattcctctgttgtttcatctctgagtaatccagttccttgtggatac Alignment from Pairagon CC------------------------------------TCCCTACCCGGAGCAGCACCCTCACTGCAAGATGAGGTGAGGGAAGCAGAGGCTGGGAGGCTAAGGGCAGTGGAACGGGAGAACCGGGAGCTTCGAGGCCAACTACAGATGCTTCAGGCACAGCTTGGCAGCCAG ttgagtagggcaacatgaccagacagaatctgtcttgctctttcctgcagCGTCATTGGAGGATTGTCCTGTTGATTGCGATGAACAATCCCTTCCTGGCCCAGCACCCTCACTGCAGGATGAGGTGAGGAAAGTAGAGGGTGGCCGTCTTAGGGCAGTGGATCGGGAAAATCGGGAGCTTCGAGGTCAA---------CATATGGCACAGCTTGGGAGCCAGgtaattcctctgttgtttcatctctgagtaatccagttccttgtggatac Alignment from Exonerate_protein2genome CCTCCCTACCCGGAGCAGCACCCTCACTGCAAGATGAGGTGAGGGAAGCAGAGGCTGGGAGGCTAAGGGCAGTGGAACGGGAGAACCGGGAGCTTCGAGGCCAACTACAGATGCTTCAGGCACAGCTTGGCAGCCAG ttgagtagggcaacatgaccagacagaatctgtcttgctctttcctgcagcgtcattggaggattgtcctgttgattgcgatgaacAATCCCTTCCTGGCCCAGCACCCTCACTGCAGGATGAGGTGAGGAAAGTAGAGGGTGGCCGTCTTAGGGCAGTGGATCGGGAAAATCGGGAGCTTCGAGGTCAA---------CATATGGCACAGCTTGGGAGCCAGgtaattcctctgttgtttcatctctgagtaatccagttccttgtggatac Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise -----------------------------------GCCTCCCTACCCGGAGCAGCACCCTCACTGCAAGATGAGGTGAGGGAAGCAGAGGCTGGGAGGCTAAGGGCAGTGGAACGGGAGAACCGGGAGCTTCGAGGCCAACTACAGATGCTTCAGGCACAGCTTGGCAGCCAG ttgagtagggcaacatgaccagacagaatctgtcttgctctttcctgcagCGTCATTGGAGGATTGTCCTGTTGATTGCGATGAACAATCCCTTCCTGGCCCAGCACCCTCACTGCAGGATGAGGTGAGGAAAGTAGAGGGTGGCCGTCTTAGGGCAGTGGATCGGGAAAATCGGGAGCTTCGAGGTCAACATATG---------GCACAGCTTGGGAGCCAGgtaattcctctgttgtttcatctctgagtaatccagttccttgtggatac #### Ccdc88b_ID1837_12 --> 0 - 1 Original Alignment GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTGGGGAGg aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCT------ggtgagacatgcttgtagcagacaggatttggcaaggaacctttagtctta Alignment from CESAR GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTGGGGAGg aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCT------ggtgagacatgcttgtagcagacaggatttggcaaggaacctttagtctta Alignment from Spaln_aa2Genome GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTGGGGAGGCCT aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCTGGTGAGACATgcttgtagcagacaggatttggcaaggaacctttagtctta Alignment from Spaln_nt2Genome GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTG aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCTGgtgagacatgcttgtagcagacaggatttggcaaggaacctttagtctta Alignment from Pairagon GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTGGGGAG--------------------------------------------- aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCTGGTGAGACATGCTTGTAGCAGACAGGATTTGGCAAGGAACCTTTAGTCTTA Alignment from Exonerate_protein2genome GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTG aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCTGgtgagacatgcttgtagcagacaggatttggcaaggaacctttagtctta Alignment from Exonerate_coding2genome GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTG aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCTGgtgagacatgcttgtagcagacaggatttggcaaggaacctttagtctta Alignment from GeneWise GACCTGGACTCTCTGCGGCATCAGCTGGAGCAGCTGGTGGAAGAGAATGTGGAGCTGGAGCTGGAACTTCAGAGGAGTCTGGAGCCACCCCCAGGCTCCCCTG aggcctaatggacagacagctctggcacaattccatcatttgtttcttagGACCTGGACTCACTGCGGCATCAGTTGGAACAGTTAGTGGAAGAGAATGTAGAGCTAGAGTTGGAACTACAAAGAAGTTTGGAGCCACCTCCAGGCTCCCCTGgtgagacatgcttgtagcagacaggatttggcaaggaacctttagtctta #### Ccs_ID661_7 --> 0 - 2 Original Alignment GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAG---------------------------ag gTTGGCCT gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTGGAGAAAAAACTTTGCGGCCGGGTAGCCTCTGATaggtgagtcatataacaatcaactctcctgttcccatcttacagaCTCTCAT Alignment from CESAR GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAG---------------------------ag gTTGGCCT gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTGGAGAAAAAACTTTGCGGCCGGGTAGCCTCTGATaggtgagtcatataacaatcaaccccatttcccgctctccacagaCTCTCAT Alignment from Spaln_aa2Genome GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAGG-------------------------- -TTGGCCT gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTGGAGAAAAAACTTTGCGGCCGGGTAGCCTCTGATAGgtgagtcatataacaatcaactctcctgttcccatcttacagACTCTCAT Alignment from Spaln_nt2Genome GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGA--------GGTTGG CCT----- gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTGGAGAAAAAACTTTGCGGCCGGgtagcctctgataggtgagtcatataacaatcaactctcctgttcccatcttacagACTCTCAT Alignment from Pairagon GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAGGTTGG---------------------------------------------------------------------------------CCT gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAAT------------TTGGAGAAAAAACTTTGCGGCCGGGTAGCCTCTGATAGGTGAGTCATATAACAATCAACTCTCCTGTTCCCATCTTACAGACTCTCAT Alignment from Exonerate_protein2genome GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAGGTT G---GCCT gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTGGAGAAAAAACTttgcggccgggtagcctctgataggtgagtcatataacaatcaactctcctgttcccatcttacagACTCTCAT Alignment from Exonerate_coding2genome gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcaggtttgggatgtgattgcccgcaccctggttattgatgagggagaagatgatgtgggctgggggggccaccctttatccaagattactgggaatttggagaaaaaactttgcggccgggtagcctctgataggtgagtcatataacaatcaactctcctgttcccatcttacagactctcat Alignment from GeneWise GTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGGGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAATTCTGGGAAGAGGTTG----------------------- ----GCCT gcacatatgcagggcagatgaagctgaccatgttgtctgtccgttctcagGTTTGGGATGTGATTGCCCGCACCCTGGTTATTGATGAGGGAGAAGATGATGTGGGCTGGGGGGGCCACCCTTTATCCAAGATTACTGGGAATTTGGAGAAAAAACTTTGCGGCCGGGTAGCCTCTGATAGgtgagtcatataacaatcaactctcctgttcccatcttacagACTCTCAT #### Cd274_ID6274_5 --> 2 - 1 Original Alignment tgAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATg ccttactaacattctaactcacattggttccttgctattctgtctcccagtg------CTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATggtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from CESAR tgAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATg gtttgtccttactaacattctaactggttccttgctattctgtctcccagtg------CTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATggtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from Spaln_aa2Genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATG ccttactaacattctaactcacattggttccttgctattctgtctcccagTG------CTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGgtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from Spaln_nt2Genome TGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATG ccttactaacattctaactcacattggttccttgctattctgtctcccagTGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGgtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from Pairagon TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAATG ccttactaacattctaactcacattggttccttgctattctgtctcccag------TGCTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATGgtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from Exonerate_protein2genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT ccttactaacattctaactcacattggttccttgctattctgtctcccagTG------CTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATggtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from Exonerate_coding2genome TGAGAATGCTAGATGTGGAGAAATGTGGCGTTGAAGATACAAGCTCAAAAAACCGAAAT ccttactaacattctaactcacattggttccttgctattctgtctcccagTG------CTGGAT---GAGAAATGCAGTGTTGAGCATATAAGCTCAAAAAACCGGAATggtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta Alignment from GeneWise ccttactaacattctaactcacattggttccttgctattctgtctcccagtgctggatgagaaatgcagtgttgagcatataagctcaaaaaaccggaatggtaaggggatcaatgtacagaaattttggtgaccattaaacaccagatta #### Cdc42bpg_ID1573_3 --> 0 - 0 Original Alignment GTTGCCGTGGTGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcag---------GTGAGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from CESAR GTTGCCGTGGTGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ttgatccttctgtgagtccagtcactgtggcattttttgatctcctgcag---------GTGAGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from Spaln_aa2Genome GTTGCCGTGGTGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcag---------GTGAGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from Spaln_nt2Genome GTGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcagGTGAGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from Pairagon GGAGGTTGCCGTGGTGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcag-------------GTGAGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from Exonerate_protein2genome TGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcaggTGAGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from Exonerate_coding2genome ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcaggtgaggcagagaggaagtggccagatctttgcaatgaatatgtttcataagtgggaaatgttgaagagggctgaggtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca Alignment from GeneWise GTTGCCGTGGTGAGGCAGAGGGGCAGTGGCCAGATCTTTGCCATGAAGATGCTGCATAAGTGGGAGATGCTGAAGAGGGCTGAG ctgtgagtccagtcacatttcatgctgtggcattttttgatctcctgcagGTG---------AGGCAGAGAGGAAGTGGCCAGATCTTTGCAATGAATATGTTTCATAAGTGGGAAATGTTGAAGAGGGCTGAGgtaagttggcacaaatgtaaaatctatccctacatgtttgcttgtataca #### Cdc42bpg_ID1574_4 --> 0 - 0 Original Alignment ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG atgtttgcttgtatacagacaacctgttatgttctctcttttctctttag---ACCTGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from CESAR ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG tacatgtttgcttgtatacagacaagttatgttctctcttttctctttagACC---TGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from Spaln_aa2Genome ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG atgtttgcttgtatacagacaacctgttatgttctctcttttctctttagACC---TGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from Spaln_nt2Genome ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG atgtttgcttgtatacagacaacctgttatgttctctcttttctctttagA---CCTGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from Pairagon ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG atgtttgcttgtatacagacaacctgttatgttctctcttttctctttagA---CCTGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from Exonerate_protein2genome ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG atgtttgcttgtatacagacaacctgttatgttctctcttttctctttagACC---TGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from Exonerate_coding2genome atgtttgcttgtatacagacaacctgttatgttctctcttttctctttagacctgtctccgcgaggagcgagatgttctagtgaaggaagaccattgttgggtgacagttttacattactcattccaggatgaggagttcttagtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt Alignment from GeneWise ACGGCCTGTTTCCGGGAGGAGCGAGATGTTCTAGTGAAGGGAGACAGCCGCTGGGTGACTGCTCTGCACTACGCCTTCCAGGATGAAGAGTACCTG atgtttgcttgtatacagacaacctgttatgttctctcttttctctttagACC---TGTCTCCGCGAGGAGCGAGATGTTCTAGTGAAGGAAGACCATTGTTGGGTGACAGTTTTACATTACTCATTCCAGGATGAGGAGTTCTTAgtaaaatgccctatgtcacaagggagccaccctgacagtactgtcttttt #### Cdc42bpg_ID1575_5 --> 0 - 2 Original Alignment TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCTC---ACGCTGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGC------------TATGTCCACag tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGCTATGCC---aggtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from CESAR TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCTCACG---CTGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGCTATGTCCAC---------ag tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGCTATGCCaggtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from Spaln_aa2Genome TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCTCACG---CTGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGCTATGTCCACAGG-------- tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGCTATGCCAGgtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from Spaln_nt2Genome TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCTCACGC---TGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGCTATGTCCACAGGGATGTGAA tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGCTATGCCAGgtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from Pairagon TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCT---CACGCTGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGCTATGTCCACAG--------- tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGCTATGCCAGgtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from Exonerate_protein2genome TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCTC---ACGCTGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGCTATGTCCACAG tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGctatgccaggtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from Exonerate_coding2genome tgcaatcagacttctggttggataactactgactgtctcctctacctcagtacctgctgatggatttttatgctggtggtgatcttctaaaaagattactgagctgctttgaagaccgtctcccgcctgaactagctcaaatatatttggctgagatggtgttggctattcactccttgcaccagctaggctatgcccacagctatgccaggtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc Alignment from GeneWise TACCTGGTGATGGACTACTATGCTGGCGGGGACCTTCTC---ACGCTGCTGAGCCGCTTTGAGGACCGCCTCCCACCTGAGCTGGCCCAGTTCTATCTGGCTGAGATGGTTCTGGCCATCCACTCACTGCACCAGCTGGGCTATGTCCAC---------AG tgcaatcagacttctggttggataactactgactgtctcctctacctcagTACCTGCTGATGGATTTTTATGCTGGTGGTGATCTTCTAAAAAGATTACTGAGCTGCTTTGAAGACCGTCTCCCGCCTGAACTAGCTCAAATATATTTGGCTGAGATGGTGTTGGCTATTCACTCCTTGCACCAGCTAGGCTATGCCCACAGCTATGCCAGgtgagcactaagctagaggtgtgttgttgaggtattgggatcattccttc #### Cdc42bpg_ID1576_6 --> 1 - 0 Original Alignment gGATGTGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccaga---GTGGAGCCAGACAATGTTCTA---AGCATGAATGGGCAT---TGCTTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from CESAR gGATGTGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG ggacacacacatacttacaccaaaggcttaatacttgctcttcttgccaga---GTGGAGCCAGACAATGTT---CTAAGCATGAATGGGCAT---TGCTTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from Spaln_aa2Genome -GTGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccagAGTGGAGCCAGACAATGTT---CTAAGCATGAATGGGCAT---TGCTTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from Spaln_nt2Genome --TGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccagAGTGGAGCCAGACAA---TGTTCTAAGCATGAATGGGCA---TTGCTTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from Pairagon GGATGTGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccagagtggagccagacaatgttctaag------------------------------CATGAATGGGCA---TTGCTTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from Exonerate_protein2genome GGATGTGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccagA---GTGGAGCCAGACAATGTT---CTAAGCATGAATGGGCATTGC---TTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from Exonerate_coding2genome cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccagagtggagccagacaatgttctaagcatgaatgggcattgcttagctgattttggcacctgcctatgcctcaacatcaacaccaaggtaagtaaaccacctagaaattcatagataagtataaagacatttagtta Alignment from GeneWise TGTGAAGCCTGACAACATCCTGCTGGACATGAATGGCCACATCCGCCTGGCAGACTTTGGCTCCTGCCTGCGTCTCAACAACAATGGCATG cacacacatacttacaccaaagaacgcttaatacttgctcttcttgccagAGTGGAGCCAGACAATGTTCTA---AGCATGAATGGGCATTGC---TTAGCTGATTTTGGCACCTGCCTATGCCTCAACATCAACACCAAGgtaagtaaaccacctagaaattcatagataagtataaagacatttagtta #### Cdc42bpg_ID1586_16 --> 1 - 0 Original Alignment gATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGAACGG--------- gcacttgctgtctggaattggcaaaatattttttccctccactttttaaggATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAGTGGACCAAGTCAgtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from CESAR gATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGAACGG--------- gcacttgctgtctggaattggcaaaatattttttccctccactttttaaggATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAGTGGACCAAGTCAgtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from Spaln_aa2Genome GATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGAACGG--------- gcacttgctgtctggaattggcaaaatattttttccctccactttttaagGATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAGTGGACCAAGTCAgtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from Spaln_nt2Genome GATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGAACGGC---- gcacttgctgtctggaattggcaaaatattttttccctccactttttaagGATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAGTGGACCAAgtcagtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from Pairagon GATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGAACGG----- gcacttgctgtctggaattggcaaaatattttttccctccactttttaagGATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAGTGGACCAAgtcagtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from Exonerate_protein2genome GATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGA gcacttgctgtctggaattggcaaaatattttttccctccactttttaagGATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAgtggaccaagtcagtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from Exonerate_coding2genome gcacttgctgtctggaattggcaaaatattttttccctccactttttaaggatcagtgttggtaaaatggaggttctatgccatctacaggcagtgaaccagcagctgagtcgagaacaggagtggaccaagtcagtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt Alignment from GeneWise GATCAGTGTTGGGAAAGAGGAGGTTCTGTGCCGATTGCAGGAGGAAAACCAGCGGCTGAGCCGGGAGCAGGAA---------CGG gcacttgctgtctggaattggcaaaatattttttccctccactttttaagGATCAGTGTTGGTAAAATGGAGGTTCTATGCCATCTACAGGCAGTGAACCAGCAGCTGAGTCGAGAACAGGAGTGGACCAAGTCAgtgcggatcaagtatgacaaagccagggttgccaccactggcttgtgggt #### Cdc42bpg_ID1590_20 --> 1 - 1 Original Alignment cCGCCTGCAGGAGGCTGAGAAGCAAAGTCAGGCCCTGCAG---CAGGAGGTGGCTGAGCTCCGGGAGGAACTGCAAGCTCGAGGACCGGGGg cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagcCACCTGCAGGAAGCTGAGACACAAAGTAAGACACTCCAGCAGCAGGGGGTGGCTGTGCTGAAG---------------------------ggtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from CESAR cCGCCTGCAGGAGGCTGAGAAGCAAAGTCAGGCCCTGCAGCAGGAG---GTGGCTGAGCTCCGGGAGGAACTGCAAGCTCGAGGACCGGGGg cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagcCACCTGCAGGAAGCTGAGACACAAAGTAAGACACTCCAGCAGCAGGGGGTGGCTGTGCTGAAG---------------------------ggtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from Spaln_aa2Genome CCGCCTGCAGGAGGCTGAGAAGCAAAGTCAGGCCCTGCAGCAGGAG---GTGGCTGAGCTCCGGG cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagCCACCTGCAGGAAGCTGAGACACAAAGTAAGACACTCCAGCAGCAGGGGGTGGCTGTGCTGAAGGgtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from Spaln_nt2Genome CCGCCTGCAGGAGGCTGAGAAGCAAAGTCAGGCCCT---GCAGCAGGAGGTGGCTGAGCTCCGGG cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagCCACCTGCAGGAAGCTGAGACACAAAGTAAGACACTCCAGCAGCAGGGGGTGGCTGTGCTGAAGGgtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from Pairagon CCGCCTGCAGGAGGCTGAGAAGCAAAGTCAGGC---CCTGCAGCAGGAGGTGGCTGAGCTCCGGGAGGAACTGCAAGCTCGAGGACCGGGGG cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagCCACCTGCAGGAAGCTGAGACACAAAGTAAGACACTCCAGCAGCAGGGGGTGGCTGTGCT---------------------------GAAGGgtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from Exonerate_protein2genome cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagccacctgcaggaagctgagacacaaagtaagacactccagcagcagggggtggctgtgctgaagggtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from Exonerate_coding2genome cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagccacctgcaggaagctgagacacaaagtaagacactccagcagcagggggtggctgtgctgaagggtaagtacccacttgaaaacaatcacacctttgcttggggtccactcttt Alignment from GeneWise CCGCCTGCAGGAGGCTGAGAAGCAAAGTCAGGCCCTGCAGCAGGAG---GTGGCTGAGCTCCGGGAGGAACTGCAAGCTCGAGGACCGGGG------------G cactgcagtgtatgagacctcctgggtgcaccccgtctttctctccgcagCCACCTGCAGGAAGCTGAGACACAAAGTAAGACACTCCAGCAGCAGGGGGTGGCTGTGCTGAAGGGTAAGTACCCACTTGAAAACAATCACACCTTTGCTTGGGgtccactcttt #### Cdc42bpg_ID1592_22 --> 0 - 0 Original Alignment AAGGATTCTGCCAAGGACCCTGGCAATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG tttaaaagtaacttctttcctttgcatccccttctcttctcttcctgcag------------------------AATTCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from CESAR AAGGATTCTGCCAAGGACCCTGGCAATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG taacacatacgtagtagctaagtttatccccttctcttctcttcctgcag------------------------AATTCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from Spaln_aa2Genome AATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG tttaaaagtaacttctttcctttgcatccccttctcttctcttcctgcagAATTCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from Spaln_nt2Genome AATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG tttaaaagtaacttctttcctttgcatccccttctcttctcttcctgcagAATTCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from Pairagon AAGGATTCTGCCAAGGACCCTGGCAATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG tttaaaagtaacttctttcctttgcatccccttctcttctcttcctgcag------------------------AATTCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from Exonerate_protein2genome AAGGATTCTGCCAAGGACCCTGGCAATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG tttaaaagtaacttctttcctttgcaTCCCCTTCTCTTCTCTTCCTGCAGAATTCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from Exonerate_coding2genome tttaaaagtaacttctttcctttgcatccccttctcttctcttcctgcagaattcagctgagggtccaaagtctggagcagaagcagagcttagaccagagggccggcgcagtctacgcatgggtgtagggtcataaccaactagaatagaactacaggggatttctgcattgac Alignment from GeneWise AAGGATTCTGCCAAGGACCCTGGCAATTCAGGAGAGGGTCCAAGGTCTGGAGCCGAAGCAGAGCTGAGGCCAGAGGGCCGCCGCAGTCTGCGCATGGGG tttaaaagtaacttctttcctttgcatccccttctcttctcttcctgcagAAT------------------------TCAGCTGAGGGTCCAAAGTCTGGAGCAGAAGCAGAGCTTAGACCAGAGGGCCGGCGCAGTCTACGCATGGGTgtagggtcataaccaactagaatagaactacaggggatttctgcattgac #### Cdc42bpg_ID1595_25 --> 2 - 0 Original Alignment ccTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCG--------- GTGCCGCGGC acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagcaTGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAgtaacctgggggggttgtggtggtctgctctgctctgcagGTACGACAGC Alignment from CESAR ccTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCG--------- GTGCCGCGGC acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagcaTGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAgtaacctgggggggttgttgtggtaacatggtttttgtagGTACGACAGC Alignment from Spaln_aa2Genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCGGTGCCGCGG C acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAgtaacctgggggggttgtggtggtctgctctgctctgcaggtacgacagC Alignment from Spaln_nt2Genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCG- GTGCCGCGGC acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAgtgaccgagtaacctgggggggttgtggtggtctgctctgctctgcagGTACGACAGC Alignment from Pairagon CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTC-------------------------------------------------GGTGCCGCGGC acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAGTAACCTGGGGGGGTTGTGGTGGTCTGCTCTGCTCTGCAGGTACGACAGC Alignment from Exonerate_protein2genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCGGTGCCGCGG C acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAgtaacctgggggggttgtggtggtctgctctgctctgcaggtacgacagC Alignment from Exonerate_coding2genome CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCGGTGCCGCGG C acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAgtaacctgggggggttgtggtggtctgctctgctctgcaggtacgacagC Alignment from GeneWise CCTGTGGCTACTTCTGTCACTCAGCTTGTGCGTCACAAGCCCCACCTTGCCCTGTGCCCCCTGAACTCCTCCGCACAGCCTTGGGGGTGCACCCCGAAACAGGCACAGGGACTGCCTATGAGGGCTTCCTGTCGGTGCCGCGG C acattatttaatgcacatatgtgtgtgttgactattatttatctttgcagCATGTGGTTATTTCTGT------GCCTGTGCCTCGCAAACCCCTCCTTGCCCTGTGCCCCCTGAACTTCTTCGCACAGCCTTGGGGGTGCACCCCAAAAAGGGAACAGAGTCAGCCTATGAGGGGTTTTTGTCAAGTGACCGAgtaacctgggggggttgtggtggtctgctctgctctgcaggtacgacagC #### Cdc42bpg_ID1597_27 --> 1 - 0 Original Alignment g---------GACCCCCAGTTCTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcaggAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from CESAR g---------GACCCCCAGTTCTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcaggAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from Spaln_aa2Genome GGACCCCCAGTTC---------TCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcagGAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from Spaln_nt2Genome GGACCCCCAGTT---------CTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcagGAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from Pairagon ---------GGACCCCCAGTTCTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcagGAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from Exonerate_protein2genome G---------GACCCCCAGTTCTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcagGAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from Exonerate_coding2genome G---------GACCCCCAGTTCTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcagGAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc Alignment from GeneWise -------AGGGACCCCCAGTTCTCAGCCACCCCTGTCTTGGCCCCAGATGTCATTCATGCCCAATCCAAGGACCTGCCACGTATCTTCAGG actgatgcgtgaacaaccaacatggatcgttatgttttgctttgtttcagGAACACGCCGGATCCCCAGTTTTCAGTGACCCCTGACTTGGCCCCAGATGTCATTCATGCCCAATCAAAGGACCTGCCACGCATCTTCAGGgtaaaaaaactaggtgatataggatttagcctccacaggctccggccagc #### Cdc42bpg_ID1601_31 --> 2 - 0 Original Alignment gtTACACAGCACCC---------TACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtaggt------GCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct Alignment from CESAR gtTACACAGCACCC---------TACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG tctcacttatgcctaaaaaccatagcttctcttcctgctcacatttgtaggt------GCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttgtgtt Alignment from Spaln_aa2Genome GTTACACA---GCACCCTACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtagGTGCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct Alignment from Spaln_nt2Genome GTTACACAGCAC----CCTACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtagG-TGCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct Alignment from Pairagon GTTACACAGCAC---------CCTACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtagGT------GCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct Alignment from Exonerate_protein2genome GTTACACA---GCACCCTACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtagGTGCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct Alignment from Exonerate_coding2genome GTTACACA---GCACCCTACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtagGTGCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct Alignment from GeneWise --GGTTACACAGCACCCTACCTAACAGTGTTCAGTGAAAACGCCCTTGATGTGTTTGACGTGAGGAGAGCAGAATGGGTACAGACTGTGCCGCTCAAGAAG ttatgcctaaaaaccataggcctgccttctcttcctgctcacatttgtagGTGCACCATACTTAACTTACCTAACTGTATTCAGTGACAATACCCTTGATGTCTTTGATGTTAGGAGAGCAGAATGGGTCCAAACTGTATCACTCAAGAAAgtgagtgctagcgctggttgtcaaattagtacattgagtggacttctgct #### Cdca5_ID1428_2 --> 2 - 0 Original Alignment ggCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG agaaataaccgattgtacacgctttgacggcctccctctgtcatctgcagga---------------------------GAGTCACTAAAACACAAGTCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGgtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from CESAR ggCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG ccatgtacctggtgatgggttatttgacggcctccctctgtcatctgcagga---------------------------GAGTCACTAAAACACAAGTCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGgtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from Spaln_aa2Genome GG---CCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG agaaataaccgattgtacacGCTTTGACGGCCTCCCTCTGTCATCTGCAGGAGAGTCACTAAAACACAAGTCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGgtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from Spaln_nt2Genome TACTAAGCCTTC GA-AGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG agAAATAACCGATTgtacacgctttgacggcctccctctgtcatctgcagGAGAGTCACTAAAACACAAGTCATGTTCAGACCTCACAAACTCATTTTCTGAAACCTGGCAACGGgtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from Pairagon GGCCCAGGACTTCACTTACTAAGCCTTCGAAGTCGTCCAAGCGGAAATCTGGCTCAGATCTCCCGAACTCGTTCTCTGAAATCTGGCCGAGG agaaataaccgattgtacacgctttgacggcctccctctgtcatctgcaggagagtcactaaaacacaagtcatgttcag---------------------------------------------------------ACCTCACAAACTCATTTTCTGAAACCTGGCAACGGgtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from Exonerate_protein2genome agaaataaccgattgtacacgctttgacggcctccctctgtcatctgcaggagagtcactaaaacacaagtcatgttcagacctcacaaactcattttctgaaacctggcaacgggtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from Exonerate_coding2genome agaaataaccgattgtacacgctttgacggcctccctctgtcatctgcaggagagtcactaaaacacaagtcatgttcagacctcacaaactcattttctgaaacctggcaacgggtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc Alignment from GeneWise agaaataaccgattgtacacgctttgacggcctccctctgtcatctgcaggagagtcactaaaacacaagtcatgttcagacctcacaaactcattttctgaaacctggcaacgggtgagtactgacctccctggtctgaaagcagctgcatacaccacaatttc #### Cep78_ID3982_4 --> 2 - 0 Original Alignment ttATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGCCAAGATCTTAAAG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagttATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATG---------------gtactgaatgttcaagctctaacgaggtaaattcagtgttactgcagttc Alignment from CESAR ttATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGCCAAGATCTTAAAG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagttATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATG------GTACTGAATgttcaagctctaacgaggtaaattcagtgttactg Alignment from Spaln_aa2Genome TTATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGCCAAGATCTTAAAG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagTTATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATGGTACTGAATGTTCAAgctctaacgaggtaaattcagtgttactgcagttc Alignment from Spaln_nt2Genome TTATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGC----------CAAGATCTTAA-AG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagTTATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATGGTACTGAATGTTCAAGCTCTAACGAGgtaaattcagtgttactgcagttc Alignment from Pairagon TTATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagTTATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATGgtactgaatgttcaagctctaacgaggtaaattcagtgttactgcagttc Alignment from Exonerate_protein2genome TTATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGCCAAGATCTTAAAG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagTTATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATGGTACTGAATGTTCAAgctctaacgaggtaaattcagtgttactgcagttc Alignment from Exonerate_coding2genome TTATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGCCAAGATCTTAAAG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagTTATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATGGTACTGAATGTTCAAgctctaacgaggtaaattcagtgttactgcagttc Alignment from GeneWise TTATTTGTCAAGGTATAAAGAACTCTGTCACTCTCAAGACCGTCAACTTTACAGGGTGTAATCTGACATGGCAAGGAGCCTGTCATATGGCCAAGATCTTAAAG tgtcagctttagagaaaggtggacaactggatatttgcctgtcattgcagTTATCTGTCAAGGCATAAAAAATTCTGTTGCCCTTAAAACTGTCAATTTTACTGGGTGTAATCGAACATGGCAGGGAGCCTGTCAGATG------GTACTGAATgttcaagctctaacgaggtaaattcagtgttactg #### Cep78_ID3983_3 --> 0 - 1 Original Alignment GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAA---a ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCagtatgttaatatattttataaccattcttggtgcctctcatatgcaccca Alignment from CESAR GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAA---a ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCagtatgttaatatattttataaccattcttggtgcctctcatatgcaccca Alignment from Spaln_aa2Genome GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAA---A ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCAgtatgttaatatattttataaccattcttggtgcctctcatatgcaccca Alignment from Spaln_nt2Genome GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAA---A ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCAgtatgttaatatattttataaccattcttggtgcctctcatatgcaccca Alignment from Pairagon GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAA---A ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCAgtatgttaatatattttataaccattcttggtgcctctcatatgcaccca Alignment from Exonerate_protein2genome GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAA---A ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCAgtatgttaatatattttataaccattcttggtgcctctcatatgcaccca Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GGACTGAGTAAATCAACCTCTTTGGTGCACTTGTCTCTTGCAAATTGTCCAATTGGAGATGGAGGTTTAGAAATT- ttggccatctcaataggtagatacccgagtgtcctctctctctgccctagGGATTGAGCAAATCAACCTCTCTGGTGCACTTGTCTCTTGCAAATTGCCCAATTGGAGATGGAGGGTTAGAACCCAgtatgttaatatattttataaccattcttggtgcctctcatatgcaccca #### Chuk_ID8920_8 --> 1 - 2 Original Alignment gCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTag tggggaatggttcttggatgcactatgctgccccatgtcttttcttataggCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAAC---------aggtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from CESAR gCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGCCTTTGTag tggggaatggttcttggatgcactatgctgccccatgtcttttcttataggCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAAC---------aggtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from Spaln_aa2Genome GCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAG tggggaatggttcttggatgcactatgctgccccatgtcttttcttatagGCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGgtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from Spaln_nt2Genome GCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAG tggggaatggttcttggatgcactatgctgccccatgtcttttcttatagGCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGgtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from Pairagon GCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAG tggggaatggttcttggatgcactatgctgccccatgtcttttcttatagGCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGgtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from Exonerate_protein2genome GCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAG tggggaatggttcttggatgcactatgctgccccatgtcttttcttatagGCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGgtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from Exonerate_coding2genome GCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAG tggggaatggttcttggatgcactatgctgccccatgtcttttcttatagGCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGgtgagtgacgcctacataacttagagcctttgggaatatgccccttatct Alignment from GeneWise GCATGAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCATGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAG tggggaatggttcttggatgcactatgctgccccatgtcttttcttatagGCATGAGGAGATTAAGAAGAAAGATCCAAAATGCATATTTGCGTGTGAAGAGATGACTGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAACAGgtgagtgacgcctacataacttagagcctttgggaatatgccccttatct #### Chuk_ID8922_6 --> 0 - 0 Original Alignment ---ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagAATACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from CESAR ---ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagAATACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from Spaln_aa2Genome ---ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTT ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagAATACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from Spaln_nt2Genome -AGACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagAATACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from Pairagon AAGACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagAATACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from Exonerate_protein2genome ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagaatACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from Exonerate_coding2genome ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagaatACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca Alignment from GeneWise ---ACAATACATAAAATAATTGATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTG ccacaagttttgtggaacttgatgacattctttgtgtgtgatctctttagAATACAGTGCATAAAATAATTGATCTGGGGTATGCCAAAGATGTTGATCAAGGAAGTCTTTGTTCAACTTTTGTAGGAACATTGAAATACTTGgtaaaggaatggcatgttaatcctgattctgttacattgttggtatttca #### Col17a1_ID10279_43 --> 2 - 1 Original Alignment gtGACAACATCAGGACTTATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGt ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactaggt---------AGGACAGATCTGCTAGGAGTTCAGGGGCCCCCTGGT------------CCTGGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAAtgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from CESAR gtGACAACATCAGGACTTATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGt agtctgaaactgtctctgtccagcatccttgttttttgtttttaaactaggt---------AGGACAGATCTGCTAGGAGTTCAGGGGCCCCCTGGT------------CCTGGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAAtgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from Spaln_aa2Genome ACATCAGGACTTATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGT ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactagGT---AGGACAGATCTGCTAGGAGTTCAGGGGCCCCCTGGT------------CCTGGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAATgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from Spaln_nt2Genome GTGACAACATCAGGACTTATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGT ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactagGT---------AGGACAGATCTGCTAGGAGTTCAGGGGCCCCCTGG------------TCCTGGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAATgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from Pairagon CAACATCAGGACTTATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGT ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactaggtaggacag--------------ATCTGCTAGGAGTTCAGGGGCCCCCTGG------------TCCTGGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAATgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from Exonerate_protein2genome ATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGT ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactagGTAGGACAGATCTGCTAGGAGTTCAGGGGCCCCCTGGT---CCTGGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAATgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from Exonerate_coding2genome ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactaggtaggacagatctgctaggagttcaggggccccctggtcctggatctgtgatcactattaagggagagacttttgattactctcaactggcaagtcatgaagttagctacctacaatgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg Alignment from GeneWise ACATCAGGACTTATCTCTCAGGGGTTCAGGGTCCCCCAGGCCCACCAGGTCCCCCAGGGCCTGTCATCACCATCACAGGAGAGACTTTCGACTACTCCCAGCTGGCAAGCCAGGTCGTAAGCTACTTGCGGT ctgtctctgtccagcatgtctttcctccttgttttttgtttttaaactagGT---AGGACAGATCTGCTAGGAGTTCAGGGGCCCCCTGGTCCT------------GGATCTGTGATCACTATTAAGGGAGAGACTTTTGATTACTCTCAACTGGCAAGTCATGAAGTTAGCTACCTACAATgtaagtttctgtggttttcacttcctcagtttgtgttgttctctgtatgg #### Col17a1_ID10282_40 --> 2 - 1 Original Alignment aaACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAg taagtcctaagcaacctgcactgcttctccctttgcctgccttgtcctagta---------AGGGGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAggtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from CESAR aaACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAg agcaaatgttaagtcctaagcaacctctccctttgcctgccttgtcctagtaAGG---------GGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAggtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from Spaln_aa2Genome TCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG taagtcctaagcaacctgcactgcttctccctttgcctgccttgtcctagTAAGGGGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAGgtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from Spaln_nt2Genome TCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG taagtcctaagcaacctgcactgcttctccctttgcctgccttgtcctagTAAGGGGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAGgtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from Pairagon AAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG taagtcctaagcaacctgcactgcttctccctttgcctgccttgtcctag---------TAAGGGGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAGgtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from Exonerate_protein2genome AAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG taagtcctaagcaacctgcactgcttctccctttgcctgccTTGTCCTAGTAAGGGGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAGgtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from Exonerate_coding2genome taagtcctaagcaacctgcactgcttctccctttgcctgccttgtcctagtaaggggccctccaggtccacctggccccccaggtccaaaaggggaccaaggtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta Alignment from GeneWise AAACCTTCTTCACTGGCCCTCCAGGTCCACCCGGCCCCCCAGGTCCCAAGGGAGACCAAG taagtcctaagcaacctgcactgcttctccctttgcctgccttgtcctagTA---------AGGGGCCCTCCAGGTCCACCTGGCCCCCCAGGTCCAAAAGGGGACCAAGgtgagcaggtgacccgaaagctgccaagtgtgatcactagtatgagacta #### Col17a1_ID10283_39 --> 2 - 1 Original Alignment ggGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCA---g attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttaggtGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACggtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from CESAR ggGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCA---g attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttaggtGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACggtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from Spaln_aa2Genome GGGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCAGAAA attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttagGTGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACGgtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from Spaln_nt2Genome GGGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCAGA-- attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttagGTGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACGgtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from Pairagon GGGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCAG--- attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttagGTGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACGgtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from Exonerate_protein2genome GGGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCA---G attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttagGTGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACGgtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from Exonerate_coding2genome attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttaggtgagggtgtgccaggtccacctgggcctccaggatcttttttgactgattctgacggtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata Alignment from GeneWise GGGAAGGCGTACCAGGCCCACCCGGGCCACCAGGATCCTTCCTGACTGACTCAGAA- attgtcaatagtgagggtaatatgacgttttttgtttgtttgttttttagGTGAGGGTGTGCCAGGTCCACCTGGGCCTCCAGGATCTTTTTTGACTGATTCTGACGgtaattatgtccatcagctctgctctgatttggccagaaaatcatgcata #### Col17a1_ID10293_29 --> 2 - 1 Original Alignment gtCCGGCTGGCGCTGATGGACAGCAAGGTTCCAGA------g tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcaggtCCAGCTGGCGCTGATGGACAACAAGGTTCACGGGAAATAggtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from CESAR gtCCGGCTGGCGCTGATGGACAGCAAGGTTCCAGA------g tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcaggtCCAGCTGGCGCTGATGGACAACAAGGTTCACGGGAAATAggtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from Spaln_aa2Genome GTCCGGCTGGCGCTGATGGACAGCAAGGTTCCAGA------G tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcagGTCCAGCTGGCGCTGATGGACAACAAGGTTCACGGGAAATAGgtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from Spaln_nt2Genome GTCCGGCTGGCGCTGATGGACAGCAAGGTTCCAG------AG tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcagGTCCAGCTGGCGCTGATGGACAACAAGGTTCACGGGAAATAGgtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from Pairagon GTCCGGCTGGCGCTGATGGACAGCAAGGTTCCAG------AG tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcagGTCCAGCTGGCGCTGATGGACAACAAGGTTCACGGGAAATAGgtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from Exonerate_protein2genome GTCCGGCTGGCGCTGATGGACAGCAAGGTTCCAGAG tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcagGTCCAGCTGGCGCTGATGGACAACAAGGTTCACGGGaaataggtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from Exonerate_coding2genome tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcaggtccagctggcgctgatggacaacaaggttcacgggaaataggtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc Alignment from GeneWise tcagaaagcccattgatcagttaacacatcttcctgttttcattcatcaggtccagctggcgctgatggacaacaaggttcacgggaaataggtacaccaatcccttgtagtttccttgatgactggttgccctttgtcctc #### Col17a1_ID10297_25 --> 2 - 1 Original Alignment gtGCTGTGGGTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAg gaaaggaatatcattgtctgaggtgactcatgtgccaattttcattgcaggt------GGAACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAggtaatgcgggtagtgaaaggtgagggctcatttgagaaggtattttaagc Alignment from CESAR gtGCTGTGGGTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAg acataggaaaggaatatcattgtctactcatgtgccaattttcattgcaggt------GGAACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAggtaatgcgggtagtgaaaggtgagggctcatttgagaaggtattttaagc Alignment from Spaln_aa2Genome GTGCTGTGGGTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAG gaaaggaatatcattgtctgaggtgactcatgtgccaattttcattgcagGT------GGAACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAGgtaatgcgggtagtgaaaggtgagggctcatttgagaaggtattttaagc Alignment from Spaln_nt2Genome G--GTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAG gaaaggaatatcattgtctgaggtgactcatgtgccaattttcattgcagGTGGAACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAGgtaatgcgggtagtgaaaggtgagggctcatttgagaaggtattttaagc Alignment from Pairagon GTGGGTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAG gaaaggaatatcattgtctgaggtgactcatgtgccaattttcattgcagGTGGA-ACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAGgtaatgcgggtagtgaaaggtgagggctcatttgagaaggtattttaagc Alignment from Exonerate_protein2genome TGCTGTGGGTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAGGTGACAAAGGACTCATGGG gaaaggaatatcattgtctgaggtgactcatgtgccaattttcatTGCAGGTGGAACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAGGTAATGCGGGTAGTGAAAGgtgagggctcatttgagaaggtattttaagc Alignment from Exonerate_coding2genome gaaaggaatatcattgtctgaggtgactcatgtgccaattttcattgcaggtggaacccagggacttcggggtgacgtgggattgcctggtgtgaaaggtaatgcgggtagtgaaaggtgagggctcatttgagaaggtattttaagc Alignment from GeneWise GTGCTGTGGGTCCCCAAGGGCTCCGAGGTGACGTGGGACTTCCTGGTGTCAAAGGTGACAAAGGAC gaaaggaatatcattgtctgaggtgactcatgtgccaattttcattgcagGT------GGAACCCAGGGACTTCGGGGTGACGTGGGATTGCCTGGTGTGAAAGGTAATGCGGGTAgtgaaaggtgagggctcatttgagaaggtattttaagc #### Col17a1_ID10300_22 --> 2 - 1 Original Alignment gaGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGA---g taactatctgtactgttgcctctttcttacagtgatttttattcctacaggaGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGTTggtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from CESAR gaGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGA---g taactatctgtactgttgcctctttcttacagtgatttttattcctacaggaGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGTTggtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from Spaln_aa2Genome GAGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGA---G taactatctgtactgttgcctctttcttacagtgatttttattcctacagGAGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGTTGgtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from Spaln_nt2Genome GAGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGAG--- taactatctgtactgttgcctctttcttacagtgatttttattcctacagGAGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGTTGgtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from Pairagon GAGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGAG--- taactatctgtactgttgcctctttcttacagtgatttttattcctacagGAGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGTTGgtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from Exonerate_protein2genome GAGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGAG taactatctgtactgttgcctctttcttacagtgatttttattcctacagGAGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGttggtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from Exonerate_coding2genome GAGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGAG taactatctgtactgttgcctctttcttacagtgatttttattcctacagGAGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGttggtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt Alignment from GeneWise GAGATCCTGGCATGGAAGGACCCATAGGCCAGAGAGGACTAGCAGGCCCCATGGGACCTCGTGGTGAACCCGGGCCTCCTGGGTCTGGAGAGAAAGGAGACAGAGGG- taactatctgtactgttgcctctttcttacagtgatttttattcctacagGAGACCCAGGCATGGAAGCACCAATAGGCCAGAGAGGATTAGCAGGTCCCATGGGACCCAGCGGTGAACCAGGGCCTCCTGGATCTGGGGAGAAAGGAGACCAAGTTGgtgagtgtcaccatcaacaatcaatgcagtgacctgcgtctttttattgt #### Col17a1_ID10308_14 --> 2 - 1 Original Alignment ctTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAAT---------------------------g atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagcaTCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAGAGAAATTATTGAGCAGCTTCTGTCAggtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from CESAR ctTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAAT---------------------------g atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagcaTCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAGAGAAATTATTGAGCAGCTTCTGTCAggtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from Spaln_aa2Genome CTTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAAT---------------------------G atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagCATCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAGAGAAATTATTGAGCAGCTTCTGTCAGgtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from Spaln_nt2Genome CTTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAATGGAGACCTAAAT-ACCGTGTCCACAAAG atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagCATCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAGAGAAATTATTGAGCAGCTTCTGTCAGgtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from Pairagon CTTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAAT---------------------------G atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagCATCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAGAGAAATTATTGAGCAGCTTCTGTCAGgtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from Exonerate_protein2genome CTTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAATG atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagCATCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAgagaaattattgagcagcttctgtcaggtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from Exonerate_coding2genome CTTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGATGTGAATGGAGACCTAAATACCGTGTCCACAAAGA atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagCATCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATGTGAATAGAGAAATTATTGAGCAGCTTCTGTCAGgtaagttctgcactctagttgcttccttacacaatcatgtctagtatact Alignment from GeneWise CTTCCTTTTCAGAAGACACCCTGAAAAAGGAGAAGCAGGCTGCATATGCCGCTGACACCTGCCTGAAGGCAGAT atgaggatataaggacagtgcgcttaagtttctccttaattgtccttaagCATCTTTCTCAGAAGATACATTGAAAAAGGAGAAGCAGGCAGCATATGCTGCTGACACCTGCCTCAAGGCAGATgtgaatagagaaattattgagcagcttctgtcaggtaagttctgcactctagttgcttccttacacaatcatgtctagtatact #### Coro1b_ID353_3 --> 0 - 1 Original Alignment GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACC------AAGCGCGTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCA---g aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGACC---CCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCggtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from CESAR GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACC---AAGCGC---GTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCA---g aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGACC---CCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCggtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from Spaln_aa2Genome GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACC------AAGCGCGTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCA---G aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTG---ACCCCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCGgtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from Spaln_nt2Genome GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACCA---AGCGCG---TGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCA---G aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGA---CCCCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCGgtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from Pairagon GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATAC-------------CAAGCGCGTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGC---AG aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGA---CCCCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATC-------TGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCGgtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from Exonerate_protein2genome GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACC------AAGCGCGTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCA---G aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGACC---CCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCGgtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from Exonerate_coding2genome GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACC------AAGCGCGTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCA---G aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGACC---CCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCGgtaagtttattatgcccagaccatgctctctactctagtttcagttcagc Alignment from GeneWise GTATGGCAGATTCCAGAAAATGGGCTGACCTCCCCTCTGACAGAGCCAGTAGTGGTGCTCGAGGGGCATACC------AAGCGCGTGGGCATTATCACCTGGCACCCCACAGCCCGAAATGTGCTTCTCAGTGCAGGT- aatgataccctctcttgatgattgacccgttttttacattttctccctagATCTGGCAGATCCCAGAGAATGGTTTGACC---CCACTGACAGAGCCTGTAGTTGTGCCTGAGGGGCATACAATTAAACGACATCTGGGTATTACTACTTGGCATCCTACTGCCCAAATTGTGATTCTTGGTGCTATCGgtaagtttattatgcccagaccatgctctctactctagtttcagttcagc #### Coro1b_ID354_4 --> 2 - 0 Original Alignment gtTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA--- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccaggaTGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactagtgtcccctccctacctc Alignment from CESAR gtTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA--- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccaggaTGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactctttccttcttccctgtga Alignment from Spaln_aa2Genome GTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA--- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccagGATGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactagtgtcccctccctacctc Alignment from Spaln_nt2Genome GTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA--- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccagGATGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactagtgtcccctccctacctc Alignment from Pairagon GTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA----------------------------------------------------- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccagGATGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCGTAACCACAAATGAGTATTCTGTTTTTGACTAGTGTCCCCTCCCTACCTC Alignment from Exonerate_protein2genome GTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA--- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccagGATGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactagtgtcccctccctacctc Alignment from Exonerate_coding2genome GTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCA--- atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccagGATGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactagtgtcccctccctacctc Alignment from GeneWise GTTGTGACAATGTGGTACTTATCTGGAATGTGGGCACTGCAGAGGAGCTGTACCGTCTGGACAGCTTGCACCCCGACCTCATCTACAACGTGAGCTGGAACCACAATGGCAGCCTCTTTTGCTCAGCTTGCAAGGACAAGAGCGTCCGAATCATCGATCCTAGGCGGGGCACCCTGGTGGCAGAA atttaattcgttacaaactcatttgcacatgtctgtccttgcctctccagGATGTGACAATGTGCTACTTATCTGGAATGTGGATGCTGCAGAAGAGCTGTACCGTTTGGACAGTTTGCATCCTGACCTTGCTTATAATGTCAGTTGGAACCACATTGGCAGCTTCTTTTGTTCAGCCTGCAAAGACAAGAGTGTTCGGATCACTGATCCTAGGCGGGATACCTTGGTTGCATGCgtaaccacaaatgagtattctgtttttgactagtgtcccctccctacctc #### Coro1b_ID357_7 --> 0 - 2 Original Alignment GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCag tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCC---CACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGT---------cggtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from CESAR GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCag tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGT---------cggtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from Spaln_aa2Genome GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGA tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTCGgtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from Spaln_nt2Genome GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGA tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCCC---ACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTCGgtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from Pairagon GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGAAATTGCCAG tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCCC---ACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGT---------CGgtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from Exonerate_protein2genome GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGA tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTCGgtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from Exonerate_coding2genome GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAGTGTGA tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAA---CCCCACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTGTCGgtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt Alignment from GeneWise GGCGATTCCAGCATCCGGTACTTTGAGATCACAGATGAGCCCCCCTACATCCACTTCCTGAATACATTTACCAGCAAAGAACCCCAGAGGGGTATGGGCAGCATGCCTAAGAGGGGCTTGGAGGTCAGCAAG- tggatactaatggacattcctttaattgactcttgtattttttttttcagGGTGATTCTAGTATCCGGTACTTTGAAAACACAGATGAACCC---CACATCCAGTTCTTGAACACATTTGCTAGCAAAGAACCCCAAAGGGGTATGGGCAGCATGCTGGAGAGGGGCCTGGCAGTCAGCAAGTgtcggtgagtacaaacgcctgtatcagtggttgtatatcagttatctcattctt #### Cpt1a_ID41_13 --> 0 - 0 Original Alignment ------TGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from CESAR ------TGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from Spaln_aa2Genome ----TGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from Spaln_nt2Genome ATGCCAGGAGGT-----CATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from Pairagon ------TGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from Exonerate_protein2genome GGAGAATGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from Exonerate_coding2genome GGAGAATGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc Alignment from GeneWise ------TGCCAGGAGGTCATAGAGACATCCCTAAGCAGTGCCAGTTTTTTGGCAAATGATGTGGACCTGCATTCCTTCCCATTTGACACCTTTGGCAAAGGCTTGATCAAGAAGTGCCGGACGAGTCCCGATGCCTTCATCCAGCTGGCACTGCAGCTCGCACATTACAAG gacctggtcgtgtgcatcccaactccaagcctctcttgtctatctctcagGGTCCATGCCAGGGGGTCATAGCAATTTCCCTCAGCAGTACAAGTTTTTTGGCAAATGATGTAGACCTGCATTCTTTCCATTTTGACACCTTTGGTGAAGGTTTGATAAAGAAATGCCAGACCAGCCCTGATGCCTTCGTCCAGCTTGCACTGCAACTAGCACAATACAAGgtgcgtgatgcactttctacagagaatttgcttttgagatgtgctaagcc #### Csf2ra_ID13430_10 --> 1 - 0 Original Alignment gTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAG------ ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcaggTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCCCCgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from CESAR gTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAG------ ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcaggTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCCCCgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from Spaln_aa2Genome GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAG------ ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCCCCgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from Spaln_nt2Genome GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAGACCC-- ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCCCCgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from Pairagon GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAGACCCTCAGGAAGGACCTCCTGCAGCCC ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCC---------------------CCCgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from Exonerate_protein2genome GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAGACC ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCcccgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from Exonerate_coding2genome GCCTGCGCAGTCCTACTGTGCGCGCTGGCGCTCGGAGTGACGTGCAGGAGGTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAGACC CCGCACGCATACTACACTACCTGCATGTGCCTGGGGTTCCGCTGC---AGGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCcccgtaagaagccataggcaactagagattcaaatgggactgggccaaaagag Alignment from GeneWise GTTCGAGGTGACGCGCCGACTCTTCCCGCCCATCCCAGGGATCAGGGACAAGGTGTCCGACGACGTGCGAGTGAACCCTGAGACCCTCAGGAAGGACCTCCTGCAGCCC ttaccgcacgcatactacactacctgcatgtgcctggggttccgctgcagGTTGGAGGTGACACGCCGTCTCTTCCCGCCAATCCCAGGAATTAGGGACAAGGTGTCTGATGATGTGCGAGTGAACCCTGAGTCCCCCGTAAGAAGCCATAGGCAACTAgagattcaaatgggactgggccaaaagag #### Csf2ra_ID13432_8 --> 0 - 1 Original Alignment GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCg caaagatatgttcttactcccatctctcttaaccatatgtgtgcccacag------GTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCggtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca Alignment from CESAR GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCg ggtccacaaagatatgttcttactcctcttaaccatatgtgtgcccacag------GTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCggtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca Alignment from Spaln_aa2Genome GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCG caaagatatgttcttactcccatctctcttaaccatatgtgtgcccacag------GTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCGgtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca Alignment from Spaln_nt2Genome GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCG caaagatatgttcttactcccatctctcttaaccatatgtgtgcccacag------GTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCGgtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca Alignment from Pairagon GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCG caaagatatgttcttactcccatctctcttaaccatatgtgtgcccacag------GTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCGgtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca Alignment from Exonerate_protein2genome GTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCG caaagatatgttcttactcccatctctcttaaccatatgtgtgcccacagGTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCGgtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca Alignment from Exonerate_coding2genome AGCGCAGAGCCAGGAAGCACACCCCGGAAGGTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCGAGGCTGAGGACACGCGAGTGCCCGGTGCGCTCCTGTATGCAGTGAC caaagatatgttcttactcccatCTCTCTTAACCATATGTGTGCCCACAG---------GTTGTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG--GTGCAGCCTCTCGGTAAGTCAACTGTTATGTTTTCATGCAAAAGATATACCTGCTGTCCAACA Alignment from GeneWise GTGCTCGTCGTGGAGGAGACCCGCCTCGCCTTCCCCAGCCCCGCCCCCCACGGAGGTCACAAGGTCAAGGTGCGCGCGGGCGACACGAGGATGAAGCACTGGGGCGAATGGAGTCCCGCCCATCCTCTCG caaagatatgttcttactcccatctctcttaaccatatgtgtgcccacagGTT------GTTGAGGAGACCCGCCTCACCTTCCCTAGTCCTGCTCCCCATGGATGGCACAGGGTCAAAGTCCGAGCAGGTGATACTAGGATGAAGCACTGGGGGAAATGG------GTGCAGCCTCTCGgtaagtcaactgttatgttttcatgcaaaagatatacctgctgtccaaca #### Csf2ra_ID13436_4 --> 2 - 2 Original Alignment gcGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTCC------------ac tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacaggcACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCATACACCATCacgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from CESAR gcGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTCC------------ac tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacaggcACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCATACACCATCacgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from Spaln_aa2Genome GCGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTCCACG----------- tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacagGCACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCATACACCATCACgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from Spaln_nt2Genome GCGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTC------------CAC tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacagGCACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCATACACCATCACgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from Pairagon GCGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTC------------CAC tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacagGCACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCATACACCATCACgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from Exonerate_protein2genome GCGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTCCAC tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacagGCACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCatacaccatcacgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from Exonerate_coding2genome tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacaggcactgcaggcactggggcagagaacctaatctgtgagattcgagcttcacgctttctttcctgtgcttggcgagaggggccagctgcacctgcagatgtccagcactcactgcaggtccttaactcaccatacaccatcacgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt Alignment from GeneWise GCGCGGCGGGCTCGGGGGCGGAGAACCTGACCTGCGAGATCCGAGCCGCGCGCTTCCTTTCCTGCGCGTGGCGGGAGGGGCCAGCGGCGCCCGCGGACGTCCGGTACTCGCTGCGAGTCCTCAACTCC------------AC tgatagaggtagtgttgaattgcacccaggtcactcccaccactccacagGCACTGCAGGCACTGGGGCAGAGAACCTAATCTGTGAGATTCGAGCTTCACGCTTTCTTTCCTGTGCTTGGCGAGAGGGGCCAGCTGCACCTGCAGATGTCCAGCACTCACTGCAGGTCCTTAACTCACCATACACCATCACgtaagttgtaaacacccagttgtctgtccgcagcacattgccactatctt #### Csf2ra_ID13437_3 --> 0 - 1 Original Alignment CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAA---------g atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACggtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from CESAR CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAA---------g atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACggtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from Spaln_aa2Genome CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAGGCGCGGCGG atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACGgtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from Spaln_nt2Genome CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAA---------G atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACGgtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from Pairagon CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAA---------G atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACGgtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from Exonerate_protein2genome CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAAGGCGCGGCGG atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACGgtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from Exonerate_coding2genome atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagccctttggttgccgctgctggttcagaaggatgatggcactgcaccatggtgtaacactagacgtcaatggcacagttggaggtgcagctgcacattggaagctcagctttgttaatgagcgactgaacggtaagtgtagatgttgtggactccaggttacactttctagctatcatatc Alignment from GeneWise CCCTTCGGTTGCCGCTGCTGGTTCAGGAGGATGATGGCGCTGCACCACGGTGTCACGCTGGATGTCAATGGCACGGTCGGGGGCGCGGCCGCGCACTGGAGGCTGAGCTTCGTCAACGAA---------G atagaatgctccgtgcattaccttaaccgcctctgtgtgtctgtccccagCCCTTTGGTTGCCGCTGCTGGTTCAGAAGGATGATGGCACTGCACCATGGTGTAACACTAGACGTCAATGGCACAGTTGGAGGTGCAGCTGCACATTGGAAGCTCAGCTTTGTTAATGAGCGACTGAACGgtaagtgtagatgttgtggactccaggttacactttctagctatcatatc #### Csf2ra_ID13438_2 --> 2 - 0 Original Alignment ctCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGC------ACCGTGACCTCGCGGGAGGCGGGGATACACCGGCGAGTCTCG aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagccCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGA------gtgagcatggataagtaagatttaatactgcacctaataatcccattagg Alignment from CESAR ctCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGC------ACCGTGACCTCGCGGGAGGCGGGGATACACCGGCGAGTCTCG aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagccCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGA------gtgagcatggataagtaagatttaatactgcacctaataatccc Alignment from Spaln_aa2Genome CTCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGC------ACCGTGACCTCGCGGGAGGCGGGGATACACCGGCGA aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagCCCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGAgtgagcatggataagtaagatttaatactgcacctaataatcccattagg Alignment from Spaln_nt2Genome CTCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGCA------CCGTGACCTCGCGGGAGGCGGGGATACACCGGCGA aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagCCCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGAgtgagcatggataagtaagatttaatactgcacctaataatcccattagg Alignment from Pairagon CTCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGC------ACCGTGACCTCGCGGGAGGCGGGGATACACCGGCGA aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagCCCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGAgtgagcatggataagtaagatttaatactgcacctaataatcccattagg Alignment from Exonerate_protein2genome CTCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGC------ACCGTGACCTCGCGGGAGGCGGGGATACACCGGCGAGTCTCG aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagCCCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGAGTGAGCatggataagtaagatttaatactgcacctaataatcccattagg Alignment from Exonerate_coding2genome aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagccccaaccactccgtatgttggctctgccctaaacttaatctttgatccttggactcgcatgctgacctgggcttgtgatgctgcagctgacaatgtcatggtaatgtcatgcatagtaactgttacatcatgggaagcatcaatacaccggcgagtgagcatggataagtaagatttaatactgcacctaataatcccattagg Alignment from GeneWise CTCCGACCACACCGGACGCCGGCTCCGCCCTCAACCTGACCTTCGACCCCTGGACTCGGACGCTGACCTGGGCCTGCGACACCGCCGCGGGGAACGTCACGGTGACGTCATGC------ACCGTGACCTCGCGGGAGGCGGGGATACACCGGCGA aggtcctccaccacccagtgccaaaccatttctatttattttttaaacagCCCCAACCACTCCGTATGTTGGCTCTGCCCTAAACTTAATCTTTGATCCTTGGACTCGCATGCTGACCTGGGCTTGTGATGCTGCAGCTGACAATGTCATGGTAATGTCATGCATAGTAACTGTTACATCATGGGAAGCATCAATACACCGGCGAgtgagcatggataagtaagatttaatactgcacctaataatcccattagg #### Ctsf_ID674_2 --> 0 - 0 Original Alignment GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAAACAGTG tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAG------gtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct Alignment from CESAR GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAAACAGTG tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAG------gtaagtcgtgcctagtggttagattgttgcagccctctgtagga Alignment from Spaln_aa2Genome GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAA tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAGgtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct Alignment from Spaln_nt2Genome GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAA tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAGgtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct Alignment from Pairagon GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAAACAGTG tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAA------Ggtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct Alignment from Exonerate_protein2genome GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAA tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAGgtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct Alignment from Exonerate_coding2genome GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAA tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAGgtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct Alignment from GeneWise GCCGGCCAGGGCTCTCTGTTCTCCCTGGAAGCCACACTAGAGGAGCCACCTTGCAATGATCCCCTGGTGTGCCCACTGCCTGAGACGAAGAAA tagtaaagggaaaggcagcattggccataagattgttgcttatttttcagGCTGGCCAGGGCTCACTGTTTTCTCTGGAATCCACGCTAGATGAGCCCCCTTGCAATGATCCTTTGGTGTGCTCTCTCCCCGAGACAAAGAAGgtaagtcgtgcctagtggttagattgttgcagccctctgtaggagaggct #### Ctsf_ID675_3 --> 0 - 1 Original Alignment CTCTGCAGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAg atatcacatctgtgactcaatatattttcatttgttgctctgctccccag------AGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTggtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from CESAR CTCTGCAGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAg tagggtatatcacatctgtgactcatttcatttgttgctctgctccccag------AGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTggtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from Spaln_aa2Genome CTCTGCAGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAG atatcacatctgtgactcaatatattttcatttgttgctctgctccccag------AGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTGgtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from Spaln_nt2Genome CTCTGCAGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAG atatcacatctgtgactcaatatattttcatttgttgctctgctccccag------AGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTGgtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from Pairagon CTCTGCAGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAG atatcacatctgtgactcaatatattttcatttgttgctctgctccccag------AGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTGgtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from Exonerate_protein2genome AGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAG atatcacatctgtgactcaatatattttcatttgttgctctgctccccagAGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTGgtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from Exonerate_coding2genome AGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAG atatcacatctgtgactcaatatattttcatttgttgctctgctccccagAGCTTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTGgtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag Alignment from GeneWise CTCTGCAGTTTTGAAGTCCTGGAAGAGCTAAAAGAACACTTGCTGCTGAGGAGGGACTGTAGCCCAGTGAATGCCAAGGTCACAG atatcacatctgtgactcaatatattttcatttgttgctctgctccccagAGC------TTTGAAGCCCTTGAAGCACTTAAGGAACACTTGCTCCTCACAAGGGACTGCAGCTCTGTGAATGCCCAGATGACTGgtgagtgattgctcaagcagatggacagaaagagataatacccaagtaag #### Ctsf_ID681_9 --> 2 - 1 Original Alignment agCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTG------g tcagacaaactcctccatagggttcctttccatattcccctccattacagagCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGggtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from CESAR agCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTG------g tcagacaaactcctccatagggttcctttccatattcccctccattacagagCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGggtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from Spaln_aa2Genome GAGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTG------ tcagacaaactcctccatagggttcctttccatattcccctccattacagAGCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGGgtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from Spaln_nt2Genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTT tcagacaaactcctccatagggttcctttccatattcccctccattacagAGCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTgtactggggtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from Pairagon AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTT------GG tcagacaaactcctccatagggttcctttccatattcccctccattacagAGCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGGgtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from Exonerate_protein2genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTG------G tcagacaaactcctccatagggttcctttccatattcccctccattacagAGCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGGgtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from Exonerate_coding2genome AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTG------G tcagacaaactcctccatagggttcctttccatattcccctccattacagAGCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGGgtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg Alignment from GeneWise AGCTCTTGGATTGTGACAAGGTGGACAAGGCCTGCTTGGGTGGATTGCCCTCCAACGCCTATGCAGCCATAAAGAATTTG------G tcagacaaactcctccatagggttcctttccatattcccctccattacagAGCTCTCACATTGTGGCAAAGAGGATAAAGCCTGTTTGGGTGGATTGCCCTCCAATGCCTATGCAGCCATAAAGAATCTGTACTGGGgtaaagtgtgccgaatccacctgaggatgatagtggctaccatggtgttg #### Ctsf_ID685_13 --> 2 - 0 Original Alignment gcTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG GGTTACTACTACT cttaagctctggtaattccttactattcagctctatctcccactccccaggtTCTAACATCCCTTACTGGGCAATCAAGAAT---------------------------gtgagtttgggtctggtttctatttgatgcttcctagGGGTACTATTACT Alignment from CESAR gcTCTAACATTCCTTACTGGGCCATCAAGAACAGCTGGGGCAGTGACTGGGGTGAGGAG cttaagctctggtaattccttactattcagctctatctcccactccccaggtTCTAACATCCCTTACTGGGCAATCAAGAAT---------------------------gtgagtttgggtctgcttttaat Alignment from Spaln_aa2Genome CGCTCTAACATTCCTTACTGGGCCATCAAGAA CAGCTGGGGCAGTG cttaagctctggtaattccttactattcagctctatctcccactccccagGTTCTAACATCCCTTACTGGGCAATCAAGAATgtgagtttgggtctggtttctatttgatgcttcctag------------- Alignment from Spaln_nt2Genome GCTCTAACATTCCTTACTGGGCCATCAAGAAC---AGCTGGGGCAGTGACTGGGGT-GAGG------AGGGTTACTACTACT cttaagctctggtaattccttactattcagctctatctcccactccccagGTTCTAACATCCCTTACTGGGCAATCAAGAATGTGAGTTTGGGTCTGGTTTCTATTTGATGCTTCCTAGGGGTACTATTACT Alignment from Pairagon GCTCTAACATTCCTTACTGGGCCATCAAGAAC AGCTGGGGCAGTG cttaagctctggtaattccttactattcagctctatctcccactccccagGTTCTAACATCCCTTACTGGGCAATCAAGAATgtgagtttgggtctggtttctatttgatgcttcctag------------- Alignment from Exonerate_protein2genome GCTCTAACATTCCTTACTGGGCCATCAAGAAC cttaagctctggtaattccttactattcagctctatctcccactccccagGTTCTAACATCCCTTACTGGGCAATCAAGAATgtgagtttgggtctggtttctatttgatgcttcctaggggtactattact Alignment from Exonerate_coding2genome cttaagctctggtaattccttactattcagctctatctcccactccccaggttctaacatcccttactgggcaatcaagaatgtgagtttgggtctggtttctatttgatgcttcctaggggtactattact Alignment from GeneWise GCTCTAACATTCCTTACTGGGCCATCAAGAAC---AGCTGGGGCAGTGACTGGGGTGAGGAG cttaagctctggtaattccttactattcagctctatctcccactccccagGTTCTAACATCCCTTACTGGGCAATCAAGAATGTGAGTTTGGGT---------------CTGgtttctatttgatgcttcct #### Ctsw_ID1017_9 --> 0 - 0 Original Alignment CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCACTCTGTC------TTGCTGGTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAGAAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAG---gtaaggtgggtacaggaacacaatgaagcatagaaaagcaatgaagcaaa Alignment from CESAR CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCACTCTGTC------TTGCTGGTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAGAAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAG---gtaaggtgggtacaggaacacaatgaagcatagaaaagcaatgaagc Alignment from Spaln_aa2Genome CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCACTCTGTC------TTGCTGGTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAGgtaaggtgggtacaggaacacaatgaagcatagaaaagcaatgaagcaaa Alignment from Spaln_nt2Genome CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCAC-----TCTG-TCTTGCTGGTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAG--AAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAGGTAAGgtgggtacaggaacacaatgaagcatagaaaagcaatgaagcaaa Alignment from Pairagon CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCACTCTGTCTTGC------TGGTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAG--AAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAGGTAAGgtgggtacaggaacacaatgaagcatagaaaagcaatgaagcaaa Alignment from Exonerate_protein2genome CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCACTCTGTC------TTGCTGGTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAGAAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAG---gtaaggtgggtacaggaacacaatgaagcatagaaaagcaatgaagc Alignment from Exonerate_coding2genome aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagtattatcagaaaggtgtcatcaaggctacacccagttcctgtgaccctcgtcaagaagaccaccccgttctgctattgttggttggttttggtaaaagggaagagggcatgcaaatggggacagtcttaacacattctcataaacgttgtcattccttctcattctgggtcttgaagaactcttggggggcccactggggtgaggtaaggtgggtacaggaacacaatgaagcatagaaaagcaatgaagcaaa Alignment from GeneWise CATTACCAGAAGGGTGTCATCAAGGCTACACCCAGCTCCTGTGACCCTCGGCAAGTGGACCACTCTGTCTTGCTG------GTGGGCTTTGGCAAGGAGAAAGAGGGCATGCAGACAGGGACAGTCTTGTCCCATTCTCGAAAACGTCGCCACTCCTCCCCATACTGGATCCTGAAGAACTCCTGGGGAGCTCACTGGGGCGAG aaatcaatccagagatctcattacactggtaccccatgtgatcgctgcagTATTATCAGAAAGGTGTCATCAAGGCTACACCCAGTTCCTGTGACCCTCGTCAAGAAGACCACCCCGTTCTGCTATTGTTGGTTGGTTTTGGTAAAAGGGAAGAGGGCATGCAAATGGGGACAGTCTTAACACATTCTCATAAACGTTGTCATTCCTTCTCATTCTGGGTCTTGAAGAACTCTTGGGGGGCCCACTGGGGTGAGgtaaggtgggtacaggaacacaatgaagcatagaaaagcaatgaagcaaa #### Ctsw_ID1018_8 --> 2 - 0 Original Alignment ca------ATTGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagtgACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from CESAR ca------ATTGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagtgACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from Spaln_aa2Genome CA------ATTGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagTGACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from Spaln_nt2Genome ---CAAT---TGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagTGACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from Pairagon ------CAATTGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagTGACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from Exonerate_protein2genome AGCAGGCAATTGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagTGACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from Exonerate_coding2genome tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagtgacaatgattggacactacctcactgcacatgggcccatcactgtgactattaacatgaagctgcttctggtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc Alignment from GeneWise -----GCAATTGCCCACTACCTGGCCGTGCATGGACCTATCACCGTGACCATCAACATGAAACTACTCCAG tggaggtagatatgccaccctctaaaatctttctggcgtttcctttccagTGACAATGATTGGACACTACCTCACTGCACATGGGCCCATCACTGTGACTATTAACATGAAGCTGCTTCTGgtacagtgtccagcacaataagaggaaggggggctctaggagctctcttc #### Ctsw_ID1020_6 --> 2 - 1 Original Alignment agCTGCTGGACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACa tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagag------GACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATagtaagttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from CESAR agCTGCTGGACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACa aaagtctctacctgcatgtgacgataatcaactattatttcaacttccagag------GACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATagtaagttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from Spaln_aa2Genome AGCTGCTGGACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACAGTGG tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagAG------GACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATAGTAAgttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from Spaln_nt2Genome AGCTGCTGGACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACA tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagA------GGACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATAgtaagttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from Pairagon AGCTGCTGGACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACA tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagA------GGACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATAgtaagttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from Exonerate_protein2genome AGCTGCTGGACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACA tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagAG------GACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATAgtaagttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from Exonerate_coding2genome tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagaggactgcaaacactgtggcaatggctgcaatgatggctttatatgggatgcatatctaactgtcctcaataatagtaagttattatggctacaagcaggtgaagtgtacttgacatcaaagttt Alignment from GeneWise GACTGCGAACGCTGTGGAAATGGTTGCAATGGTGGCTTCGTGTGGGACGCATATCTAACTGTCCTCAACAACAGTGG tctacctgcatgtgacgattaacttaatcaactattatttcaacttccagagGACTGCAAACACTGTGGCAATGGCTGCAATGATGGCTTTATATGGGATGCATATCTAACTGTCCTCAATAATAGTAAgttattatggctacaagcaggtgaagtgtacttgacatcaaagttt #### Cutc_ID8809_4 --> 2 - 1 Original Alignment gtGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAg atctcctcaggggtagcttgattctggcctgaacatactgctttttacagga---------------------------------------------ATTATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGggtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from CESAR gtGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAg tatgcctcaggggtagcttgattctggcctgaacatactgctttttacagga------------------------------ATT---------------ATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGggtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from Spaln_aa2Genome TGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAG atctcctcaggggtagcttgattctggcctgaacatactgctttttacagGAATTATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGGgtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from Spaln_nt2Genome TGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAG atctcctcaggggtagcttgattctggcctgaacatactgctttttacagGAATTATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGGgtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from Pairagon GTGTTCTTCAAGTAGTAAAACAGAGTGTTCAGATCCCAGTGTTTGTGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAG atctcctcaggggtagcttgattctggcctgaacatactgctttttacagGAATTATTCA---------------------------------------------CCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGGgtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from Exonerate_protein2genome TGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAG atctcctcaggggtagcttgattctggcctgaacatactgctttttacagGAATTATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGGgtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from Exonerate_coding2genome TGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAGCTCTTT atctcctcaggggtagcttgattctggcctgaacatactgctttttacagGAATTATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGGGTACAGgtcaagacaccagctaaaatacatgtataccatacagttgcagc Alignment from GeneWise TGATGATCCGCCCACGCGGAGGCGACTTCTTATACTCCGACCGTGAAGTTGAGGTGATGAAGGCTGACATTCGCCTTGCCAAGCTTTATGGTGCCGATGGTTTGGTGTTTGGGGCATTGACTGAAGATGGACACATTGACAAAGAGCTATGCTTGTCTCTTGTAG atctcctcaggggtagcttgattctggcctgaacatactgctttttacagGAATTATTCACCCACGAGGAGGTGACTTCCTGCACTCAGACCATGAAGTAGAAGTGATGAAAGCTGATATTCGCCTAGCCAAGCTTTATGGTGCTGACGGTTTAGTGTTTGGTGCATTGACTGAAGATGGACATGTTGACAGAGAGTTGTGTATATCTCTTGTGGgtacaggtcaagacaccagctaaaatacatgtataccatacagttgcagc #### Cyp17a1_ID9997_3 --> 2 - 0 Original Alignment taTGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAGC---------------------------GATCTGGTGGACATATTCCCGTGGTTGAAG cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagtaTGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGA---------ATGGAATCCATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATCTAGTGGAGATAATCCCATGG------gtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from CESAR taTGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAGCGATCTGGTGGACATATTCCCGTGGTTGAAG--- cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagtaTGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGA---------ATGGAATCCATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATCTAgtggagataatcccatgggtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from Spaln_aa2Genome TATGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAGCGATCTGGTGGACATATTCCCGTGGTTGAAG--- cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagTATGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGA---------ATGGAATCCATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATCTAgtggagataatcccatgggtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from Spaln_nt2Genome TATGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACA GCGATCTGGTGGACATATTCCCGTGG cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagTATGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGA---------ATGGAATCCATTGTTGTGGTCTTGGGCCACAgtgatcttgttaagaacactccatggtttgatctag---------TGGAGATAATCCCATGGgtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from Pairagon TATGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTA------------CCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAG---------------------------CGATCTGGTGGACATATTCCCGTGG cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagTATGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGAATGGAATCC---------------------ATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATCTAGTGGAGATAATCCCATGGgtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from Exonerate_protein2genome TATGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAGCGATCTGGTGGACATATTCCCGTGGTTGAAG cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagTATGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGAATG---------GAATCCATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATctagtggagataatcccatgggtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from Exonerate_coding2genome TATGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAGCGATCTGGTGGACATATTCCCGTGGTTGAAG cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagTATGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGAATG---------GAATCCATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATctagtggagataatcccatgggtcagttactacggagggaatttttatgaaagagtgacccactccccatt Alignment from GeneWise TATGTCAGGAAGCCAACTCACTGTGTGACTTGATACTTACATACGACGGGGAGTCCCGAGATCTGTCTACGCTCATCTTCAAGTCAGTAATCAATATCATCTGTACCATCTGCTTCAACATCTCTTTTGAGAACAAGGATCCGATACTGACTACCATACAGACCTTTACAGAGGGTATTGTGGATGTCCTGGGCCACAGCGATCTGGTGGACATATTCCCGTGGTTGAAGATT cgtcaagctactcctgtgctctattccattaatgccaacccatctttcagTATGCCAAGAGGCCAACTCACTGTGTGACTTGATACTTTCTTATGACGGGGAGTCCCAAGATCTATCTACACTCATTTTCAAATCAGCAATTAACATCATCTGTACCATATGTTTTAACATCTCTTTTGAGAACATGGATCCAATATTGACTATGAGAATG---------GAATCCATTGTTGTGGTCTTGGGCCACAGTGATCTTGTTAAGAACACTCCATGGTTTGATCTAgtggagataatcccatgggtcagttactacggagggaatttttatgaaagagtgacccactccccatt #### Cyp26a1_ID7414_2 --> 0 - 0 Original Alignment ------------------------------CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagCTGCTGGGTCACGGATCTCGAAATATGCAACGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from CESAR ------------------------------CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagCTGCTGGGTCACGGATCTCGAAATATGCAACGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from Spaln_aa2Genome GTGCTT---------------------CAGCGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagCTGCTGGGTCACGGATCTCGAAATATGCAACGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from Spaln_nt2Genome GAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagctgctgggtcacggatctcgaaatatgcaacgcagGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from Pairagon ------------------------------CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagCTGCTGGGTCACGGATCTCGAAATATGCAACGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from Exonerate_protein2genome ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagctgctgggtcacggatctcgaaatatgcaacgcaggaagtttgttcagatggagcacaggaagtatggctttatctacaagacacatctgtttggctggccaacagtgcgtgtgatgggtacagataacgttcgtcgtatattgctgggggagcaccgcttagtgtcagttcactggcctgcatcagtacgtattatcctgggtgctggctgcctttctaacctgtatgattcctcacacaagaaacaaaagaaggtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from Exonerate_coding2genome CGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagctgctgggtcacggatctcgaaatatgcaaCGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca Alignment from GeneWise ---------------------GTGCTTCAGCGGAGGAAGTTTCTGCAGATGAAGCGCAGGAAATACGGCTTCATCTACAAGACGCATCTGTTTGGGCGGCCCACGGTGCGGGTGATGGGCGCGGATAATGTGCGGCGCATCTTGCTGGGAGAGCACCGGTTGGTGTCGGTGCACTGGCCCGCGTCGGTGCGCACCATCCTGGGCGCTGGCTGCCTCTCCAACCTGCACGATTCCTCGCACAAGCAGCGAAAGAAG ccccttgcaaaccatggccacttccatgctttgcattcctgcatttctagCTGCTGGGTCACGGATCTCGAAATATGCAACGCAGGAAGTTTGTTCAGATGGAGCACAGGAAGTATGGCTTTATCTACAAGACACATCTGTTTGGCTGGCCAACAGTGCGTGTGATGGGTACAGATAACGTTCGTCGTATATTGCTGGGGGAGCACCGCTTAGTGTCAGTTCACTGGCCTGCATCAGTACGTATTATCCTGGGTGCTGGCTGCCTTTCTAACCTGTATGATTCCTCACACAAGAAACAAAAGAAGgtgagcactgcaaggccaattaaagtaatgactggaaggccaattctaca #### Cyp26a1_ID7415_3 --> 0 - 0 Original Alignment ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG GGCGTGAAGGCGCGGAACCTTA caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagCCTTTGTCCGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTGTACCGTgtacgtagccacactgtacttgttgaagGGTGTT---TCTCGTAATATAA Alignment from CESAR ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG GGCGTGAAGGCGCGGAACCTTA caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagCCTTTGTCCGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTGTACCGTgtaactttctggtctgcttaccttccagGGTGTT---TCTCGTAATATAA Alignment from Spaln_aa2Genome ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGGGGCGTGAAGGCGCGGAAC caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagCCTTTGTCCGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTGTACCGT---GTACGTAGCCACACTgtacttgttgaagggtgtttctcgtaatataa Alignment from Spaln_nt2Genome ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCT GTACCGGGGCGTGAAGGCGCGG caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagCCTTTGTCCGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTT---CATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTgtaccgtgtacgtagccacactgtacttgttgaagG---------GTG-TTTCTCGT Alignment from Pairagon ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGGGGCGTGAAGGCGCGGAACCTT----------------------------------------------ATAC caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagCCTTTGTCCGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTT---CATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTGTACCG---------------------TGTACGTAGCCACACTGTACTTGTTGAAGGGTGTTTCTCGTAATATAATAC Alignment from Exonerate_protein2genome GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAG ATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGGGGCGTGAAGGCGCGGAACCTTA caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagcctttgtccGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAatgacccgtaatctcgtttcccttcccattgATGTCCCGTTCA---GTGGTCTGTACCGTGTACGTAGCCACACTGTACTTGTTGAAGGGTGTT---TCTCGTAATATAA Alignment from Exonerate_coding2genome GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagcctttgtccGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTGTACCGTgtacgtagccacactgtacttgttgaagggtgtttctcgtaatataatac Alignment from GeneWise ---------GTGATTATGCAGGCCTTCAGCCGCGAGGCACTCCAGTGCTACGTGCCCGTGATCGCTGAGGAAGTCAGCAGTTGTCTGGAGCAGTGGCTAAGCTGCGGCGAGCGCGGCCTCCTGGTCTACCCCGAGGTGAAGCGCCTCATGTTCCGCATCGCCATGCGCATCCTGCTGGGCTGCGAGCCGGGTCCAGCGGGCGGCGGGGAGGACGAGCAGCAGCTCGTGGAGGCTTTCGAGGAGATGACCCGCAATCTCTTCTCTCTTCCCATTGACGTGCCCTTTAGCGGCCTGTACCGG-GGCGTGAAG------------------------GCGCGGAACCTTATAC caagcacaaagtataggttgacaaacacttccatcctgtgtcttctacagCCTTTGTCCGTCATAATGCATGCATTCAGCAGGGAAGCACTCCAGTGTTATGTCCCTGTTATAGCTGAGGAAGTCAGCAGTTGTTTGGAACAGTGGCTATGCTGTGGTGAACATGGTCTCCTTGCGTATCCTGAGGTGAAGCGCCTTATGTTC---ATTGCTATGCGAATCCTGCTAGGCTGTCAGCAAGGCTCAGCAGGAAGTGGGGAGGATGAACAGCAGCTAGTAGAGTCTTTTGAGGAAATGACCCGTAATCTCGTTTCCCTTCCCATTGATGTCCCGTTCAGTGGTCTGTACCGTGTACGTAGCCACACTGTACTTGTTGAAGGGTGTTTCTCGTAATATAATAC #### Cyp2c39_ID7783_2 --> 0 - 1 Original Alignment ---------TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTg ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctagGATGTGCGATTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAggtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from CESAR ---------TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTg ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctagGATGTGCGATTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAggtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from Spaln_aa2Genome CCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctaggatgtgcgattctcaaaagCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAGgtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from Spaln_nt2Genome ---------TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctagGATGTGCGATTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAGgtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from Pairagon ---------TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctagGATGTGCGATTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAGgtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from Exonerate_protein2genome TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctaggatgtgcgaTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAGgtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from Exonerate_coding2genome TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctaggatgtgcgaTTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAGgtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt Alignment from GeneWise ---------TTCTCAAAAGCCTATGGCCCTGTGTTCACTCTGTATTTGGGCTCACGGCCCACTGTTGTATTACATGGGTATGAAGCAGTGAAGGAAGCTCTGATTGATCATGGGGAGGAGTTTTCTGATAGAGGAAGCATTCCAATGGTAGAAAAGATTAATAACGGCCTTG ttgtagaaggccaggatcgttagtttttgggctctttggttgttctctagGATGTGCGATTCTCAAAAGCCTATGGCCCCCTTTTCACTGTGTATTTAGGTTCTTGTCCCACTGTTGTACTATATGGGTACGAAGCAGTGAAGGAGGCTCTGATCGATCATGGAGAGGAGTTCTCTGACAGAGGAAGCATCCCAATGATAGATGAGATTAATACTGGCCTAGgtaattaaattaaaaggcaagttcaggtttgaggctttgagaattaattt #### Cyp2c50_ID7862_3 --> 2 - 1 Original Alignment gcATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT------g aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagggATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATggtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from CESAR gcATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT------g aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagggATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATggtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from Spaln_aa2Genome GCATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAA------ACCAATG aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagGGATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATGgtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from Spaln_nt2Genome GCATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAAT------G aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagGGATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATGgtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from Pairagon GCATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAA------ACCAATG aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagGGATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATGgtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from Exonerate_protein2genome GCATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAA------ACCAATG aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagGGATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATGgtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from Exonerate_coding2genome GCATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAA------ACCAATG aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagGGATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATGgtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt Alignment from GeneWise GCATTATATTTAGTAAAGGAAATGTATGGAAAAACACAAGGCGCTTCTCACTCACGACTCTGCGGAATTTAGGCATGGGAAAAAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCACGTTGCCTTGTGGAGGAACTTAGGAAAACCAATGGCTCA- aggggagtatgagtgcatagcagctaggttcctttgtgttttctctttagGGATTATATTCAGTAAGGGAAATGTATGGAAAAATATAAGACATTTTGCACTTACCACTCTGCGAAATTTAGGCATTGGAAAAAGAAGCATTGAGGACCAGCTTCAGGAGGAAGCCCGTTGGCCTGTTGAGGAGCTTAGGAAGACCAATACCAATGgtgagtcgaagtgcagacccagaacctagtgtgattttaatccagttttt #### Cyp2c50_ID7863_4 --> 2 - 0 Original Alignment gcTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG--- tttcatacctagctttagtcagtggattgttcacttttctgtctttccaggcTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTT---TGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from CESAR gcTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tttcatacctagctttagtcagtggattgttcacttttctgtctttccaggcTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTTTGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from Spaln_aa2Genome GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tttcatacctagctttagtcagtggattgttcacttttctgtctttccagGCTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTTTGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from Spaln_nt2Genome GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tttcatacctagctttagtcagtggattgttcacttttctgtctttccagGCTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTTTGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from Pairagon GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGA tttcatacctagctttagtcagtggattgttcacttttctgtctttccagGCTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAgtatgccatggctttgggtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from Exonerate_protein2genome GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tttcatacctagctttagtcagtggattgttcacttttctgtctttccagGCTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTTTGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from Exonerate_coding2genome GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tttcatacctagctttagtcagtggattgttcacttttctgtctttccagGCTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTTTGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt Alignment from GeneWise GCTCACCCTGTGATCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTCATCTGCTCAATTATTTTCCAGGATCGTTTTGATTATAAAGATCGGGATTTTCTTAATTTGATGGAAAAACTGAATGAAATAACCAAGATAATGAGCACCCCTTGGTTGCAG tttcatacctagctttagtcagtggattgttcacttttctgtctttccagGCTCACTGTGTGATCCTGCCTTCATCTTGGGTTGTGCTCCCTGCAATGATATCCGCTCAATTATTTTTGATGATCGATTTGAGTATAAAGATCGGGATTTTCTCAATTTGATGGAAAAGTTAAATAAAATATCTAAAATAATGAGTATGCCATGGCTTTGGgtgatttcagatatttggaatgacacccgtttgctgttattattaagcgt #### Cyp2c54_ID7856_2 --> 0 - 1 Original Alignment ---------TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAG---GAAGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGg gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagTCCTCTTCATTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGggtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from CESAR ---------TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAG---GAAGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGg gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagTCCTCTTCATTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGggtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from Spaln_aa2Genome -------TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAG---GAAGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagTCCTCTTCATTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGGgtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from Spaln_nt2Genome TTATCAAGAGT---------TTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGA---AGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagTCCTCTTCATTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGGgtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from Pairagon ---------TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGA---AGGAAGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagTCCTCTTCATTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGGgtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from Exonerate_protein2genome TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAG---GAAGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagtcctcttcaTTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGGgtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from Exonerate_coding2genome TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAG---GAAGCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagtcctcttcaTTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGGgtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa Alignment from GeneWise ---------TTATCAAGAGTTTATGGTCCTGTGTATACTCTATATTTGGGCAGGAAGCCCACTGTGGTGTTGCATGGATATGAGGCAGTGAAGGAA---GCTCTGGTTGACCATGGGGATGTCTTTGCTGGAAGGGGAAGGCTCCCAGTTTTTGATAAAGCTACTAATGGAATGG gggtgacttcatatggttacttcatatttactgttgtgcttttggtttagTCCTCTTCATTATCACGAGTTTATGGTCCATTTTATACTTTATATCTAGGGAGGAAGCCAACTGTTGTTTTACATGGGTATGAGGCTGTGAAGGAGGAAGTTCTTGCTGACCAAGGGGATATTTTTGCTGGAAGGGGTAGTCTCCCATTTTTTGGTAAAGCTACCAATGGAATGGgtgagctctggggcgtgtaccatgcatggttgcactactatgatatccaa #### D19Bwg1357e_ID5846_6 --> 2 - 2 Original Alignment gcGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTAT---gg tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttaggtGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCgggtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from CESAR gcGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTAT---gg tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttaggtGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCgggtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from Spaln_aa2Genome GCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTATGGAAG tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttagGTGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCGGgtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from Spaln_nt2Genome GCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTAT---GG tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttagGTGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCGGgtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from Pairagon GCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTAT---GG tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttagGTGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCGGgtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from Exonerate_protein2genome GCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTATGGAAG tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttagGTGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCGGgtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from Exonerate_coding2genome GCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTATGGAAG tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttagGTGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCGGgtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata Alignment from GeneWise GCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTATGGAAG tatgtttccctgcccagcagtgattatgtagtttcttttttcttttttagGTGACTTAGTGGAGTTAAGCAGAGCAAAACATACCCAGAATATTGTTAAGAAATTTATTACCTATAGCGGgtgagggcaggattgtgtattgaggcttccctaaaatactaaattgaata #### D19Ertd737e_ID13192_2 --> 0 - 1 Original Alignment AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCAAAAAAg atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTCA------ggtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag Alignment from CESAR AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCAAAAAAg atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTCA------ggtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag Alignment from Spaln_aa2Genome AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCC- atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTCAGgtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag Alignment from Spaln_nt2Genome AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCAAAAAAG atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTC------AGgtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag Alignment from Pairagon AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCAAAAAAG atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAG-----------AAAGAGgtcaggtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag Alignment from Exonerate_protein2genome AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCAAAAAAG atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTCA------Ggtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag Alignment from Exonerate_coding2genome AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCAAAAAAGGCAAATTGAAGAATGAAAAGGAATCTCACAG atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTCAGGTATACCTCCAAGTAGCTTAGGAATGTTGGCTTACATttaaattaagtag Alignment from GeneWise AAATTTCAAGAATTGCATAAAAAAAATTCTGAACAGAAAAATTCAACGCCAAGATTCAGACAGAAAAAAAGAAAACGCTCCA atgcccatcttctgcctacgtgtacacaggggtttttcttttattttaagAAGTTTCAAGAATTGCATAAAAAAAACTCAGAACAAAAGAATTTAACACTAAGATTCAGGCAGAAAAAAAGAAAGAGGTCAGgtatacctccaagtagcttaggaatgttggcttacatttaaattaagtag #### Dagla_ID2755_15 --> 1 - 0 Original Alignment gATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCCAAA ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccaggGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCC---gtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctatatg Alignment from CESAR gATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCCAAA ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccaggGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCC---gtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctat Alignment from Spaln_aa2Genome GATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCC ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccagGGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCCgtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctatatg Alignment from Spaln_nt2Genome GATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCC ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccagGGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCCgtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctatatg Alignment from Pairagon GATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCC ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccagGGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCCgtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctatatg Alignment from Exonerate_protein2genome GATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCCAAA ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccagGGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCC---gtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctat Alignment from Exonerate_coding2genome GATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCCAAA ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccagGGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAACCC---gtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctat Alignment from GeneWise GATTGGCCTTTCCCAGCTGGAAGGTTTCCGTCGGCAGCTTCTGGATGTCCTGCAGCGGAGCACCAAGCCCAAA ggacagagatgttggtaaagaaggaaacaaatgttttgatgattctccagGGTTGGCCTTTCCCAACTAGAAGGATTTTGCAGGCAGCTTTTAGATGTCTTGCAACGGAGTACTAAA---CCCgtaagtaatactggtcagagctacagaaccaaaaaacgcctgtctatatg #### Dagla_ID2759_11 --> 0 - 0 Original Alignment GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG ttacacttcacttttgttacactaccacttatctctctcctactacacagGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTG---------gtgtgtggtgtgccgcggtaactgatgttccagtgtctcacagttgctct Alignment from CESAR GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG ttacacttcacttttgttacactaccacttatctctctcctactacacagGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTG---------gtgtgtggtgtgccgcggtaactgatgttccagtgtctcac Alignment from Spaln_aa2Genome GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG ttacacttcacttttgttacactaccacttatctctctcctactacacagGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTGGTGTGTGGTgtgccgcggtaactgatgttccagtgtctcacagttgctct Alignment from Spaln_nt2Genome GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG ttacacttcacttttgttacactaccacttatctctctcctactacacagGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTGG--TGTGTGgtgtgccgcggtaactgatgttccagtgtctcacagttgct Alignment from Pairagon GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTT--------------------------------------------------- ttacacttcacttttgttacactaccacttatctctctcctactacacagGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTGGTGTGTGGTGTGCCGCGGTAACTGATGTTCCAGTGTCTCACAGTTGCTCT Alignment from Exonerate_protein2genome GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTG ttacacttcacttttgttacactaccacttatctctctcctactacacagGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTGgtgtgtggtgtgccgcggtaactgatgttccagtgtctcacagttgctct Alignment from Exonerate_coding2genome ttacacttcacttttgttacactaccacttatctctctcctactacacaggatgccttaactgatttaacaggtgatgcagagcaccttcctgcagagacacacagagttgcctggttggtgtgtggtgtgccgcggtaactgatgttccagtgtctcacagttgctct Alignment from GeneWise --------------------------------------------------GATGCCCTGACTGACCTGACAGGCGATGCTGAGCGCCTCCCTGTGGAGGGACACAGAGGCACCTGGTTGGGCCACAAG TTACACTTCACTTTTGTTACACTACCACTTATCTCTCTCCTACTACACAGGATGCCTTAACTGATTTAACAGGTGATGCAGAGCACCTTCCTGCAGAGACACACAGAGTTGCCTGGTTGGTGTGTGGTgtgccgcggtaactgatgttccagtgtctcacagttgctct #### Dagla_ID2760_10 --> 0 - 0 Original Alignment GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcag---TATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAgtgctagccattgtattcaaatttacacttcacttttgttacactaccac Alignment from CESAR GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG tcgcttatcagctttccaaaattccgttcttttttgtgccccttgctcag---TATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAgtgctagccattgtattcaaatttacacttcacttttgttacactaccac Alignment from Spaln_aa2Genome GTCTATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcagTATGAAACTCCCTTTTAT---GTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAgtgctagccattgtattcaaatttacacttcacttttgttacactaccac Alignment from Spaln_nt2Genome TATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcagTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAgtgctagccattgtattcaaatttacacttcacttttgttacactaccac Alignment from Pairagon TATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCA---------------------------------------------------- cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcagTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAGTGCTAGCCATTGTATTCAAATTTACACTTCACTTTTGTTACACTACCAC Alignment from Exonerate_protein2genome TATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcagTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAgtgctagccattgtattcaaatttacacttcacttttgttacactaccac Alignment from Exonerate_coding2genome cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcagtatgaaactcccttttatgttgctgttgaccatgataagaagaaagtagtggtcagcatcagggggactttatccccgaaagtgctagccattgtattcaaatttacacttcacttttgttacactaccac Alignment from GeneWise TATGAAACTCCCTTCTACGTAGCTGTGGACCATGACAAGAAGAAAGTGGTGATCAGTATCCGGGGAACACTGTCCCCCAAG cttatcagctttccaaaattccttcgttcttttttgtgccccttgctcagTATGAAACTCCCTTTTATGTTGCTGTTGACCATGATAAGAAGAAAGTAGTGGTCAGCATCAGGGGGACTTTATCCCCGAAAgtgctagccattgtattcaaatttacacttcacttttgttacactaccac #### Dak_ID2897_16 --> 0 - 0 Original Alignment CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTCAAG ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTC---gtaagtagtcactcactagtaagtcagctcaccattaaggacctaaggat Alignment from CESAR CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTCAAG ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTC---gtaagtagtcactcactagtaagtcagctcaccattaaggacctaag Alignment from Spaln_aa2Genome CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTC ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTCgtaagtagtcactcactagtaagtcagctcaccattaaggacctaaggat Alignment from Spaln_nt2Genome CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTCA-AG ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTCGTAAgtagtcactcactagtaagtcagctcaccattaaggacctaaggat Alignment from Pairagon CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTC ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTCgtaagtagtcactcactagtaagtcagctcaccattaaggacctaaggat Alignment from Exonerate_protein2genome CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTC ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTCgtaagtagtcactcactagtaagtcagctcaccattaaggacctaaggat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTGGATTCTCTGTGGGCAGCAGCACAGGAGTTCCAAGCCTGGAAGAGCCCAGGGGCCAGTCTCCTCCCAGTCCTGACTAAAGCAGTC ttggccccccctatggtgctaagattggctgcagtctctgatccctgcagCTAGACTCCCTGTGGTCAGCAGCACAGGAGTTCCAAGCCTGGAAAAGTCCCGGCGCTAGCCTCCTTCCAGTCCTTACAAAAGCTGTCgtaagtagtcactcactagtaagtcagctcaccattaaggacctaaggat #### Dak_ID2899_14 --> 0 - 2 Original Alignment CTCTATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGaa ttactacagctagtacaaatttattacgtccaactaccatgtgtgcccag---TATGGATTGTTCCTCACTGCTTCAGCCCAACCTCTG------AAAACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGaagtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc Alignment from CESAR CTCTATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGaa gccttactacagctagtacaaatttacgtccaactaccatgtgtgcccag---TATGGATTGTTCCTCACTGCTTCAGCCCAACCTCTG------AAAACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGaagtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc Alignment from Spaln_aa2Genome CTCTATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGAA ttactacagctagtacaaatttattacgtccaactaccatgtgtgcccag---TATGGATTGTTCCTCACTGCTTCAGCCCAACCTCTG------AAAACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGAAgtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc Alignment from Spaln_nt2Genome CTCTATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGAA ttactacagctagtacaaatttattacgtccaactaccatgtgtgcccag---TATGGATTGTTCCTCACTGCTTCAGCCCAACCTCT------GAAAACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGAAgtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc Alignment from Pairagon CTCTATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGAA ttactacagctagtacaaatttattacgtccaactaccatgtgtgcccag---TATGGATTGTTCCTCACTGCTTCAGCCCAACCTCT------GAAAACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGAAgtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc Alignment from Exonerate_protein2genome TATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGAA ttactacagctagtacaaatttattacgtccaactaccatgtgtgcccagTATGGATTGTTCCTCACTGCTTCAGCCCAACCTCTG------AAAACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGAAgtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --------------------------------------------------TATGGCCTGTTCCTGACTGCAGCTGCCCAGCCTCTCAAGGCCAAGACTGACCTCCCAACCTGGTCTGCTGCCATGGATGCCGGCTTAGAGTCCATGCAGAA TTACTACAGCTAGTACAAATTTATTACGTCCAACTACCATGTGTGCCCAGTATGGATTGTTCCTCACTGCTTCAGCCCAACCTCTGAAA------ACTGACCTGCCAACCTGGTCTGCTGCCATGGATGCTGGCCTAGACTCCATGCAGAAgtaaggcagtctttttacctctcaacaaaaagtgaggttgtgccatatgc #### Dak_ID2901_12 --> 2 - 1 Original Alignment gtGTAACATCAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAg tagggaatgtagaggttcatgttttgttctaaccctgtgatctctcctaggt---------AAGCAGGTAGCCCTGGTA---TATCGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGCA---GAGAGAGCTGCTGGTGATGGA------GATTCCATGCACAGCCGTGCTTCCAAGggtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc Alignment from CESAR gtGTAACATCAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAg gcacatgcatagggaatgtagaggtgttctaaccctgtgatctctcctaggt---------AAGCAGGTAGCCCTGGTA---TATCGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGCA---GAGAGAGCTGCTGGTGATGGAGAT------TCCATGCACAGCCGTGCTTCCAAGggtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc Alignment from Spaln_aa2Genome CAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAG tagggaatgtagaggttcatgttttgttctaaccctgtgatctctcctagGTAAGCAGGTAGCCCTGGTATAT---CGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGCA---GAGAGAGCTGCTGGTGATGGAGAT------TCCATGCACAGCCGTGCTTCCAAGGgtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc Alignment from Spaln_nt2Genome CAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAG tagggaatgtagaggttcatgttttgttctaaccctgtgatctctcctagGTAAGCAGGTAGCCC---TGGTATATCGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGC---AGAGAGAGCTGCTGGTGATGGAGA------TTCCATGCACAGCCGTGCTTCCAAGGgtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc Alignment from Pairagon GTGTAACATCAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAG tagggaatgtagaggttcatgttttgttctaaccctgtgatctctcctagGT---------AAGCAGGTAGCCCTGGTAT---ATCGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGC---AGAGAGAGCTGCTGGTGATGGAGA------TTCCATGCACAGCCGTGCTTCCAAGGgtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc Alignment from Exonerate_protein2genome CAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAG tagggaatgtagaggttcatgttttgttctaaccctgtgatctctcctagGTAAGCAGGTAGCCCTGGTATAT---CGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGCA---GAGAGAGCTGCTGGTGATGGAGAT------TCCATGCACAGCCGTGCTTCCAAGGgtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CAAAGCAGATGGCACTTGTGCTGGATCGGATATGCACCACCCTCATCGGACTGGAGGAGCACCTGAATGCCTTGGACAGGGCTGCTGGTGATGGGGATTGTGGTTCTACCCATAGCCGTGCTGCCAAAG tagggaatgtagaggttcatgttttgttctaaccctgtgatctctcctagGTAAGCAGGTAGCCCTGGTATAT---CGGATATGTGCCACCCTCATAGGATCTGAAGAGCACCTGAATGCA---GAGAGAGCTGCTGGTGATGGAGAT------TCCATGCACAGCCGTGCTTCCAAGGgtgaggttccttcttccggccacaaaggccaatctttgggcctagctgtc #### Dak_ID2902_11 --> 2 - 1 Original Alignment atGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTG------------------ACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAg ctgtatgaatgggactgtctaggacctaaaaccttggcttctcttggcagat---------------AAACGT---TAT---ATGACCAAAGTCTCTGTCATGACCAAAGTCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGggtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag Alignment from CESAR atGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTGACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAg atcaaggcactactgctgtatgaatctaaaaccttggcttctcttggcagatAAACGTTATATGACCAAAGTC---TCTGTCATGACCAAAGTCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGggtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag Alignment from Spaln_aa2Genome ATGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTGACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAG ctgtatgaatgggactgtctaggacctaaaaccttggcttctcttggcagATAAACGTTATATGACCAAAGTC---TCTGTCATGACCAAAGTCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGGgtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag Alignment from Spaln_nt2Genome ATGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTGACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAG ctgtatgaatgggactgtctaggacctaaaaccttggcttctcttggcagATAAACGTTATATGACCAAAGTCT---CTGTCATGACCAAAGTCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGGgtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag Alignment from Pairagon ATGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTGACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAG ctgtatgaatgggactgtctaggacctaaaaccttggcttctcttggcagataaacgttatatgaccaaagtctctgtcatgaccaaag------------------------------------------TCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGGgtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag Alignment from Exonerate_protein2genome ATGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTGACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAG ctgtatgaatgggactgtctaggacctaaaaccttggcttctcttggcagATAAACGTTATATGACCAAAGTC---TCTGTCATGACCAAAGTCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGGgtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ATGCTGAAACTACTGCAAAAGCCTGGCCTCACATGGCCAAGGTCTCTGTGACTGGGAGGAAGCGGATTCGGGCAGCTCCCACAGAGCCTCCAGAAGCCCCTGAAGCCACTGCAGCAGGAG ctgtatgaatgggactgtctaggacctaaaaccttggcttctcttggcagATAAACGTTATATGACCAAAGTC---TCTGTCATGACCAAAGTCTCCATAACTGGGAGGAAACAGATCCGGGCATCCCCCACAGAGCCACCTGAGTCCCCGGAAGCTACTGTTGCAGGGGgtgagtagtccagatgtgaatactaaggacaaggaaggcttacctagcag #### Dak_ID2904_9 --> 2 - 1 Original Alignment gc---TCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGg gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcaggtCAGTCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTggtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc Alignment from CESAR gc---TCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGg gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcaggtCAGTCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTggtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc Alignment from Spaln_aa2Genome GCTCTTCAGTGGTGCTGATA---GTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcagGTCAGTCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTGgtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc Alignment from Spaln_nt2Genome GCTCTTCAGTGGT---GCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcagGTCAGTCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTGgtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc Alignment from Pairagon GTCAGGCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcagGTCAG--TCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTGgtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc Alignment from Exonerate_protein2genome GC---TCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcagGTCAGTCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTGgtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --GGCTCTTCAGTGGTGCTGATAGTCAACAATCTGGGTGGCCTGTCTTTCCTGGAACTGGGCATCATAGCTGATGCTGCCATACGCTTGCTGG gtgtgtctaggcatgctccaagcatgctgtacctctcccctttcttgcagGTCAGTCATCAGTGGTACTGATAGTGAATAATCTTGGTGGTCTGTCCTTCCGGGAACTGGGTATCACTGCTGATGCTGCCATACATTTGCTTGgtaaagaacctcatcaggcatccatatggaaaccctttaatgcctatgcc #### Ddb1_ID2930_15 --> 2 - 1 Original Alignment agATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGCTCTTTTCTACTTTGGGCTCAACATCGAGACAg ccatagagcttattccttggtcaccctatggtgaactatttatccttcagagATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGG---------------------------------ggtaccactgtagatgatttgaatgctgggtattaagccctaacctcttga Alignment from CESAR agATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGCTCTTTTCTACTTTGGGCTCAACATCGAGACAg ccatagagcttattccttggtcaccctatggtgaactatttatccttcagagATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGG---------------------------------ggtaccactgtagatgatttgaatgctgggtattaagccctaacctcttga Alignment from Spaln_aa2Genome AGATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGCTCTTTTCTACTTTGGGCTCAACATCGAG- ccatagagcttattccttggtcaccctatggtgaactatttatccttcagAGATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGGTACCACTGTAGATGATTTGAATGCTGGGTattaagccctaacctcttga Alignment from Spaln_nt2Genome AGATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGG ccatagagcttattccttggtcaccctatggtgaactatttatccttcagAGATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGgtaccactgtagatgatttgaatgctgggtattaagccctaacctcttga Alignment from Pairagon AGATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGG ccatagagcttattccttggtcaccctatggtgaactatttatccttcagAGATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGgtaccactgtagatgatttgaatgctgggtattaagccctaacctcttga Alignment from Exonerate_protein2genome AGATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGCTCTTTTCTACTTTGGGCTCAACA ccatagagcttattccttggtcaccctatggtgaactatttatccttcagAGATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGGTACCACTGTAGATGATTTGAATGctgggtattaagccctaacctcttga Alignment from Exonerate_coding2genome AGATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGCTCTTTTCTACTTTGGGCTCAACA ccatagagcttattccttggtcaccctatggtgaactatttatccttcagAGATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGGTACCACTGTAGATGATTTGAATGctgggtattaagccctaacctcttga Alignment from GeneWise AGATCATTCCTCGATCCATCCTGATGACCACTTTTGAGAGTAGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGCTCTTTTCTACTTTGGGCTCAACATC-- ccatagagcttattccttggtcaccctatggtgaactatttatccttcagAGATCATTCCTCGATCCATATTGATGACCACCTTTGAAGGTGGCCACTACCTCCTTTGTGCCTTGGGAGATGGGGGTACCACTGTAGATGATTTGAATGCTGGgtattaagccctaacctcttga #### Ddb1_ID2931_16 --> 2 - 2 Original Alignment gtTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGAC---ag gtaacaacttcgccctattttgcttcccatttttcctctttttcttttaggtTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATaggtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from CESAR gtTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGAC---ag gtaacaacttcgccctattttgcttcccatttttcctctttttcttttaggtTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATaggtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from Spaln_aa2Genome GTTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACAGT-- gtaacaacttcgccctattttgcttcccatttttcctctttttcttttagGTTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATAGgtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from Spaln_nt2Genome GTTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGAC---AG gtaacaacttcgccctattttgcttcccatttttcctctttttcttttagGTTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATAGgtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from Pairagon GTTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGAC---AG gtaacaacttcgccctattttgcttcccatttttcctctttttcttttagGTTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATAGgtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from Exonerate_protein2genome GTTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGAC---AG gtaacaacttcgccctattttgcttcccatttttcctctttttcttttagGTTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATAGgtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from Exonerate_coding2genome GTTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGAC---AG gtaacaacttcgccctattttgcttcccatttttcctctttttcttttagGTTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATAGgtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt Alignment from GeneWise GTTTACTGAGTGACCGTAAAAAGGTGACTTTGGGCACCCAGCCCACGGTGTTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTCATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAGGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACAGT-- gtaacaacttcgccctattttgcttcccatttttcctctttttcttttagGTTTATTGAGCGACCGTAAAAAGGTAACCTTGGGCACCCAGCCCACTGTGCTGAGGACATTCCGTTCTCTTTCTACCACCAACGTCTTTGCTTGCTCTGACCGGCCCACTGTGATCTATAGCAGCAATCACAAGTTGGTCTTCTCCAATGTCAACCTCAAGGAAGTGAACTATATGTGTCCTCTCAACTCAGATGGCTATCCTGACCATAGgtaagtgttcctaggtgtcccaagcagaggtcacatatcattttctgatt #### Ddb1_ID2932_17 --> 1 - 2 Original Alignment tCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCag actggagttgtacatcatggtggggctcttccttttggacaatgctttagt---GCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTaggtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from CESAR tCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCag gacactggagttgtacatcatggtgctcttccttttggacaatgctttagt---GCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTaggtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from Spaln_aa2Genome TCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCAG actggagttgtacatcatggtggggctcttccttttggacaatgctttagT---GCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTAGgtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from Spaln_nt2Genome TCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCAG actggagttgtacatcatggtggggctcttccttttggacaatgctttagT---GCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTAGgtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from Pairagon TCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCAG actggagttgtacatcatggtggggctcttccttttggacaatgctttagT---GCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTAGgtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from Exonerate_protein2genome TCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCAG actggagttgtacatcatggtggggctcttccttttggacaatgcttTAGTGCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTAGgtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from Exonerate_coding2genome TCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCAG actggagttgtacatcatggtggggctcttccttttggacaatgcttTAGTGCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTAGgtaacattacacctgagatttacacctaagaagtgggaatggggcagggt Alignment from GeneWise TCTGGCATTGGCCAATAACAGCACTCTCACCATTGGCACCATCGATGAGATCCAGAAGCTCCATATTCGCACAGTTCCCCTCTATGAGTCTCCCAG actggagttgtacatcatggtggggctcttccttttggacaatgctttagT---GCATTGGCCAATAACAGTACTCTCACAATTGGTACCATTGATGAAATGCAGAAGCTCCACATCCGGACAGTCCCCCTCTATGAGTCTCCTAGgtaacattacacctgagatttacacctaagaagtgggaatggggcagggt #### Ddb1_ID2936_21 --> 2 - 0 Original Alignment gaAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacctcagga---------ACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from CESAR gaAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG cctgaggagaagtctatcaagcacttcttgactcttctttcccacctcagga---------ACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from Spaln_aa2Genome GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacctcagGA---------ACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from Spaln_nt2Genome AGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacctcagGAACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from Pairagon GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacctcagGA---------ACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from Exonerate_protein2genome ACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacCTCAGGAACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from Exonerate_coding2genome ACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacCTCAGGAACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat Alignment from GeneWise GAAAACTACAGACTGTGGCTGAAAAGGAAGTAAAAGGAGCTGTGTACTCTATGGTGGAGTTTAATGGGAAGCTGCTTGCCAGCATCAATAGCACG gagaagtctatcaagcactggcttatcttgactcttctttcccacctcagGA---------ACTGTCACTGATAAGGAAGTAAAAGGGGCAGTGTACTCAATGGTCGACTTTAATGGGAAATTATTGGCCAGCACGAATAGCACAgtgagtgacaagggtttttaggctgaactctgatgacccacatttggaat #### Ddb1_ID2939_24 --> 1 - 1 Original Alignment tGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCTACA---CAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAg ttggtagaggggagtgctctggtctcccgaggtctttgtggaatctgcagt------ACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAggtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt Alignment from CESAR tGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCTACA---CAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAg taaggcttggtagaggggagtgctccccgaggtctttgtggaatctgcagt------ACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAggtaagagctgtgggatggcttgcttatgcaaagttgccactctttcctta Alignment from Spaln_aa2Genome TGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCT---ACACAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAG ttggtagaggggagtgctctggtctcccgaggtctttgtggaatctgcagT------ACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAGgtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt Alignment from Spaln_nt2Genome CACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCTACA---CAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAG ttggtagaggggagtgctctggtctcccgaggtctttgtggaatctgcagTACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAGgtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt Alignment from Pairagon TGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCTACA---CAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAG ttggtagaggggagtgctctggtctcccgaggtctttgtggaatctgcagT------ACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAGgtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt Alignment from Exonerate_protein2genome TGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCT---ACACAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAG ttggtagaggggagtgctctggtctcccgaggtctttgtggaatCTGCAGTACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAGgtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt Alignment from Exonerate_coding2genome TGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCT---ACACAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAG ttggtagaggggagtgctctggtctcccgaggtctttgtggaatCTGCAGTACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAGgtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt Alignment from GeneWise TGCTGCCACCACTGATGAGGAGCGGCAGCACCTACAGGAGGTTGGTCTCTTCCACCTGGGCGAGTTTGTCAATGTGTTCTGCCATGGCTCCCTAGTTATGCAGAATCTGGGCGAGGCTTCTACCCCTACA---CAGGGCTCGGTGCTCTTTGGCACAGTCAACGGCATGATAG ttggtagaggggagtgctctggtctcccgaggtctttgtggaatctgcagT------ACAACTGTTGAGGAACGTCAGCATTTACAGGAAATAGTTCTCTTCCATCTAGGGGAGTTTGTCATTGTGTTTTGCCACAGCTCTCTAGTTATGAAGAATCTGGGTGAGGCCTCCACTCCTACGACTCAGGGATCAGTCCTTTTTGGCACAGTCAATGTCATGATAGgtaagagctgtgggatggcttgcttatgcaaagcttgatcctgtgtcttt #### Dkk1_ID6483_2 --> 0 - 1 Original Alignment CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATg ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---GTTGAT------CAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGC------cgtgagtcattaagtaccccagtatctattgatggctttggttaacaagtt Alignment from CESAR CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATg ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---GTTGAT------CAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGC------cgtgagtcattaagtaccccagtatctattgatggctttggttaacaagtt Alignment from Spaln_aa2Genome CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGC- ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCCgtgagtcattaagtaccccagtatctattgatggctttggttaacaagtt Alignment from Spaln_nt2Genome CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCA AA ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGC---------TGTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCCgtgagtcattaagtaccccagtatctattgatggctttggttaacaagTT Alignment from Pairagon CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCA ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCCgtgagtcattaagtaccccagtatctattgatggctttggttaacaagtt Alignment from Exonerate_protein2genome CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAA ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCCGTGAgtcattaagtaccccagtatctattgatggctttggttaacaagtt Alignment from Exonerate_coding2genome CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAA ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCT---------GTTGATCAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCCGTGAgtcattaagtaccccagtatctattgatggctttggttaacaagtt Alignment from GeneWise CCCTACCCTTGCGCTGAAGATGAGGAGTGCGGCTCTGACGAGTACTGCTCCAGCCCCAGCCGCGGGGCAGCCGGCGTCGGAGGTGTACAGATCTGTCTGGCTTGCCGAAAGCGCAGGAAGCGCTGCATGAGGCACGCTATGTGCTGCCCCGGGAACTACTGCAAAAATGGAATA- ttatttgggaactcaactgatctacctgtaacaattctcattcttctcagCCATTCCCTTGTGTTATAGATGAGGAGTGTGGTTCTGATAAACATAGTCCCAGTCCCAGCTGTGGAGCGGCTGTTGAT---------CAGATCTGCTTGGCTTGCCGAAGACACAGAAAGTGTTGTGTAAGGCATGCCATGTGTTGCCCTGAGAACCACTGCCGTGAGTCATTAAgtaccccagtatctattgatggctttggttaacaagtt #### Dnmbp_ID8855_11 --> 0 - 0 Original Alignment AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACT---GAGCGAGCGGAGAAGCTGAAGGACAAGAAGACTCTGGAGGAGCTGCAGTCAGCCCGAAACAACTACGAGGCCCTGAACTCGCAGCTGCTGGACGAGCTGCCCAAGTTCCAGCAGTACGCCCAGAGCCTCTTCACCAACTGCATCCACGGCTATGCCGAAGCCCACTGTGACTTCGTGCAGCAAGCCCTGGAGCAGCTGCAGCCGCTGCTGTCG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTTG------------GCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTGAT---------------------------AAATCTTTGGAGGAACTGCAGTCAACCCGAAACAATCATGAGGCTCTAAACACTAAGCTGCTAGATGCACTGCCCAAATTCCAGCAGTATGACCAGAGTCTCTTTGCCAACTGTGTCTATGGATATGCTAAAGCCCATTGTGACTTTCTTCAGCAGGCACTGGAGCAA------------------gtaatgcgtcgggtcttctccttgccaatggcaaatgattactagtgaag Alignment from CESAR AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACTGAGCGAGCGGAGAAGCTGAAGGACAAGAAGACTCTGGAGGAGCTGCAGTCAGCCCGAAACAACTACGAGGCCCTGAACTCGCAGCTGCTGGACGAGCTGCCCAAGTTCCAGCAGTACGCCCAGAGCCTCTTCACCAACTGCATCCACGGCTATGCCGAAGCCCACTGTGACTTCGTGCAGCAAGCCCTGGAGCAGCTGCAGCCGCTGCTGTCG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTTG------------GCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTGAT------------------------AAATCTTTGGAGGAACTGCAGTCAACCCGAAACAATCATGAGGCTCTAAACACTAAGCTGCTAGATGCACTGCCCAAATTCCAGCAGTATGACCAGAGTCTCTTTGCCAACTGTGTCTATGGATATGCTAAAGCCCATTGTGACTTTCTTCAGCAGGCACTGGAGCAA------------------gtaatgcgtcgggtcttctccttgccaatggc Alignment from Spaln_aa2Genome AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACTGAGCGAGCGGAGAAGCTGAAGGACAAGAAGACTCTGGAGGAGCTGCAGTCAGCCCGAAACAACTACGAGGCCCTGAACTCGCAGCTGCTGGACGAGCTGCCCAAGTTCCAGCAGTACGCCCAGAGCCTCTTCACCAACTGCATCCACGGCTATGCCGAAGCCCACTGTGACTTCGTGCAGCAAGCCCTGGAGCAGCTGCAGCCGCTGCTGTCG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTTG------------GCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTGAT------------------------AAATCTTTGGAGGAACTGCAGTCAACCCGAAACAATCATGAGGCTCTAAACACTAAGCTGCTAGATGCACTGCCCAAATTCCAGCAGTATGACCAGAGTCTCTTTGCCAACTGTGTCTATGGATATGCTAAAGCCCATTGTGACTTTCTTCAGCAGGCACTGGAGCAAGTA------ATGCGTCGGgtcttctccttgccaatggcaaatgattacta Alignment from Spaln_nt2Genome AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACTGAGCGAGCGGAGAAGCTGAAGGACAAGAAGACTCTGGAGGAGCTGCAGTCAGCCCGAAACAACTACGAGGCCCTGAACTCGCAGCTGCTGGACGAGCTGCCCAAGTTCCAGCAGTACGCCCAGAGCCTCTTCACCAACTGCATCCACGGCTATGCCGAAGCCCACTGTGACTTCGTGCAGCAAGCCCTGGAGCAG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTT------------GGCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTG------------------------ATAAATCTTTGGAGGAACTGCAGTCAACCCGAAACAATCATGAGGCTCTAAACACTAAGCTGCTAGATGCACTGCCCAAATTCCAGCAGTATGACCAGAGTCTCTTTGCCAACTGTGTCTATGGATATGCTAAAGCCCATTGTGACTTTCTTCAGCAGGCACTGGAGCAAgtaatgcgtcgggtcttctccttgccaatggcaaatgattactagtgaag Alignment from Pairagon AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACTGAGCGAGCGGAGAAGCTGAAGGACAAGAAGACTCTGGAGGAGCTGCAGTCAGCCCGAAACAACTACGAGGCCCTGAACTCGCAGCTGCTGGACGAGCTGCCCAAGTTCCAGCAGTACGCCCAGAGCCTCTTCACCAACTGCATCCACGGCTATGCCGAAGCCCACTGTGACTTCGTGCAGCAAGCCCTGGAGCAG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTT------------GGCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTG------------------------ATAAATCTTTGGAGGAACTGCAGTCAACCCGAAACAATCATGAGGCTCTAAACACTAAGCTGCTAGATGCACTGCCCAAATTCCAGCAGTATGACCAGAGTCTCTTTGCCAACTGTGTCTATGGATATGCTAAAGCCCATTGTGACTTTCTTCAGCAGGCACTGGAGCAAgtaatgcgtcgggtcttctccttgccaatggcaaatgattactagtgaag Alignment from Exonerate_protein2genome AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACTGAGCGAGCG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTTG------------GCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTGATAAATCTttggaggaactgcagtcaacccgaaacaatcatgaggctctaaacactaagctgctagatgcactgcccaaattccagcagtatgaccagagtctctttgccaactgtgtctatggatatgctaaagcccattgtgactttcttcagcaggcactggagcaagtaatgcgtcgggtcttctccttgccaatggcaaatgattactagtgaag Alignment from Exonerate_coding2genome ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagaaacagcggacagagcagcttattatcaaccctttaaaccaattgttggcaccatacaaactgttacaaaggcgttttgacaaacttcttgacttatacaactgcattgataaatctttggaggaactgcagtcaacccgaaacaatcatgaggctctaaacactaagctgctagatgcactgcccaaattccagcagtatgaccagagtctctttgccaactgtgtctatggatatgctaaagcccattgtgactttcttcagcaggcactggagcaagtaatgcgtcgggtcttctccttgccaatggcaaatgattactagtgaag Alignment from GeneWise AAAGAGAGGACCGAGCGGCTCGTCATCAATCCCTTAAACCAGTTGTTGAACATGTTCACGGGGCCCTACAAGCTGGTGCAGAAGCGGTTCGACAAGCTCCTGGACTTCTACAACTGCACTGAGCGAGCGGAGAAGCTGAAGGACAAGAAGACTCTGGAGGAGCTGCAGTCAGCCCGAAACAACTACGAGGCCCTGAACTCGCAGCTGCTGGACGAGCTGCCCAAGTTCCAGCAGTACGCCCAGAGCCTCTTCACCAACTGCATCCACGGCTATGCCGAAGCCCACTGTGACTTCGTGCAGCAAGCCCTGGAGCAGCTGCAGCCGCTGCTGTCG ccaaccagtgtaccattactgagggctacactctcgtgtttgaaaattagAAACAGCGGACAGAGCAGCTTATTATCAACCCTTTAAACCAATTGTTG------------GCACCATACAAACTGTTACAAAGGCGTTTTGACAAACTTCTTGACTTATACAACTGCATTGAT------------------------AAATCTTTGGAGGAACTGCAGTCAACCCGAAACAATCATGAGGCTCTAAACACTAAGCTGCTAGATGCACTGCCCAAATTCCAGCAGTATGACCAGAGTCTCTTTGCCAACTGTGTCTATGGATATGCTAAAGCCCATTGTGACTTTCTTCAGCAGGCACTGGAGCAAGTA------ATGCGTCGGgtcttctccttgccaatggcaaatgattacta #### Dock8_ID5395_16 --> 0 - 2 Original Alignment ---GTCATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATaa ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTGAGG---CCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACaagtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from CESAR ---GTCATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATaa ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTG---AGGCCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACaagtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from Spaln_aa2Genome GTCATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATAA ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTGAGGCCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACAAgtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from Spaln_nt2Genome GTC---ATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATAA ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTGA---GGCCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACAAgtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from Pairagon ---GTCATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATAA ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTGA---GGCCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACAAgtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from Exonerate_protein2genome GTCATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATAA ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTGAGGCCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACAAgtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from Exonerate_coding2genome ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagctcgtgatctatggaaagttgaggcctgaatttttgcaggaagtctatacagctattatgtaccataacaagtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta Alignment from GeneWise ---GTCATCTTTGGCAAGTCCAGTGGGCCTGAATTTCTGCAGGAAGTATATACAGCTATTACATACCATAATAA ttgattgtagagtccaatattacaccgagctggtgcttctgtctcatcagCTCGTGATCTATGGAAAGTTGAGG---CCTGAATTTTTGCAGGAAGTCTATACAGCTATTATGTACCATAACAAgtaaatagcaggaatctctcagactaccactatgaaatcctgtcctctta #### Dock8_ID5396_17 --> 1 - 0 Original Alignment g---TCTCCTGACTTTTACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactaggAAATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from CESAR g---TCTCCTGACTTTTACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactaggAAATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from Spaln_aa2Genome GTCTCCTGACTTT---TACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactagGAAATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from Spaln_nt2Genome G---TCTCCTGACTTTTACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactagGAAATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from Pairagon G---TCTCCTGACTTTTACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactagGAAATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from Exonerate_protein2genome GTCTCCTGACTTTTACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactaggaaATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from Exonerate_coding2genome gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactaggaaatctcctgacttttatgaagaagtgaaaatcaagctaccagcgaagctgacagtgaatcatcatcttctcttcactttctatcacatcagctgtcagcagaagcaaggggcctccggagagagccttctggggtactcagtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc Alignment from GeneWise -AAGTCTCCTGACTTTTACGAAGAAGTGAAAATTAAGCTCCCTGCCAAGCTCACAGTGAATCATCACCTCCTCTTCACCTTCTACCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAAAGCCTTCTGGGGTACTCG gcctgcgcttcagatcacgattgcttgcccaaatggtgtgttctcactagGAAATCTCCTGACTTTTATGAAGAAGTGAAAATCAAGCTACCAGCGAAGCTGACAGTGAATCATCATCTTCTCTTCACTTTCTATCACATCAGCTGTCAGCAGAAGCAAGGGGCCTCCGGAGAGAGCCTTCTGGGGTACTCAgtaagttctggtggtttccaaccttccaatttaggttcacatgtgttagc #### Dock8_ID5412_31 --> 0 - 0 Original Alignment CCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG------ ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGGCCAAAgtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from CESAR CCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG------ ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGGCCAAAgtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from Spaln_aa2Genome TTGCCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG ttctatactctggccttaccactccaaggtttcttttccttgtctttcag---CCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGgccaaagtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from Spaln_nt2Genome -CCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGgccaaagtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from Pairagon CCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG------ ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGGCCAAAgtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from Exonerate_protein2genome CCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGgccaaagtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from Exonerate_coding2genome CCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAG ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGgccaaagtaagcactgggaatgaaacactagttattcttccattccaaccttcttc Alignment from GeneWise CCCTATAAGCAGTACAACATGCTGAATGCAGACACCACCCGCCACCTCATGATTTGCTTCCTGTGGATCATGAAAAATGCTGATCAGAGCCTCATCAGGAAGTGGATCGCTGACCTGCCTTCCATGCAGCTCAATAGGATTCTGGACCTGCTGTTCATCTGTGTCTCCTGCTTTGAATACAAGGGAAAG ttctatactctggccttaccactccaaggtttcttttccttgtctttcagCCCTATAAGCAGTATAATATGCTGAATGCAGATGCTACTCACCACCTCATGATCTGCTTTCTCTGGATCATGAGGAATGCTGATCAGAGCCTCATCAGGAGGTGGATTGCTGACCTGCCTTCCATGCAGCTCAACAGGGTTTTAGACCTACTGTTCATCTGTGTCTCCTGTTTTGAATACAAGGCCAAAgtaagcactgggaatgaaacactagttattcttccattccaaccttcttc #### Dpp3_ID742_11 --> 0 - 0 Original Alignment ---GACCTGTATATCCGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagTTGGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from CESAR ---GACCTGTATATCCGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagTTGGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from Spaln_aa2Genome GACCTGTAT---ATCCGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagTTGGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from Spaln_nt2Genome GGACCTGTATATC--CGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagTTGGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from Pairagon ---GACCTGTATATCCGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagTTGGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from Exonerate_protein2genome GACCTGTATATCCGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagttgGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from Exonerate_coding2genome aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagttggatctgtatatccactggaaaggtccatcatttgatgtacaggtgggcttacatgagctattaagccatggcagtggcaagctctttgtacaggtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta Alignment from GeneWise ---GACCTGTATATCCGCTGGAAGGGGCCGTCCTTTGATGTGCAGGTGGGGTTACACGAGCTGTTGGGCCATGGCAGCGGCAAGCTCTTTGTACAG aaggttgctacagctggtgtggatagtgcctacaccttgtctcactgcagTTGGATCTGTATATCCACTGGAAAGGTCCATCATTTGATGTACAGGTGGGCTTACATGAGCTATTAAGCCATGGCAGTGGCAAGCTCTTTGTACAGgtatgtggtcccaaaggtagatcctgttatcagtgctactgatcatggta #### Drap1_ID984_6 --> 0 - 2 Original Alignment GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTTTCAGag gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCAC------aggtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac Alignment from CESAR GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTTTCAGag gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCAC------aggtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac Alignment from Spaln_aa2Genome GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTT gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCACAGgtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac Alignment from Spaln_nt2Genome GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTTTCAGAG gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCACAGGTA-AGgtagaattttacttaggaagtgtaccagttttttcaccctgaca Alignment from Pairagon GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTTTCAGAG gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCAC------AGgtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac Alignment from Exonerate_protein2genome GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTTTCAGAG gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCAC------AGgtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac Alignment from Exonerate_coding2genome AGGAGGATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTTTCAGAG gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctaggATAAGTCTGAGGATATGGATACAGAT------GGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCAC------AGgtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac Alignment from GeneWise GATGAGTCTGAGGATACAGATACTGATGGGGAAGAAGAGACACCACAGCTTCCACCCCAAGCCAGTCACCCTCCTGCCCACTT gcattgttaaattttgtgtcccaaaatcttgtgtttctgctatcttctagGATAAGTCTGAGGATATGGATACAGATGGAGAGGAGGAGACACCCCAGCTTCCACCTCAGGCCAGTCACCCCCTTGCTCACAGgtaaggtagaattttacttaggaagtgtaccagttttttcaccctgacac #### Drap1_ID985_5 --> 1 - 0 Original Alignment CCTCGAag gGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAGGAG CCTCGAaggtatgcggctagggacctgctaaccatgcactttcttcctagaGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAA---gtaaccactggactagctagtgatgagttatggtttttgtagccaagcta Alignment from CESAR CCTCGAag gGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAGGAG CCTCGAaggcaagtggctagggacctgctaaccatgcactttcttcctagaGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAA---gtaaccactggactagctagtgatgagttatggtttttgtagccaag Alignment from Spaln_aa2Genome CCTCGAAG GGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAG CCTCGAAGgtatgcggctagggacctgctaaccatgcactttcttcctagAGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAAgtaaccactggactagctagtgatgagttatggtttttgtagccaagcta Alignment from Spaln_nt2Genome CCTCGAAG GGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAG CCTCGAAGgtatgcggctagggacctgctaaccatgcactttcttcctagAGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAAgtaaccactggactagctagtgatgagttatggtttttgtagccaagcta Alignment from Pairagon CCTCGAAGG------------------------------------------GGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAG CCTCGAAGGTATGCGGCTAGGGACCTGCTAACCATGCACTTTCTTCCTAGAGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAAgtaaccactggactagctagtgatgagttatggtttttgtagccaagcta Alignment from Exonerate_protein2genome CCTCGAAG GGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAGGAG CCTCGAAGgtatgcggctagggacctgctaaccatgcactttcttcctagAGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAA---gtaaccactggactagctagtgatgagttatggtttttgtagccaag Alignment from Exonerate_coding2genome CCTCGAAGGGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAA---GGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAGG CCTCGAAGGTATGCGGCTAGGGACCTGCTAACCATGCACTTTCTTCCTAGAGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGgtaaagataaaaagctctctgggacagattccgaacaagtaaccactggactagctagtgatgagttatggtttttgtagccaagcta Alignment from GeneWise CCTCGAAGG------------------------------------------GGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCACGGGAAGCAAAGGCAAAGACAAGAAGCTGTCCGGGACAGACTCTGAGCAG CCTCGAAGGTATGCGGCTAGGGACCTGCTAACCATGCACTTTCTTCCTAGAGGCTGTAAACCAGGTAGCAGTGGAAAGAAAAATGGCGGCACAGGAAGCAAGGGTAAAGATAAAAAGCTCTCTGGGACAGATTCCGAACAAgtaaccactggactagctagtgatgagttatggtttttgtagccaagcta #### Drap1_ID986_4 --> 1 - 2 Original Alignment gAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGGTCCTCGAag gGGCCGGA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagaATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAG---------aggtatacggcttaattcggtaaagtctctctccatccttgcagaGGCTGTA Alignment from CESAR gAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGGTCCTCGAag gGGCCGGA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagaATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAG---------aggtatacggcttaattcgtgctaaccatgcactttcttcctagaGGCTGTA Alignment from Spaln_aa2Genome GAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGG TCCTCGAA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagAATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAGAGgtatacggcttaattcggtaaagtctctctccatccttgcagA------- Alignment from Spaln_nt2Genome GAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGGTCCTCGAAG GGGCCGGA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagAATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAG---------AGgtatacggcttaattcggtaaagtctctctccatccttgcagAGGCTGTA Alignment from Pairagon GAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGG---------------------------------TCCTCGAAGGGGCCGGA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagAATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAGAGGTATACGGCTTAATTCGGTAAAGTCTCTCTCCATCCTTGCAGAGGCTGTA Alignment from Exonerate_protein2genome GAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGGTCCTCGAAG GGGCCGGA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagAATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAGAGGTATACGGCttaattcggtaaagtctctctccatccttgcagAGGCTGTA Alignment from Exonerate_coding2genome GAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGGTCCTCGAAGGGGCCGGAAACCGGGCAGCAGCGGCAGGAAGAACGGAGGCA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagAATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAGAGGTATACGGCTTAATTCGGTAAAGTCTCTCTCCATCCTTGCAGAGGCTGTA Alignment from GeneWise GAAGCAGTGCATTGAACTCGAGCAGCAGTTTGACTTCTTGAAAGACTTGGTGGCATCAGTGCCTGACATGCAGGGGGATGGGGAGGACAACCACGTGGATGGGGACAAGGGT---------------------------------CCTCGAAGGGGCCGGA tttccgaagttgtttagtggcagccaaccctttattttgatctctttcagAATGCAATGCATTGATGTTGAGCAACAATTTGACTTCTTGAAAGCACTAGTAGCATCAGTACCTGACATGCAGGGGGACAGGGAAGACAACCATGTGGATGGGGAAAAGAGGTATACGGCTTAATTCGGTAAAGTCTCTCTCCATCCTTGCAGAGGCTGTA #### Drap1_ID988_2 --> 0 - 1 Original Alignment ---GCGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCt tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTtgtaccaacctcaagcccagttattctgaggtggaattataccacacatct Alignment from CESAR ---GCGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCt tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTtgtaccaacctcaagcccagttattctgaggtggaattataccacaccaca Alignment from Spaln_aa2Genome GCGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCT tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTTgtaccaacctcaagcccagttattctgaggtggaattataccacacatct Alignment from Spaln_nt2Genome G---CGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCT tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTTgtaccaacctcaagcccagttattctgaggtggaattataccacacatct Alignment from Pairagon G---CGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCT tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTTgtaccaacctcaagcccagttattctgaggtggaattataccacacatct Alignment from Exonerate_protein2genome ---GCGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCT tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTTgtaccaacctcaagcccagttattctgaggtggaattataccacacatct Alignment from Exonerate_coding2genome GCGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCT tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacaggatACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTTgtaccaacctcaagcccagttattctgaggtggaattataccacacatct Alignment from GeneWise ---GCGCGGATCAAAAAGATCATGCAGACGGACGAAGAGATTGGGAAGGTGGCGGCAGCTGTGCCTGTCATCATCT tgcttcccccatgtgttgggagtacagtccgctctaccttcatcccacagGATACGCGGATCACAAAGATCATGCAGACAGATGAAGAAATTGGAAAAGTTGCAGCTGCTGTACCAGTCATCATTTgtaccaacctcaagcccagttattctgaggtggaattataccacacatct #### Eef1g_ID2567_9 --> 2 - 0 Original Alignment ggATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG------------------ agtatgggaatacagagtcaggaaggattttcacttacttcatgttttaggtATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCATTTTATGGAAGACCTTGGgtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from CESAR ggATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG------------------ agtatgggaatacagagtcaggaaggattttcacttacttcatgttttaggtATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCATTTTATGGAAGACCTTGGgtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from Spaln_aa2Genome GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG------------------ agtatgggaatacagagtcaggaaggattttcacttacttcatgttttagGTATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCATTTTATGGAAGACCTTGGgtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from Spaln_nt2Genome GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCC------------------G agtatgggaatacagagtcaggaaggattttcacttacttcatgttttagGTATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCATTTTATGGAAGACCTTGGgtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from Pairagon GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCC------------------G agtatgggaatacagagtcaggaaggattttcacttacttcatgttttagGTATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCATTTTATGGAAGACCTTGGgtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from Exonerate_protein2genome GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG agtatgggaatacagagtcaggaaggattttcacttacttcatgttttagGTATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCAttttatggaagaccttgggtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from Exonerate_coding2genome GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG agtatgggaatacagagtcaggaaggattttcacttacttcatgttttagGTATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCAttttatggaagaccttgggtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa Alignment from GeneWise GGATGTTTCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTGTTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCG------------------ agtatgggaatacagagtcaggaaggattttcacttacttcatgttttagGTATGTTCCAACGGCTGGACAAGCTGCGGAAGAATGCCTTTGCTAGTGTTATACTCTTTGGAACAAATAACAGCAGTTCTCTTTCTGGAGTTTGGGTCTTTCGTGGCCAGGAGCTTGCCTATCCATTTTATGGAAGACCTTGGgtaggtcctcagtatgagagcttcatggtgggggcttagaagttttggaa #### Efemp2_ID1035_8 --> 2 - 2 Original Alignment at------ATTGACGAGTGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACaa gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagagGGCATTTTAGGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTAC---CGTGTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACaagtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from CESAR at---ATT---GACGAGTGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACaa gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagagGGCATTTTAGGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACCGT---GTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACaagtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from Spaln_aa2Genome AT------ATTGACGAGTGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACAA gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagAGGGCATTTTAGGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACCGT---GTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACAAgtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from Spaln_nt2Genome GAG--TGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACAA gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagagggcattttagGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACC---GTGTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACAAgtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from Pairagon ATATTGACGAG--TGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACAA gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagagggcattttag--------GAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACC---GTGTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACAAgtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from Exonerate_protein2genome AT------ATTGACGAGTGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACAA gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagAGGGCATTTTAGGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACCGT---GTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACAAgtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from Exonerate_coding2genome AT------ATTGACGAGTGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACAA gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagAGGGCATTTTAGGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACCGT---GTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACAAgtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg Alignment from GeneWise -----GATATTGACGAGTGTGAAACAGGTGCACACCAATGTTCTGAGGCCCAAACCTGTGTCAACTTCCATGGGGGTTACCGCTGTGTGGACACCAACCGTTGTGTGGAGCCCTATGTCCAAGTGTCAGACAA gtgagtgagtatggaactaagacactccaaatttggatttattcacaaagAGGGCATTTTAGGAGACTGTGAGACAGGTGTACACCAGTGTTCTGAGGCCCAAACTTGTGTTAATTTCCATGCTGGTTACCGT---GTCGAGATCAACCGCTGTGTAGAGCCATATGTTCATGTGTCAGACAAgtgaggaccccacgcacttgctgacttgcataagttagggagatcttggg #### Ehbp1l1_ID1220_15 --> 0 - 1 Original Alignment ---------CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAg gtagcttaggtgaggcaacctgtcctctgtccccctctacccttctaaagGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAggtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from CESAR ---------CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAg gtagcttaggtgaggcaacctgtcctctgtccccctctacccttctaaagGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAggtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from Spaln_aa2Genome -------CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAG gtagcttaggtgaggcaacctgtcctctgtccccctctacccttctaaagGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAGgtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from Spaln_nt2Genome ---------CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAG gtagcttaggtgaggcaacctgtcctctgtccccctctacccttctaaagGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAGgtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from Pairagon -----------------------------------------------------------CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAG GTAGCTTAGGTGAGGCAACCTGTCCTCTGTCCCCCTCTACCCTTCTAAAGGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAGgtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from Exonerate_protein2genome ---CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAG gtagcttaggtgaggcaacctgtcctctgtccccctctacccttctaaaggtcctgGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAGgtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from Exonerate_coding2genome GTGGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTGCAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAG gtaGCTTAGGTGAGGCAACCTGTCCTCTGTCCCCCTCTACCCTTCTAAAGGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAGgtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca Alignment from GeneWise ---------CAACGGTTCCAGGACACAAGTCAGTACGTGTGCGCAGAGCTGCAAGCCCTGGAGCAGGAACAGGGACAGATAGATGGGAGGGCCGCTGAGGTGGAGAAGCAGCTGAGGAGCCTCATGGAATCAG gtagcttaggtgaggcaacctgtcctctgtccccctctacccttctaaagGTCCTGGCCCATCGGTTACAGGACACAAGCCAGTATGTGTGTGCAGAGCAACAAGCCCTTGAGCAGGAACAGGGACAGGTTGATGGCAGGGCTCCTGAAGTGCAGAGACAATTTCGGAGCCTGATGGAATCAGgtaaagccccctagtttcatctgtgcttaaaacctgatacagttgagaca #### Ehbp1l1_ID1221_14 --> 2 - 0 Original Alignment gtGGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccataggt---------CCTACTGAAAAGTCGTCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtattgctacactgaatggtggttattactttcctgagtagcttag Alignment from CESAR gtGGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG gactagaatttctttttttcactggtttcctgatttcctttaaaccataggt---------CCTACTGAAAAGTCGTCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtattgctacactgaatggtggttattactttcctgagtagcttag Alignment from Spaln_aa2Genome GTGGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccatagGT---------CCTACTGAAAAGTCGTCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtattgctacactgaatggtggttattactttcctgagtagcttag Alignment from Spaln_nt2Genome CTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccatagGTCCTACTGAAAAGTCGTCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtattgctacactgaatggtggttattactttcctgagtagcttag Alignment from Pairagon GTGGGCCCCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccatagG---------TCCTACTGAAAAGTCGTCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtattgctacactgaatggtggttattactttcctgagtagcttag Alignment from Exonerate_protein2genome CCCTCCTACTGAGGAGTCATCACCCAGCCTGGGGGAAGAGACAGGCCTG ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccatAGGTCCTACTGAAAAGTCGTCTCGTAGCTTGGAAGAAGAGACAGGGCTGgtgagtattgctacactgaatggtggttattactttcctgagtagcttag Alignment from Exonerate_coding2genome CCCTCCTA ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccataggtcctactgaaaagtcgtctcgtagcttggaagaagagacagggctggtgagtattgctacactgaatggtggttattactttcctgagTAGCTTAG Alignment from GeneWise ttctttttttcactggaaaaaatgatttcctgatttcctttaaaccataggtcctactgaaaagtcgtctcgtagcttggaagaagagacagggctggtgagtattgctacactgaatggtggttattactttcctgagtagcttag #### Ehbp1l1_ID1227_8 --> 2 - 2 Original Alignment ctGCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAag tggcaatccaaacctccaaaagccattcttgcttttttactttctacaagct---AGACCCTCTAGTGCTGAAAAGACAAGTCCCGCCCCGGTAAGTGCCCCTGCGCCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACTGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGGACTCCACCTGAGACAaagtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from CESAR ctGCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAag ggatggcaatccaaacctccaaaagttcttgcttttttactttctacaagct---AGACCCTCTAGTGCTGAAAAGACAAGTCCCGCCCCGGTAAGTGCCCCTGCGCCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACTGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGGACTCCACCTGAGACAaagtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from Spaln_aa2Genome CTGCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG tggcaatccaaacctccaaaagccattcttgcttttttactttctacaagCT---AGACCCTCTAGTGCTGAAAAGACAAGTCCCGCCCCGGTAAGTGCCCCTGCGCCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACTGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGGACTCCACCTGAGACAAAgtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from Spaln_nt2Genome CAGACCCTC-TAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG tggcaatccaaacctccaaaagccattcttgcttttttactttctacaagCTAGACCCTCTAGTGCTGAAAAGACAAGTCCCGCCCCGGTAAGTGCCCCTGCGCCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACTGCCATGACTGATGG---AGTGGGGCATGAGACCCTAGAGCCCCCAGGGACTCCACCTGAGACAAAgtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from Pairagon -------------------------------------------------GCCAGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG TGGCAATCCAAACCTCCAAAAGCCATTCTTGCTTTTTTACTTTCTACAAGCTAGACCCTCTAGTGCTGAAAAGACAAGTCCCGCCCCGGTAAGTGCCCCTGCGCCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACTGCCATGACTGATGG---AGTGGGGCATGAGACCCTAGAGCCCCCAGGGACTCCACCTGAGACAAAgtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from Exonerate_protein2genome tggcaatccaaacctccaaaagccattcttgcttttttactttctacaagctagaccctctagtgctgaaaagacaagtcccgccccggtaagtgcccctgcgccccaagttagagcaatccggggccaaggggatccaactgccatgactgatggagtggggcatgagaccctagagcccccagggactccacctgagacaaagtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from Exonerate_coding2genome tggcaatccaaacctccaaaagccattcttgcttttttactttctacaagctagaccctctagtgctgaaaagacaagtcccgccccggtaagtgcccctgcgccccaagttagagcaatccggggccaaggggatccaactgccatgactgatggagtggggcatgagaccctagagcccccagggactccacctgagacaaagtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta Alignment from GeneWise --AGACCCTCTAGTGCTGAAGACACCAGCCCTGCCCCAGTGAGTGCCCCTGCACCCCCGGTCAGGGCCTTCCGGGGCCAGGGGTCAGAACCAGCTGCTATAACCGGGGGCCAGGTGGGGCCTGAAACCCCAGAGCCCCCGCCATCCCCACCAGAGACAAG tggcaatccaaacctccaaaagccattcttgcttttttactttctacaagCTAGACCCTCTAGTGCTGAAAAGACAAGTCCCGCCCCGGTAAGTGCCCCTGCGCCCCAAGTTAGAGCAATCCGGGGCCAAGGG---GATCCAACTGCCATGACTGATGGA---GTGGGGCATGAGACCCTAGAGCCCCCAGGGACTCCACCTGAGACAAAgtaggaatcatctcagcttctcaggcaagattgcgccattgcagtgtcta #### Ehbp1l1_ID1229_6 --> 1 - 1 Original Alignment gGATGATGACATGCAGAGTCTGGCCAGCCTCATGAGTGTGAAGCCTAGTGACGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTCCGGACTCGAGGCCCCCAGTCAg tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcaga---GATGATATGCAAAGTCTTGCCAGCCTCATGAGTGTGAAGCCTAGTGATGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTTCAGACCAGAGGCCCCCAGTCAggtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from CESAR gGATGATGACATGCAGAGTCTGGCCAGCCTCATGAGTGTGAAGCCTAGTGACGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTCCGGACTCGAGGCCCCCAGTCAg tcatagatgatgtgtgaaccatctgcttttatggacccttcctcctgcagaGATGAT---ATGCAAAGTCTTGCCAGCCTCATGAGTGTGAAGCCTAGTGATGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTTCAGACCAGAGGCCCCCAGTCAggtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from Spaln_aa2Genome GGATGATGACATGCAGAGTCTGGCCAGCCTCATGAGTGTGAAGCCTAGTGACGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTCCGGACTCGAGGCCCCCAGTCAG tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcagA---GATGATATGCAAAGTCTTGCCAGCCTCATGAGTGTGAAGCCTAGTGATGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTTCAGACCAGAGGCCCCCAGTCAGgtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from Spaln_nt2Genome GGATGATGACATGCAGAGTCTGGCCAGCCTCATGAGTGTGAAGCCTAGTGACGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTCCGGACTCGAGGCCCCCAGTCAG tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcagAGATGAT---ATGCAAAGTCTTGCCAGCCTCATGAGTGTGAAGCCTAGTGATGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTTCAGACCAGAGGCCCCCAGTCAGgtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from Pairagon GGATGATGACATGCAGAGTCTGGCCAGCCTCATGAGTGTGAAGCCTAGTGACGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTCCGGACTCGAGGCCCCCAGTCAG tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcagAGATGAT---ATGCAAAGTCTTGCCAGCCTCATGAGTGTGAAGCCTAGTGATGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTTCAGACCAGAGGCCCCCAGTCAGgtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from Exonerate_protein2genome tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcagagatgatatgcaaagtcttgccagcctcatgagtgtgaagcctagtgatgtgggaaacctggatgactttgctgagagtgatgaggaggaagctaatggccctggggctcctgaggttcagaccagaggcccccagtcaggtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from Exonerate_coding2genome tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcagagatgatatgcaaagtcttgccagcctcatgagtgtgaagcctagtgatgtgggaaacctggatgactttgctgagagtgatgaggaggaagctaatggccctggggctcctgaggttcagaccagaggcccccagtcaggtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc Alignment from GeneWise GGATGATGACATGCAGAGTCTGGCCAGCCTCATGAGTGTGAAGCCTAGTGACGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTCCGGACTCGAGGCCCCCAGTCAG tagatgatgtgtgaaccatctggctcttttatggacccttcctcctgcagAGATGAT---ATGCAAAGTCTTGCCAGCCTCATGAGTGTGAAGCCTAGTGATGTGGGAAACCTGGATGACTTTGCTGAGAGTGATGAGGAGGAAGCTAATGGCCCTGGGGCTCCTGAGGTTCAGACCAGAGGCCCCCAGTCAGgtaaggatactgttattcaggttgcaggtacctgaggcggatacttgtcc #### Eif1ad_ID949_2 --> 0 - 1 Original Alignment GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---g acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGggtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from CESAR GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---g acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGggtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from Spaln_aa2Genome GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---G acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGGgtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from Spaln_nt2Genome GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---G acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGGgtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from Pairagon GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---G acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGGgtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from Exonerate_protein2genome GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---G acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGGgtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from Exonerate_coding2genome GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGA---G acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGGgtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc Alignment from GeneWise GTCCTCAGGACTCCTGGGAACAATCTGCATGAGGTGGAAACAGCACAGGGGCAGCGCTTCCTGGTGAGCATGCCCTCCAAATACCGCAAGAACATCTGGATCAAGAGAGGG- acaatgcaaattctagataatgagtgattctttttctttgctgtcttcagGTCCTCAGGACCCCAGGGAACAATTTGCATGAGGTGGAAACTGCTCAGGGGCAACGCTTCCTGGTCAGCATGCCCTCCAAATACCGTAAGAACATCTGGATCAAGAGAACGGgtaagatctttttgctttttcaactaccaaacatgataccaccttgtccc #### Eif3a_ID13317_13 --> 0 - 0 Original Alignment GACCTTGAAGAACTGGATCCAGATTTTATTATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagaaactttacacctcctccaacccctgactcag------------------------------ATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from CESAR GACCTTGAAGAACTGGATCCAGATTTTATTATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG caagtacctaaagctgtagaactttacacctcctccaacccctgactcag------------------------------ATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from Spaln_aa2Genome AAGACCTTGAAGAACTGGATCCAGATTTTATTATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagAAACTTTACACCTCCTCCAACCCCTGACTCAGATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from Spaln_nt2Genome ATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagaaactttacacctcctccaacccctgactcagATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from Pairagon GACCTTGAAGAACTGGATCCAGATTTTATTATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagaaactttacacctcctccaacccctgactcag------------------------------ATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from Exonerate_protein2genome ATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagaaactttacacctcctccaacccctgactcagATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from Exonerate_coding2genome ATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagaaactttacacctcctccaacccctgactcagATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac Alignment from GeneWise --GACCTTGAAGAACTGGATCCAGATTTTATTATGGCCAAACAGGTTGAACAACTGGAGAAAGAAAAGAAGGAACTTCAGGAACGCCTGAAGAATCAAGAAAAGAAG cgtggtttgataaatcagAAACTTTACACCTCCTCCAACCCCTGACTCAGATGGCCAAACAGGTAGAACAGCTGGAAAAGGAAAAGAAAGAACTTCAAGAACGCCTCAAGACGCAAGAAGAGAAGgtaccagtggatcactgataagttctgtaagtaaagtagatcaaaagaac #### Eml3_ID2506_5 --> 1 - 1 Original Alignment cCGGGGGAACAAAGACCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAg gacacaagttttactctgtgtaatgatgcgctaggttgtctgtcttccagt---------------CCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAggtaggttaaggaaggagaatggcattaacactgactagtaacacacacca Alignment from CESAR cCGGGGGAACAAAGACCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAg tcatcgctggcagtggacacaagttatgcgctaggttgtctgtcttccagt---------------CCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAggtaggttaaggaaggagaatggcattaacactgactagtaacacacacca Alignment from Spaln_aa2Genome CCGGGGGAACAAAGACCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAG gacacaagttttactctgtgtaatgatgcgctaggttgtctgtcttccagT---------------CCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAGgtaggttaaggaaggagaatggcattaacactgactagtaacacacacca Alignment from Spaln_nt2Genome CCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAG gacacaagttttactctgtgtaatgatgcgctaggttgtctgtcttccagTCCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAGgtaggttaaggaaggagaatggcattaacactgactagtaacacacacca Alignment from Pairagon CCGGGGGAACAAAGACCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAG gacacaagttttactctgtgtaatgatgcgctaggttgtctgtcttccag---------------TCCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAGgtaggttaaggaaggagaatggcattaacactgactagtaacacacacca Alignment from Exonerate_protein2genome CCGGGGGAACAAAGACCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAG gacacaagttttactctgtgtaatgatgcgctaggTTGTCTGTCTTCCAGTCCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAGgtaggttaaggaaggagaatggcattaacactgactagtaacacacacca Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCGGGGGAACAAAGACCCTCTGTCCAGTCCTGGGGGTCCCGGATCTCGGAGGAGCAATTATAACTTAG gacacaagttttactctgtgtaatgatgcgctaggttgtctgtcttccagT---------------CCTCTGTCCAGTCCTGGGGGTCCTGGATCTCGGAGGAGCAATTATAATTTAGgtaggttaaggaaggagaatggcattaacactgactagtaacacacacca #### Eml3_ID2508_7 --> 1 - 2 Original Alignment tTATGGGTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGAtg ctgctaatccccccccatagcctattctctcttttcttccacttttaaagt------TATAGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGAtggtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa Alignment from CESAR tTATGGGTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGAtg ttacttctgctaatccccccccatatctctcttttcttccacttttaaagtTAT------AGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGAtggtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa Alignment from Spaln_aa2Genome TTATGGGTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGATG ctgctaatccccccccatagcctattctctcttttcttccacttttaaagT------TATAGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGATGgtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa Alignment from Spaln_nt2Genome GTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGATG ctgctaatccccccccatagcctattctctcttttcttccacttttaaagTTATAGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGATGgtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa Alignment from Pairagon TTATGGGTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGATG ctgctaatccccccccatagcctattctctcttttcttccacttttaaagTTAT------AGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGATGgtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa Alignment from Exonerate_protein2genome GTTTATGGGTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGATG ctgctaatccccccccatagcctattctctcttttcttccacTTTTAAAGTTATAGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGATGgtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TTATGGGTACAGGGGTCGTGATTCTCGCTCTAATCTATTTGTGCTGCGCTCTGGGGAGGTGGTCTACTTTATTGCCTGTGTAGTGGTGCTGTACCGGCCTGGGGGAGGCCCAGGGGGTCCTGGAGGTGGCGGCCAGAGACATTACCGGGGTCACACAGACTGCGTTCGATG ctgctaatccccccccatagcctattctctcttttcttccacttttaaagT------TATAGAGGTCAGGATTCTCGCTCAAATTTATTTGTGCTACGCCCTGGTGATGTTGTCTACTTTATTGCCTGTGTAGTGGTACTGTACCGGCCGGGAGGAGGCCCAGGTGGGCCAGGAGGTGGTGGTCAGAGACATTATCGGGGCCACACAGACTGTGTTCGATGgtaagaaccgtggtagtggtaaacacttaattcctgttgacttcaaggaa #### Eml3_ID2509_8 --> 1 - 0 Original Alignment cCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGATGGAAAG gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagtCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAGGAT------gtaagtcccaaggccagcatgcagatggcaatgagatcattgatcaagtt Alignment from CESAR cCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGATGGAAAG gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagtCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAGGAT------gtaagtcccaaggccagcatgcagatggcaatgagatcattgat Alignment from Spaln_aa2Genome CCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGAT------GGAAAG gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagTCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAGGATGTAAGTCCCAAGgccagcatgcagatggcaatgagatcattgatcaagtt Alignment from Spaln_nt2Genome CCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGAT gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagTCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAGGATgtaagtcccaaggccagcatgcagatggcaatgagatcattgatcaagtt Alignment from Pairagon CCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGATGGAA---------------------------------------------- gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagTCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAGGATGTAAGTCCCAAGGCCAGCATGCAGATGGCAATGAGATCATTGATCAAGTT Alignment from Exonerate_protein2genome CCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGAT gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagTCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAGGATgtaagtcccaaggccagcatgcagatggcaatgagatcattgatcaagtt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCTTGCTGTTCACCCTGATGGTGTTCGTGTAGCCTCAGGACAGACAGCTGGAGTGGACAAGGATGGAAAG gtacttcagtgtaaccggtgattttatgatttttttccttctactcttagTCTTGCTGTACATCCTGATGGAGTTCATGTTGCTTCAGGGCAGACAGCTGGCGTGGACAAG------GATgtaagtcccaaggccagcatgcagatggcaatgagatcattgatcaagtt #### Eml3_ID2512_11 --> 0 - 0 Original Alignment AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTT------gtaaagtcaggccgggtaaggtaaacaaacgcatggcataataacacact Alignment from CESAR AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTT------gtaaagtcaggccgggtaaggtaaacaaacgcatggcataataa Alignment from Spaln_aa2Genome AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTT------GGGAAA ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTTGTAAAGTCAGGCCGGgtaaggtaaacaaacgcatggcataataacacact Alignment from Spaln_nt2Genome AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGG ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTTGTAAAgtcaggccgggtaaggtaaacaaacgcatggcataataacacact Alignment from Pairagon AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTT ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTTgtaaagtcaggccgggtaaggtaaacaaacgcatggcataataacacact Alignment from Exonerate_protein2genome AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTTGGG ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTTGTAAAGtcaggccgggtaaggtaaacaaacgcatggcataataacacact Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AGTACAAATGACTCAGTCCTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGCTGTATTGTCACCAGTGGGAAATCGCATGTCCACTTTTGGAACTGGAGCGGTGGGACAGGGGCTCCCGGGAATGGGCTCCTCGCCCGGAAGCAGGGTGTTTTT------GGGAAA ttcagccctcatgacaacagttgtagtactgccttctgtcccctctgtagAGTACAAATGACTCCGTACTCGCTGTTGGCTTCAGCCCTCGTGACAGCAGTTGTATTGTTACTAGTGGAAAATCACATGTTCACTTTTGGAATTGGAGTGGTGGTACAGGGGCTCCTGGGAATGGAATCCTTGCACGGAAGCAGGATGTTGTAAAGTCAGGCCGGgtaaggtaaacaaacgcatggcataataacacact #### Eml3_ID2515_14 --> 0 - 0 Original Alignment ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCTGTTATCCAG------ ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAGTAATCCAGTCGCCAgtgagaactctgtaagacactgagggagggacccccactgttgccccagc Alignment from CESAR ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCTGTTATCCAG------ ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAGTAATCCAGTCGCCAgtgagaactctgtaagacactgagggagggacccccactgttgccccagc Alignment from Spaln_aa2Genome ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCTGTTATCCAGGGCCAC ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAGTAATCCAGTCGCCAgtgagaactctgtaagacactgagggagggacccccactgttgccccagc Alignment from Spaln_nt2Genome ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCTGTTATCCAG------ ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAGTAATCCAGTCGCCAgtgagaactctgtaagacactgagggagggacccccactgttgccccagc Alignment from Pairagon ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCTGTTATCCAG------ ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAGTAATCCAGTCGCCAgtgagaactctgtaagacactgagggagggacccccactgttgccccagc Alignment from Exonerate_protein2genome ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCT ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAgtaatccagtcgccagtgagaactctgtaagacactgagggagggacccccactgttgccccagc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ATTCCAGAACACTTTGGAGCTGTGAGGGCCATTGCTGAAGGGCTTGGCTCTGAGCTGCTGGTGGGAACCACAAAGAATGCATTACTGAGGGGAGATCTGGCTCAAGGCTTCTCCCCTGTTATCCAGGGCCAC ggatggggagacatgggaaatagtataatgacattgtgttttatttctagGTGCCAGAACATTTCGGTTCAGTAAGTGCGATTGCTGATGGACTTGGAGCTGAACTACTGGTGGGGACCACAAAGAATGCCTTACTAAGAGCAGATCTTGCCCAAGGTTTCTCTCCAGTAATCCAGTCGCCAgtgagaactctgtaagacactgagggagggacccccactgttgccccagc #### Eml3_ID2518_17 --> 1 - 1 Original Alignment gTGGTTGGTTTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAg gcaagatcttatctctatgtgacatctctttgctaactctttcccccaagg---------TTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGggtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc Alignment from CESAR gTGGTTGGTTTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAg aagtgtaaggcaagatcttatctctctctttgctaactctttcccccaagg---------TTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGggtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc Alignment from Spaln_aa2Genome GTGGTTGGTTTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAG gcaagatcttatctctatgtgacatctctttgctaactctttcccccaagG---------TTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGGgtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc Alignment from Spaln_nt2Genome TTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAG gcaagatcttatctctatgtgacatctctttgctaactctttcccccaagGTTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGGgtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc Alignment from Pairagon GTGGTTGGTTTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAG gcaagatcttatctctatgtgacatctctttgctaactctttcccccaagG---------TTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGGgtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc Alignment from Exonerate_protein2genome GTGGTTGGTTTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAG gcaagatcttatctctatgtgacatctctttgctaactctttcccccaagG---------TTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGGgtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTGGTTGGTTTTGGACACAGAGACCAGAGAGATTGTATCCGATGTCACTGACGGCAATGAACAGCTCTCAGTTGTCCGGTACAGCCCAG gcaagatcttatctctatgtgacatctctttgctaactctttcccccaagG---------TTGGACACCGAGACCAGGGAAATTGTGTCTGATGTCACAGATGGCAATGAGCAACTCTCAGTTGTCCGGTACAGCCCGGgtagccacacttccccatgcctgaatgctgctcggaatcctggcttgttc #### Eno4_ID12833_5 --> 2 - 0 Original Alignment gaCGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGATCAG tttccagttttctacttccaaaaagacatgatttggggctggtcccacaggaCGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGAT---gtgtggagttaatattgtgggcatgagtgtggaaaaagagttggtggcag Alignment from CESAR gaCGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGATCAG tttccagttttctacttccaaaaagacatgatttggggctggtcccacaggaCGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGAT---gtgtggagttaatattgtgggcatgagtgtggaaaaagagttggtgg Alignment from Spaln_aa2Genome GACGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGAT tttccagttttctacttccaaaaagacatgatttggggctggtcccacagGACGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGATgtgtggagttaatattgtgggcatgagtgtggaaaaagagttggtggcag Alignment from Spaln_nt2Genome GACGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGATCA tttccagttttctacttccaaaaagacatgatttggggctggtcccacagGACGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGATGTgtggagttaatattgtgggcatgagtgtggaaaaagagttggtggcag Alignment from Pairagon GACGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGA--------------------------------------------------- tttccagttttctacttccaaaaagacatgatttggggctggtcccacagGACGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGATGTGTGGAGTTAATATTGTGGGCATGAGTGTGGAAAAAGAGTTGGTGGCAG Alignment from Exonerate_protein2genome GACGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGATCAG tttccagttttctacttccaaaaagacatgatttggggctggtcccacagGACGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGATGTGtggagttaatattgtgggcatgagtgtggaaaaagagttggtggcag Alignment from Exonerate_coding2genome GACGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGATCAG tttccagttttctacttccaaaaagacatgatttggggctggtcccacagGACGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGATGTGtggagttaatattgtgggcatgagtgtggaaaaagagttggtggcag Alignment from GeneWise GACGGAGGGATACGCTTTTGGAGAAACCTGTTTCACCCCCGGAGCCCCCTGAACCAGTCCTCCATGGTAGCATGGCCATAGGCGCTGTGTCCCTGGCAGTGGCCAAAGCCAGCGCAACCTTGGCCAGCGATCCTCTCTACTTAACCCTGGCGTCACTGAAGCATGAT tttccagttttctacttccaaaaagacatgatttggggctggtcccacagGACGGAGGGATATGCTTTTGGAGAGACCTGTGTCGCCCCAAGAGCCACCTGAACCAGTTCAGCATGGAAGTATGGCCCTAGGTGCTGTGTTACTGGCAGTGGCTAAAGCTAGTGCTACCTTGGCCCATGACCCTCTCTACTCAGCCCTGGCATCACTGAAGCAAGATgtgtggagttaatattgtgggcatgagtgtggaaaaagagttggtggcag #### Exosc1_ID8332_7 --> 0 - 1 Original Alignment ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAg taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAG------------------------------ggtgggtcagtaactaaatttgctgtcccagacgaaagtcaatttaaatcc Alignment from CESAR ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACTGCT---GAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAg taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAG------------------------------ggtgggtcagtaactaaatttgctgtcccagacgaaagttctttgtttatc Alignment from Spaln_aa2Genome ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGG CGTTGTGGTGGCC taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAGGGTGGgtcagtaactaaatttgctgtcccagacgaaagTCAATTTAAATCC Alignment from Spaln_nt2Genome ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACTGCTG---AAAACGAGC-TGG GCGTTGTGGTGGC taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAGGGTGGgtcagtaactaaatttgctgtcccagacgaaagTCAATTT--AAAT Alignment from Pairagon ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACTGCT---GAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAG------------------------------Ggtgggtcagtaactaaatttgctgtcccagacgaaagtcaatttaaatcc Alignment from Exonerate_protein2genome ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAGGGTGGGTCAGTAACTAAATTTGCTGTCCCAGacgaaagtcaatttaaatcc Alignment from Exonerate_coding2genome ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACT---GCTGAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAGTCAG taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAGGGTGGGTCAGTAACTAAATTTGCTGTCCCAGacgaaagtcaatttaaatcc Alignment from GeneWise ATCTCCCTAGGCGATGCACAGTCCAATTACCTGCTGACTACTGCT---GAAAACGAGCTGGGCGTTGTGGTGGCCCACAGTGAG------------------------ taatggttatataagaaaggtcaaacactcctcgttcctctcttccccagATATCGCTAGGGGCTGCACAGTCCAATTATCTGTTAACCACTGCTGCCGAAAACGAGGGTGGGTCAGTAACTAAATTTGCTGTCCCAGACGAAAGTCAATTTAAATCC #### Exosc1_ID8337_2 --> 2 - 0 Original Alignment gc---------GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcaggcacttggctttctccttttgcataggtAACAGCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from CESAR gc---------GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcaggcacttggctttctccttttgcataggtAACAGCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from Spaln_aa2Genome GC---------GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcaggcacttggctttctccttttgcatagGTAACAGCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from Spaln_nt2Genome GC--GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcaggcacttggctttctccttttgcataggtaacagCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from Pairagon GC-----------------------------------GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcagGCACTTGGCTTTCTCCTTTTGCATAGGTAACAGCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from Exonerate_protein2genome GC---------GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcaggcacttggctttctccttttgcatagGTAACAGCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from Exonerate_coding2genome GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG acacttttgcatattatgttgcaggcacttggctttctccttttgcataggtaacagccatGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg Alignment from GeneWise GCACCACCGGTGAGGTACTGCATCCCCGGC------GAACGTCTGTGTAACTTGGAGGAAGGCAGCCCCGGCAGCGGCACCTACACCCGGCATGGCTACATCTTTTCGTCGCTGGCTGGCTGCCTGATGAAGACCAGCGAGAATGGCGCG ttgcatattatgttgcaggcacttg------GCTTTCTCCTTTTGCATAGGTAACAGCCATGAACATCTGTGCAACTTAGAAGAAGGCAGTCCTGGCAGTGGCACCTACACCTGGCATGGCTACATATCCTCATCATTGGCTGGCTGTCCTACGAAGACCAGCAAGAATGGTGCAgtaattaaggaggctccctatacggggttcactcctgccctccccatggg #### Fads1_ID2689_3 --> 0 - 0 Original Alignment ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagCAAAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from CESAR ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagCAAAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from Spaln_aa2Genome ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagCAAAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from Spaln_nt2Genome ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagCAAAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCC---CATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from Pairagon ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagCAAAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCC---CATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from Exonerate_protein2genome AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagcaaAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from Exonerate_coding2genome AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagcaaAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta Alignment from GeneWise ---AAAGCGCTAACTGATGAATTCCGGGAGCTGCGGGCCACAGTAGAGCGAATGGGCCTCATGAAGGCCAACCACCTCTTCTTCCTGGTCTACCTGCTTCACATCCTGCTGCTGGATGTGGCTGCCTGGCTCACCCTTTGGATCTTTGGAACTTCCTTGGTGCCCTTCATCCTCTGTGCAGTACTGCTCAGTACAGTTCAG gcactttgagattagttaggctgatgttcctccttcggttccttccctagCAAAAAGTAATATCTGATGAATTTCGAGAACTGCGGGCCACTGTAGAGCGAATAGGTCTCATGAAAGCTAATCATCTCTTCCTTTTGGTATACCTGCTTCGCATTCCCCTGCTTGATGTAGCTGCCTGGCTAACACTATGGATCTTTGGAACATCCTTGGTGCCC---ATACTTTGTGCAGTATTACTCAGCACTGTTCAGgtgaggcctacttctcagcctaaaccacaaatactgaagagtggtttgta #### Fads1_ID2694_8 --> 0 - 2 Original Alignment ------GACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGC---CTTTTCTTCATTGTCag caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagCACAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTaggtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from CESAR ------GACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCCTT---TTCTTCATTGTCag caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagCACAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTaggtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from Spaln_aa2Genome GACTTGGCCTGG------ATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCCTT---TTCTTCATTGTCAG caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagCACAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTAGgtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from Spaln_nt2Genome GGACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCCTT---TTCTTCATTGTCAG caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagcacagCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTAGgtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from Pairagon ------GACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCC---TTTTCTTCATTGTCAG caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagCACAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTAGgtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from Exonerate_protein2genome GTGGACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCCTT---TTCTTCATTGTCAG caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagcacAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTAGgtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from Exonerate_coding2genome GTGGACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCCTT---TTCTTCATTGTCAG caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagcacAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTAGgtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac Alignment from GeneWise ------GACTTGGCCTGGATGCTCAGCTTCTATGCCCGCATCTTCTTCACTTACATGCCGCTGCTGGGGCTGAAAGGCTTCCTGGGCCTT---TTCTTCATTGTCAG caatcctttgaaaaaacaaaaaccctgctttctgttttcttttaccttagCACAGCGATTTGGCCTGGATGGTTAGTTTCTACGCTCACATCTTTTTAGCCTATATATCACTCTCAGGGTTGAAGGGCTTCTTGGGGCTCATCTTCTTCATTGTTAGgtattgacaagcagtgagtttaaaatagtaagcccaaacaccaccagaac #### Fads1_ID2695_9 --> 1 - 0 Original Alignment gTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG--------- accaccagaaccttgttactagctctgcgaccttcacccacgcccctcaggTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGGGAGACATTgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from CESAR gTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG--------- accaccagaaccttgttactagctctgcgaccttcacccacgcccctcaggTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGGGAGACATTgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from Spaln_aa2Genome GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG--------- accaccagaaccttgttactagctctgcgaccttcacccacgcccctcagGTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGGGAGACATTgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from Spaln_nt2Genome GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG--------- accaccagaaccttgttactagctctgcgaccttcacccacgcccctcagGTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGGGAGACATTgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from Pairagon GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG--------- accaccagaaccttgttactagctctgcgaccttcacccacgcccctcagGTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGGGAGACATTgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from Exonerate_protein2genome GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accaccagaaccttgttactagctctgcgaccttcacccacgcccctcagGTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGggagacattgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from Exonerate_coding2genome GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG accaccagaaccttgttactagctctgcgaccttcacccacgcccctcagGTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGggagacattgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat Alignment from GeneWise GTTCCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCCCCATGCACATTGATCACGACCGGAATGTGGACTGGGTCTCCACCCAG--------- accaccagaaccttgttactagctctgcgaccttcacccacgcccctcagGTTTCTGGAAAGCAACTGGTTTGTGTGGGTGACACAGATGAACCATATCTCCATGCACATTGATCCAGATAGGAATGTGGATTGGGTCTCAACACAGGGAGACATTgtggggtgtagtctacccagctgtgaagcttcggagttcagatcatgaat #### Fads1_ID2696_10 --> 0 - 2 Original Alignment ---CTGCAGGCAACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACca taatccctacactgatacatggaaatttcttactctgcttgtctttgtagCTGCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACcagtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg Alignment from CESAR ---CTGCAGGCAACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACca taatccctacactgatacatggaaatttcttactctgcttgtctttgtagCTGCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACcagtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg Alignment from Spaln_aa2Genome CTGCAGGCAACCTGC---AACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACCA taatccctacactgatacatggaaatttcttactctgcttgtctttgtagCTGCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACCAgtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg Alignment from Spaln_nt2Genome GCTGCAGGCA--ACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACCA taatccctacactgatacatggaaatttcttactctgcttgtctttgtagCTGCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACCAgtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg Alignment from Pairagon ---CTGCAGGCAACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACCA taatccctacactgatacatggaaatttcttactctgcttgtctttgtagCTGCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACCAgtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg Alignment from Exonerate_protein2genome CTGCAGGCAACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACCA taatccctacactgatacatggaaatttcttactctgcttgtctttgtagctgCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACCAgtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg Alignment from Exonerate_coding2genome CTGCAGGCAACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACCACCTCTTCCCCACCATGCCGCGGCAC taatccctacactgatacatggaaatttcttactctgcttgtctttgtagctgCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACCAGTGCGGTGATAGTGCAAGGAAACATgggatggcacagggtctaggtgagg Alignment from GeneWise ---CTGCAGGCAACCTGCAACGTTCACCAATCAGCCTTCAACAACTGGTTCAGTGGCCACCTAAATTTCCAGATTGAACACCA taatccctacactgatacatggaaatttcttactctgcttgtctttgtagCTGCTGCAGGCAACATGCAATGTCCACCAATCTGCCTTCAACAACTGGTTCAGTGGACATCTGAATTTCCAGATTGAACACCAgtgcggtgatagtgcaaggaaacatgggatggcacagggtctaggtgagg #### Fads3_ID2664_7 --> 2 - 0 Original Alignment ttGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGACG--------- tatcatttgtataccccatggctgagggctttgtaccactcaccccacagttGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTTGGCTTCCAgtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca Alignment from CESAR ttGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGACG--------- tatcatttgtataccccatggctgagggctttgtaccactcaccccacagttGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTTGGCTTCCAgtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca Alignment from Spaln_aa2Genome TTGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGACG--------- tatcatttgtataccccatggctgagggctttgtaccactcaccccacagTTGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTTGGCTTCCAgtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca Alignment from Spaln_nt2Genome TTGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGAC--G tatcatttgtataccccatggctgagggctttgtaccactcaccccacagTTGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTTGgcttccagtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca Alignment from Pairagon TTGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGAC------------------------------------------------------------ tatcatttgtataccccatggctgagggctttgtaccactcaccccacagTTGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTTGGCTTCCAGTACCAGACTCGACTTCAAAAGCTAAGGCATGAAAGCTTTCAACAGACCA Alignment from Exonerate_protein2genome TTGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGACG tatcatttgtataccccatggctgagggctttgtaccactcaccccacagTTGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTtggcttccagtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca Alignment from Exonerate_coding2genome TTGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGACG tatcatttgtataccccatggctgagggctttgtaccactcaccccacagTTGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTtggcttccagtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca Alignment from GeneWise TTGGCCCTCCGCTGCTCACCTTGGTGAACTTTGAAGTTGAAAATCTGGCGTACATGCTGGTGTGCATGCAGTGGACG--------- tatcatttgtataccccatggctgagggctttgtaccactcaccccacagTTGGCCCACCACTCTTCACTTTAGTGAATTATGAAGTTGAAAATCTGGCTTACATGTTGGTATGCATGCAGTGGACTTGGCTTCCAgtaccagactcgacttcaaaagctaaggcatgaaagctttcaacagacca #### Fads3_ID2665_8 --> 0 - 2 Original Alignment GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTC------------------ag ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGGGAATGTATCTTGTGATCcggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from CESAR GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTC---ag ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGGGAatgtatcttgtgatccggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from Spaln_aa2Genome GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTCAGG-- ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGGGAATgtatcttgtgatccggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from Spaln_nt2Genome GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTCAG--- ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGGGAATgtatcttgtgatccggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from Pairagon GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTG------------------TCAG ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGGGAATGTATCTTGTGATCCGgtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from Exonerate_protein2genome GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTC ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGggaatgtatcttgtgatccggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from Exonerate_coding2genome GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTC ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGggaatgtatcttgtgatccggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta Alignment from GeneWise GACTTGCTGTGGGCTGCCAGTTTCTACTCCCGCTTTTTCTTGTCCTACTCTCCCTTCTATGGTGCCACTGGGACACTGCTCCTCTTTGTTGCTGTCAGG-- ttgaacaggcaaagtgattccagtttagtagtttaattatcttcccacagGACTTACTGTGGGCTGCCAGCTTCTACACCCACTTTTTTTTGTCCTACTCACCCTTCTATGGAGTCACTGGGACACTAATCCTCTTTGTCGTTGTGGGAATgtatcttgtgatccggtaagatgctacttgctgagcaccaaatctatttaactcccttggcctta #### Fads3_ID2666_9 --> 1 - 0 Original Alignment gGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagg---------------------------ATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from CESAR gGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG ttgagtcatctcgattgaatgattccatgctattccaactgtccctacagg---------------------------ATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from Spaln_aa2Genome GATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from Spaln_nt2Genome GATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from Pairagon GATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagGATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from Exonerate_protein2genome GTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagG---ATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from Exonerate_coding2genome GTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagG---ATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc Alignment from GeneWise GGTGCTGGAGAGCCACTGGTTCGTGTGGATCACGCAGATGAACCACATCCCCAAGGAGATTGGCCATGAAAAGCATCGGGACTGGGCAAGCTCTCAG atcggcttgcagcattaagcggttccatgctattccaactgtccctacagG---------------------------ATCACACAGATGAACCATATCCCCAAGAAGATAGGACATGAAAAACATCGGGACTGGGCAACCTCTCAGgtaagtctcttgagtgcttaagtgcatactagtggcaaaagtgtctgtgc #### Fads3_ID2668_11 --> 1 - 2 Original Alignment cCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCgg caagataacatcattatgggggtatcacctgtggttgctggctgccgcagcCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGAGATC---gggtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from CESAR cCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCgg caagataacatcattatgggggtatcacctgtggttgctggctgccgcagcCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGAG---ATCgggtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from Spaln_aa2Genome CCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCGG caagataacatcattatgggggtatcacctgtggttgctggctgccgcagCCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGAG---ATCGGgtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from Spaln_nt2Genome CCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCGG caagataacatcattatgggggtatcacctgtggttgctggctgccgcagCCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGA---GATCGGgtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from Pairagon CCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCGG caagataacatcattatgggggtatcacctgtggttgctggctgccgcagCCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGA---GATCGGgtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from Exonerate_protein2genome CCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCGG caagataacatcattatgggggtatcacctgtggttgctggctgccgcagCCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGAG---ATCGGgtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from Exonerate_coding2genome CCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCGG caagataacatcattatgggggtatcacctgtggttgctggctgccgcagCCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGAG---ATCGGgtgcgtagcagatgtttggagccaagcaacctgggtccaacttcataagt Alignment from GeneWise CCTCTTCCCCACGATGCCAAGGCACAACTACCGGAGGGTGGCCCCCCTGGTCAAGGCGTTCTGCGCCAAGCACGGCCTACACTACGAGGTGAAGCCTTTCCTCACCGCTCTGGTGGATATCATCGGGTCCCTGAAGAAGTCTGGCGACATCTGGCTGGATGCATACCTCCATCAA caagataacatcattatgggggtatcacctgtggttgctggctgccgcagCCTTGTTCCTACTATGTCCAGGCACAACTACCGGAGAGTGGCACCCCTTGTTGAGGCATTCTGTGCTACACATGGACTACACCGTAAGGTAAAGCCATTTCTTATGGCATTGGTGGAGATC---GGGTGCGTA---------GCAGATGTTTGGAGCCAAGCAACCTGGGTCCAAc #### Fam160b1_ID12353_4 --> 0 - 0 Original Alignment TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGGCAGCCC------CTGCTTCCACACATCAACGTACACAGGCCTGTGCAG--------- AAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGCTTTCTTTTgtaggtaagtatagttgaatatcatgacgtcatggtctccacagCAGTTG Alignment from CESAR TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGGCAGCCC------CTGCTTCCACACATCAACGTACACAGGCCTGTGCAG--------- AAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGCTTTCTTTTgtaggtaagtatagttgaatataatgttctactttttgtcccagCAGTTG Alignment from Spaln_aa2Genome TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGG------CAGCCCCTGCTTCCACACATCAACGTACACAGGCCTGTGCAG--------- AAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGCTTTCTTTTgtaggtaagtatagttgaatatcatgacgtcatggtctccacagCAGTTG Alignment from Spaln_nt2Genome TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGGCAGCCCC------TGCTTCCACACATCAACGTACACAGGCCTGTGCAGA----------AA TTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGCTTTCTTTTGTAGgtaagtatagttgaatatcatgacgtcatggtctccacagcagTTG Alignment from Pairagon TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGGCAGCCC------CTGCTTCCACACATCAACGTACACAGGCCTGTG-----------------------------------------------------CAGAAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGCTTTCTTTTGTAGGTAAGTATAGTTGAATATCATGACGTCATGGTCTCCACAGCAGTTG Alignment from Exonerate_protein2genome TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGG------CAGCCCCTGCTTCCACACATCAACGTACACAGGCCTGTGCAG AAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGctttcttttgtaggtaagtatagttgaatatcatgacgtcatggtctccacagCAGTTG Alignment from Exonerate_coding2genome TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGG------CAGCCCCTGCTTCCACACATCAACGTACACAGGCCTGTGCAG AAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGctttcttttgtaggtaagtatagttgaatatcatgacgtcatggtctccacagCAGTTG Alignment from GeneWise TGCCCTCCAGGAATGAAGCAGCAGGTTTTGGTGTTCTATACCAAGCTTCTGGGACGAATCCGGCAGCCC------CTGCTTCCACACATCAACGTACACAGGCCTGTGCAG--------- AAATTA ataaatgtaggttcaccttgtctgtaatggatttttatttttacaattagTGCCCTCCAGGAATGAAACAGCAGGTGTTACTACTTTACACCAAACTACTTGAACAAATCCAGCAGCCCCAACCACTACTCCCACATGTCAATGTGCACAGGCCAGTGCAGCTTTCTTTTgtaggtaagtatagttgaatatcatgacgtcatggtctccacagCAGTTG #### Fas_ID6926_7 --> 2 - 0 Original Alignment taTTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT acagtgacaactactgacactctcgcttatgattttattttcatacatagta---------AGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTgtaagaatctagtgcaatacagggatgccctttccaatactcccaatcaa Alignment from CESAR taTTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT atgagatatacagtgacaactactgcttatgattttattttcatacatagta---------AGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTgtaagaatctagtgcaatacagggatgccctttccaatactcccaatcaa Alignment from Spaln_aa2Genome TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT acagtgacaactactgacactctcgcttatgattttattttcatacatagTA---------AGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTgtaagaatctagtgcaatacagggatgccctttccaatactcccaatcaa Alignment from Spaln_nt2Genome TATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT acagtgacaactactgacactctcgcttatgattttattttcatacatagTA-AGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTgtaagaatctagtgcaatacagggatgccctttccaatactcccaatcaa Alignment from Pairagon TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGT acagtgacaactactgacactctcgcttatgattttattttcatacatagTA---------AGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTgtaagaatctagtgcaatacagggatgccctttccaatactcccaatcaa Alignment from Exonerate_protein2genome TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGTGAAACCATACCAATGAATGCCTCAA acagtgacaactactgacactctcgcttatgattttattttCATACATAGTAAGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTGTAAGAATCTAGTGCAAT---ACAGggatgccctttccaatactcccaat Alignment from Exonerate_coding2genome TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGTGAAACCATACCAATGAATGCCTCAA acagtgacaactactgacactctcgcttatgattttattttCATACATAGTAAGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTGTAAGAATCTAGTGCAAT---ACAGggatgccctttccaatactcccaat Alignment from GeneWise TATTTATATATCGAAAGTACCGGAAAAGAAAGTGCTGGAAAAGGAGACAGGATGACCCTGAATCTAGAACCTCCAGTCGTGAAACCATA-- acagtgacaactactgacactctcgcttatgattttattttcatacatagTA---------AGAAAGTACCGAAAAAGAAAGTGCTGGAAAAGGAGACAAGATGACCCCGAATCTAGAACCTCGAGTCGTGTAAGAATCTAgtgcaatacagggatgccctttccaatactcccaatcaa #### Fau_ID1402_2 --> 0 - 1 Original Alignment GATCATGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAg tactgactacataggaccagatactggctgcctatcttcttactgtgcag------GTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTggtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from CESAR GATCATGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAg ttcacttactgactacataggaccaggctgcctatcttcttactgtgcag------GTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTggtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from Spaln_aa2Genome GATCATGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAG tactgactacataggaccagatactggctgcctatcttcttactgtgcag------GTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTGgtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from Spaln_nt2Genome GTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAG tactgactacataggaccagatactggctgcctatcttcttactgtgcagGTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTGgtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from Pairagon GATCATGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAG tactgactacataggaccagatactggctgcctatcttcttactgtgcag------GTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTGgtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from Exonerate_protein2genome GATCATGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAG tactgactacataggaccagatactggctgcctatcttcttactGTGCAGGTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTGgtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from Exonerate_coding2genome GATCATGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAG tactgactacataggaccagatactggctgcctatcttcttactGTGCAGGTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTGgtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata Alignment from GeneWise GTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCCTAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAG tactgactacataggaccagatactggctgcctatcttcttactgtgcagGTTGCATCACTTGAAGGCATGGCTCCTGAGGATCAGGCTGTACTCTTGGCAGGTTCCCCACTGGAAGATGATGCAACCCTGGGCCAGTGTGGTGTAAAAGCACCAACTACTCTAGAGGTGGCAGGTCGCATGCTTGGTGgtatgtgataccctgtgagctatcacaaggtaactgccagtgcatgtata #### Fau_ID1403_3 --> 2 - 0 Original Alignment gtAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAAGTGAGAGGTCAGACTCCCAAG ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccaggcATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAGTC------------------gtagggagcaggggtgaaaccgggtcttgtcgccacgcttccttcaagtc Alignment from CESAR gtAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAAGTGAGAGGTCAGACTCCCAAG ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccaggcATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAGTC------------------gtagggagcaggggtgaaaccgggtcttgtcg Alignment from Spaln_aa2Genome GTAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAA ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccagGCATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAgtcgtagggagcaggggtgaaaccgggtcttgtcgccacgcttccttcaagtc Alignment from Spaln_nt2Genome GTAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAAGTGAGAGGTCAGACTCCCAAG ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccagGCATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAGTCGTAGG---GA--GCAGGGgtgaaaccgggtcttgtcgccacgcttccttc Alignment from Pairagon GTAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAAGTG ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccagGCATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAGTCgtagggagcaggggtgaaaccgggtcttgtcgccacgcttccttcaagtc Alignment from Exonerate_protein2genome GTAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAAGTGAGAGGTCAGACTCCCAAG ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccagGCATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAGTCGTAGGGAGCAGGGGTGAAaccgggtcttgtcgccacgcttccttcaagtc Alignment from Exonerate_coding2genome GTAAAGTTCACGGTTCCCTGGCTCGGGCTGGAAAAGTGAGAGGTCAGACTCCCAAG ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccagGCATAGTTCATGGCTCCCTGGCCCGGGCTGGAAAAGTCGTAGGGAGCAGGGGTGAAaccgggtcttgtcgccacgcttccttcaagtc Alignment from GeneWise ttttaagaggagaagaggagttcgtctaaatctacctctttaatgaccaggcatagttcatggctccctggcccgggctggaaaagtcgtagggagcaggggtgaaaccgggtcttgtcgccacgcttccttcaagtc #### Fbxl15_ID9850_2 --> 1 - 0 Original Alignment g---CTCCTGGACCTGCCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAG atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagaTGTTTCCTAGACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCAA---CTTCGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAgtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from CESAR g---CTCCTGGACCTGCCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAG atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagaTGTTTCCTAGACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCAA---CTTCGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAgtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from Spaln_aa2Genome G----CTCCTGGACCTGCCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAG atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagATGTTTCCTAGACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCAA---CTTCGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAgtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from Spaln_nt2Genome GGCTCCTGGACCTG--CCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAG atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagATGTTTCCTAGACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCA---ACTTCGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAgtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from Pairagon GCTCCTGGACCTGCCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAG atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagatgtttcctag--------ACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCA---ACTTCGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAgtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from Exonerate_protein2genome G---CTCCTGGACCTGCCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAG atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagATGTTTCCTAGACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCAA---CTTCGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAgtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from Exonerate_coding2genome atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagatgtttcctagacctgccttgggaagaattgctgctccttcatgttgtaaactgggtcccacttcaccaacttcgactgcagcaggtgagtagaacttttggggcacttgttcagttgcacttggccaggttacgccgctttgatgctgctcaagtgagttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt Alignment from GeneWise -AGGCTCCTGGACCTGCCCTGGGAAGACGTGCTGCTCCCGCACGTCCTGAACTGGGTCCCGCTGCGCCAGCTGCTCCGGCTGCAGCGCGTCAGTCGCGCCTTCCGGGCGCTCGTTCAGCTGCACTTGGCGAGGCTGCGCCGCTTCGACGCCGCTCAGGTG- atcttattggtacttgttcccttactgatgcgaaattacttcccaatcagATGTTTCCTAGACCTGCCTTGGGAAGAATTGCTGCTCCTTCATGTTGTAAACTGGGTCCCACTTCACCAACTT---CGACTGCAGCAGGTGAGTAGAACTTTTGGGGCACTTGTTCAGTTGCACTTGGCCAGGTTACGCCGCTTTGATGCTGCTCAAGTGAgttggtaagcaggggtgctcttgtcgttgtactgttgtgctcttgt #### Fgf8_ID9567_2 --> 1 - 0 Original Alignment gCTGTTGCACTTGCTGGTTCTCTGCCTCCAAGCCCAG accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagaCTTTTACAATCACTAGTTTTTTGCCTCCAGGCA---gtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatgtca Alignment from CESAR gCTGTTGCACTTGCTGGTTCTCTGCCTCCAAGCCCAG accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagaCTTTTACAATCACTAGTTTTTTGCCTCCAGGCA---gtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatg Alignment from Spaln_aa2Genome GCTGTTGCACTTGCTGGTTCTCTGCCTCCAAGCC accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagACTTTTACAATCACTAGTTTTTTGCCTCCAGGCAgtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatgtca Alignment from Spaln_nt2Genome GCTGTTGCACTTGCTGGTTCTCTGCCTCCAAGCC accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagACTTTTACAATCACTAGTTTTTTGCCTCCAGGCAgtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatgtca Alignment from Pairagon accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagacttttacaatcactagttttttgcctccaggcagtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatgtca Alignment from Exonerate_protein2genome GCTGTTGCACTTGCTGGTTCTCTGCCTCCAAGCCCAG accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagACTTTTACAATCACTAGTTTTTTGCCTCCAGGCA---gtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatg Alignment from Exonerate_coding2genome accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagacttttacaatcactagttttttgcctccaggcagtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatgtca Alignment from GeneWise accactctgtcttttgggccacattttgtctggctcctgtccctgtgcagacttttacaatcactagttttttgcctccaggcagtcagtagcattgtgcttaagcaatgagtggggagatcaggtggatgtca #### Fibp_ID1012_9 --> 0 - 2 Original Alignment TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGATGGCTTCcg agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTG---------cggtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from CESAR TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGATGGCTTCcg agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTG---------cggtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from Spaln_aa2Genome TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGA agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTGCGgtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from Spaln_nt2Genome TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGATGGCTTCCG agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTC---------CTTGCGgtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from Pairagon TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGATGGCTTCCG agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTG---------CGgtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from Exonerate_protein2genome TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGA agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTGCGgtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from Exonerate_coding2genome TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGA agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTGCGgtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt Alignment from GeneWise TTTGTGGAACCCTGCCGCTCTGACCACTGGCCACTGAGTGATGTGCGGCTCTTCCTCAGCCAGTATTCAGCGTCAGTCCACTCCCTGGA agaatttgttgtactaactttttggtgaacctgtttcctttcttttccagTTTGTAGAACCATGCCGGTCTGACCACTGGCCACTGAGTGATGTCCAGCTTTTTCTTAGCCAGTATTCAGTTTCAGTACATTCCTTGCGgtgagtagatcatgggcaagagatagacatatatttgtttggtctagttt #### Fkbp2_ID1946_3 --> 1 - 1 Original Alignment gATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTG---------g gttgactttcggctagctttttttatacccactttctccctgatccacaggATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCCGTATGggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from CESAR gATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTG---g gttgactttcggctagctttttttatacccactttctccctgatccacaggATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCcgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from Spaln_aa2Genome GATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTGGGG- gttgactttcggctagctttttttatacccactttctccctgatccacagGATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCCgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from Spaln_nt2Genome GATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTGG--- gttgactttcggctagctttttttatacccactttctccctgatccacagGATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCCgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from Pairagon GATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTGG--- gttgactttcggctagctttttttatacccactttctccctgatccacagGATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCCgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from Exonerate_protein2genome GATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTG---G gttgactttcggctagctttttttatacccactttctccctgatccacagGATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCCgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from Exonerate_coding2genome gttgactttcggctagctttttttatacccactttctccctgatccacaggatgtgtgaaggagagaggcagaagttgttcatcctgtcagaactggcccgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg Alignment from GeneWise GATGTGTGAAGGGGAAAAGCGGAAGTTGGTGATCCCATCCGAGCTGGGG- gttgactttcggctagctttttttatacccactttctccctgatccacagGATGTGTGAAGGAGAGAGGCAGAAGTTGTTCATCCTGTCAGAACTGGCCCgtatgggtgatgtaacgtagtgtccagaacaaatttagaactaggccagtttaatg #### Frmd8_ID1284_4 --> 2 - 0 Original Alignment atGAGCCTTCCCTTCAGTTCCGAAGGAATGTTTTTTTCCCAAGGCGCCGAGAGCTCCAG agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagat---------------------------------TTCCCCAGACAGCGTGAGCTCCAGgtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from CESAR atGAGCCTTCCCTTCAGTTCCGAAGGAATGTTTTTTTCCCAAGGCGCCGAGAGCTCCAG tatctttgaaggcttaggaaacaatgaaacatttctgacctgtaccccagat---------------------------------TTCCCCAGACAGCGTGAGCTCCAGgtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from Spaln_aa2Genome TTCCCAAGGCGCCGAGAGCTCCAG agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagATTTCCCCAGACAGCGTGAGCTCCAGgtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from Spaln_nt2Genome TTTTCCCAAGGCGCCGAGAGCTCCAG agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagATTTCCCCAGACAGCGTGAGCTCCAGgtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from Pairagon ATGAGCCTTCCCTTCAGTTCCGAAGGAATGTTTTTTTCCCAAGGCGCCGAGAGCTCCAG agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagA---------------------------------TTTCCCCAGACAGCGTGAGCTCCAGgtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from Exonerate_protein2genome TTTTCCCAAGGCGCCGAGAGCTCCAG agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagATTTCCCCAGACAGCGTGAGCTCCAGgtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from Exonerate_coding2genome agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagatttccccagacagcgtgagctccaggtgaggcaggacttatctaaggtcacactattttagtatgtccatatttg Alignment from GeneWise ATGAGCCTTCCCTT agcgtgcagaataggttgaaacaatgaaacatttctgacctgtaccccagatttccccagacagcgtgagctccaggtgaggcaggacttatctaaggtcacactattttagTATGTCCATATTTG #### Ganab_ID2467_6 --> 1 - 2 Original Alignment tTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTag tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagt---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCaggtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from CESAR tTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTag tggtagtaagacaatggtgggacagtctggtgtcgttgtgtctcccatagt---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCaggtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from Spaln_aa2Genome TTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTAG tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagT---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCAGgtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from Spaln_nt2Genome TTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTAG tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagT---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCAGgtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from Pairagon TTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTAG tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagT---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCAGgtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from Exonerate_protein2genome TTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTAG tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagT---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCAGgtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from Exonerate_coding2genome TTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTAG tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagT---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCAGgtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc Alignment from GeneWise TTTCTCGGATAAAGTTAGTCTCGCGCTCGGTAGCGTGTGGGATAAGATCAAGAACCTTTTCTCTAG tagtaagacaatggtgggacagaaatctggtgtcgttgtgtctcccatagT---TCTGATAAAGTTAGCCTGACACTCAGCAGTGTGTGGGATAAGATCAAGAACCTTTTTTCCAGgtgagcgcctcattatatacctattgtgttctgcactggccaccagcctc #### Ganab_ID2468_7 --> 1 - 0 Original Alignment gCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgcagg---GAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from CESAR gCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG cagtgaacatcctaacttcactatataacttccatttgcctcttctgcagg---GAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from Spaln_aa2Genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgcagG---GAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from Spaln_nt2Genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgcagG---GAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from Pairagon GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgcagG---GAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from Exonerate_protein2genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgCAGGGAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from Exonerate_coding2genome GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgCAGGGAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat Alignment from GeneWise GCAAGAATCAAAAGACCCAGCTGAAGGCAATGGAGCCCAGCCTGAAGCAACACCTGGGGATGGTGACAAG tgaacatcctaacttcactataggttaacttccatttgcctcttctgcagG---GAATCAAAAGACCCTGCGGAGGGCAATGGGGCCCAGCCCGAGGCGACACCTGGGGATGGCGACAAGgtgggttgaatgtgagatttttacctctttaggaggcggcaagttggtat #### Ganab_ID2469_8 --> 0 - 1 Original Alignment CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATg tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGC---------ggtaggtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from CESAR CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATg tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGC---------ggtaggtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from Spaln_aa2Genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGC- tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCGgtaggtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from Spaln_nt2Genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCA tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCGgtaggtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from Pairagon CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCCTTATG tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGC---------Ggtaggtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from Exonerate_protein2genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCC tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCGGTAGgtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from Exonerate_coding2genome CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCAAGCC tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCGGTAGgtaattcgacattctggcaagccttgatgctaattttggaattgtc Alignment from GeneWise CCAGAGGAGACCCAGGAAAAGGCTGAGAAGGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACACATTCTGACAGCA tttaggaggcggcaagttggtatgaatttgcctttgccctctaactgcagCCAGAGGAGACCCAAGAAAAGGCTGAGAAGGATGAGCCAGGAGCTTGGGAGGAAACATTCAAAACACCTTCTGACAGCGgtaggtaattcgacattctggcaagccttgatgctaattttggaattgtc #### Ganab_ID2470_9 --> 2 - 2 Original Alignment gcCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACT------ga tgcaacatgcatacagccttaatactaacatgactcttcttcttttctaggtCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGGAAAgagtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from CESAR gcCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACT------ga tgcaacatgcatacagccttaatactaacatgactcttcttcttttctaggtCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGGAAAgagtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from Spaln_aa2Genome GCCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACTGAG----- tgcaacatgcatacagccttaatactaacatgactcttcttcttttctagGTCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGGAAAGAgtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from Spaln_nt2Genome GCCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACTG------A tgcaacatgcatacagccttaatactaacatgactcttcttcttttctagGTCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGGAAAGAgtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from Pairagon GCCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACT------GA tgcaacatgcatacagccttaatactaacatgactcttcttcttttctagGTCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGGAAAGAgtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from Exonerate_protein2genome GCCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACTGA tgcaacatgcatacagccttaatactaacatgactcttcttcttttctagGTCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGgaaagagtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from Exonerate_coding2genome GCCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACTGA tgcaacatgcatacagccttaatactaacatgactcttcttcttttctagGTCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGgaaagagtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga Alignment from GeneWise GCCCCACGTCTGTAGGTTTGGACTTTTCTCTGCCAGGAATGGAACATGTGTATGGGATCCCTGAGCATGCTGACAGCCTGAGACTGAAGGTCACT------GA tgcaacatgcatacagccttaatactaacatgactcttcttcttttctagGTCCCATGTCTGTTGGTTTAGACTTTTCTCTACCGTGGATGGAACATGCATACGGGATCCCTGAACATGCTGACAGCTTAAGACTGAAGGTTACTGGGAAAGAgtgagtccttgtgataacagtaacagcaaaagacctaattttcatgatga #### Ganab_ID2475_14 --> 2 - 0 Original Alignment Ag gcTCAGCTAGTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG Aggtaagcaatgaagttttttcttacctatgtgacctttgttccgtttaggc---------TACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from CESAR Ag gcTCAGCTAGTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG Aggtaagttccatgaccaatgaagtcctatgtgacctttgttccgtttaggc---------TACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from Spaln_aa2Genome AG GCTCAGCTAGTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG AGgtaagcaatgaagttttttcttacctatgtgacctttgttccgtttagGC---------TACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from Spaln_nt2Genome AG GCTCAGCTAGTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG AGgtaagcaatgaagttttttcttacctatgtgacctttgttccgtttagGC---------TACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from Pairagon AG GCTCAGCTAGTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG AGgtaagcaatgaagttttttcttacctatgtgacctttgttccgtttagGC---------TACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from Exonerate_protein2genome AGGCTCAGCTA GTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG AGGTAAGCAATgaagttttttcttacctatgtgacctttgttccgtttagGCTACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from Exonerate_coding2genome AGGCTCAGCTA GTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG AGGTAAGCAATgaagttttttcttacctatgtgacctttgttccgtttagGCTACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat Alignment from GeneWise AG GCTCAGCTAGTTACCCTGACTTCACTAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAG AGgtaagcaatgaagttttttcttacctatgtgacctttgttccgtttagGC---------TACCCTGACTACACCAATCCAAGGATGAGGGCCTGGTGGTCTAACATGTTCAGCTTTGACAATTATGAGgtgggtaattgggccagttggtaatccacataattttgattattagtcat #### Ganab_ID2476_15 --> 0 - 0 Original Alignment GGTTCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctag---TCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from CESAR GGTTCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG gttactgtaatctttttttccttctatctgattttttttttttttcctag---TCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from Spaln_aa2Genome GGTTCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctag---TCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from Spaln_nt2Genome GGTTCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctag---TCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from Pairagon GGTTCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctag---TCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from Exonerate_protein2genome TCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctagTCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from Exonerate_coding2genome TCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctagTCTGCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg Alignment from GeneWise GGTTCAGCTCCTAATCTTTATGTTTGGAATGACATGAATGAACCGTCTGTGTTCAATGGTCCTGAGGTCACCATGTTGAAGGATGCTGTGCATTATGGAGGCTGGGAGCACCGGGACATCCATAACATCTATGGCTTATATGTG actgtaatctttttttccttctccaatctgattttttttttttttcctagTCT---GCCCCCAATCTGTATGTATGGATAGAAATGAATGAACCTTCTGTCTTCAATGGTCCTGAGGTCACCATGTTAAAGGATGCAGTGCACTATGGAGGCTGGGAGCACCGGGATATCCACAATTTTTATGGATTATATGTGgtgagctgagtaaatcacaaggcagtcaagcaaagaggacaaaaaagttg #### Ganab_ID2481_20 --> 2 - 0 Original Alignment gtGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ccaggctgctcagatgcgtacaaaacctttgtggtccttttttcttgtaggt---ACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from CESAR gtGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ggaccaggctgctcagatgcgtacacctttgtggtccttttttcttgtaggt---ACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from Spaln_aa2Genome GTGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ccaggctgctcagatgcgtacaaaacctttgtggtccttttttcttgtagGT---ACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from Spaln_nt2Genome GTGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ccaggctgctcagatgcgtacaaaacctttgtggtccttttttcttgtagG---TACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from Pairagon -------------------------------------------------GATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA CCAGGCTGCTCAGATGCGTACAAAACCTTTGTGGTCCTTTTTTCTTGTAGGTACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from Exonerate_protein2genome GTGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ccaggctgctcagatgcgtacaaaacctttgtggtccttttttcttgtagGT---ACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from Exonerate_coding2genome GTGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ccaggctgctcagatgcgtacaaaacctttgtggtccttttttcttgtagGT---ACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt Alignment from GeneWise GTGATGCACTCCTTATTCACCCTGTATCGGATGCTGGGGCCCACGGAGTGCAGGTCTATTTGCCTGGCCAAGAAGAA ccaggctgctcagatgcgtacaaaacctttgtggtccttttttcttgtagGT---ACACTCCTTATTCACCCTGTATCAGATGCCGGGGCCCATGGTGTGCAGGTCTATTTGCCCGGCCAAGAAGAAgtaaaatgccaaatagcaaagcccaaatggcaaataatacataggtgtgt #### Ganab_ID2483_22 --> 0 - 0 Original Alignment ---ATCCCCGTGTTCCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagCCCATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from CESAR ---ATCCCCGTGTTCCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagCCCATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from Spaln_aa2Genome ATCCCCGTGTTC---CAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagCCCATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from Spaln_nt2Genome TATCCCCGTGTT--CCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagCCCATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from Pairagon ---ATCCCCGTGTTCCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagCCCATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from Exonerate_protein2genome ATCCCCGTGTTCCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagcccATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from Exonerate_coding2genome ATCCCCGTGTTCCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagcccATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc Alignment from GeneWise ---ATCCCCGTGTTCCAGCGTGGCGGAACCATTGTGCCTCGATGGATGCGTGTGAGGCGCTCTTCAGACTGTATGAAGGACGATCCTATCACTCTCTTTGTTGCTCTCAGTCCCCAG gtatagcataaaagaaatgaagtcatgatgacaatcttaatttccttcagCCCATCCCTGTGTTCCAGTGTGGTGGCACCATTGTCCCTCGATGGATGCGTGTCAGGCGCCCTTCAGACTGCATGAAGGATGATCCTATCACTCTTTTTGTTGCTCTCAGTCCCCAGgtaagcatttaatcaccaggactgggtccattatagatttattttaaatc #### Ganab_ID2484_23 --> 0 - 2 Original Alignment GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCT------ag ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCCTGGaggtcagtcttatgccctgcctccagtttctgctacctgtgcttgtgattcc Alignment from CESAR GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCT------ag ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCCTGGaggtcagtcttatgccctgcctccagtttctgctacctgtgattgagtcttt Alignment from Spaln_aa2Genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGT----- ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCCTGGAGgtcagtcttatgccctgcctccagtttctgctacctgtgcttgtgattcc Alignment from Spaln_nt2Genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCT------AG ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCCTGGAGgtcagtcttatgccctgcctccagtttctgctacctgtgcttgtgattcc Alignment from Pairagon GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGT-------------------------------------------------------------- ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCCTGGAGGTCAGTCTTATGCCCTGCCTCCAGTTTCTGCTACCTGTGCTTGTGATTCC Alignment from Exonerate_protein2genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAG ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCctggaggtcagtcttatgccctgcctccagtttctgctacctgtgcttgtgattcc Alignment from Exonerate_coding2genome GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAG ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCctggaggtcagtcttatgccctgcctccagtttctgctacctgtgcttgtgattcc Alignment from GeneWise GGTACTGCCCAAGGAGAGCTCTTTCTAGATGATGGACACACCTTTAACTATCAGACTCGCCATGAGTTCCTGTTGCGGCGGTTCTCTTTCTCTGGCAGCACACTGGTCTCTAGTTCA-- ataggtggacagaccacactgtctgttagactcagaacctctgttcacagGGTACTGCGCAGGGAGAGCTTTTCCTGGATGATGGCCACACCTTTAACTATCAGACTCGGCATGAGTTCCTGTTGCGGCGGTTTTCTTTTTCTGGTAGCACACTGGTATCTGCCTGGAGgtcagtcttatgccctgcctccagtttctgctacctgtgcttgtgattcc #### Ganab_ID2485_24 --> 1 - 1 Original Alignment tTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAA---g gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagcCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCAAGCAAAGGCTggttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from CESAR tTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAA---g gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagcCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCAAGCAAAGGCTggttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from Spaln_aa2Genome TTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAA---G gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagCCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCAAGCAAAGGCTGgttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from Spaln_nt2Genome TTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAAG gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagCCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCA-AGCAAAGgctggttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from Pairagon TTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAAG gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagCCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCA-AGCAAAGgctggttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from Exonerate_protein2genome TTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAAG gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagCCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCAAGCAAAGGctggttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from Exonerate_coding2genome TTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAAG gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagCCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCAAGCAAAGGctggttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc Alignment from GeneWise TTCAGCAGACCCCAAAGGCCACCTTGAGACACCTATTTGGATTGAGCGAGTAGTCATCATGGGGGCTGGAAAGCCAGCAGCTGTGGTGCTCCAGACCAAAGGA- gccctgcctccagtttctgctacctgtgattgagtctttgtctctcccagCCTAGCCGACCCTAAAGGCCATCAGGAGACTCCTATCTGGGTGGAGCAAGTTATTATAATGGGGGCTGGGAAGCCAGCTGCTGTGGTGCACCAAGCAAAGGCTGgttagaagatgcaatatgaattgatagaaacagtattagagatgaccagc #### Gbf1_ID9795_14 --> 0 - 1 Original Alignment AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAACAAGt cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAAC---tgtgagctgtaacttaattattttattattactactctttaaacccatgct Alignment from CESAR AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAACAAGt cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAAC---tgtgagctgtaacttaattattttattattactactctttaaacccatgct Alignment from Spaln_aa2Genome AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAAC- cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAACTgtgagctgtaacttaattattttattattactactctttaaacccatgct Alignment from Spaln_nt2Genome AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAACAAGT cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAAC---Tgtgagctgtaacttaattattttattattactactctttaaacccatgct Alignment from Pairagon AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAACAAGT cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAAC---Tgtgagctgtaacttaattattttattattactactctttaaacccatgct Alignment from Exonerate_protein2genome AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAACAAGT cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAAC---Tgtgagctgtaacttaattattttattattactactctttaaacccatgct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AATGCCTTTCCTGTGTCTGGTCAGCTTTATACAACACACCTGCTGTCTCTTGATGCCCTTTTGACAGTTATTGACAGCACTGAGTCTCATTGTCAGGCCAAAGTCCTCAACACCCTCAACCAGCAAGAGAAGAAAGAGACAGCCAGACCTGGCTTTGAGGCAGTGGATGGCAACCCAGAAACTAACA cccacttgacagtatacaggttaaatagtcatttctgttcacctttttagAATGTATTTCCTGTATCTGGTCAACTTGATACTACACATCTTCTGTCCCTTGATGCCCTTTTAACTTCTATTGACAGTAATGAGCTTCATTCTCAAGCCAAGGTTCTCAATGCCCTTAACCAGCAAGAGAATAAGGAGACGTCAAGGCCTGGTTTTGAAGCAGTTGAT---AACCCAGATGCTAACTgtgagctgtaacttaattattttattattactactctttaaacccatgct #### Gbf1_ID9800_19 --> 0 - 0 Original Alignment ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca Alignment from CESAR ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca Alignment from Spaln_aa2Genome AGTTGTAAT---GGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca Alignment from Spaln_nt2Genome AGTTGTAATGGCT---CCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca Alignment from Pairagon ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca Alignment from Exonerate_protein2genome ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---AGTTGTAATGGCTCCCCATTTGCTAATAGTGATGCCTGCTTTGCCCTGGCCTATGCTGTCATCATGCTTAACACTGACCAACATAACCACAATGTTCGAAAGCAGAATGCACCCATGACCCTGGAG ggtaaacatttcattatgaggtgttacactcctcctcctcctcctctcagGATAGCTGCAATGGCTCTCCTTTTGCTAATAGTGGTGCCTGTTCTGCGCTAGCCTATGGTGCCATCATGCTGAACACTGACCAGCATAACCACAATGTTCAAAAACAGAATACAACCACAACTCTAGAAgtatgtgcagaatagttgtctacctatagtcgggacagcaccactcgaca #### Gbf1_ID9803_22 --> 1 - 0 Original Alignment gAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG ggaaatgtgcaccaggtgtttcttttcttgtgctcctccttgttttccaga------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc Alignment from CESAR gAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG gggcctggaaatgtgcaccaggtgttcttgtgctcctccttgttttccaga------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc Alignment from Spaln_aa2Genome GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG ggaaatgtgcaccaggtgtttcttttcttgtgctcctccttgttttccagA------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc Alignment from Spaln_nt2Genome GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG ggaaatgtgcaccaggtgtttcttttcttgtgctcctccttgttttccag------AGCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc Alignment from Pairagon GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG ggaaatgtgcaccaggtgtttcttttcttgtgctcctccttgttttccag------AGCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc Alignment from Exonerate_protein2genome GAAGTGTGCCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG ggaaatgtgcaccaggtgtttcttttcttgtgctcctccttgttttccagA------GCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCATGATCTCCGCCCACTATGGCCTCAGCGATGTGTTTGACAATCTCATCATCTCTCTGTGCAAATTCACAGCTCTAAGTAGTGAG ggaaatgtgcaccaggtgtttcttttcttgtgctcctccttgttttccagagCCACAATCTCTGCCCACTATGGCCTCAGTGATGTCTTTGACAATCTGATCATTTCCCTGTGCAAATTCACAGCTTTAAGTAGTGAGgtgagtaattaccaagtaaactaatcagaggctaatgctgcacatcctcc #### Gbf1_ID9804_23 --> 0 - 0 Original Alignment TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGAG--------- agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAGCTAAAAGATgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta Alignment from CESAR TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGAG--------- agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAGCTAAAAGATgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta Alignment from Spaln_aa2Genome TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGAG--------- agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAGCTAAAAGATgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta Alignment from Spaln_nt2Genome TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGA agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAgctaaaagatgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta Alignment from Pairagon TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGAG--------- agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAGCTAAAAGATgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta Alignment from Exonerate_protein2genome TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGAG agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAGctaaaagatgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TCTATTGAGAACCTTCCCAGTGTATTTGGAAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTCCATTTGGCCCATCGTCATGGTGACATCCTTCGGGAGGGCTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCCCAACTTTTACCCAAGGCTATGGTGGAG--------- agggtttcctagactgaacctggctaacatgttcgctctattatttttagTCTATAGAAAACCTTCCCAGTGTTTTTGGTAGCAACCCTAAAGCCCACATAGCAGCCAAGACAGTATTTCATTTGGCCCATCGTCATGGTGACATCCTTCGAGAGGGGTGGAAGAATATCATGGAGGCCATGTTGCAGCTTTTCCGAGCTCAACTTTTACCTAAAGCTATGGTTGAGCTAAAAGATgtgtgtgctaatcaaggctccttggcatactatagcctcatgtcccacta #### Gbf1_ID9807_26 --> 0 - 0 Original Alignment CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG ctgggctttctttgtttatcataaagtgggcttttgtccttttattttag------GACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca Alignment from CESAR CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG cttacactgggctttctttgtttatgtgggcttttgtccttttattttag------GACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca Alignment from Spaln_aa2Genome CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG ctgggctttctttgtttatcataaagtgggcttttgtccttttattttag------GACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca Alignment from Spaln_nt2Genome CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG ctgggctttctttgtttatcataaagtgggcttttgtccttttattttag------GACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca Alignment from Pairagon CAATGTGACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG ctgggctttctttgtttatcataaagtgggcttttgtccttttattttag------GACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca Alignment from Exonerate_protein2genome GACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG ctgggctttctttgtttatcataaagtgggcttttgtccttttattttagGACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GACCCAGAAAAAATGATCACAGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAGCTCATGAAG ctgggctttctttgtttatcataaagtgggcttttgtccttttattttagGACCCAGAAAAGATGATCACGGAAAGCAAGTTCCTCCAGCTGGAATCACTGCAGGAACTCATGAAGgtgagttatgaacagatcatggaaaaatagaattgtactggtgcagtgca #### Gbf1_ID9815_34 --> 2 - 0 Original Alignment gaATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAG--- cacacttggtgactttcacaattgcttcagtgtccttcatttttccacaggaATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg Alignment from CESAR gaATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAG--- cacacttggtgactttcacaattgcttcagtgtccttcatttttccacaggaATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg Alignment from Spaln_aa2Genome GAATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAG--- cacacttggtgactttcacaattgcttcagtgtccttcatttttccacagGAATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg Alignment from Spaln_nt2Genome GAATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAG--- cacacttggtgactttcacaattgcttcagtgtccttcatttttccacagGAATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg Alignment from Pairagon GAATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAG--- cacacttggtgactttcacaattgcttcagtgtccttcatttttccacagGAATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg Alignment from Exonerate_protein2genome GAATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAG--- cacacttggtgactttcacaattgcttcagtgtccttcatttttccacagGAATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAATCGCCTGCTTATGCTGTGACGCCCGGCGCCAGGTACGGATGCAGGCCCTGACATATCTGCAGCGAGCCCTTCTGGTGCATGACCTACAGAAGCTAGATGCCCTGGAGTGGGAGTCCTGTTTTAACAAGGTG cacacttggtgactttcacaattgcttcagtgtccttcatttttccacagGAATTGCTTGCTTATGCTGTGATGCTCGACGCCAGGTGCGGATGCAGGCCTTGACATATCTCCAACATGCACTTCTTGTGCCCGACCTGCAGAAACTGGATGCCCTGGAGTGGGAGTCTTGTTCAAACAAGCTCgtaaggctcactcataatagatgctggttcacaacatacaccccaaaggg #### Gbf1_ID9816_35 --> 0 - 0 Original Alignment ---------GTGCTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG tcacaacatacaccccaaagggttgatatttttcccttacgtttcaccagCTTTATACAGTGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag Alignment from CESAR ---------GTGCTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG tcacaacatacaccccaaagggttgatatttttcccttacgtttcaccagCTTTATACAGTGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag Alignment from Spaln_aa2Genome TGCTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG tcacaacatacaccccaaagggttgatatttttcccttacgtttcaccagctttatacagTGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag Alignment from Spaln_nt2Genome GTGCTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG tcacaacatacaccccaaagggttgatatttttcccttacgtttcaccagctttatacag-TGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag Alignment from Pairagon -----------------------------------------------------------GTGCTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG TCACAACATACACCCCAAAGGGTTGATATTTTTCCCTTACGTTTCACCAGCTTTATACAGTGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag Alignment from Exonerate_protein2genome GTGCTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG tcacaacatacaccccaaagggttgatatttttcccttacgtttcaccagctttatacaGTGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --CTGTTTCCTCTCCTGACCAAGCTTTTGGAAAATATCAGCCCTGCAGATGTGGGCGGGATGGAGGAGACCCGGATGCGGGCTTCCACACTGCTCTCAAAG tcacaacatacaccccaaagggttgatatttttcccttacgtttcaccagctttatacagTGCTATTTCCCCTTCTTTCCAAGCTCTTAGAGAATATTAGTCCTGCAGAGGTAGGTGGGATGGAAGAGACACGAATGCGGGCATCTACACTCCTTTCAAAGgtgtgttaccttgtttgcacactgacaagatggttatctcatcactggag #### Gbf1_ID9818_37 --> 0 - 1 Original Alignment TCAGAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGg cattcaaactactacttctcctgctgcgctccctccatcaatcatggcag------GCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAggtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from CESAR TCAGAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGg agtgtccattcaaactactacttctgcgctccctccatcaatcatggcag------GCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAggtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from Spaln_aa2Genome TCAGAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGG cattcaaactactacttctcctgctgcgctccctccatcaatcatggcag------GCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAGgtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from Spaln_nt2Genome GCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGG cattcaaactactacttctcctgctgcgctccctccatcaatcatggcagGCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAGgtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from Pairagon TCAGAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGG cattcaaactactacttctcctgctgcgctccctccatcaatcatggcag------GCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAGgtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from Exonerate_protein2genome TCA---GAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGG cattcaaactactacttctcctgctgcgctccctccatcaaTCATGGCAGGCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAGgtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from Exonerate_coding2genome TCA---GAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGG cattcaaactactacttctcctgctgcgctccctccatcaaTCATGGCAGGCTATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAGgtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc Alignment from GeneWise TCAGAAGCTATCCCCGAGTCTCTGAAGAACATGCTGCTGGTGATGGACACAGCGGAGATTTTCCACAGTGCAGATGCAAGAGGAGGAGGCCCCTCTGCTCTCTGGGAGATTACCTGGGAGCGCATCGACTGCTTCTTGCCACACTTGCGTGACGAGCTCTTCAAGCAGACTGTCATCCAGG cattcaaactactacttctcctgctgcgctccctccatcaatcatggcagGCT------ATCCCTGAGTCTCTGAAGAACATGCTACTGCTAATGGATACAGCAGAGATTTTCCATAGTGCTGATGCTAGAGGAGGAGGTCCTACTACCCTCTGGGAGATAACATGGGAGCGCATTGTATGCTTCTTGCCACACTTGCGTGATGAACTCTTCAAGCAGACTGTAATCCAAGgtaatggcagatttgataaccaagcagtttatgaactaacagaactaccc #### Gif_ID3279_3 --> 2 - 1 Original Alignment ac---CTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAa tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagacATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACTCTG---AGGAAAATGGAAAACTGGTCACCTTCAagtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from CESAR ac---CTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAa tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagacATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAagtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from Spaln_aa2Genome AC---CTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagACATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACTCTGAGGAAA---ATGGAAAACTGGTCACCTTCAAgtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from Spaln_nt2Genome ACCTG---ACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagACATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACTCT---GAGGAAAATGGAAAACTGGTCACCTTCAAgtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from Pairagon AC---CTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagACATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAAgtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from Exonerate_protein2genome AC---CTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagACATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAAgtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from Exonerate_coding2genome AC---CTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagACATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACT---CTGAGGAAAATGGAAAACTGGTCACCTTCAAgtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa Alignment from GeneWise --GACCTGACAAGTGGGCAGCTTGCCCTCACCGTTATGGCTCTCACGTCCTCCTGCAGAGACCCTGGAAGTAAAGTGTCCACTCTACTGAAGAAAATGGAGAACTGGTCACCTTCAA tcctccctctgtcttgtgtagtttgtctaaaattcctctcatccccacagACATGTTGACAAGTGGGCAGCTGGCCCTCACTGTTATGGCTTTCACATCCTCTTGCAGAGATCCAGGTAGTAAGGTTTCTACTCTG---AGGAAAATGGAAAACTGGTCACCTTCAAgtacgtgtggcttgtgggggcattgagagggagagagtgtcatgcatgaa #### Gm815_ID5778_2 --> 0 - 1 Original Alignment TCCTTAGGAACGATGCTTCTGTGCTGCGTAGAAGCCCATGCCATGGGATTCCAGAACACTTCCTTCTCTACGTTTAGAACTGCTTCCCATACTTTTTTCCCCCACt tttacaccacaccttattcctgtattatgacactgctgttttgccttcag---------ACCATGCTTCTATGT------------------------------------------------------------TCACAGACC------CACCACtgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from CESAR TCCTTAGGAACGATGCTTCTGTGCTGCGTAGAAGCCCATGCCATGGGATTCCAGAACACTTCCTTCTCTACGTTTAGAACTGCTTCCCATACTTTTTTCCCCCACt cagcttttttttacaccacaccttatatgacactgctgttttgccttcag---------ACCATGCTTCTATGTTCA------------------------CAG------------------------------ACCCAC------------CACtgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from Spaln_aa2Genome ATGGCCCTGTCTGAGTCCTTAGGAACGATGCTTCTGTGCTGCGTAGAAGCCCATGCCAT tttacaccacaccttattcctgtattATGACACTGCTGTTTTGCCTTCAGACCATGCTTCTATGTTCACAGACCCACCACTGTCTgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from Spaln_nt2Genome TTTTCCCCCACT tttacaccacaccttattcctgtattatgacactgctgttttgccttcagaccatgcttctatgttcacag--ACCCACCACTgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from Pairagon tttacaccacaccttattcctgtattatgacactgctgttttgccttcagaccatgcttctatgttcacagacccaccactgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from Exonerate_protein2genome tttacaccacaccttattcctgtattatgacactgctgttttgccttcagaccatgcttctatgttcacagacccaccactgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from Exonerate_coding2genome tttacaccacaccttattcctgtattatgacactgctgttttgccttcagaccatgcttctatgttcacagacccaccactgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta Alignment from GeneWise tttacaccacaccttattcctgtattatgacactgctgttttgccttcagaccatgcttctatgttcacagacccaccactgtctgtaaaaaaaaagatgagcccgtaatcttagtaaagttgatgggtta #### Got1_ID8751_4 --> 2 - 0 Original Alignment ag---------AACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagagACCCATGACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from CESAR ag---------AACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagagACCCATGACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from Spaln_aa2Genome AG---------AACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagAGACCCATGACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from Spaln_nt2Genome AGA---------ACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagAGACCCATGACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from Pairagon AG---------AACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagAGACCCATGACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from Exonerate_protein2genome AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagagacccatgACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from Exonerate_coding2genome AGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagagacccatgACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc Alignment from GeneWise --------GAGAACCATAATGCTGTGTTTTCTGCCGCCGGTTTTAAGGACATTCGGCCCTATTGCTACTGGGATGCGGAGAAGAGAGGACTGGACCTCCAGGGTTTCCTGAATGATCTGGAG gttttatatctccattaataatggataacatgtctcattttgtctcctagAGACCCATGACAACCATAATGCTGTATTCTCTGCTGCTGGTTTCAAGGATATTCGTCCCTATTGCTACTGGGATGCTGAGAAAAGAGGATTAGACCTTCAGGGTTTCCTTAATGATCTGGAGgtaacagaagataagaatagatgcccaggcttagtgcaggagggttttcc #### Gpha2_ID1505_2 --> 2 - 0 Original Alignment ccTTCAATGTG---ACGGTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTCAGAAAG tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagcaTTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTT------gtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac Alignment from CESAR ccTTCAATGTG---ACGGTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTCAGAAAG tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagcaTTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTT------gtgagttttcccgcactgagtctctgtgtcttcaaagttacact Alignment from Spaln_aa2Genome CCTTCAATGTG---ACGGTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTC tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagCATTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTTgtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac Alignment from Spaln_nt2Genome CCTTCAATGTGACGG---TGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCT- tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagCATTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTTgtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac Alignment from Pairagon -------------------------------------------------------------------GTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTC TGATAGGTAGTTTATTTTAGTTTGTCAAGGCAAGCTGCTGTCTGCTGTAGCATTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTTgtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac Alignment from Exonerate_protein2genome CCTTCAATGTG---ACGGTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTC tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagCATTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTTgtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac Alignment from Exonerate_coding2genome CCTTCAATGTG---ACGGTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTC tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagCATTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTTgtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac Alignment from GeneWise CCTTCAATGTGACG---GTGCGCAGTGATCGCCTCGGCACTTGCCAGGGCTCCCACGTGGCACAGGCCTGTGTAGGACACTGTGAGTCTAGTGCTTTCCCTTCCCGGTACTCTGTGCTGGTGGCCAGTGGCTATCGGCACAACATCACCTCTTCCTCCCAGTGCTGCACCATCAGCAGCCTC tgataggtagtttattttagtttgtcaaggcaagctgctgtctgctgtagCATTCAATATTGCAGCAGTGCATAGTGACCACCTTGGAGAATGTCAGGCATCCCAATTATCACAGGCCTGTGTGGGATATTGTGAGTCCAGTGCTTTTCCTTCCCAGTATTCTGTATTGGTGGTCAGTGGTTATTGGCACAATACTACATCATCATCACCCTGCTGCACTATTAGCAGTCTTgtgagttttcccgcactgagtctctgtgtcttcaaagttacactttgaac #### Gpr137_ID1885_6 --> 0 - 2 Original Alignment AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCACCag ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGC---aggtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from CESAR AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCACCag ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGC---aggtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from Spaln_aa2Genome AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCAC ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGCAGgtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from Spaln_nt2Genome AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCAC ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGCAGgtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from Pairagon AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCAC ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGCAGgtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from Exonerate_protein2genome AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCAC ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGCAGgtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from Exonerate_coding2genome AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGCAC ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGCAGgtgagcagtacccagctctttacccaaataggagaggctgctctttaccc Alignment from GeneWise AGCACCAGTCGAATCCTCAATGGGCAGGTTTTTGGCTCCCGATCCTACTTCTTTGACCGGGCTGGCCACTGTGAGGATGAGGGCTGCTCCTGGGAGCATAGCCGGAGTGAGAGC-- ggttgtagtagaaagggtggaaccccagttaccattaatttgcctaacagAGCACCAGTCAAATCCTTAATGGCCAAGTCTTTGGTTCCCGATCGTACTTCTTTGATAGGGCTGGACACTGTGAGGATGACAGCTGCTCCGGTGAGCACAGCCAAAGCAAGAGCAGgtgagcagtacccagctctttacccaaataggagaggctgctctttaccc #### Gpr137_ID1886_5 --> 0 - 0 Original Alignment ---GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagATGGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTC---TTTTGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from CESAR ---GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagATGGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from Spaln_aa2Genome GCAGATCTGGTG---AATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagATGGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from Spaln_nt2Genome GGCAGATCTGG--TGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagATGGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCT---TTTGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from Pairagon ----------------------------------------------------GGCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG GGGCTAACAGGGTTGCACATTAGCAAATTGCCTGCCCTTTCCCCTTCTAGATGGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCT---TTTGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from Exonerate_protein2genome GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagatgGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from Exonerate_coding2genome GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagatgGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta Alignment from GeneWise ---GCAGATCTGGTGAATGACCTAGGGAACAAAGGCTACCTGGTGTTTGGTCTCATCCTCTTCGTTTGGGAACTGCTGCCCACCACATTGCTGGTGGGCTTCTTCCGGGTACACCGGCCCCCACAGGATCTG gggctaacagggttgcacattagcaaattgcctgccctttccccttctagATGGCAGATCTGGTCAATGACCTAGTGAACAAAGGTTACCTTGTGTTTGGTCTAATTCTCTTT---TGGCAATTGCTACCTACCACGTGGCTGGTGGGCTTCTTCCGCGTACACCGGCCCCCACAGGATCTGgtaggtaacatgtgtcccttaatagagatgtcctgtcatcttccaaacta #### Gpr137_ID1888_3 --> 1 - 0 Original Alignment g---------------CTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggACAAGACTAACAATACTGGCTGTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGT------GCTCTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from CESAR g---------------CTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggACAAGACTAACAATACTGGCTGTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from Spaln_aa2Genome G---------CTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAA ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggacaagACTAACAATACTGGCTGTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from Spaln_nt2Genome GGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggacaagactaacaatactggctgttcagGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from Pairagon G---------------CTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcagGACAAGACTAACAATACTGGCTGTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from Exonerate_protein2genome GCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggacaagactaacaatACTGGCTGTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from Exonerate_coding2genome TCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggacaagactaacaatactggctgTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCT------CTTGCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact Alignment from GeneWise -------TTGCTGGCTGTCCGAGGGGCCTTCGTGGGTGCTTCACTGCTCTTTTTGCTGGTGAATGTACTGTGTGCAGTGCTGTCTCGCCAGCGCCAGGCACAGCCCTGGGTCCTTCTGCTGGTACGTGTCCTGGTGAGCGACTCTCTCTTCGTCATCTGTGCCCTCTCGCTTGCTGCCTGCCTCTGCCTTGTGGCCCGTCGAGCCCCTTCCACCAGCATCTACTTAGAGGCCAAG ggctatagcccctgcactgaaggtgtccctgtgggccctcatgtcttcaggacaagACTAACAATACTGGCTGTTCAGGGTGCCTTTGTGGGTGCTTCATTGCTTTTTTTATTGGTTAATGTACTGTGTGCAGTTCTATCATGCCAGCGTCAACAACAACCCTGGATACTTTCACTGGAACATGTCTTGGTAAGTGACTCTCTCTTTGTCATCTGTGCTCTT------GCTGGATGCCTCTGCCTAGTAGCCCGTCGTGCCCCAACCACCAGCATCTACTTAGATGCAAAGgtaaaggtgcaatatagatgtggcattgttggatttgtggacagaatact #### Hectd2_ID7162_18 --> 2 - 0 Original Alignment agTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttattttccccagag---------CTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from CESAR agTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tgttctccttttagacccaatgtccacttttgttttgttattttccccagag---------CTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from Spaln_aa2Genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttattttccccagAG---------CTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from Spaln_nt2Genome AGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttattttccccagAGCTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from Pairagon AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttattttccccag---------AGCTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from Exonerate_protein2genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttatTTTCCCCAGAGCTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from Exonerate_coding2genome AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttatTTTCCCCAGAGCTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca Alignment from GeneWise AGTATGTACAGCTTTATACTGACTTCCTGTTGAACAAATCTATCTATAAGCAATTTGCTGCATTTTACTGTGGATTTCATAGTGTGTGTGCTTCAAATGCCCTAATG tttagacccaatgtccttcacctcaacttttgttttgttattttccccagAG---------CTCTATACTGACTTCCTGTTAAACAAGTCTATTTATAAGCAATTTGCTGCATTCTACTGTGGCTTTCATAGTGTGTGTGCTTCCAATGCATTGATGgtaagtttagatttcaattgaacgggtctaataattgataactgatccca #### Hells_ID7708_15 --> 0 - 0 Original Alignment ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGT------gtgagcactcgcacagctaaaatttatgctgtccagtgcagtctggatca Alignment from CESAR ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGT------gtgagcactcgcacagctaaaatttatgctgtccagtgcagtct Alignment from Spaln_aa2Genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGT gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGTgtgagcactcgcacagctaaaatttatgctgtccagtgcagtctggatca Alignment from Spaln_nt2Genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGT gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGTgtgagcactcgcacagctaaaatttatgctgtccagtgcagtctggatca Alignment from Pairagon ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGT gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGTgtgagcactcgcacagctaaaatttatgctgtccagtgcagtctggatca Alignment from Exonerate_protein2genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGT------gtgagcactcgcacagctaaaatttatgctgtccagtgcagtct Alignment from Exonerate_coding2genome ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGTCACAAG gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGT------gtgagcactcgcacagctaaaatttatgctgtccagtgcagtct Alignment from GeneWise ATTGATGAAGAGTTGGTAACAAATTCTGGGAAGTTCTTAATTTTGGATCGAATGCTGCCCGAACTTAAAAAAAGAGGT gtttcattcaaaattacaagctgtgatttaatgaaaatctccatccccagAATGATGAAGAGTTTGTAACAAATTCTGGGAGGTTCTTAATTTCAGATCGAATGCTGCCAGAACTTAAGAAAAGAGGTgtgagcactcgcacagctaaaatttatgctgtccagtgcagtctggatca #### Hnrnpul2_ID2409_13 --> 0 - 0 Original Alignment GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTAT------------------gtacctttatgggataggctgaattatccgacacgtgagcagaagaaagg Alignment from CESAR GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTAT------------------gtacctttatgggataggctgaattatccgac Alignment from Spaln_aa2Genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTAC tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTATgtacctttatgggataggctgaattatccgacacgtgagcagaagaaagg Alignment from Spaln_nt2Genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTATGTAC-CTTTATGGGATAGgctgaattatccgacacgtgagcagaagaaag Alignment from Pairagon GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATT------------------ATgtacctttatgggataggctgaattatccgacacgtgagcagaagaaagg Alignment from Exonerate_protein2genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTATGTACCTTTATGGGATAGGctgaattatccgacacgtgagcagaagaaagg Alignment from Exonerate_coding2genome GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAACCGGGAT tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTATGTACCTTTATGGGATAGGctgaattatccgacacgtgagcagaagaaagg Alignment from GeneWise GGCTACCGTAATTTCTATGATCGATACAGAGGTGACTATGAACGATTCTACAGTCGAGATTATGAGTACAACAGATACAGAGACTATTAC tgatcttaaatgcctataaaggattgagcccatgtcctttctccttccagGGCTACCGCAATTTCTATGATCGATACAAGGGTGACTATGAACGATTCTATAGTCGGGATTACAAATACAATAGATATAGGGGATATTATgtacctttatgggataggctgaattatccgacacgtgagcagaagaaagg #### Hps1_ID8614_14 --> 1 - 2 Original Alignment gGAGAGGCTTCTGGACTGGAAGGACTTCCTGTTGGTGAAGAGCCGGAGA---AATGTCACCATGGTGtc aatggttagaagatgcaactagttattgtctttcccttgagcatcaataggGAGAGACTTTTGTACTGGAAGGATTTTTCCTTGGTGAATAGCTGGAGAAGAAATGTCACC------gcgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from CESAR gGAGAGGCTTCTGGACTGGAAGGACTTCCTGTTGGTGAAGAGC---CGGAGAAATGTCACCATGGTGtc aatggttagaagatgcaactagttattgtctttcccttgagcatcaataggGAGAGACTTTTGTACTGGAAGGATTTTTCCTTGGTGAATAGCTGGAGAAGAAATGTCACC------gcgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from Spaln_aa2Genome GGAGAGGCTTCTGGACTGGAAGGACTTCCTGTTGGTGAAGAGCCGGAGAAATGTCACCATGGTGTC aatggttagaagatgcaactagttattgtctttcccttgagcatcaatagGGAGAGACTTTTGTACTGGAAGGATTTTTCCTTGGTGAATAGCTGGAGAAGA---AATGTCACCGCgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from Spaln_nt2Genome GGAGAGGCTTCTGGACTGGAAGGACTTCCTGTTGGTGAAGAGCCGGAGAA---ATGTCACCATGGTGTC aatggttagaagatgcaactagttattgtctttcccttgagcatcaatagGGAGAGACTTTTGTACTGGAAGGATTTTTCCTTGGTGAATAGCTGGAGAAGAAATGTCACC------GCgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from Pairagon GGAGAGGCTTCTGGACTGGAAGGACTTCCTGTTGGTGAAGAGCCGG---AGAAATGTCACCATGGTGTC aatggttagaagatgcaactagttattgtctttcccttgagcatcaatagGGAGAGACTTTTGTACTGGAAGGATTTTTCCTTGGTGAATAGCTGGAGAAGAAATGTCACCG------Cgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from Exonerate_protein2genome aatggttagaagatgcaactagttattgtctttcccttgagcatcaatagggagagacttttgtactggaaggatttttccttggtgaatagctggagaagaaatgtcaccgcgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from Exonerate_coding2genome aatggttagaagatgcaactagttattgtctttcccttgagcatcaatagggagagacttttgtactggaaggatttttccttggtgaatagctggagaagaaatgtcaccgcgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga Alignment from GeneWise aatggttagaagatgcaactagttattgtctttcccttgagcatcaatagggagagacttttgtactggaaggatttttccttggtgaatagctggagaagaaatgtcaccgcgtaagtcgaaaatattgattgtatgttcatgagattattcaagctattga #### Hps1_ID8617_11 --> 0 - 0 Original Alignment AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAG tactccgcttggctcccccactctccttcgtttttgctttctcttcccag---------GCCCCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAAC---AACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAGgtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from CESAR AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAG gacctgtcttactccgcttggctcccttcgtttttgctttctcttcccag---------GCCCCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAAC---AACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAGgtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from Spaln_aa2Genome AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAG tactccgcttggctcccccactctccttcgtttttgctttctcttcccag---------GCCCCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAAC---AACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAGgtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from Spaln_nt2Genome AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAG tactccgcttggctcccccactctccttcgtttttgctttctcttcccag---------GCCCCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAACA---ACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAGgtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from Pairagon AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAG tactccgcttggctcccccactctccttcgtttttgctttctcttcccag---------GCCCCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAACA---ACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAGgtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from Exonerate_protein2genome AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAG tactccgcttggctcccccactctccttcgtttttgctttcTCTTCCCAGGCCCCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAAC---AACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAGgtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from Exonerate_coding2genome tactccgcttggctcccccactctccttcgtttttgctttctcttcccaggccccactaacccaaatcctatgccaactgctggatggattctcccttctggagaaaaggttgaaggagggccaggaggctggtagtgctttacgatcccagccctttgtgaccgacccacaccagaacaacaagttcatcaagaatcgggtcgggcaggaggtccaggtactgtcacagaactaatgtggactgattttgggaccctggctacagcc Alignment from GeneWise AGCCCCAGCACCCCACTGGCCCTGATCCTGTACCAACTGCTGGATGGCTTCTCCCTCCTGGAGAAAAAGCTGAAGGAAGGTCAGGAGGCCGGAAGTGCCCTGCGATCCCAGCCCTTTGTTGCAGACCTGCGCCAGAAGATGGACAAGTTTATCAAGAATCGAGTTGGGCAGGAGATTCAGAACACCTGGCTGGA tactccgcttggctcccccactctccttcgtttttgctttctcttcccagGCC---------CCACTAACCCAAATCCTATGCCAACTGCTGGATGGATTCTCCCTTCTGGAGAAAAGGTTGAAGGAGGGCCAGGAGGCTGGTAGTGCTTTACGATCCCAGCCCTTTGTGACCGACCCACACCAGAAC---AACAAGTTCATCAAGAATCGGGTCGGGCAGGAGGTCCAG---------GTACTgtcacagaactaatgtggactgattttgggaccctg #### Hps1_ID8625_3 --> 0 - 2 Original Alignment ---TTTGGAGAGTACCTGTTCGTCGCCATCAACGGAGACCACAGTGAGAGCGAGGGGGACCTGCGGAGGAAACTGTGTGTGCTCAAGTATCTATTCGAGGTGCACTTCGGGCTGGTGACTGTGGACGGCCAGCTCATCCGGAAGga tgatattaaatacacattttgactgccttgtacctttattttattcatagATCTTTGAAGAGTACCTGTTTGCTGTAATCAATGGAGACCACACTGAGAGTAAAGGGGAGCTACTGAGA---CTGTGTGTGCTTAAGTACTTATTTGGGGTGCACTTTGGGCTCGTGACTGTTGATGGCCAACTTATCTGGAAAgagtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from CESAR ---TTTGGAGAGTACCTGTTCGTCGCCATCAACGGAGACCACAGTGAGAGCGAGGGGGACCTGCGGAGGAAACTGTGTGTGCTCAAGTATCTATTCGAGGTGCACTTCGGGCTGGTGACTGTGGACGGCCAGCTCATCCGGAAGga tgatattaaatacacattttgactgccttgtacctttattttattcatagATCTTTGAAGAGTACCTGTTTGCTGTAATCAATGGAGACCACACTGAGAGTAAAGGGGAGCTACTGAGA---CTGTGTGTGCTTAAGTACTTATTTGGGGTGCACTTTGGGCTCGTGACTGTTGATGGCCAACTTATCTGGAAAgagtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from Spaln_aa2Genome TTTGGAGAGTACCTGTTCGTCGCCATCAACGGAGACCACAGTGAGAGCGAGGGGGACCTGCGGAGGAAACTGTGTGTGCTCAAGTATCTATTCGAGGTGCACTTCGGGCTGGTGACTGTGGACGGCCAGCTCATCCGGAAGGA tgatattaaatacacattttgactgccttgtacctttattttattcatagATCTTTGAAGAGTACCTGTTTGCTGTAATCAATGGAGACCACACTGAGAGTAAAGGGGAGCTACTGAGA---CTGTGTGTGCTTAAGTACTTATTTGGGGTGCACTTTGGGCTCGTGACTGTTGATGGCCAACTTATCTGGAAAGAgtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from Spaln_nt2Genome ---TTTGGAGAGTACCTGTTCGTCGCCATCAACGGAGACCACAGTGAGAGCGAGGGGGACCTGCGGAGGAAACTGTGTGTGCTCAAGTATCTATTCGAGGTGCACTTCGGGCTGGTGACTGTGGACGGCCAGCTCATCCGGAAGGA tgatattaaatacacattttgactgccttgtacctttattttattcatagATCTTTGAAGAGTACCTGTTTGCTGTAATCAATGGAGACCACACTGAGAGTAAAGGGGAGCTACTGAG---ACTGTGTGTGCTTAAGTACTTATTTGGGGTGCACTTTGGGCTCGTGACTGTTGATGGCCAACTTATCTGGAAAGAgtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from Pairagon ---TTTGGAGAGTACCTGTTCGTCGCCATCAACGGAGACCACAGTGAGAGCGAGGGGGACCTGCGGAGGAAACTGTGTGTGCTCAAGTATCTATTCGAGGTGCACTTCGGGCTGGTGACTGTGGACGGCCAGCTCATCCGGAAGGA tgatattaaatacacattttgactgccttgtacctttattttattcatagATCTTTGAAGAGTACCTGTTTGCTGTAATCAATGGAGACCACACTGAGAGTAAAGGGGAGCTACTGAG---ACTGTGTGTGCTTAAGTACTTATTTGGGGTGCACTTTGGGCTCGTGACTGTTGATGGCCAACTTATCTGGAAAGAgtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from Exonerate_protein2genome tgatattaaatacacattttgactgccttgtacctttattttattcatagatctttgaagagtacctgtttgctgtaatcaatggagaccacactgagagtaaaggggagctactgagactgtgtgtgcttaagtacttatttggggtgcactttgggctcgtgactgttgatggccaacttatctggaaagagtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from Exonerate_coding2genome tgatattaaatacacattttgactgccttgtacctttattttattcatagatctttgaagagtacctgtttgctgtaatcaatggagaccacactgagagtaaaggggagctactgagactgtgtgtgcttaagtacttatttggggtgcactttgggctcgtgactgttgatggccaacttatctggaaagagtgagtggccagatcaacctctaattccttactgcttcagataacatctg Alignment from GeneWise ---TTTGGAGAGTACCTGTTCGTCGCCATCAACGGAGACCACAGTGAGAGCGAGGGGGACCTGCGGAGGAAACTGTGTGTGCTCAAGTATCTATTCGAGGTGCACTTCGGGCTGGTGACTGTGGACGGCCAGCTCATCCGGAAGGA tgatattaaatacacattttgactgccttgtacctttattttattcatagATCTTTGAAGAGTACCTGTTTGCTGTAATCAATGGAGACCACACTGAGAGTAAAGGGGAGCTACTGAGA---CTGTGTGTGCTTAAGTACTTATTTGGGGTGCACTTTGGGCTCGTGACTGTTGATGGCCAACTTATCTGGAAAGAgtgagtggccagatcaacctctaattccttactgcttcagataacatctg #### Incenp_ID2604_15 --> 0 - 0 Original Alignment ------GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGATGTGCAG taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagCTCCTGGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATGTAAGAgtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from CESAR ------GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGATGTGCAG taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagCTCCTGGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATGTAAGAgtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from Spaln_aa2Genome ----GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGATGTGCAG taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagCTCCTGGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATGTAAGAgtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from Spaln_nt2Genome ------GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGATGTGCAG taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagCTCCTGGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATGTAAGAgtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from Pairagon ------GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGAT taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagCTCCTGGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATgtaagagtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from Exonerate_protein2genome GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGATGTGCAG taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagctcctgGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATGTAAGAgtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from Exonerate_coding2genome taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagctcctggaggagaagcagcacctggctaagcaggagccacaggagcaacaggcatggaaagcaaaggaggtcgcagcagccagaagggtgctcaacatgatggtggatgtaagagtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg Alignment from GeneWise ------GAAGAGCAACAGCGCCTGGCTGAGCAGCAACTGCAGGAGGAGCAGGCAAAGAAAGCTAAGGAGGTGGCAGCAGCCAGGAAAGTCCTGAACATGACTGTGGATGTGCAG taacgaggtgagtgatgctgtgggggagcttcctgcttctcctgccttagCTCCTGGAGGAGAAGCAGCACCTGGCTAAGCAGGAGCCACAGGAGCAACAGGCATGGAAAGCAAAGGAGGTCGCAGCAGCCAGAAGGGTGCTCAACATGATGGTGGATGTAAGAgtaagagctgaaagttagcatccaaatcagatatatgcttactgtgaatg #### Jak2_ID6240_16 --> 0 - 1 Original Alignment AAGCTGCAGTTCTATGAAGATAAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAg gtgcgcacacgctaagtccgttggcatctccctctaatttcttcttccag---------------------AAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAAT---AGTATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTggtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from CESAR AAGCTGCAGTTCTATGAAGATAAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAg atagatccaaccttcccagatgtgcatctccctctaatttcttcttccag---------------------AAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATAGT---ATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTggtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from Spaln_aa2Genome AAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAG gtgcgcacacgctaagtccgttggcatctccctctaatttcttcttccagAAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATAGT---ATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTGgtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from Spaln_nt2Genome AAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAG gtgcgcacacgctaagtccgttggcatctccctctaatttcttcttccagAAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATA---GTATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTGgtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from Pairagon AAGCTGCAGTTCTATGAAGATAAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAG gtgcgcacacgctaagtccgttggcatctccctctaatttcttcttccag---------------------AAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATA---GTATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTGgtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from Exonerate_protein2genome AAGCTGCAGTTCTATGAAGATAAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAG gtgcgcacacgctaagtccgttggcatctCCCTCTAATTTCTTCTTCCAGAAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATAGT---ATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTGgtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from Exonerate_coding2genome AAGCTGCAGTTCTATGAAGATAAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAG gtgcgcacacgctaagtccgttggcatctCCCTCTAATTTCTTCTTCCAGAAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATAGT---ATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTGgtattctggttctttacctctgatggatttgatttgtctaacttgagaat Alignment from GeneWise -----------------------------AAGCTGCAGTTCTATGAAGATAAGCATCAGCTTCCTGCACCCAAGTGGACAGAGTTAGCAAACCTTATAAATAATTGCATGGACTATGAGCCAGATTTCAGGCCTGCTTTCAGAGCTGTCATCCGTGATCTTAACAGCCTGTTTACTCCAG GTGCGCACACGCTAAGTCCGTTGGCATCTCCCTCTAATTTCTTCTTCCAGAAGCATCAGCTTCCTGCCCCTGGGTGGACAGAGTTAGCAAACCTTATAAATAGT---ATGGACTATGAACCAGATTTCAGACCTGCTTTCAGAGCTCTTGTACGTGATCTTAACAGTCTTTTTACACCTGgtattctggttctttacctctgatggatttgatttgtctaacttgagaat #### Kat5_ID1110_12 --> 2 - 2 Original Alignment gc---------------------------TATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCaa tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcaggcTCACCCTGTGATCCCACCACCTTCATCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCaagtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from CESAR gc---------------------------TATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCaa tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcaggcTCACCCTGTGATCCCACCACCTTCATCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCaagtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from Spaln_aa2Genome GTTCAGCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcaggctcaccctgtgatcccaccacCTTCATCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCAAgtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from Spaln_nt2Genome GTTCAGCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcaggctcaccctgtgatcccaccacCTTCATCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCAAgtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from Pairagon G---------------------------CTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcagGCTCACCCTGTGATCCCACCACCTTCATCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCAAgtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from Exonerate_protein2genome CTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcaggctcaccctgtgatcccaccaccttcatCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCAAgtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from Exonerate_coding2genome CTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcaggctcaccctgtgatcccaccaccttcatCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCAAgtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta Alignment from GeneWise --------------------------AGCTATGAACTCTCGAAAGTAGAAGGGAAGACCGGAACTCCTGAGAAACCCCTGTCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTGATGGGGCTGAAGTCGGAGAGCGGGGAGAGGCCACAGATCACCATCAA tgggcctataccagggaaaggagcagggcaaagggcttctcttgttgcagGCTCACCCTGTGATCCCACCACCTTCATCTATGAACTCTCAAAAGTTGATGGGAAAACTGGCACCCCTGAGAAACCCCTATCAGATCTTGGCCTCCTATCCTACCGAAGTTACTGGTCCCAAACCATCTTGGAGATCCTTATGGGGCTGAAGTCAGAGAGTGGGGAGAGGCCCCAGATCACCATCAAgtcagggaaggtgcaaataagcaggatgtgctatggatctcacagatgta #### Kat5_ID1111_11 --> 0 - 1 Original Alignment GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCa cccaccaacctgttggccatatgttagatgtctgtctgtcatgcttccag---------------GAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCagtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from CESAR GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCa agagagttgcaattacccaccaaccagatgtctgtctgtcatgcttccag---------------GAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCagtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from Spaln_aa2Genome GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCA cccaccaacctgttggccatatgttagatgtctgtctgtcatgcttccag---------------GAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCAgtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from Spaln_nt2Genome GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCA cccaccaacctgttggccatatgttagatgtctgtctgtcatgcttccag---------------GAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCAgtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from Pairagon GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCA cccaccaacctgttggccatatgttagatgtctgtctgtcatgcttccag---------------GAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCAgtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from Exonerate_protein2genome GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCA cccaccaacctgttggccatatgttagatgtctgtCTGTCATGCTTCCAGGAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCAgtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from Exonerate_coding2genome GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCA cccaccaacctgttggccatatgttagatgtctgtCTGTCATGCTTCCAGGAAGATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCAgtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag Alignment from GeneWise GAAAAGGAATCCACAGAAGATTACAATGTGGCCTGCATCTTGACTCTGCCTCCCTACCAGCGCCGGGGCTATGGCAAGCTGCTTATTGAGTTCA cccaccaacctgttggccatatgttagatgtctgtctgtcatgcttccagGAA---------------GATTACAACATTGCTTGCATCTTAACCCTACCCCCCTACCAACGGCGTGGCTATGGTAGATTGCTTATTGAGTTCAgtaaggctatactacctgctcatggtctgagctaaatagatcaggttgag #### Kat5_ID1114_8 --> 0 - 0 Original Alignment GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccag------CAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from CESAR GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG gctccccccagtactcacccgctgacctcacccacatctgccctccccag------CAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from Spaln_aa2Genome GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccag------CAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from Spaln_nt2Genome CAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccagCAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from Pairagon GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccag------CAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from Exonerate_protein2genome CAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccagCAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from Exonerate_coding2genome CAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccagCAGGATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga Alignment from GeneWise GATTCTCAGGACAGCTCAGATGGAATACCGTCAGCACCACGAATGACTGGCAGTCTGGTGTCTGACCGGAGCCACGACGACATTGTCACCCGGATGAAGAACATTGAGTGTATTGAGCTTGGCCGGCACCGCCTCAAGCCGTGGTACTTCTCCCCGTACCCACAAGAGCTTACCACGCTACCCGTCCTCTACCTGTGCGAATTTTGCCTCAAATATGGCCGTAGCCTCAAGTGTCTGCAACGCCACTTG cccagtactcacccgctgacacaagcctcacccacatctgccctccccagCAG------GATAGCTCAGATGGGATACCAACAGCTCCACAAATGACAGGTAGTCTAGTATCTGACCAGGGGCATGATGACATTGTCACCCAAATGAAGAATATTGAGTGCATTGAACTTGGCAGGCATCACCTTAAGCCATGGTATTTCTCCCCATAC---CAGGTGCTCACCATCATACCTATCCTCTATCTGTGTGAATCTTGCCTGAAGTATGGCCATAGTCTCAAGTGCCTTAAGCGCCACCTTgtaaggggtgacttagacatcagtgtggtttagcgctagttattggtgga #### Kat5_ID1119_3 --> 2 - 1 Original Alignment ccCTGGCTGAGATCCTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACt gtcatctctaaacttgctcttggttgattttttctttctttctgcttcagca---------------AGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACtgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from CESAR ccCTGGCTGAGATCCTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACt aggctggccccaattgtcatctctagattttttctttctttctgcttcagca---------------AGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACtgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from Spaln_aa2Genome CCCTGGCTGAGATCCTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACT gtcatctctaaacttgctcttggttgattttttctttctttctgcttcagCA---------------AGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACTgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from Spaln_nt2Genome CTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACT gtcatctctaaacttgctcttggttgattttttctttctttctgcttcagC-AAGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACTgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from Pairagon CCCTGGCTGAGATCCTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACT gtcatctctaaacttgctcttggttgattttttctttctttctgcttcagC---------------AAGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACTgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from Exonerate_protein2genome CCCTGGCTGAGATCCTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACT gtcatctctaaacttgctcttggttgattttttctTTCTTTCTGCTTCAGCAAGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACTgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from Exonerate_coding2genome gtcatctctaaacttgctcttggttgattttttctttctttctgcttcagcaagtgtgaaggacattagtggcaggaagcttttctatgtttactacattgactgtagggccaccctagaagatggttactcttgaagattagaagatcgacac Alignment from GeneWise CCCTGGCTGAGATCCTGAGCGTGAAGGACATCAGTGGCCGAAAGCTTTTCTATGTCCATTACATTGACT gtcatctctaaacttgctcttggttgattttttctttctttctgcttcagCA---------------AGTGTGAAGGACATTAGTGGCAGGAAGCTTTTCTATGTTTACTACATTGACTgtagggccaccctagaagatggttactcttgaagattagaagatcgacac #### Kat5_ID1120_2 --> 0 - 1 Original Alignment GGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGG---c atccaccaatggctatcaatacacatcctccaggcttcccattcctgcagGGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCcgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from CESAR GGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGG---c atccaccaatggctatcaatacacatcctccaggcttcccattcctgcagGGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCcgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from Spaln_aa2Genome GGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGG---C atccaccaatggctatcaatacacatcctccaggcttcccattcctgcagGGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCCgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from Spaln_nt2Genome GGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGGCCCC atccaccaatggctatcaatacacatcctccaggcttcccattcctgcagGGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCCgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from Pairagon GGGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGGCCCC atccaccaatggctatcaatacacatcctccaggcttcccattcctgcaGGGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCCgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from Exonerate_protein2genome GGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGG---C atccaccaatggctatcaatacacatcctccaggcttcccattcctgcagGGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCCgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from Exonerate_coding2genome atccaccaatggctatcaatacacatcctccaggcttcccattcctgcagggtgagataagtgagggctgctgcctacctgtccttcggcgcaatcaagataatgaagatgagtggatccgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg Alignment from GeneWise GCGGAGGTGGGGGAGATAATCGAGGGCTGCCGCCTGCCCGTGCTGCGGCGCAACCAGGACAACGAAGATGAGTGGCCC- atccaccaatggctatcaatacacatcctccaggcttcccattcctgcag---------GGTGAGATAAGTGAGGGCTGCTGCCTACCTGTCCTTCGGCGCAATCAAGATAATGAAGATGAGTGGATCCgtaagtgtgtcctgagggtactctgaaggaacaaaaggcaaggtcccagg #### Kazald1_ID9301_3 --> 0 - 1 Original Alignment TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTGCAACCCTCACAGTGCTCACACCAg acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCA------------------------ggtaagaattaattgtgggtagtaggtaaatgcgatcctagccatccaaca Alignment from CESAR TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTGCAACCCTCACAGTGCTCACACCAg acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCA------------------------ggtaagaattaattgtgggtagtaggtaaatgcgatcctagccatccaaca Alignment from Spaln_aa2Genome TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTG acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCAGgtaagaattaattgtgggtagtaggtaaatgcgatcctagccatccaaca Alignment from Spaln_nt2Genome TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTG acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCAGgtaagaattaattgtgggtagtaggtaaatgcgatcctagccatccaaca Alignment from Pairagon TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTGCAACCCTCACAGTGCTCACACCAG acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCT------------------------CAGgtaagaattaattgtgggtagtaggtaaatgcgatcctagccatccaaca Alignment from Exonerate_protein2genome TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTGCAACCCTCACAGTGCTCACACCAG acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCAGGTAAGAATTAATTGTGGGTAGTAGgtaaatgcgatcctagccatccaaca Alignment from Exonerate_coding2genome TTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTGCAACCCTCACAGTGCTCACACCAG acggggttattgcccacaaggttatgggttcttacttgctactcatacagTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCAGGTAAGAATTAATTGTGGGTAGTAGgtaaatgcgatcctagccatccaaca Alignment from GeneWise --------------------------------------------GTGCAGTTTAGGGGTGGACCTCAGAAGTTTGAGGTGACTGGCTGGCTACAGATTCAAGCTTTGCGCCCTAGTGATGAGGGCACCTACCGTTGCCTTGCCCGGAATGCTCTGGGCCAAGCGGAAGCTTCTG ACGGGGTTATTGCCCACAAGGTTATGGGTTCTTACTTGCTACTCATACAGTTCAGAGGTGGACCACAAGAATTTAAGGTGACTAGTTCACTACAGATTCAGGCATTGCACCATAGTGATGAAGGCACATACCGCTGTCTCACCCGAAATGTTCTCAGCCAAGCTGAAGCCTCAGgtaagaattaattgtgggtagtaggtaaatgcgatcctagccatccaaca #### Kcnip2_ID9603_9 --> 0 - 0 Original Alignment AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG--------- gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGTATCGACATgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from CESAR AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG--------- gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGTATCGACATgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from Spaln_aa2Genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG--------- gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGTATCGACATgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from Spaln_nt2Genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACA gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAgtatcgacatgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from Pairagon AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG--------- gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGTATCGACATgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from Exonerate_protein2genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGtatcgacatgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from Exonerate_coding2genome AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAG gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGtatcgacatgtaggtaaatgcaagaagggttggggtttgaaaaggggttctaggttcaa Alignment from GeneWise AAGATGGACAGAAACAAGGACGGCGTGGTGACCATTGAGGAATTCATTGAGTCTTGTCAACAGGACGAGAACATCATGAGGTCCATGCAACTCTTTGATAATGTCATC gtttctctcaacttgccttgaaactgagttactgccctcttttctcctagAAGATGGATAGAATCAAGGATGGTGTGGTGACCATTGAGGAATTCATTGCGTCTTGTCAACAGTATCGACATGTAGGTAAATGCAAGAAGGGTTGGGGTTTGAAAAGGggttctaggttcaa #### Kcnip2_ID9604_8 --> 0 - 0 Original Alignment GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGC---------gtatgtgtttcgaacgccgcaacttctggaatagtgggacatgtccagtc Alignment from CESAR GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGC---------gtatgtgtttcgaacgccgcaacttctggaatagtgggaca Alignment from Spaln_aa2Genome GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTC ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGCGTATGTgtttcgaacgccgcaacttctggaatagtgggacatgtccagtc Alignment from Spaln_nt2Genome GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGC TT ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGCgtatgtgtttcgaacgccgcaacttctggaatagtgggacatgtccag-T Alignment from Pairagon GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGC ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGCgtatgtgtttcgaacgccgcaacttctggaatagtgggacatgtccagtc Alignment from Exonerate_protein2genome GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCT ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGCGTATgtgtttcgaacgccgcaacttctggaatagtgggacatgtccagtc Alignment from Exonerate_coding2genome GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCT ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGCGTATgtgtttcgaacgccgcaacttctggaatagtgggacatgtccagtc Alignment from GeneWise GAAATGCTCGACATCATGAAGTCCATCTATGACATGATGGGCAAGTACACCTACCCTGCCCTCCGGGAGGAGGCCCCGAGGGAACACGTGGAGAGCTTCTTCCAG ctcagtggtgcggggtgttatgctacccctcctctactttgttgtcccagGACATGATTGACATCATGAAATCCATCTATGACATGATGGGCAAATACACCTACCCTGCACTCCGGGAGGAAGCCCCACGGGAACACGTGGAAAGCGTA---TGTgtttcgaacgccgcaacttctggaatagtgggacatgtcca #### Kcnip2_ID9607_5 --> 0 - 1 Original Alignment ---------------------------GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAg atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcagGTGCCTGCAGATGAAAGAGGCGCCTGGGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAggttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa Alignment from CESAR gtgcattccatagttcaagtgggcttagtggggctagaggctgtatgagaa Alignment from Spaln_aa2Genome -------------------------GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAG atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcagGTGCCTGCAGATGAAAGAGGCGCCTGGGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAGgttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa Alignment from Spaln_nt2Genome GGTCCTGTACA-----GAGGCTTCAAGAACGAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAG atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcagGTGCCTGCAGATGAAAGAGGCGCCTGG---GAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAGgttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa Alignment from Pairagon -----------------GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAG atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcaggtgcctgcagATGAAAGAGGCGCCTGGGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAGgttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa Alignment from Exonerate_protein2genome GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAG atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcaggtgcctgcagatgaaagaggcgcctggGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAGgttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa Alignment from Exonerate_coding2genome GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAG atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcaggtgcctgcagatgaaagaggcgcctggGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAGgttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa Alignment from GeneWise ---------------------------GAATGTCCCAGCGGAATTGTCAACGAGGAGAACTTCAAGCAAATTTATTCTCAGTTCTTTCCCCAAGGAG atgtgcgaatctcatgattggttatatttcactcagtgctctgtgtgcagGTGCCTGCAGATGAAAGAGGCGCCTGGGAATGTCCCAGTGGCATTGTCAATGAAAAGAACTTCAAGCAGGTCTATTCTCAGTTCTTTCCACAAGAAGgttggtcacaggtatagtgggaagatgtaagcatggtatagccaagagaa #### Kcnip2_ID9608_4 --> 2 - 0 Original Alignment acAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAG---TTGCAGGTCCTGTACAGAGGCTTCAAGAAC tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagatAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAAA---gtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttctaa Alignment from CESAR acAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAGTTG---CAGGTCCTGTACAGAGGCTTCAAGAAC tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagatAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAAA---gtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttc Alignment from Spaln_aa2Genome ACAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAG---TTGCAGGTCCTGTACAGAGGCTTCAAG tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagATAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAAAgtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttctaa Alignment from Spaln_nt2Genome ACAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAGTTGCAG---GTCCTGTACAGAGGCTTCAAGA tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagATAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAA-Agtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttctaa Alignment from Pairagon ACAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAGT---TGCAGGTCCTGTACAGAGGCTTCAAG tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagATAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAAAgtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttctaa Alignment from Exonerate_protein2genome ACAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAG---TTGCAGGTCCTGTACAGAGGCTTCAAGAAC tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagATAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAAA---gtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttc Alignment from Exonerate_coding2genome ACAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAG---TTGCAGGTCCTGTACAGAGGCTTCAAGAAC tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagATAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTCAAA---gtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttc Alignment from GeneWise ACAGCGTGGAGGATGAGTTTGAACTATCCACGGTGTGCCACCGGCCTGAGGGTCTGGAACAACTCCAGGAACAAACCAAGTTCACACGCAGAGAGTTG---CAGGTCCTGTACAGAGGCTTCAAGAAC tgaagggctagtgccagtcatgaagtattttctctctctccaatatttagATAGTGTTGAGGATGAGTTTGAACTGTCAATGATTTGTCACCGGCCAGAAAGTTTGGAACAGCTACAGAAACACGCCAAGTTTGCACATAGAGAGTTGCTGCAAGTCTTGTATAGAGGATTC---AAAgtatgaaggggggaatgaaaccacctgcggtagaccctccaaacttctaa #### Kcnk4_ID1877_3 --> 2 - 0 Original Alignment TTTTCTCGGGGACCATCATCACTACCATCg gc---------------------TATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGATG---CTG---CTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATctgtgagtatgcatccctccatcctcattacttgatttgtagtcGACCCGAGGGATTGCGAGTCTtgtttcatttccctctaggcTATGGAAATATACTCCTACACACTAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCACTATGCGGGATAGGGCTGTTGCTTGTAGGAGTTGGGGACCAGCTAGGCTCCTCGCTGCGTCGAGGC------AAAATTGGAGCAATCTTCTCGgtaagcacct Alignment from CESAR ctgaaaccacctaggtggcatgagcctaatttcttctctataaggacataa Alignment from Spaln_aa2Genome TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTC------GGGATGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtgagtatgcatccctccatcctcattacttgatttgtagtcgacccgagggattgcgagtcttgtttcatttccctctagGCTATGGAAATATACTCCTACACACTAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCACTATGCGGGATAGGGCTGTTGCTTGTAGGAGTTGGGGACCAGCTAGGCTCCTCGCTGCGTCGA------GGCAAAATTGGAGCAATCTTCTCGgtaagcacct Alignment from Spaln_nt2Genome TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGA------TGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtgagtatgcatccctccatcctcattacttgatttgtagtcgacccgagggattgcgagtcttgtttcatttccctctagGCTATGGAAATATACTCCTACACACTAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCACTATGCGGGATAGGGCTGTTGCTTGTAGGAGTTGGGGACCAGCTAGGCTCCTCGCTGCGTCGAGGCA------AAATTGGAGCAATCTTCTCGgtaagcacct Alignment from Pairagon TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTGTTCGGGA------TGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtgagtatgcatccctccatcctcattacttgatttgtagtcgacccgagggattgcgagtcttgtttcatttccctctagGCTATGGAAATATACTCCTACACACTAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCACTATGCGGGATAGGGCTGTTGCTTGTAGGAGTTGGGGACCAGCTAGGCTCCTCGCTGCGTCGAGGCA------AAATTGGAGCAATCTTCTCGgtaagcacct Alignment from Exonerate_protein2genome TTTTCTCGGGGACCATCATCACTACCATCG GCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTG------TTCGGGATGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTgtgagtatgcatccctccatcctcattacttgatttgtagtcgacccgagggattgcgagtcttgtttcatttccctctagGCTATGGAAATATACTCCTACACACTAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCACTATGCGGGATAGGGCTGTTGCTTGTAGGAGTTGGGGACCAGCTAGGCTCCTCGCTGCGTCGA------GGCAAAATTGGAGCAATCTTCTCGgtaagcacct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TTTTCTCGGGGACCATCATCACTACCATC---------------------------------------------------------------------------------GGCTATGGCAATATAGTCTTACACACAGATGCCGGGCGTCTCTTTTGTATCTTCTATGCACTGGTGGGGATCCCACTG------TTCGGGATGCTGCTGGCGGGAGTCGGGGACCGGCTGGGCTCCTCTCTGCGCCGGGGCATCGGCCACATCGAAGCAATCTTCTTG TTTTTTCAGGATCTATTGTGACAAACATCTGTGAGTATGCATCCCTCCATCCTCATTACTTGATTTGTAGTCGACCCGAGGGATTGCGAGTCTTGTTTCATTTCCCTCTAGGCTATGGAAATATACTCCTACACACTAAGGCTGTATGTCTCTTCTGTGTCTTTGATGCACTAGTGGGGATTCCACTATGCGGGATAGGGCTGTTGCTTGTAGGAGTTGGGGACCAGCTAGGCTCCTCGCTGCGTCGAGGC------AAAATTGGAGCAATCTTCTCGgtaagcacct #### Kif11_ID7318_8 --> 0 - 0 Original Alignment GTTGATCTTGCAGGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacag------------GGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from CESAR GTTGATCTTGCAGGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG tcaaactatggaagctgcagcttgatggtcacctctgattttcacaacag------------GGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from Spaln_aa2Genome GGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacagGGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from Spaln_nt2Genome GGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacagGGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from Pairagon GTTGATCTTGCAGGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacag------------GGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from Exonerate_protein2genome GGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacagGGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from Exonerate_coding2genome GGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacagGGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca Alignment from GeneWise GGAAGTGAAAATATTGGGCGTTCTGGAGCTGTTGACAAGAGGGCCCGGGAAGCTGGAAATATCAACCAATCCCTCTTGACTCTGGGAAGAGTTATTACTGCTCTTGTGGAAAGAACACCTCATATTCCTTATCGAGAATCTAAACTAACTAGAATCCTGCAAGATTCTCTTGGGGGACGTACAAGAACATCTATAATTGCAACCATTTCCCCTGCATCTTTCAATCTTGAG agctgcagcttgaccagcccacctttggtcacctctgattttcacaacagGGAAGTGAAAATATTGGGCATTCTGGAGCGGTAGTCAAGAGAGCACGCAAAGCTGGAAATATCAACCAATCTCTCTTAACTCTGGGAAGAGTAATTACTGCACTCTTGGAGAGAACACCCCATATTCCCTACCGAGAATCTAAACTAACCAGAATCCTACAAGATTCTCTTGGTGGACGTACTAGGACTTCTATAATTGCAACTATTTCACCAGCGTCTTTCAATCTTGAAgtgagtcagatagtagccatgacacacaaactcattggtctcttcagcca #### Kif20b_ID6998_3 --> 0 - 0 Original Alignment GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGTGGCA---------CAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgacccag------GTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTA---CGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from CESAR GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG ctggctataaacacagtctctcacgtatcattgctttctttctgacccag------GTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from Spaln_aa2Genome GTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgacccagGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from Spaln_nt2Genome GTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCACTTA---AGTGAGAAGAGCTCTGGACAGGT------GGCACAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgacccagGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from Pairagon GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGT------GGCACAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgacccag------GTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from Exonerate_protein2genome GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgACCCAGGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from Exonerate_coding2genome GGCTGTGTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgACCCAGGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt Alignment from GeneWise GTGCAAGTTTTGGATTCACAGTCTGTTCTGCTGAAAGACCCTCAAAGCATCCTTGGCCAC---TTAAGTGAGAAGAGCTCTGGACAGGTG------GCACAGAAATTCAGTTTTTCTAAG gctataaacacagtctctcacgagatatcattgctttctttctgacccagGTGCAAATTTTGGATTCACACTCTGTTTTGCTGGAAGACCCACAGAGTATGCTTGGTCACTTGTTGAGTCAGAAAAGCTCTGGCCAGGTACGCCAGGTACAGGAATTTAGCTTTTCTAAGgtaagtgtaagtatggtggattgaccacgttgaacgctctatcaagaggt #### Kif20b_ID7004_9 --> 1 - 2 Original Alignment tCACAGCATATTCACTATTAGAATATTACAGATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTga ccaaggccgggctagtattataaatttgtcttctctacctcctggataagt------------------------------ATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTgagtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from CESAR tCACAGCATATTCACTATTAGAATATTACAGATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTga tatttgaatggaagtcctcctaaatttgtcttctctacctcctggataagt------------------------------ATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTgagtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from Spaln_aa2Genome GAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTG ccaaggccgggctagtattataaatttgtcttctctacctcctggataagtatagAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTGAgtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from Spaln_nt2Genome GATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTGA ccaaggccgggctagtattataaatttgtcttctctacctcctggataagTATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTGAgtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from Pairagon TCACAGCATATTCACTATTAGAATATTACAGATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTGA ccaaggccgggctagtattataaatttgtcttctctacctcctggataagT------------------------------ATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTGAgtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from Exonerate_protein2genome TCACAGCATATTCACTATTAGAATATTACAGATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTGA ccaaggccgggctagtattaTAAATTTGTCTTCTCTACCTCCTGGATAAGTATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTGAgtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from Exonerate_coding2genome TCACAGCATATTCACTATTAGAATATTACAGATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTGA ccaaggccgggctagtattaTAAATTTGTCTTCTCTACCTCCTGGATAAGTATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTGAgtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag Alignment from GeneWise TCACAGCATATTCACTATTAGAATATTACAGATAGAAGATTCTGAAATACCTCGTGTAACACGAGTTAGTGA ccaaggccgggctagtattataaatttgtcttctctacctcctggataagT------------------------------ATAGAAGATTCTGAGATACCTCGTGTTACACGAGTTAGTGAgtaagcgggtttcaaagctgtgggtcgttttggaaagaaagtctctgcag #### Kif20b_ID7005_10 --> 1 - 2 Original Alignment aTTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAaa cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcaggTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAG---aagtaccaagtgccagttgtgtcatagaatctgctgttctgagtactttcta Alignment from CESAR aTTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAaa cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcaggTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAG---aagtaccaagtgccagttgtgtcatagaatctgctgttctgagtactttcta Alignment from Spaln_aa2Genome ATTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTC cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcagGTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAGAAgtaccaagtgccagttgtgtcatagaatctgctgttctgagtactttcta Alignment from Spaln_nt2Genome ATTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAAA cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcagGTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAG---AAgtaccaagtgccagttgtgtcatagaatctgctgttctgagtactttcta Alignment from Pairagon ATTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAAA cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcagGTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAG---AAgtaccaagtgccagttgtgtcatagaatctgctgttctgagtactttcta Alignment from Exonerate_protein2genome ATTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAAAGGTTCAGCATGTG cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcagGTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAGAAGTACCAAGTGCCAGTTgtgtcatagaatctgctgttctgagtactttcta Alignment from Exonerate_coding2genome ATTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAAAGGTTCAGCATGTG cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcagGTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAGAAGTACCAAGTGCCAGTTgtgtcatagaatctgctgttctgagtactttcta Alignment from GeneWise ATTGTCTCTATGTGATCTTGCTGGTTCAGAACGAAGCATGAAGACACAAAACGAAGGTGAAAGGTTAAGAGAGGCTGGGAATATCAACACTTCTTTATTGACTCTGGGAAAGTGTATCAATGTTTTGAAGAACAGTGAAAAGTCAAAGGTTCAGCATGTGCC cgttttggaaagaaagtctctgcagcactaggactgatgttgccttgcagGTTGTCGCCGTGTGATCTTGCAGGTTCAGAACAAAGCATGAAGACGCAGAATGAAGGTGAGAGGCCAAGAGAAGCAGGAAATATCAACACACCCTTGTTGACCTTGGGAATGTGTGTCAATGTATTAAAGAACAGTGAGAAGAAGTACCAAGTGCCAGTTGTgtcatagaatctgctgttctgagtactttcta #### Klc2_ID859_7 --> 0 - 0 Original Alignment ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from CESAR ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from Spaln_aa2Genome ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from Spaln_nt2Genome ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from Pairagon ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from Exonerate_protein2genome ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from Exonerate_coding2genome ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa Alignment from GeneWise ---GTCCTGGGCAAGTTTCACCCAGATGTGGCCAAGCAGCTCAGCAACCTGGCCTTGCTGTGCCAGAACCAGGGCAAAGCTGAGGAGGTGGAATACTACTACCGGAGAGCCCTGGAGATCTATGCCACACGCCTTGGTCCTGATGACCCCAATGTGGCGAAGACCAAGAACAACCTG aatgccatacagcaccatgactaggaaccatccccttgtccactttttagATTGTCCTTGGAAAGTTT------GATGTGGCTGAGCCACTTAGCAACCTGGTTTTGTTATGCCAGAACCAGGACAGAGCTGAAGAGGTGGAATACTATTACCCACGGGGCTTGAAGATATATGCCAAACGCCTCAGTCCTGAAGATCCCAATGCAGCAAAAACTAAGAACAACCTGgtgagttgtaatgtaatggatcctataaagatgacaccacccatgttgaa #### Ldb1_ID9692_8 --> 0 - 0 Original Alignment GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCGA--------------- tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGGCGCCTGTATGGACGGgtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from CESAR GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCGA--------------- tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGGCGCCTGTATGGACGGgtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from Spaln_aa2Genome GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTC---------------CGA tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGGCGCCTGTATGGACGGgtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from Spaln_nt2Genome GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCG tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGgcgcctgtatggacgggtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from Pairagon GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGT tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATgcggattttcaaatacagctattaagtactttcggcgcctgtatggacgggtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from Exonerate_protein2genome GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCG tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGgcgcctgtatggacgggtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from Exonerate_coding2genome GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCG tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGgcgcctgtatggacgggtcagggtggagggccacaatataaattagcttttgttaccattacaggc Alignment from GeneWise GCCCAGGACCCCCAGATGCTGGATCAGCTGTCCAAAAACATTACCCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCGA--------------- tttggagtccacatcttaatcaggtgaagagaatgtgttgtgttttctagGCTCAGGACCCCCAGATGCTGGATCAGCTATCCAAAAACATTACTCGATGCGGATTTTCAAATACAGCTATTAAGTACTTTCGGCGCCTGTATGGACGGgtcagggtggagggccacaatataaattagcttttgttaccattacaggc #### Ldb1_ID9694_6 --> 2 - 0 Original Alignment ccATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagccATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTT------gtaagggtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from CESAR ccATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagccATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTGTAAGGgtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from Spaln_aa2Genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTGTAAGGgtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from Spaln_nt2Genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTGTAAGGgtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from Pairagon CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTT ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTgtaagggtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from Exonerate_protein2genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTGTAAGGgtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from Exonerate_coding2genome CCATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG ggctctgggtgagatgctttctctctttaccaaggtgccttgtcccctagCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTGTAAGGgtgactaaagtgcagggatagcgtaacctaataccatgagacag Alignment from GeneWise ----------------------------------------------------ATTGGCCGGACCCTGATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGCTGTACTACGTGCTCAAGCACCCCAAGGAGGCATTCCACAGCAACTTCGTGTCCCTCGACTGTGACCAGGGCAGCATGGTGACCCAGCACGGCAAACCCATGTTTACCCAG GGCTCTGGGTGAGATGCTTTCTCTCTTTACCAAGGTGCCTTGTCCCCTAGCCATTGGCCGGACCCTAATACCACGCTACTTCCGAAGCATTTTTGAGGGGGGTGCCACAGAGTTGTACTACGTGCTCAAGCACCCTAAGGAGGCATTCCACAGCAACTTTGTGTCCCTTGAATGTGATGAGGGCAGCATGGTGACCCAGCATGGCAAACCCATGTTTGTAAGGgtgactaaagtgcagggatagcgtaacctaataccatgagacag #### Ldb1_ID9696_4 --> 1 - 0 Original Alignment gAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG--------------------- ttggctacatatgtccacacacctatttatggatggcttttgctttctaggAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAACAGATGATACTCTCCTACTTCgtaagccaggatgagaggttgatgggggtgtgcctttggacccccattcc Alignment from CESAR gAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG--------------------- ttggctacatatgtccacacacctatttatggatggcttttgctttctaggAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAACAGATGATACTCTCCTACTTCgtaagccaggatgagaggttgatgggggtgtgcctttcactcttctacat Alignment from Spaln_aa2Genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG--------------------- ttggctacatatgtccacacacctatttatggatggcttttgctttctagGAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAACAGATGATACTCTCCTACTTCgtaagccaggatgagaggttgatgggggtgtgcctttggacccccattcc Alignment from Spaln_nt2Genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAGGAG------------------ ttggctacatatgtccacacacctatttatggatggcttttgctttctagGAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAACAGATGATACTCTCCTACTTCgtaagccaggatgagaggttgatgggggtgtgcctttggacccccattcc Alignment from Pairagon GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAG------------------------------------------------------------------------- ttggctacatatgtccacacacctatttatggatggcttttgctttctagGAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAACAGATGATACTCTCCTACTTCGTAAGCCAGGATGAGAGGTTGATGGGGGTGTGCCTTTGGACCCCCATTCC Alignment from Exonerate_protein2genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG ttggctacatatgtccacacacctatttatggatggcttttgctttctagGAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAAcagatgatactctcctacttcgtaagccaggatgagaggttgatgggggtgtgcctttggacccccattcc Alignment from Exonerate_coding2genome GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG ttggctacatatgtccacacacctatttatggatggcttttgctttctagGAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAAcagatgatactctcctacttcgtaagccaggatgagaggttgatgggggtgtgcctttggacccccattcc Alignment from GeneWise GAGGCACACACCATATGGTAACCAAACCGACTATAGAATATTTGAGCTTAACAAACGGCTACAGAACTGGACAGAG----------------------------------------------------------------------- ttggctacatatgtccacacacctatttatggatggcttttgctttctagGAGGCACAGTCCATACGGTAATCAGACTGACTATAGGATATTTGAGCTAAACAAGCGGCTACAGAATTGGACAGAACAGATGATACTCTCCTACTTCGTAAGCCAGGATGAGAGGTTGATGGGGGTGTGCCTTTGGACCCCCATTCC #### Lipf_ID6846_2 --> 0 - 1 Original Alignment ---AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTTATGGGAAGAAAAATTCTGAGAATATCg gtccactcaatcacactactatttttcttgaccccggccctggtctgtagCAAAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAggtgataatatcctgtgaatgggaagaaaaatcttgagcaagtcaatccac Alignment from CESAR ---AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTTATGGGAAGAAAAATTCTGAGAATATCg gtccactcaatcacactactatttttcttgaccccggccctggtctgtagCAAAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAggtgataatatcctgtgaatgggaagaaaaatcttgagcaagtcaatccac Alignment from Spaln_aa2Genome GTTAGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTTATGGGAAGAAAAATTCTGAGAATATCG gtccactcaatcacactactatttttcttgaccccggccctggtctgtagCAAAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAGgtgataatatcctgtgaatgggaagaaaaatcttgagcaagtcaatccac Alignment from Spaln_nt2Genome ---AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTT--------------------------------------------ATGGGAAGAAAAATTCTGAG-AA gtccactcaatcacactactatttttcttgaccccggccctggtctgtagCAAAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAGGTGATAATATCCTGTGAATGGGAAGAAAAATCTTGAGCAAgtcaatccac Alignment from Pairagon ---AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTT--------------------------------------------ATGGGAAGAAAAATTCTGA gtccactcaatcacactactatttttcttgaccccggccctggtctgtagCAAAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAGGTGATAATATCCTGTGAATGGGAAGAAAAATCTTGAgcaagtcaatccac Alignment from Exonerate_protein2genome AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTTATGGGAAGAAAAATTCTGAGAATATCG gtccactcaatcacactactatttttcttgaccccggccctggtctgtagcaaAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAGgtgataatatcctgtgaatgggaagaaaaatcttgagcaagtcaatccac Alignment from Exonerate_coding2genome AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTTATGGGAAGAAAAATTCTGAGAATATCG gtccactcaatcacactactatttttcttgaccccggccctggtctgtagcaaAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAGgtgataatatcctgtgaatgggaagaaaaatcttgagcaagtcaatccac Alignment from GeneWise ---AGTCAGATGATAACTTACTGGGGATATCCAAGTGAGGAATATGAAGTTGTTACTGAAGATGGCTACATTCTGGGGGTCTATAGAATTCCTTATGGGAAGAAAAATTCTGAGAATATCG gtccactcaatcacactactatttttcttgaccccggccctggtctgtagCAAAGTCAAATTGTAACTTATTGGGGATATCCAAGTGAAGAATATGAAGGGGCGTCTGAAGATGGATATATTCTGGGGATCTATAGAATTCCATATAGCAAAAGGAACTCCGAAAACATAGgtgataatatcctgtgaatgggaagaaaaatcttgagcaagtcaatccac #### Ltbp3_ID1252_4 --> 0 - 1 Original Alignment TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---t ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATtgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from CESAR TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---t ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATtgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from Spaln_aa2Genome TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---T ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATTgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from Spaln_nt2Genome TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---T ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATTgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from Pairagon TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---T ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATTgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from Exonerate_protein2genome TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---T ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATTgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from Exonerate_coding2genome TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAG---T ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATTgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag Alignment from GeneWise TGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGCGGTAGCATCGGTACTGCCTGGGGACAAAGCAAGTGTCACAAGTGCCCACAGCTTCAGTAT- ctattccaaccatcaaaccagtgctgatgaatgtttgtgatctcttacagTGTGGCAGCAACCCTTTGCCTGGCCTTACCAAGCAGGAAGATTGCTGTGGTAGCATAGGTACTGCCTGGGGACCAAGCAAGTGTCACAAGTGCCCACAGCTTCAGGATTgtaagtgcttaacatggactcacaattttctctccgatcatgattagtag #### Ltbp3_ID1253_5 --> 2 - 1 Original Alignment at------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGg taccgagctcactctcttttttcactatgatcccgctctttgttctacagatTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGggttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from CESAR at------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGg taccgagctcactctcttttttcactatgatcccgctctttgttctacagatTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGggttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from Spaln_aa2Genome AT------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccgagctcactctcttttttcactatgatcccgctctttgttctacagATTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from Spaln_nt2Genome AT------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccgagctcactctcttttttcactatgatcccgctctttgttctacagATTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGGGT---GGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from Pairagon AT------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccgagctcactctcttttttcactatgatcccgctctttgttctacagATTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGG---GGTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from Exonerate_protein2genome AT------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccgagctcactctcttttttcactatgatcccgctctttgttctacagATTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from Exonerate_coding2genome AT------ACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccgagctcactctcttttttcactatgatcccgctctttgttctacagATTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg Alignment from GeneWise -----TATACAGGGGTGCAGAAGCCTGGACCTGTACGTGGGGAGGTGGGTGCTGACTGCCCCCAGGGCTACAAGAGGCTCAACAGCACCCACTGCCAGG taccgagctcactctcttttttcactatgatcccgctctttgttctacagATTCCCTAACAGGAGTGCAAAAGCCTGGACCTGTTCGAGGG---GTGGGCACTGACTGCCCCAAAGGCTATAAAAGACTTAATAGCACCCATTCCCAGGgttaatatcaccaatcaccaaaggttccattaattgtgatgtgaggaagg #### Ltbp3_ID1255_7 --> 2 - 1 Original Alignment ccGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTACA---------g c agcacagtaagattgcctctccacactgttaaagacacaattttctgcagctGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCGCGGGCTCggtaatcttgtagagtcttgggattgcactctcttggattctcctcccagc Alignment from CESAR ccGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTACAg c agcacagtaagattgcctctccacactgttaaagacacaattttctgcagctGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGcgcgggctcggtaatcttgtagagtcttgggattgcatccctacaatctcctgttgcagc Alignment from Spaln_aa2Genome CCGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTACAG C agcacagtaagattgcctctccacactgttaaagacacaattttctgcagCTGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCgcgggctcggtaatcttgtagagtcttgggattgcactctcttggattctcctcccagC Alignment from Spaln_nt2Genome CCGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTA----CAG C agcacagtaagattgcctctccacactgttaaagacacaattttctgcagCTGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCGCGGgctcggtaatcttgtagagtcttgggattgcactctcttggattctcctcccagC Alignment from Pairagon CCGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTA----------------------------------------------------------CAGC agcacagtaagattgcctctccacactgttaaagacacaattttctgcagCTGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCGCGGGCTCGGTAATCTTGTAGAGTCTTGGGATTGCACTCTCTTGGATTCTCCTCCCAGC Alignment from Exonerate_protein2genome CCGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTACAG C agcacagtaagattgcctctccacactgttaaagacacaattttctgcagCTGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCgcgggctcggtaatcttgtagagtcttgggattgcactctcttggattctcctcccagC Alignment from Exonerate_coding2genome CCGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTACAG C agcacagtaagattgcctctccacactgttaaagacacaattttctgcagCTGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCgcgggctcggtaatcttgtagagtcttgggattgcactctcttggattctcctcccagC Alignment from GeneWise CCGACAAACCAGAGGAGAAGAGCCTGTGTTTCCGCCTTGTGAGCACCGAACACCAGTGCCAGCACCCTCTGACCACACGCCTAACCCGCCAGCTCTGCTGCTGTAGTGTGGGTAAAGCCTGGGGTGCCCGGTGCCAGCGCTGCCCGGCAGATGGTACA---------G C agcacagtaagattgcctctccacactgttaaagacacaattttctgcagCTGACAAACCAAAGGAGAAAAGCTTGTGTTTCCGCCTTGTGAGCACTGAACACCAGTGCCAGCATCCTTTAACTACACGTTTGACCCATCAGCTCTGCTGTTGTAGTGTTGGTAAGGCTTGGGGGGCCCGGTGCCAGCGTTCTCCAGCAGATGGCATGCGCGGGCTCGgtaatcttgtagagtcttgggattgcactctcttggattctcctcccagC #### Ltbp3_ID1258_10 --> 0 - 1 Original Alignment ---CCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTACCCAg tattacgacttggactaccaacatgaggttcctattttccccctctatagTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCCTTggtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from CESAR ---CCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTACCCAg tattacgacttggactaccaacatgaggttcctattttccccctctatagTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCCTTggtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from Spaln_aa2Genome CCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTACCCAG tattacgacttggactaccaacatgaggttcctattttccccctctatagTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCCTTGgtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from Spaln_nt2Genome ---CCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTACCCAG tattacgacttggactaccaacatgaggttcctattttccccctctatagTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCCTTGgtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from Pairagon ---CCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACC---CCACT tattacgacttggactaccaacatgaggttcctattttccccctctatagTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTgttacctcaccatctcaacctttccttggtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from Exonerate_protein2genome TGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTACCCAG tattacgacttggactaccaacatgaggttcctattttccccctctatagtacccagTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCCTTGgtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from Exonerate_coding2genome ATCCACCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTAC tattacgacttggactaccaacatgaggttcctattttccccctctatAGTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCcttggtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct Alignment from GeneWise CCACCAGTGAGTGAGGAGCGATCGGTGCAGCAGAGCCACCCCACTACCACCACCTCACCCCCCCGGCCTTACCCAG tattacgacttggactaccaacatgaggttcctattttccccctctatagTACCCAGTGAGTGAGGAGCGATCTGTACAACAGAGCCATCCTGCCACTGTTACCTCACCATCTCAACCTTTCCTTGgtaatgtggttggtggagggcaagccataccaacaggggtaagcctagct #### Ltbp3_ID1261_13 --> 2 - 1 Original Alignment atGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGg actggtcaattctagacatatctaacagatatccttagctataatcacagat------GGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGggtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from CESAR atGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGg gatgtgactggtcaattctagacatcagatatccttagctataatcacagat------GGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGggtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from Spaln_aa2Genome ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG actggtcaattctagacatatctaacagatatccttagctataatcacagAT------GGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGGgtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from Spaln_nt2Genome ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG actggtcaattctagacatatctaacagatatccttagctataatcacagAT------GGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGGgtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from Pairagon ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG actggtcaattctagacatatctaacagatatccttagctataatcacagAT------GGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGGgtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from Exonerate_protein2genome ATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG actggtcaattctagacatatctaacagatatccttagctataaTCACAGATGGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGGgtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from Exonerate_coding2genome actggtcaattctagacatatctaacagatatccttagctataatcacagatgggtgtggggctgagccctgtggccctggaaaaggtatctgtatgactactggtggatcatataattgtcattgcaaccggggctaccgccttcatgtaggtgcagggggccgactctgtgtgggtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc Alignment from GeneWise -----GATGTGAACGAGTGCGAGGCAGAGCCCTGCGGCCCCGGGAAAGGCATCTGTATGAACACTGGTGGCTCCTACAATTGTCACTGCAACCGAGGCTACCGCCTCCACGTGGGTGCAGGGGGCCGCTCGTGCGTGG actggtcaattctagacatatctaacagatatccttagCTATAATCACAGATGGGTGTGGGGCTGAGCCCTGTGGCCCTGGAAAAGGTATCTGTATGACTACTGGTGGATCATATAATTGTCATTGCAACCGGGGCTACCGCCTTCATGTAGGTGCAGGGGGCCGACTCTGTGTGGgtgagtatacttgggtagcacacacctgtgtgcatttctgacaccagacc #### Ltbp3_ID1262_14 --> 2 - 1 Original Alignment acCTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAg accagaccctctccttcctgtgtgtgtgcagagggtcctctctgcttcagat---------TGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAggtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from CESAR acCTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAg atttctgacaccagaccctctccttgtgcagagggtcctctctgcttcagat---------TGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAggtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from Spaln_aa2Genome ACCTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAG accagaccctctccttcctgtgtgtgtgcagagggtcctctctgcttcagAT---------TGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAGgtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from Spaln_nt2Genome ACCTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAG accagaccctctccttcctgtgtgtgtgcagagggtcctctctgcttcag---------ATTGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAGgtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from Pairagon ACCTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAG accagaccctctccttcctgtgtgtgtgcagagggtcctctctgcttcag---------ATTGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAGgtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from Exonerate_protein2genome ACCTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAG accagaccctctccttcctgtgtgtgtgcagagggtcctctctgcttcagAT---------TGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAGgtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from Exonerate_coding2genome accagaccctctccttcctgtgtgtgtgcagagggtcctctctgcttcagattgcacaaagccccatctgtgtggtgatggtggcttctgcatcaatttcccaggccactacacatgcaactgttatcctggttacaggctcaaggcctccagaccaccaatctgggaaggtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat Alignment from GeneWise ----------CTGAACGAGTGCACCAAGCCTCACCTGTGTGGGGACGGTGGCTTCTGCATCAACTTCCCTGGTCACTACAAATGCAACTGCTATCCTGGCTACCGGCTCAAGGCCTCCCGACCGCCCATTTGCGAAG accagaccctctccttcctgtgtgtgtgcagagGGTCCTCTCTGCTTCAGATTGCACAAAGCCCCATCTGTGTGGTGATGGTGGCTTCTGCATCAATTTCCCAGGCCACTACACATGCAACTGTTATCCTGGTTACAGGCTCAAGGCCTCCAGACCACCAATCTGGGAAGgtgagatgtcatcctacttctcctcctggccttaggttggatgagtgcat #### Ltbp3_ID1268_20 --> 2 - 1 Original Alignment agGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCA---g gctatagcttagcagatattaattggaaaattgtaatgattttgatccagagGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAggtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from CESAR agGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCA---g gctatagcttagcagatattaattggaaaattgtaatgattttgatccagagGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAggtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from Spaln_aa2Genome AGGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAGCCG gctatagcttagcagatattaattggaaaattgtaatgattttgatccagAGGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAGgtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from Spaln_nt2Genome AGGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCA---G gctatagcttagcagatattaattggaaaattgtaatgattttgatccagAGGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAGgtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from Pairagon AGGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTC---AG gctatagcttagcagatattaattggaaaattgtaatgattttgatccagAGGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAGgtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from Exonerate_protein2genome AGGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAGCCG gctatagcttagcagatattaattggaaaattgtaatgattttgatccagAGGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAGgtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from Exonerate_coding2genome gctatagcttagcagatattaattggaaaattgtaatgattttgatccagaggtggagcagcctcaccataagaaggaatgctaccttaactttgatgacacagtgttctgtgacagcatactagctactaatgttactcaacaggaatgctgctgctctctgggagcgggatggggagaccactgtgaaatctatccctgtcctatcttcagctcattaggtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct Alignment from GeneWise AGGTGGAGCAGCCCCACCACAAGAAGGAGTGCTACCTTAACTTCGATGACACAGTGTTCTGTGACAGCGTATTGGCTACCAATGTCACTCAGCAGGAATGCTGTTGCTCTCTGGGAGCTGGTTGGGGAGACCACTGCGAAATCTATCCCTGTCCAGTCTACAGCTCAGCC- gctatagcttagcagatattaattggaaaattgtaatgattttgatccagAGGTGGAGCAGCCTCACCATAAGAAGGAATGCTACCTTAACTTTGATGACACAGTGTTCTGTGACAGCATACTAGCTACTAATGTTACTCAACAGGAATGCTGCTGCTCTCTGGGAGCGGGATGGGGAGACCACTGTGAAATCTATCCCTGTCCTATCTTCAGCTCATTAGgtaagacaatgggctgaatcttggtcctatcaaacaggcctgtgaattct #### Ltbp3_ID1274_26 --> 2 - 1 Original Alignment acGAAGACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGg gtatgcaaagtctatgataggctctcttaaagactttgtctctcccacagat------AGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAggtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from CESAR acGAAGACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGg gtgattgtatgcaaagtctatgatacttaaagactttgtctctcccacagat------AGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAggtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from Spaln_aa2Genome CT---CCGCGAGACGAAGACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGG gtatgcaaagtctatgataggctctcttaaagACTTTGTCTCTCCCACAGATAGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAGgtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from Spaln_nt2Genome ACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGG gtatgcaaagtctatgataggctctcttaaagactttgtctctcccacagATAGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAGgtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from Pairagon ------------------------------------------------AGACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGG GTATGCAAAGTCTATGATAGGCTCTCTTAAAGACTTTGTCTCTCCCACAGATAGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAGgtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from Exonerate_protein2genome CT---CCGCGAGACGAAGACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGG gtatgcaaagtctatgataggctctcttaaagACTTTGTCTCTCCCACAGATAGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAGgtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from Exonerate_coding2genome gtatgcaaagtctatgataggctctcttaaagactttgtctctcccacagatagctcagaggaagattcagatgagtgccgttgtgtcattgggcactgtgccccgcgtcccggtggggctgtatgtgagtgtcctggtggctttccattggatgcctcccgtgcccgacgagtaggtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta Alignment from GeneWise --TCTCCGCGAGACGAAGACAGCTCAGAGGAGGATTCAGATGAGTGCCGTTGTGTGAGCGGACGCTGTGTGCCACGGCCAGGCGGGGCGGTATGCGAGTGTCCTGGAGGCTTTCAGCTGGACGCCTCCCGTGCCCGCTGCGTGG gtatgcaaagtctatgataggctctcttaaagACTTTGTCTCTCCCACAGATAGCTCAGAGGAAGATTCAGATGAGTGCCGTTGTGTCATTGGGCACTGTGCCCCGCGTCCCGGTGGGGCTGTATGTGAGTGTCCTGGTGGCTTTCCATTGGATGCCTCCCGTGCCCGACGAGTAGgtaagtatgacatcagggggcagatgggggtggaagacatcatgaaccta #### Macrod1_ID2051_6 --> 2 - 0 Original Alignment atGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGC---CTGGACCTGCTGCTGGAGCACCGGCTGCGCTCAGTG gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagatGTCATT------GTGGGGCTCATTGCAGTAGGG------------AGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTGTGTCCA---gtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa Alignment from CESAR atGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGC---CTGGACCTGCTGCTGGAGCACCGGCTGCGCTCAGTG gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagatGTCATT------GTGGGGCTCATTGCAGTAGGG------------AGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTGTGTCCA---gtaagaagatggtggactcaagggcaaaagctggcattacactagta Alignment from Spaln_aa2Genome ATGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGC---CTGGACCTGCTGCTGGAGCACCGGCTGCGCTCA gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagATGTCATT------GTGGGGCTCATTGCAGTAGGG------------AGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTGTGTCCAgtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa Alignment from Spaln_nt2Genome ATGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGCCTG---GACCTGCTGCTGGAGCACCGGCTGCGCTCA gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagATGTCAT------TGTGGGGCTCATTGCAGTAGG------------GAGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTGTGTCCAgtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa Alignment from Pairagon ATGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGCCTG---GACCTGCTGCTGGAGCACCGGCTGCGCTCA gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagATGTCATT------GTGGGGCTCATTGCAGTAGG------------GAGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTGTGTCCAgtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa Alignment from Exonerate_protein2genome ATGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGC---CTGGACCTGCTGCTGGAGCACCGGCTGCGCTCA gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagATGTCATT------GTGGGGCTCATTGCAGTAGGG------------AGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTGTGTCCAgtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa Alignment from Exonerate_coding2genome gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagatgtcattgtggggctcattgcagtagggagtgaggcggctgaattccacagttgttatctgagcagtccgttagacctactgctagaacacagattgtgtccagtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa Alignment from GeneWise ATGTCATCCACACGGTGGGGCCCATCGCCGTGGGCCAACCCACTGCCAGCCAGGCGGCCGAGCTCCGCAGCTGCTACTTGAGCAGC---CTGGACCTGCTGCTGGAGCACCGG-- gagtagaagacatcattggtacacccccccccccctcgtctgcctctcagATGTCATT------GTGGGGCTCATTGCAGTAGGG------------AGTGAGGCGGCTGAATTCCACAGTTGTTATCTGAGCAGTCCGTTAGACCTACTGCTAGAACACAGATTgtgtccagtaagaagatggtggactcaagggcaaaagctggcattacactagtagaa #### Macrod1_ID2054_9 --> 0 - 1 Original Alignment GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTA---------------g ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAAATGATGTGTATGAAggtaactataagtggctcctatacttgaagggaccagtacttttccttata Alignment from CESAR GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTA---------------g ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAAATGATGTGTATGAAggtaactataagtggctcctatacttgaagggacctactgcccttctcctg Alignment from Spaln_aa2Genome GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAAATgatgtgtatgaaggtaactataagtggctcctatacttgaagggaccagtacttttccttata Alignment from Spaln_nt2Genome GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAAATgatgtgtatgaaggtaactataagtggctcctatacttgaagggaccagtacttttccttata Alignment from Pairagon GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAAATgatgtgtatgaaggtaactataagtggctcctatacttgaagggaccagtacttttccttata Alignment from Exonerate_protein2genome GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTA ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAaatgatgtgtatgaaggtaactataagtggctcctatacttgaagggaccagtacttttccttata Alignment from Exonerate_coding2genome ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcaggtggatcgactcattatctgtgtatgcttggagaaagaagagggcatttacagggaacatcttccgcattatttcccagtaaatgatgtgtatgaaggtaactataagtggctcctatacttgaagggaccagtacttttccttata Alignment from GeneWise GTGGATCGGCTCATCATCTGTGTGTTCCTGGAGAAGGACGAGGGCATTTACCGGGAGCGCCTTCCCCATTATTTCCCAGTAGCC ttcacctgatatggtcgaagtttaagtacattctgtgaccttaaatgcagGTGGATCGACTCATTATCTGTGTATGCTTGGAGAAAGAAGAGGGCATTTACAGGGAACATCTTCCGCATTATTTCCCAGTAAATgatgtgtatgaaggtaactataagtggctcctatacttgaagggaccagtacttttccttata #### Map3k11_ID1202_3 --> 1 - 1 Original Alignment cTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAACTCATGGCTg acTGCTGGGCACAGG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagtTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAA---------ggtaaggtgatcatagctgtgacccgatggttccagatTGCTGGGCACAGG Alignment from CESAR cTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAACTCATGGCTg acTGCTGGGCACAGG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagtTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAA---------ggtaaggtgatattgctgcttctctctctgttgcagatTGCTGGGCACAGG Alignment from Spaln_aa2Genome CTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAA- CTCATGGCTGACTGCT taaaggctgataattccacttcgatcaatgtttttatggatttccttcagTTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAAGgtaaggtgatcatagctgtgacccgatggttcca gATTGCT Alignment from Spaln_nt2Genome CTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAACTCATGGCTG ACTGCTGGGCACAGG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagTTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAA---------GgtaaggtgatcatagctgtgacccgatggttccagATTGCTGGGCACAGG Alignment from Pairagon CTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAACTCATGGCTG ACTGCTGGGCACAGG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagTTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAA---------GgtaaggtgatcatagctgtgacccgatggttccagATTGCTGGGCACAGG Alignment from Exonerate_protein2genome CTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAACTCATGGCTG ACTGCTGGGCACAGG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagTTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAA---------GgtaaggtgatcatagctgtgacccgatggttccagATTGCTGGGCACAGG Alignment from Exonerate_coding2genome CTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAACTCATGGCTG ACTGCTGGGCACAGG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagTTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAA---------GgtaaggtgatcatagctgtgacccgatggttccagATTGCTGGGCACAGG Alignment from GeneWise CTTTGGAGTGCTGCTGTGGGAACTGCTGACTGGGGAGGTGCCCTACCGTGGCATCGACTGTCTTGCCGTAGCCTATGGTGTGGCTGTAAACAAGTTAACGTTACCCATCCCATCTACCTGCCCTGAGCCCTTTGCACAA---------------------------CTCATGGCTGACTGCTGGGCACAG taaaggctgataattccacttcgatcaatgtttttatggatttccttcagTTTTGGAGTGTTATTGTGGGAGCTGCTGACTGGCAAAGTGCCGTACCGGGGCATTGACTGTCTCACAGTGGTTTATGGTGTGGCTGTGAATAAATTAACATTACCTATTCCATCTACTTGTCCTGAGCCCTTTGCACAAGGTAAGGTGATCATAGCTGTGACCCG-ATGGTTCCAGATTGCTGGGCACAG #### Map4k2_ID1622_2 --> 0 - 1 Original Alignment GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGACCCAg attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGAC---ggtaagtagtggataggcacagagtgcttcgtccagctgggtaacacggaa Alignment from CESAR GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGACCCAg attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGAC---ggtaagtagtggataggcacagagtgcttcgtccagctgggtaacacggaa Alignment from Spaln_aa2Genome GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGAC- attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGACGgtaagtagtggataggcacagagtgcttcgtccagctgggtaacacggaa Alignment from Spaln_nt2Genome GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGACCC-AG attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGACGGTAAgtagtggataggcacagagtgcttcgtccagctgggtaacacggaa Alignment from Pairagon GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGACCCAG attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGAC---Ggtaagtagtggataggcacagagtgcttcgtccagctgggtaacacggaa Alignment from Exonerate_protein2genome GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGACC attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGACGgtaagtagtggataggcacagagtgcttcgtccagctgggtaacacggaa Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GCCCGTGACACCGTCACGTCCGAACTGGCCGCGGTGAAGATCGTCAAGCTAGAC- attcctacattttaagcaagtgatgtcattcattttcatttttctcttagGCTCATGACACCGTCACATCTGAGCTGGCTGCAGTGAAGATTGTCAAGCTAGACGgtaagtagtggataggcacagagtgcttcgtccagctgggtaacacggaa #### Map4k2_ID1623_3 --> 2 - 2 Original Alignment ggGACGACATCAGCTCTCTTCAGCAGGAAATCACCATCCTTCGTGAATGCCGCCACCCCAATGTCGTGGCCTACATCGGCAGCTACCTCag aaagatcaatgcactcttatggacagtgattctgttaacactgcctacaggg------ATCAGCTCTCTTCAGCAGGAAATCACCATCCTCCGTGAATGCCGCCACCCCAATGTTGTGGCCTACATCACTAGCTACCTCaggtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from CESAR ggGACGACATCAGCTCTCTTCAGCAGGAAATCACCATCCTTCGTGAATGCCGCCACCCCAATGTCGTGGCCTACATCGGCAGCTACCTCag tcaggaaaagatcaatgcactcttagtgattctgttaacactgcctacaggg------ATCAGCTCTCTTCAGCAGGAAATCACCATCCTCCGTGAATGCCGCCACCCCAATGTTGTGGCCTACATCACTAGCTACCTCaggtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from Spaln_aa2Genome ACATCAGCTCTCTTCAGCAGGAAATCACCATCCTTCGTGAATGCCGCCACCCCAATGTCGTGGCCTACATCGGCAGCTACCTCAG aaagatcaatgcactcttatggacagtgattctgttaacactgcctacagGGATCAGCTCTCTTCAGCAGGAAATCACCATCCTCCGTGAATGCCGCCACCCCAATGTTGTGGCCTACATCACTAGCTACCTCAGgtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from Spaln_nt2Genome GGGACGACATCAGCTCTCTTCAGCAGGAAATCACCATCCTTCGTGAATGCCGCCACCCCAATGTCGTGGCCTACATCGGCAGCTACCTCAG aaagatcaatgcactcttatggacagtgattctgttaacactgcctacagGG------ATCAGCTCTCTTCAGCAGGAAATCACCATCCTCCGTGAATGCCGCCACCCCAATGTTGTGGCCTACATCACTAGCTACCTCAGgtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from Pairagon GGGACGACATCAGCTCTCTTCAGCAGGAAATCACCATCCTTCGTGAATGCCGCCACCCCAATGTCGTGGCCTACATCGGCAGCTACCTCAG aaagatcaatgcactcttatggacagtgattctgttaacactgcctacagGG------ATCAGCTCTCTTCAGCAGGAAATCACCATCCTCCGTGAATGCCGCCACCCCAATGTTGTGGCCTACATCACTAGCTACCTCAGgtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from Exonerate_protein2genome aaagatcaatgcactcttatggacagtgattctgttaacactgcctacagggatcagctctcttcagcaggaaatcaccatcctccgtgaatgccgccaccccaatgttgtggcctacatcactagctacctcaggtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from Exonerate_coding2genome aaagatcaatgcactcttatggacagtgattctgttaacactgcctacagggatcagctctcttcagcaggaaatcaccatcctccgtgaatgccgccaccccaatgttgtggcctacatcactagctacctcaggtaaggctactcagatctacatacccaggtgcctcactcttagttgctca Alignment from GeneWise CTCTCTTCAGCAGGAAATCACCATCCTTCGTGAATGCCGCCACCCCAATGTCGTGGCCTACATCGGCAGCTACCTCAG aaagatcaatgcactcttatggacagtgattctgttaacactgcctacagggatcagCTCTCTTCAGCAGGAAATCACCATCCTCCGTGAATGCCGCCACCCCAATGTTGTGGCCTACATCACTAGCTACCTCAGgtaaggctactcagatctacatacccaggtgcctcactcttagttgctca #### Map4k2_ID1628_7 --> 0 - 1 Original Alignment TAAG------ ------GGTGCCAACCTTCTGCTCACTCTGCAGGGTGATGTCAAGCTGg TAAGGTAGGAgtaagcatctaggtggttgttttttgttttcttttggcagCTTCCTGGTGCAAACCTCCTGCTCACATTGCAGGGAGAGGTGCAATTGtgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from CESAR TAAG ------GGTGCCAACCTTCTGCTCACTCTGCAGGGTGATGTCAAGCTGg TAAGgtaggagtagaaatctaggtggttgttttttgttttcttttggcagCTTCCTGGTGCAAACCTCCTGCTCACATTGCAGGGAGAGGTGCAATTGtgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from Spaln_aa2Genome TAAG GGTGCCAACCTT------CTGCTCACTCTGCAGGGTGATGTCAAGCTGG TAAGgtaggagtaagcatctaggtggttgttttttgttttcttttggcagCTTCCTGGTGCAAACCTCCTGCTCACATTGCAGGGAGAGGTGCAATTGTgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from Spaln_nt2Genome TAAG ------GGTGCCAACCTTCTGCTCACTCTGCAGGGTGATGTCAAGCTGG TAAGgtaggagtaagcatctaggtggttgttttttgttttcttttggcagCTTCCTGGTGCAAACCTCCTGCTCACATTGCAGGGAGAGGTGCAATTGTgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from Pairagon TAAG----------------------------------------------------GGTGCCAACCTTCTGCTCACTCTGCAGGGTGATGTCAAGCTGG TAAGGTAGGAGTAAGCATCTAGGTGGTTGTTTTTTGTTTTCTTTTGGCAGCTTCCTGGTGCAAACCTCCTGCTCACATTGCAGGGAGAGGTGCAATTGTgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from Exonerate_protein2genome taaggtaggagtaagcatctaggtggttgttttttgttttcttttggcagcttcctggtgcaaacctcctgctcacattgcagggagaggtgcaattgtgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from Exonerate_coding2genome taaggtaggagtaagcatctaggtggttgttttttgttttcttttggcagcttcctggtgcaaacctcctgctcacattgcagggagaggtgcaattgtgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc Alignment from GeneWise TAAG ------GGTGCCAACCTTCTGCTCACTCTGCAGGGTGATGTCAAGCTGG TAAGgtaggagtaagcatctaggtggttgttttttgttttcttttggcagCTTCCTGGTGCAAACCTCCTGCTCACATTGCAGGGAGAGGTGCAATTGTgtaagtgttgtgtggacttcagagtcaatcaatggcacaagctggggctc #### Map4k2_ID1629_8 --> 2 - 2 Original Alignment cgGACTTTGGGGTGTCAGGCGAGCTGACAGCATCTGTGGCCAAAAGACGTTCTTTCATTGGCACTCCATACtg cactctctcataggcagtccatactggttttccaggtgtttctttttcagctGATTTTGGGGTCACGGATGGAGCTACAACATCTGTTGCTAAGAGGCACTCTCTCATAGGCAGT------tggtacgagttgagtgttccagagcatcggtgaagcctccctttggcctcct Alignment from CESAR CGTTCTTTCATTGGCACTCCATACtg CACTCTCTCATAGGCAGTCCATACtggttttccaggtgtttctttttcagctgattttggggtcacggatggagctacaacatctgttgctaagaggcactctctcataggcagttggtacgagttgagtgttccagagcatcggtgaagttattatttatttattt Alignment from Spaln_aa2Genome CGGACTTTGGGGTGTCAGGCGAGCTGACAGCATCTGTGGCCAAAAGACGTTCTTTCATTGGCACTCCATACTG cactctctcataggcagtccatactggttttccaggtgtttctttttcagCTGATTTTGGGGTCACGGATGGAGCTACAACATCTGTTGCTAAGAGGCACTCTCTCATAGGCAGTTGGTACGAgttgagtgttccagagcatcggtgaagcctccctttggcctcct Alignment from Spaln_nt2Genome CGTTCTTTCATTGGCACTCCATACTG CACTCTCTCATAGGCAGTCCATACTGgttttccaggtgtttctttttcagctgattttggggtcacggatggagctacaacatctgttgctaagaggcactctctcataggcagttggtacgagttgagtgttccagagcatcggtgaagcctccctttggcctcct Alignment from Pairagon CGTTCTTTCATTGGCACTCCATACTG CACTCTCTCATAGGCAGTCCATACTGgttttccaggtgtttctttttcagctgattttggggtcacggatggagctacaacatctgttgctaagaggcactctctcataggcagttggtacgagttgagtgttccagagcatcggtgaagcctccctttggcctcct Alignment from Exonerate_protein2genome cactctctcataggcagtccatactggttttccaggtgtttctttttcagctgattttggggtcacggatggagctacaacatctgttgctaagaggcactctctcataggcagttggtacgagttgagtgttccagagcatcggtgaagcctccctttggcctcct Alignment from Exonerate_coding2genome cactctctcataggcagtccatactggttttccaggtgtttctttttcagctgattttggggtcacggatggagctacaacatctgttgctaagaggcactctctcataggcagttggtacgagttgagtgttccagagcatcggtgaagcctccctttggcctcct Alignment from GeneWise CGTTCTTTCATTGGCACTCCATACTG CACTCTCTCATAGGCAGTCCATACTGgttttccaggtgtttctttttcagctgattttggggtcacggatggagctacaacatctgttgctaagaggcactctctcataggcagttggtacgagttgagtgttccagagcatcggtgaagcctccctttggcctcct #### Map4k2_ID1630_9 --> 1 - 2 Original Alignment gATGGCACCAGAGGTTGCCGCTGTGGAACGCAAGGGTGGCTACAATGAGCTGTGTGACGTCTGGGCCCTGGGCATCACTGCCATTGAGTTGGGCGAGCTGCAACCGCCACTGTTCCACCTGCACCCCATG------------------------------ag ttccagagcatcggtgaagcctgctttattatttatttatttatttataggATGGCTCCGGAAGTTGCTGCTGTGGAGTGTAAGGGAGGCTACAATGAGCTATGTGACATATGGGCACTAGGTATTACTCCAGTGGAATCAAGTGAACTCCAACATCTGTTACTCCAGCTGCACCCCATGGCACTAAAACAATCATCAACAGAACTCCTCaggtaagttcagaacttgcagtgtgtctgttcttattccctccacctctttg Alignment from CESAR gATGGCACCAGAGGTTGCCGCTGTGGAACGCAAGGGTGGCTACAATGAGCTGTGTGACGTCTGGGCCCTGGGCATCACTGCCATTGAGTTGGGCGAGCTGCAACCGCCACTGTTCCACCTGCACCCCATGag ttccagagcatcggtgaagcctgctttattatttatttatttatttataggATGGCTCCGGAAGTTGCTGCTGTGGAGTGTAAGGGAGGCTACAATGAGCTATGTGACATATGGGCACTAGGTATTACTCCAGTGGAATCAAGTGAACTCCAACATCTGTTACTCCAGCTGCACCCCATGgcactaaaacaatcatcaacagaactcctcaggtaagttcagaacttgcagtgtgtctgttcttattccctccaccaatgct Alignment from Spaln_aa2Genome GATGGCACCAGAGGTTGCCGCTGTGGAACGCAAGGGTGGCTACAATGAGCTGTGTGACGTCTGGGCCCTGGGCATCACTGCCATTGAGTTGGGCGAGCTGCAACCGCCACTGTTCCACCTGCACCCCATGAGG----------------------------- ttccagagcatcggtgaagcctgctttattatttatttatttatttatagGATGGCTCCGGAAGTTGCTGCTGTGGAGTGTAAGGGAGGCTACAATGAGCTATGTGACATATGGGCACTAGGTATTACTCCAGTGGAATCAAGTGAACTCCAACATCTGTTACTCCAGCTGCACCCCATGGCACTAAAACAATCATCAACAGAACTCCTCAGgtaagttcagaacttgcagtgtgtctgttcttattccctccacctctttg Alignment from Spaln_nt2Genome GATGGCACCAGAGGTTGCCGCTGTGGAACGCAAGGGTGGCTACAATGAGCTGTGTGACGTCTGGGCCCTGGGCATCACTGCCATTGAGTTGGGCGAGCTGCAACCGCCACTGTTCCACCTGCACCCCATG ttccagagcatcggtgaagcctgctttattatttatttatttatttatagGATGGCTCCGGAAGTTGCTGCTGTGGAGTGTAAGGGAGGCTACAATGAGCTATGTGACATATGGGCACTAGGTATTACTCCAGTGGAATCAAGTGAACTCCAACATCTGTTACTCCAGCTGCACCCCATGgcactaaaacaatcatcaacagaactcctcaggtaagttcagaacttgcagtgtgtctgttcttattccctccacctctttg Alignment from Pairagon GATGGCACCAGAGGTTGCCGCTGTGGAACGCAAGGGTGGCTACAATGAGCTGTGTGACGTCTGGGCCCTGGGCATCACTGCCATTGAGTTGGGCGAGCTGCAACCGCCACTG---------------------------TTCCACCTGCACCCCATG---------------------------------------------------------------------------------- ttccagagcatcggtgaagcctgctttattatttatttatttatttatagGATGGCTCCGGAAGTTGCTGCTGTGGAGTGTAAGGGAGGCTACAATGAGCTATGTGACATATGGGCACTAGGTATTACT---------------------------CCAGTGGAATCAAGTGAACTCCAACATCTGTTACTCCAGCTGCACCCCATGGCACTAAAACAATCATCAACAGAACTCCTCAGGTAAGTTCAGAACTTGCAGTGTGTCTGTTCTTATTCCCTCCACCTCTTTG Alignment from Exonerate_protein2genome ttccagagcatcggtgaagcctgctttattatttatttatttatttataggatggctccggaagttgctgctgtggagtgtaagggaggctacaatgagctatgtgacatatgggcactaggtattactccagtggaatcaagtgaactccaacatctgttactccagctgcaccccatggcactaaaacaatcatcaacagaactcctcaggtaagttcagaacttgcagtgtgtctgttcttattccctccacctctttg Alignment from Exonerate_coding2genome ttccagagcatcggtgaagcctgctttattatttatttatttatttataggatggctccggaagttgctgctgtggagtgtaagggaggctacaatgagctatgtgacatatgggcactaggtattactccagtggaatcaagtgaactccaacatctgttactccagctgcaccccatggcactaaaacaatcatcaacagaactcctcaggtaagttcagaacttgcagtgtgtctgttcttattccctccacctctttg Alignment from GeneWise GATGGCACCAGAGGTTGCCGCTGTGGAACGCAAGGGTGGCTACAATGAGCTGTGTGACGTCTGGGCCCTGGGCATCACTGCCATTGAGTTGGGCGAGCTGCAACCGCCACTGTTCCACCTGCACCCCATG------------------------------AG ttccagagcatcggtgaagcctgctttattatttatttatttatttatagGATGGCTCCGGAAGTTGCTGCTGTGGAGTGTAAGGGAGGCTACAATGAGCTATGTGACATATGGGCACTAGGTATTACTCCAGTGGAATCAAGTGAACTCCAACATCTGTTACTCCAGCTGCACCCCATGGCACTAAAACAATCATCAACAGAACTCCTCAGgtaagttcagaacttgcagtgtgtctgttcttattccctccacctctttg #### Map4k2_ID1633_12 --> 0 - 0 Original Alignment CACCCATTCACGACCCAGCATCTCCCTCCGGCCCTCCTCACCCAGCTCCTCGACAAGGCCAGTGACCCCCACCTGGGAACCCTCTCCCCTGAAGACAGTGAGCTGGAG--------- gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagCATCCTTTTACAACCCAACATCTCCCTCCAGCACTTCTTACCCAACTCCTTGACAAGACTAGTGACCCCCATTTAGGTACCCTCTCCCCTGAAGACAGTAAGCTAAAGAAATCAGATgtacagcagttaaccaggtatagcctgtggggtaggtgttttccacaaga Alignment from CESAR CACCCATTCACGACCCAGCATCTCCCTCCGGCCCTCCTCACCCAGCTCCTCGACAAGGCCAGTGACCCCCACCTGGGAACCCTCTCCCCTGAAGACAGTGAGCTG---------GAG gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagCATCCTTTTACAACCCAACATCTCCCTCCAGCACTTCTTACCCAACTCCTTGACAAGACTAGTGACCCCCATTTAGGTACCCTCTCCCCTGAAGACAGTAAGCTAAAGAAATCAGATgtacagcagttaaccaggtatagcctgtggggtaggtgttttccacaaga Alignment from Spaln_aa2Genome CACCCATTCACGACCCAGCATCTCCCTCCGGCCCTCCTCACCCAGCTCCTCGACAAGGCCAGTGACCCCCACCTGGGAACCCTCTCCCCTGAAGACAGTGAGCTG---------GAG gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagCATCCTTTTACAACCCAACATCTCCCTCCAGCACTTCTTACCCAACTCCTTGACAAGACTAGTGACCCCCATTTAGGTACCCTCTCCCCTGAAGACAGTAAGCTAAAGAAATCAGATgtacagcagttaaccaggtatagcctgtggggtaggtgttttccacaaga Alignment from Spaln_nt2Genome CACCCATTCACGACCCAGCATCTCCCTCCGGCCCTCCTCACCCAGCTCCTCGACAAGGCCAGTGACCCCCACCTGGGAACCCTCTCCCCTGAAGACAGTGAGCTGGAGA-------- gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagCATCCTTTTACAACCCAACATCTCCCTCCAGCACTTCTTACCCAACTCCTTGACAAGACTAGTGACCCCCATTTAGGTACCCTCTCCCCTGAAGACAGTAAGCTAAAGAAATCAGATgtacagcagttaaccaggtatagcctgtggggtaggtgttttccacaaga Alignment from Pairagon CACCCATTCACGACCCAGCATCTCCCTCCGGCCCTCCTCACCCAGCTCCTCGACAAGGCCAGTGACCCCCACCTGGGAACCCTCTCCCCTGAAGACAGTGAGCTGGAG---------------------------------------- gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagCATCCTTTTACAACCCAACATCTCCCTCCAGCACTTCTTACCCAACTCCTTGACAAGACTAGTGACCCCCATTTAGGTACCCTCTCCCCTGAAGACAGTAAGCTAAAGAAATCAGATGTACAGCAGTTAACCAGGTATAGCCTGTGGGgtaggtgttttccacaaga Alignment from Exonerate_protein2genome gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagcatccttttacaacccaacatctccctccagcacttcttacccaactccttgacaagactagtgacccccatttaggtaccctctcccctgaagacagtaagctaaagaaatcagatgtacagcagttaaccaggtatagcctgtggggtaggtgttttccacaaga Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CACCCATTCACGACCCAGCATCTCCCTCCGGCCCTCCTCACCCAGCTCCTCGACAAGGCCAGTGACCCCCACCTGGGAACCCTCTCCCCTGAAGACAGTGAGCTGGAG--------- gaaaaggtgaaagattttgaaaaagggaacttgtgcctctgtccttccagCATCCTTTTACAACCCAACATCTCCCTCCAGCACTTCTTACCCAACTCCTTGACAAGACTAGTGACCCCCATTTAGGTACCCTCTCCCCTGAAGACAGTAAGCTAAAGAAATCAGATgtacagcagttaaccaggtatagcctgtggggtaggtgttttccacaaga #### Map4k2_ID1635_14 --> 2 - 0 Original Alignment ttCACCAAGTGAAATTCGGT------------------GCTCCTCGCCGGAAGGAGACAGATCCTCTCAATGAACCG aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagttCACCAAGTGGAACTCACAGCTCCACACCAGAAGGAGACTCCCCAACAGGAAGAGACAGAC---------------gtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct Alignment from CESAR ttCACCAAGTGAAATTCGGTGCTCCTCGCCGGAAGGAGACAGATCCTCTCAATGAACCG--- aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagttCACCAAGTGGAACTCACAGCTCCACACCAGAAGGAGACTCCCCAACAGGAAGAGACAGACgtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct Alignment from Spaln_aa2Genome TTCACCAAGTGAAATTCGGTGCTCCTCGCCGGAAGGAGACAGATCCTCTCAATGAACCG--- aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagTTCACCAAGTGGAACTCACAGCTCCACACCAGAAGGAGACTCCCCAACAGGAAGAGACAGACgtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct Alignment from Spaln_nt2Genome TTCACCAAGTGAAATTCGGTGCTCCTCGCCGGAAGGAGACAGATCCTCTCAATGA-ACCG-- aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagTTCACCAAGTGGAACTCACAGCTCCACACCAGAAGGAGACTCCCCAACAGGAAGAGACAGACgtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct Alignment from Pairagon TTCACCAAGTGAAATTCGGTGCTCCTCGCCGGAAGGAGAC---------------------- aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagTTCACCAAGTGGAACTCACAGCTCCACACCAGAAGGAGACTCCCCAACAGGAAGAGACAGACgtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct Alignment from Exonerate_protein2genome aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagttcaccaagtggaactcacagctccacaccagaaggagactccccaacaggaagagacagacgtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TTCACCAAGTGAAATTCGGTGCTCCTCGCCGGAAGGAGACAGATCCTCTCAATGAACCGTGG aatgagatgaggtaactgcaacgggaccatcaatggtgttcactacttagTTCACCAAGTGGAACTCACAGCTCCACACCAGAAGGAGACTCCCCAACAGGAAGAGACAGACgtatggtaaccgtgattgatgtacaggggggaaggctaagggcgactcct #### Map4k2_ID1636_15 --> 0 - 2 Original Alignment TGGGAGGAGGAGTGGACGCTCCTGGGAAAAGAGGAACTGAGTgg gtgtgtttactttttttaagatatatttatacttactatgtctttcccag---------GAGTGGACACTCCTGGGAAAAGAAGAACTAAGTgggtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from CESAR TGGGAGGAGGAGTGGACGCTCCTGGGAAAAGAGGAACTGAGTgg ctttccattgtgtgtttactttttttttatacttactatgtctttcccag---------GAGTGGACACTCCTGGGAAAAGAAGAACTAAGTgggtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from Spaln_aa2Genome GAGTGGACGCTCCTGGGAAAAGAGGAACTGAGTGG gtgtgtttactttttttaagatatatttatacttactatgtctttcccagGAGTGGACACTCCTGGGAAAAGAAGAACTAAGTGGgtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from Spaln_nt2Genome GAGTGGACGCTCCTGGGAAAAGAGGAACTGAGTGG gtgtgtttactttttttaagatatatttatacttactatgtctttcccagGAGTGGACACTCCTGGGAAAAGAAGAACTAAGTGGgtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from Pairagon AGATCCTCTCAATGAACCGTGGGAGGAGGAGTGGACGCTCCTGGGAAAAGAGGAACTGAGTGG gtgtgtttactttttttaagatatatttatacttactatgtctttcccag----------------------------GAGTGGACACTCCTGGGAAAAGAAGAACTAAGTGGgtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from Exonerate_protein2genome GAGGAGGAGTGGACGCTCCTGGGAAAAGAGGAACTGAGTGG gtgtgtttactttttttaagatatatttatacttactatgtcttTCCCAGGAGTGGACACTCCTGGGAAAAGAAGAACTAAGTGGgtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from Exonerate_coding2genome gtgtgtttactttttttaagatatatttatacttactatgtctttcccaggagtggacactcctgggaaaagaagaactaagtgggtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta Alignment from GeneWise gtgtgtttactttttttaagatatatttatacttactatgtctttcccaggagtggacactcctgggaaaagaagaactaagtgggtaatagacagtggttagcaaagtaagggtccagatgtaccctgttggta #### Map4k2_ID1642_21 --> 0 - 1 Original Alignment ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCTGTGACTCGAg cagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCT---------ggtgggtgtggcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from CESAR ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCTGTGACTCGAg gagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCT---------ggtgggtgtggcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from Spaln_aa2Genome ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCTGTGACTCGAG cagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCTGGTGGGTGTGgcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from Spaln_nt2Genome ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCTGTGACTCGAG cagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCTGGTGGGTGTGgcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from Pairagon ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCTG cagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCTGgtgggtgtggcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from Exonerate_protein2genome ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCTGTGACTCGAG cagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCTGGTGGGTGTGgcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from Exonerate_coding2genome cagtggttccattgtcttagctcactggggatgttatgacactcctgtagatgggggcatgcttcacaaaggtctctaacggctgtcctctgcagattcatgccgctgttacttgggtccaccctggtgggtgtggcgatacgcggcaaactaaaggggataacttaggcacctat Alignment from GeneWise ATGGGTGCCTGCTTCTCCAAGGTCTTCAATGGCTGCCCCCTGCAGATCCATGCTGCTGTCACTTGGGTTCACCCT- cagtggttccattgtcttagctcactggggatgttatgacactcctgtagATGGGGGCATGCTTCACAAAGGTCTCTAACGGCTGTCCTCTGCAGATTCATGCCGCTGTTACTTGGGTCCACCCTGgtgggtgtggcgatacgcggcaaactaaaggggataacttaggcacctat #### Map4k2_ID1644_23 --> 0 - 1 Original Alignment CGAGGACACAATGGAGAAG CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCA---g TGAAGATCGAATGGAAAAGgtcgagctgtccttagaatatctatttacagCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGTTggtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from CESAR CGAGGACACAATGGAGAAG CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCA---g TGAAGATCGAATGGAAAAGgtgcgtctgtccttagaatatctatttacagCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGTTggtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from Spaln_aa2Genome CGAGGACACAATGGAGAAG CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCA---G TGAAGATCGAATGGAAAAGgtcgagctgtccttagaatatctatttacagCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGTTGgtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from Spaln_nt2Genome CGAGGACACAATGGAGAAG-------------------------------CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCAG--- TGAAGATCGAATGGAAAAGGTCGAGCTGTCCTTAGAATATCTATTTACAGCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGTTGgtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from Pairagon CGAGGACACAATGGAGA-------------------------------AGCTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCAG--- TGAAGATCGAATGGAAAAGGTCGAGCTGTCCTTAGAATATCTATTTACAGCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGTTGgtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from Exonerate_protein2genome CGAGGACACAATGGAGAAG CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCAG TGAAGATCGAATGGAAAAGgtcgagctgtccttagaatatctatttacagCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGttggtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from Exonerate_coding2genome CGAGGACACAATGGAGAAG CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCAG TGAAGATCGAATGGAAAAGgtcgagctgtccttagaatatctatttacagCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGttggtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt Alignment from GeneWise CGAGGACACAATGGAGAAG CTCATCTCCCAGCGCTGCTCCTGGCTCTACTGTGTGAACAATGTGTTGCTGTCGCTCTCAGGG- TGAAGATCGAATGGAAAAGgtcgagctgtccttagaatatctatttacagCTGATCTCTCAGCACTACACATGGCTCTACTGTGTGAATAATGTACTTCTAGCACTCCCAGTTGgtgagtgatggcagctatagaaccagcctggataacacgttcccaagagt #### Map4k2_ID1647_26 --> 2 - 0 Original Alignment ttCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTGAAG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagtcCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTT---gtgagtagggactttttaatacatagagctgcatggcaacatggtgtttt Alignment from CESAR ttCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTGAAG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagtcCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTT---gtgagtagggactttttaatacatagagctgcatgtttcttggttgg Alignment from Spaln_aa2Genome TTCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagTCCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTTgtgagtagggactttttaatacatagagctgcatggcaacatggtgtttt Alignment from Spaln_nt2Genome TTCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagTCCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTTgtgagtagggactttttaatacatagagctgcatggcaacatggtgtttt Alignment from Pairagon TTCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagTCCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTTgtgagtagggactttttaatacatagagctgcatggcaacatggtgtttt Alignment from Exonerate_protein2genome TTCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTGAAG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagTCCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTT---gtgagtagggactttttaatacatagagctgcatggcaacatggtgt Alignment from Exonerate_coding2genome TTCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTGAAG gtgggagtgccatgcaactggccccaccgtgatgtttttctgtgttatagTCCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTT---gtgagtagggactttttaatacatagagctgcatggcaacatggtgt Alignment from GeneWise -------------------------------------------------GTTCGAAACCCCTATACCGGCAGTACGTTCCTGCTGGCCGCCCTGCCTGCCAGCCTGCTTCTGCTGCAATGGTATGAGCCACTGCAGAAATTCCTGCTGCTG-------------------------------------------------- GTGGGAGTGCCATGCAACTGGCCCCACCGTGATGTTTTTCTGTGTTATAGTCCACAATCCTTATACTAGCAGCACATTCCTGCTGGCTGCTCTACCTGCAAGCCTCCTGCTTTTAGAATGGTATGAGCCCCTGCAGAAATTTCTCCTGCTTGTGAGTAGGGACTTTTTAATACATAGAGCTGCATGGCAACATGGTGTTTT #### Mark2_ID2106_15 --> 1 - 2 Original Alignment cCTAACCATGCCAGGGTCCCGGGCCTCCACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCag cagattcatgttcttgagctgtgggtttcattttgacccttttggtgtagc------------------------------GCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCaggtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from CESAR cCTAACCATGCCAGGGTCCCGGGCCTCCACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCag cccatctaactcttcactcagtgggtttcattttgacccttttggtgtagc------------------------------GCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCaggtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from Spaln_aa2Genome GGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCAG cagattcatgttcttgagctgtgggtttcattttgacccttttggtgtagCGCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCAGgtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from Spaln_nt2Genome GGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCAG cagattcatgttcttgagctgtgggtttcattttgacccttttggtgtagCGCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCAGgtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from Pairagon CCTAACCATGCCAGGGTCCCGGGCCTCCACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCAG cagattcatgttcttgagctgtgggtttcattttgacccttttggtgtagC------------------------------GCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCAGgtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from Exonerate_protein2genome CCTAACCATGCCAGGGTCCCGGGCCTCC--ACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCAG cagattcatgttcttgagCTGTGGGTTTCATTTTGACCCTTTTGGTGTAGCGCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCAGgtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from Exonerate_coding2genome CCTAACCATGCCAGGGTCCCGGGCCTCC--ACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCAG cagattcatgttcttgagCTGTGGGTTTCATTTTGACCCTTTTGGTGTAGCGCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCAGgtaggcctacagggatagctatacatctatggcaccatgctggacactcg Alignment from GeneWise CCTAACCATGCCAGGGTCCCGGGCCTCCACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCCGTACACCCCAACAAGGCCTCTGGGTTGCCCCCCACGGAGAGTAACTGTGAGGTGCCTCGGCCCAG cagattcatgttcttgagctgtgggtttcattttgacccttttggtgtagC------------------------------GCTTCTGCTTCTGCCGCAGTTTCAGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCTGCCTCTGTGCACCCCAACAAGGCTTCTGGGTTGCCCCCCACAGAGAGTAACTGTGAGGTGCCTCAGCCCAGgtaggcctacagggatagctatacatctatggcaccatgctggacactcg #### Mark2_ID2107_14 --> 0 - 2 Original Alignment AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAAGAC---ag gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATaggtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from CESAR AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAAGAC---ag gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATaggtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from Spaln_aa2Genome AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAAGACAGC-- gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATAGgtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from Spaln_nt2Genome AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAAGAC---AG gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATAGgtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from Pairagon -------------------------------------------------GAACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAAGAC---AG GACTAAGTGCACTACTTTAGAGGCAATACACTTGCCTCCCCTGGGCTCAGAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATAGgtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from Exonerate_protein2genome AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAA---GACAG gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATAGgtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from Exonerate_coding2genome AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAA---GACAG gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATAGgtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta Alignment from GeneWise AACAGCGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGACAGGGCCAGCCTTGGCCAGGCCTCCATCCAGAATGGTAAAGACAGC-- gactaagtgcactactttagaggcaatacacttgcctcccctgggctcagAACGGTGTCCTTTCCACCAGCACAAACCGAAGCAGGAACTCCCCACTTTTGGATAGGGCCAGTCTTGGCCAGGCTTCCATTCAGAATGGAAAAGACGATAGgtaagttaattaagtctggttccttttccaaagaagaatgcagtgcttta #### Mark2_ID2111_10 --> 0 - 1 Original Alignment CAAATTATG---------------AAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAg agttacattttgctccctggatattgtgactgccctttcttcccctccag---------GAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAggtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from CESAR ------CAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAg tttgaaaatagttacattttgctccgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAggtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from Spaln_aa2Genome ---GAGCAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACA agttacattttgctccctggatattgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAGgtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from Spaln_nt2Genome CAAATT------ATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAG agttacattttgctccctggatattgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAGgtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from Pairagon ------------ATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAG agttacattttgctccctggatattgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAGgtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from Exonerate_protein2genome TTAGAGCAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAG agttacattttgctccctggatattgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAGgtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from Exonerate_coding2genome TTAGAGCAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAG agttacattttgctccctggatattgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAGgtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat Alignment from GeneWise ------CAAATTATGAAAGATCGGTGGATGAACGTGGGGCATGAGGACGATGAGCTAAAGCCTTATGTGGAACCTCTCCCTGACTACAAGGACCCCCGGCGGACAG agttacattttgctccctggatattgtgactgccctttcttcccctccagGAGGATCAGTGGATGAAAGATCAGTGGATGAACGTGGGGCATGAGGATGTCGAACTAAAGATTTATGTGCAACCCTTTCCTGACTATAGGGAACCACGGCAAACAGgtgcggctgtgtggtgctgcatgtctgagataaggccacattgtgtcaat #### Mark2_ID2112_9 --> 0 - 0 Original Alignment GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAG--- atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag Alignment from CESAR GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAG--- atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag Alignment from Spaln_aa2Genome GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAGCAA atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag Alignment from Spaln_nt2Genome GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAGCAA atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag Alignment from Pairagon GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAG------------------------------------------------------- atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATGTAAGCAACCTGAGATAACAGTCAGGAAAGGAGAGCAATGTACCAATTAG Alignment from Exonerate_protein2genome GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAGCAA atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag Alignment from Exonerate_coding2genome GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAGCAA atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag Alignment from GeneWise GAGCTGCGGGAACGGGTACTGAGGGGGAAATACCGTATTCCGTTCTACATGTCCACGGACTGTGAAAATCTGCTTAAGAAATTTCTCATACTTAATCCTAGTAAGAGAGGCACTTTAGAGCAA atgctctgcaataacttatatgtcagataactgctcttctctttttccagGAGCTACGGGAACGGGTGTTGAGGGGGAAATACCGTATTCCGTTCTACATATCCACTGACTGTGAAAATCTACTTAAGAAATTCCTTATACTTAATCCTAGTAAAAGAGGCACTCTAGATAATgtaagcaacctgagataacagtcaggaaaggagagcaatgtaccaattag #### Mark2_ID2113_8 --> 0 - 0 Original Alignment GCAGAAAACCTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttccctgacag------AAGCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from CESAR GCAGAAAACCTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gagcctgtatacattgtcactatccaaatgatttcccttttccctgacag------AAGCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from Spaln_aa2Genome CTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttccctgacagaagCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from Spaln_nt2Genome GCAGAAAACCTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttccctgacag------AAGCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACT------AGGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from Pairagon GCAGAAAACCTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttccctgacag------AAGCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from Exonerate_protein2genome GCAGAAAACCTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttcccTGACAGAAGCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from Exonerate_coding2genome GCAGAAAACCTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttcccTGACAGAAGCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc Alignment from GeneWise CTGCTCCTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTTAGCAACGAATTCACCTTTGGGAACAAGCTGGATACTTTCTGTGGCAGTCCTCCTTATGCTGCCCCAGAACTTTTCCAGGGCAAAAAGTATGATGGTCCTGAGGTGGATGTCTGGAGCCTGGGAGTCATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAG gtatacattgtcactatccatcatgaaatgatttcccttttccctgacagaagCTGCTTTTGGATGCCGACATGAACATTAAGATTGCAGACTTTGGATTTAGCAACAAGTTCACTTTTGGGAATGTACTGGACACTTTTTGTGGCAGTCCTCCTTATGCTGCTCCAGAGTATTTCCAGGCTAAAAAGTATGATGGCCATGAAGTAGATGTTCGGAGCCTTGGAGTCATTCTTTATACACTA------GGATCTCTGCCCTTTGATGGACGAAATTTAATGgtatggaaactgagcatggacagctttttgctttgagcccttctcggacc #### Men1_ID1613_4 --> 0 - 0 Original Alignment AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG--------- tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGGATAGGCTGgtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from CESAR AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG--------- tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGGATAGGCTGgtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from Spaln_aa2Genome AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG--------- tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGGATAGGCTGgtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from Spaln_nt2Genome AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG--------- tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGGATAGGCTGgtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from Pairagon AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG--------- tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGGATAGGCTGgtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from Exonerate_protein2genome AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGgataggctggtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from Exonerate_coding2genome AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAG tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGgataggctggtaagtcacttataggtagcttggtggggacggcattgaaccta Alignment from GeneWise AGCTGGCTGTACCTGAAGGGGTCGTACATGCGCTGCGACCGTAAGATGGAGGTGGCGTTCATGGTGTGTGCCATCAACCCTTCCATCGATCTTCACACTGACTCTTTGGAACTGTTGCAACTACAGCAGAAGCTGCTC tgtaggatacgtctgtaaaaattgcatttctaagtaatttttaaattttactttagAGCTGGTTATATCTCCAGGGGTCATATATGCAGTGTGACCGTAAAATGGAAGTGGCATTCATGGTGTGTGCAATCAATTCTTCTATTGATCTTCACCCAGACTCCCTGGAACTTCTTCTCCTGCAACAGGATAGGCTGgtaagtcacttataggtagcttggtggggacggcattgaaccta #### Men1_ID1618_9 --> 0 - 0 Original Alignment GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG--- agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from CESAR GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGA---CAG agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from Spaln_aa2Genome GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGA---CAG agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from Spaln_nt2Genome GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG--- agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from Pairagon GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAG--- agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from Exonerate_protein2genome GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAG---GGACAG agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from Exonerate_coding2genome GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAG---GGACAG agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg Alignment from GeneWise GGCACCCAGGGCCAAGGTTCTGCTCTCCAGGACCCAGAATGCTTTGCCCACCTGCTGCGATTTTATGATGGCATCTGCAAATGGGAGGAGGGTAGCCCCACACCAGTACTGCACGTAGGCTGGGCAACTTTCCTTGTGCAGTCCCTAGGCCGCTTCGAGGGACAGGTG agacttagaaggcatgcaatccttttgattgccatctccttattctcgtcctgcagGGTACACAGGGACAAGGTTCTGCTCTACAAGACCCAGAGTGTTTTGCCCATTTGCTTAGATTTTATGATGGGATATGCAAATGGGAAGAGGGCAGTCTCACTCCAGTCTTGCATGTGGGCTGGGCAACTTTCCTTGTTGAGTCTCTAGGGCGCTTCAAGAGACAACAAgtacgtgggtatcaaaggatagaggggaagaacagacctacgtg #### Mrpl16_ID3289_2 --> 2 - 1 Original Alignment at---TCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAa gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagatGCAGCT---GCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAagtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from CESAR atTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAa gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagatGCAGCTGCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAagtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from Spaln_aa2Genome ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagATGCAGCTGCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAAgtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from Spaln_nt2Genome ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagATGCAGCTGCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAAgtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from Pairagon ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagatgcagCT------GCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAAgtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from Exonerate_protein2genome ATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagATGCAGCTGCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAAgtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from Exonerate_coding2genome TTTTCAGATTCTTGGGCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA gtaaggggtctgagcacctataaacctcttgtgtgtgttgattTGGACAGATGCAGCTGCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAAgtattgtgtaccctgaggattactacataactccagctatgccacatatg Alignment from GeneWise --GCAGCCCTTCCCACCAGTGCTGGTCTGAAGACGCTCCTCCCAGTTCCAACTTTTGAAA gtaaggggtctgagcacctataaacctcttgtgtgtgttgatttggacagatgcagCTGCAACCCTTCCCACCAGTGATGGCCTGAAAACTCTCTTCCCTGTTCCAACATATGAAAgtattgtgtaccctgaggattactacataactccagctatgccacatatg #### Mrpl43_ID9260_2 --> 1 - 1 Original Alignment gGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATAC------------c ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagaGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTTTGGAGTGCTGtgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca Alignment from CESAR gGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATAC------------c ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagaGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTTTGGAGTGCTGtgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca Alignment from Spaln_aa2Genome GGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATACCTT---------- ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagAGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTTTGGAGTGCTGTgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca Alignment from Spaln_nt2Genome GGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATACCTT--- ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagAGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTTTGGAgtgctgtgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca Alignment from Pairagon GGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATACCTT------------------------------------------------------------ ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagAGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTTTGGAGTGCTGTGTAAGTCCAGCTGAGTGAGGGCAGGGGTATCCAGTACTTAATCTATTACA Alignment from Exonerate_protein2genome GGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATACC ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagAGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTttggagtgctgtgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca Alignment from Exonerate_coding2genome GGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATACC ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagAGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTttggagtgctgtgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca Alignment from GeneWise GGAGTTCGTGGAACGCGAGGTGACCGACTTCGCCCGACGGAACCCAGGAGTCGTAGTATACGTGAACCCGCGCCCGTGCGCCATGCCACGAATAGTGGCCGAATAC---------CTT- ggcacaaaacttagaactagcctaatacgtaattttattttcttttgtagAGAGTTAGTTGAACGTGAGGTTACTGACTTTGCCCAATGGAACCCAGGAGTTGTGGTATATGTGAACTCTTGGCCTTGCACCATGCCACGAATGGTGGCAGAATACTTTGGAGTGCTGTgtaagtccagctgagtgagggcaggggtatccagtacttaatctattaca #### Ms4a10_ID3085_2 --> 0 - 0 Original Alignment GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGAACTGTCTCT gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGA---------gtaaataagaaaagcgcatgcctatagcaaccagcgaagtgcctaggatg Alignment from CESAR GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGAACTGTCTCT gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGA---------gtaaataagaaaagcgcatgcctatagcaaccagcgaagtg Alignment from Spaln_aa2Genome GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGAACTGTC------TCT gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGAGTAAATAAGAAAAGCgcatgcctatagcaaccagcgaagtgcctaggatg Alignment from Spaln_nt2Genome GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGA gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGAgtaaataagaaaagcgcatgcctatagcaaccagcgaagtgcctaggatg Alignment from Pairagon GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGA gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGAgtaaataagaaaagcgcatgcctatagcaaccagcgaagtgcctaggatg Alignment from Exonerate_protein2genome GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGAACTGTCTCT gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGAGTAAATAAGaaaagcgcatgcctatagcaaccagcgaagtgcctaggatg Alignment from Exonerate_coding2genome GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGAACTGTCTCT gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGGGGAGTAAATAAGaaaagcgcatgcctatagcaaccagcgaagtgcctaggatg Alignment from GeneWise GGCTTTCACATCGCCATTGCTTTTGCACACTTGGCCTTTGGTGGCTACTTGATCTCCACAGTCAAGAATCTGCACCTGGTGGTGTTGAAGTGCTGGTATCCACTCTGGGGAACTGTCTCT gtccagacacagctcagcattagtgaggatttctgtggtctcttatgcagGGATTTCACATTACCATTGCCTTTGCTCATTTAGCCTTTGGTGGGTACTTGATCTCCACAGTCAAGAATCTGCACCTTGTAGTACTGAAATGTTGGTATCCACTTTGG---------GGAgtaaataagaaaagcgcatgcctatagcaaccagcgaagtgcctaggatg #### Mta2_ID2532_5 --> 1 - 0 Original Alignment gGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcagg---AAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from CESAR gGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG aatgacttgtgtctctacatcctaacccccactcggcctctggtttgcagg---AAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from Spaln_aa2Genome GGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcagG---AAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from Spaln_nt2Genome GAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcagGAAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from Pairagon GGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcag---GAAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from Exonerate_protein2genome GGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcagG---AAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from Exonerate_coding2genome GGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcagG---AAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag Alignment from GeneWise GGGGAAGTGCAGCGTGACTCTCTTGAACGAGACAGACATCTTAAACCAGTATCTAGACAAGGAG gacttgtgtctctacatcctaagttcccccactcggcctctggtttgcagG---AAATGCAGTGTGAGTCTTTTGAACGAGACAGACATCTTAAATCAGTATCTAGACAAGGAGgtgagtagccatctggagaaaaaggcgggtggatattgaatgtaggtgag #### Mta2_ID2538_11 --> 0 - 2 Original Alignment ---AAAAGATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTta gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagCTGAAAAGGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCtagtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from CESAR ---AAAAGATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTta gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagCTGAAAAGGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCtagtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from Spaln_aa2Genome ATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTTA gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagctgaaaagGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCTAgtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from Spaln_nt2Genome ---AAAAGATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTTA gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagCTGAAAAGGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCTAgtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from Pairagon ---AAAAGATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTTA gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagCTGAAAAGGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCTAgtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from Exonerate_protein2genome AAAAGATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTTA gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagctgAAAAGGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCTAgtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from Exonerate_coding2genome gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagctgaaaaggctaaaagctgccgaagcagacagtatattgaaacaggtgtatatccccacctagtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct Alignment from GeneWise ---AAAAGATTGAAAGCTGCTGAAGCAGACAGCAAACTGAAACAGGTCTACATCCCCACTTA gtgctcatgggatgactccaagtttggctgagctcctgcttcctttgtagCTGAAAAGGCTAAAAGCTGCCGAAGCAGACAGTATATTGAAACAGGTGTATATCCCCACCTAgtaagtctcattccaaaataagaacacctaatcatggtgacctaatgtct #### Mta2_ID2539_12 --> 1 - 1 Original Alignment tACCAAGCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACa gtaggagaaagtctagtggcctctctttctttttctcttttcctatccagc------CCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATagtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from CESAR tACCAAGCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACa atcgcggtaggagaaagtctagtggtttctttttctcttttcctatccagc------CCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATagtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from Spaln_aa2Genome TACCAAGCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACA gtaggagaaagtctagtggcctctctttctttttctcttttcctatccagC------CCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATAgtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from Spaln_nt2Genome GCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACA gtaggagaaagtctagtggcctctctttctttttctcttttcctatccagCCCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATAgtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from Pairagon TACCAAGCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACA gtaggagaaagtctagtggcctctctttctttttctcttttcctatccag------CCCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATAgtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from Exonerate_protein2genome TACCAAGCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACA gtaggagaaagtctagtggcctctctttctttttctcttttcctATCCAGCCCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATAgtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from Exonerate_coding2genome GCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACA gtaggagaaagtctagtggcctctctttctttttctcttttcctatccagCCCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATAgtaagttacacatctgatatatcccttactattagatattcatggtttgt Alignment from GeneWise GCCAAACCCTAACCAGATCATTTCTGTGGGTTCAAAACCTGGCATGAATGGGGCTGGATTCCAGAAGGGCCTGACTTGTGAGAGCTGCCACA gtaggagaaagtctagtggcctctctttctttttctcttttcctatccagCCCAAATCCAAACCAGATTATCTCTGTGGGTTCAAAGCCTGGCATGAATGGGGCTGGATTCCAGAAAGGACTGACTTGTGAGAGCTGTCATAgtaagttacacatctgatatatcccttactattagatattcatggtttgt #### Mta2_ID2540_13 --> 2 - 0 Original Alignment ccACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA--------- gaatcactataatacagcaattcctttaaagtttgaacttttacttttagcaACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCCTGGGCgtaatggtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from CESAR ccACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGG---------------GGCACCACA gaatcactataatacagcaattcctttaaagtttgaacttttacttttagcaACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCCTGGGCGTAATGgtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from Spaln_aa2Genome CCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA--------- gaatcactataatacagcaattcctttaaagtttgaacttttacttttagCAACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCCTGGGCgtaatggtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from Spaln_nt2Genome CCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACAGAGCCACACT---CAAGAGG gaatcactataatacagcaattcctttaaagtttgaacttttacttttagCAACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAAC-----AACCACCCTGGGCGTAATGgtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from Pairagon CCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGG------------------------ gaatcactataatacagcaattcctttaaagtttgaacttttacttttagCAACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCCTGGGCGTAATGgtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from Exonerate_protein2genome CCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGG---GGCACCACA gaatcactataatacagcaattcctttaaagtttgaacttttacttttagCAACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCctgggcgtaatggtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from Exonerate_coding2genome CCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGG---GGCACCACA gaatcactataatacagcaattcctttaaagtttgaacttttacttttagCAACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCctgggcgtaatggtgagtgtgtctggagcgaccataagaattgaacctaaggaaga Alignment from GeneWise CCACACAGTCTGCCCAGTGGTATGCCTGGGGACCCCCTAACATGCAGTGCCGACTTTGTGCTTCCTGTTGGATTTATTGGAAGAAATACGGGGGACTGAAGACCCCTACCCAACTTGAAGGGGCTGCTCGGGGCACCACA--------- gaatcactataatacagcaattcctttaaagtttgaacttttacttttagCAACACAGTCTGCACAGTGGTATGCCTGGGGACCACCCAATATGCAGTACCGACTTTGTGCTTCTTGTTGGGTTTATTGGAAGACATATGGAGGCTTGAAAACTCCTACCCAGCTAGAAGGAGCAGCTCGGATAACAACCACCCTGGGCgtaatggtgagtgtgtctggagcgaccataagaattgaacctaaggaaga #### Mta2_ID2542_15 --> 2 - 1 Original Alignment gc---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGg gctggtgaccctggagacctttctctcccctaaagctgttctttttccaggcGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGggtgaggaggatcacattcccaagccaggtcagtggtcttgttctttccat Alignment from CESAR gc---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGg gctggtgaccctggagacctttctctcccctaaagctgttctttttccaggcGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGggtgaggaggatcacattcccaagccaggtcagattaatgtttttgttctt Alignment from Spaln_aa2Genome GC---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGG gctggtgaccctggagacctttctctcccctaaagctgttctttttccagGCGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGGgtgaggaggatcacattcccaagccaggtcagtggtcttgttctttccat Alignment from Spaln_nt2Genome GC---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGG gctggtgaccctggagacctttctctcccctaaagctgttctttttccagGCGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGGgtgaggaggatcacattcccaagccaggtcagtggtcttgttctttccat Alignment from Pairagon GC---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGG gctggtgaccctggagacctttctctcccctaaagctgttctttttccagGCGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGGgtgaggaggatcacattcccaagccaggtcagtggtcttgttctttccat Alignment from Exonerate_protein2genome GC---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGG gctggtgaccctggagacctttctctcccctaaagctgttctttttccagGCGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGGgtgaggaggatcacattcccaagccaggtcagtggtcttgttctttccat Alignment from Exonerate_coding2genome GC---------TCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGATCTGG gctggtgaccctggagacctttctctcccctaaagctgttctttttccagGCGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGGgtgaggaggatcacattcccaagccaggtcagtggtcttgttctttccat Alignment from GeneWise --------TGCTCGATCCGACTTCCTAAGGCTGCCAAGACGCCACTGAAAATTCACCCTCTGGTGCGGCTGCCCTTGGCAACTATCGTCAAAGAT------------------------------------------------------ gctggtgaccctggagacctttctctcccctaaagctgttctttttccagGCGGATCCAATTCAATCCGATTTCCTAAGTCTGCCAAGACTCCATTGAAAATTCACCCTCTTGTGCGGCTGCCTTTGGCAACTATCATCAAAGATCTGGGTGAGGAGGATCACATTCCCAAGCCAGGTCAGTGGTCTTGTTCTTTCCAT #### Mta2_ID2543_16 --> 2 - 0 Original Alignment tgGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT gaatcacattcccaagccaggtcagattgactcttcttctctctctctaggt---CAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from CESAR tgGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT ggaggatcacattcccaagccaggtattgactcttcttctctctctctaggt---CAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from Spaln_aa2Genome GTGGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT tcacattcccaagccaggtcagattgactcttcttctctctctcta gGTCAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from Spaln_nt2Genome TGGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT gaatcacattcccaagccaggtcagattgactcttcttctctctctctag---GTCAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from Pairagon -----------------------------------------------TGGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT GAATCACATTCCCAAGCCAGGTCAGATTGACTCTTCTTCTCTCTCTCTAGGTCAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from Exonerate_protein2genome TGGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT gaatcacattcccaagccaggtcagattgactcttcttctctctctcTAGGTCAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from Exonerate_coding2genome TGGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT gaatcacattcccaagccaggtcagattgactcttcttctctctctcTAGGTCAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat Alignment from GeneWise ----------------------------------------------GTGGCTCAGGCACCTCTGAAACCAAAAACACCTCGGGGTACCAAGACACCAATCAACAGAAACCAGCTGACCCAGAATCGAGGCCTGGGGGGCATTATGGTGAAACGTTCCTATGAGACT GAATCACATTCCCAAGCCAGGTCAGATTGACTCTTCTTCTCTCTCTCTAGGTCAGTCACTTCTAAAGCCAAAAACACCCAGGGGTACTGAGACACCAATCAACAGAAACCAACTGACCCAGAATCGAGGCCTGGGGGGAATTATGGTGAAACGCTCATACGAGACAgtgacttgaccagaataagagcataccagtaattaccttacttttttaat #### Mus81_ID1041_15 --> 1 - 2 Original Alignment t------------------------------CTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGag agccatatcatgctgacaactccactccacaactgttgctgtccccacagcGAATGGCGTGCCATTGATCTATATGCGCAGCTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAaggtgagttaggcttccaccattaaagccactgaagtactggatttctctag Alignment from CESAR cttacttattgtggattgcctgactctgtatattaagttctgagtgttgcc Alignment from Spaln_aa2Genome GCCAGTCTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGAG agccatatcatgctgacaactccactccacaactgttgctgtccccacagcgaatggcgtgccattgatctatatgcgcag------CTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAAGgtgagttaggcttccaccattaaagccactgaagtactggatttctctag Alignment from Spaln_nt2Genome TCTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGAG agccatatcatgctgacaactccactccacaactgttgctgtccccacagcgaatggcgtgccattgatctatatgcgcag-CTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAAGgtgagttaggcttccaccattaaagccactgaagtactggatttctctag Alignment from Pairagon TCTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGAG agccatatcatgctgacaactccactccacaactgttgctgtccccacagcgaatggcgtgccattgatctatatgcgcag-CTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAAGgtgagttaggcttccaccattaaagccactgaagtactggatttctctag Alignment from Exonerate_protein2genome TCTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGAG agccatatcatgctgacaactccactccacaactgttgctgtccccacagcgaatggcgtgccattgatctatatgcgcaGCTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAAGgtgagttaggcttccaccattaaagccactgaagtactggatttctctag Alignment from Exonerate_coding2genome TCTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGAGG agccatatcatgctgacaactccactccacaactgttgctgtccccacagcgaatggcgtgccattgatctatatgcgcaGCTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAAGGtgagttaggcttccaccattaaagccactgaagtactggatttctctag Alignment from GeneWise ----------------------------AGTCTCCTGGCTGCTTATGATGCCTGTGCCACCGCGAAGGAGCAGGAGATGCTCTTGAGCACCATCAAGTGTGGGCGTCTGCAGAG agccatatcatgctgacaactccactccacaactgttgctgtccccacagCGAATGGCGTGCCATTGATCTATATGCGCAGCTCCTGGCAGCTTACCATGCTTGTGCCACTGCAAGAGAGCAGAAGATTCTTTTGATCACCATCAAGTGTGGTTGTCTACAAAGgtgagttaggcttccaccattaaagccactgaagtactggatttctctag #### Mus81_ID1042_14 --> 0 - 2 Original Alignment GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC------ag atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTGAAAaggtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from CESAR GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC------ag atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTGAAAaggtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from Spaln_aa2Genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAGT----- atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTGAAAAGgtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from Spaln_nt2Genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC------AG atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTGAAAAGgtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from Pairagon GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC------AG atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTGAAAAGgtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from Exonerate_protein2genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAG atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTgaaaaggtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from Exonerate_coding2genome GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCCAG atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTgaaaaggtgagctacttacagtacatatgaccccttctaccacagctagtgataca Alignment from GeneWise GCCCAGTCTGTGCGAGAAGTATTTGCCCGGCAGCTGATGCAGGTGCGTGGACTGAGTGGGGAGAAGGCAGCAGCCGTGGTGGATCGATACAGCACCCCTGCC------AG atgaatggaacacgctatctttcacaaatggcaatgcttgtgtcctgcagGCTCAGTCTGTGCGGGAGGTATTTGCCCGACAACTGATGCAGCTGCGTGGACTGAGTGGTGAGAAGGCAGCAGCTGTAGTAGATCGTTACAGCACCCCTGCCGTGAAAAGgtgagctacttacagtacatatgaccccttctaccacagctagtgataca #### Mus81_ID1043_13 --> 0 - 0 Original Alignment ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCACTC---ACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from CESAR ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCA---CTCACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from Spaln_aa2Genome CAGGGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCA---CTCACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from Spaln_nt2Genome ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCA---CTCACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from Pairagon ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCA---CTCACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from Exonerate_protein2genome ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCA---CTCACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from Exonerate_coding2genome ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCA---CTCACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca Alignment from GeneWise ---GGCCACACCCTACGCAGCCGCCCTTGGGGGGCCCCAGGGGCTGCTGAATCAGAAGCAAAGCCTTCCACAAACCCTCTCTGCTCACTCCTCACCTTCAGTGACTTCAATGCAGAAGCTGTCAAGAACAAG cggtgcttggacttgaagggcctgctctactgtgcctgcctctccaccagAGAGGTCATACCCTTCACAGCCACCCTTGGGGAGCCCCAGGGGCTGCTGAATCTGAAGCAAAACCATCAAGAAAACCTTTGTGCTCACTC---ACCTTCAGTGATTTTAATTCAGAAGCTGTAAAGAACAAAgtgagtaccttacttcattcctttgctgatttataccaatgaatggaaca #### Mus81_ID1044_12 --> 0 - 0 Original Alignment GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTACCAG agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTAT---gtgagtagcaagtgctgagtctcatctggctttggttgaggaggatgtat Alignment from CESAR GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTACCAG agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTAT---gtgagtagcaagtgctgagtctcatctggctttggttgaggaggatg Alignment from Spaln_aa2Genome GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTAC agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTATgtgagtagcaagtgctgagtctcatctggctttggttgaggaggatgtat Alignment from Spaln_nt2Genome GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTAC CAG agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTATgtgagtagcaagtgctgagtctcatctggctttggttgaggagGATgtat Alignment from Pairagon GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTAC agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTATgtgagtagcaagtgctgagtctcatctggctttggttgaggaggatgtat Alignment from Exonerate_protein2genome GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTACCAG agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTAT---gtgagtagcaagtgctgagtctcatctggctttggttgaggaggatg Alignment from Exonerate_coding2genome GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTACCAG agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTAT---gtgagtagcaagtgctgagtctcatctggctttggttgaggaggatg Alignment from GeneWise GTCATTGATGGCTTTTTTGTGAAGCGAACCATGGATATTAAGGAGTCGGCTGGCTACCTGGCGCTTTTGACAAAGGGCCTGGAAAGACTGTAC agagaacaacctagtggctagtggcttattctctgtctcttgcctggtagGTCATTGATGGGTTCTTTGTAAAGAGAACTATGGACATTAAGGAGTCAGCCGGATTCCTTTCACTCTTGACTAAGGGTCTGGAATGTTTGTATgtgagtagcaagtgctgagtctcatctggctttggttgaggaggatgtat #### Mus81_ID1045_11 --> 0 - 0 Original Alignment TTCCGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcag---CGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from CESAR TTCCGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG tgtacaacttgggtgattgggccaactcggcctgcctgcttgtgctgcag---CGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from Spaln_aa2Genome TTCCGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcag---CGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from Spaln_nt2Genome CGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcagCGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from Pairagon TTCCGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcag---CGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from Exonerate_protein2genome CGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcagCGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from Exonerate_coding2genome CGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcagCGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag Alignment from GeneWise CGCCTGAAGCGCTGTGGCCTGGGGCACCGGGTATACTTAGTGGAAGAACATGGGTCTGTCCACAACCTTAGCCTTCCCGAGAGCACCTTGCTGCAGGCTGTCACAAACACCCAG acaacttgggtgattgggccaatagctcggcctgcctgcttgtgctgcagCGCCTGAAGCACTGTGTCCTGGGGCACCGAGTATACCTTGTGGAAGAACATGGGTCTGTCCACAACCTAAGCCTACCAGAAAGTACCTTGTTGCAGGCTGTCACAAACACCCAGgtgagtcatataggcagcaagcagatacgacagataagagaacaacctag #### Mus81_ID1046_10 --> 2 - 0 Original Alignment aa---AGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagagCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from CESAR aa---AGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagagCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from Spaln_aa2Genome AAAGACCTGGGGAGCTG---GTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagAGCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from Spaln_nt2Genome AA---AGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGCTTT---CGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagAGCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from Pairagon AA---AGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCG---CTTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagAGCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from Exonerate_protein2genome AA---AGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagAGCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from Exonerate_coding2genome AA---AGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagAGCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt Alignment from GeneWise --GAAAGACCTGGGGAGCTGGTCCTGGACCACATTGTGGAACGCAAGCGGCTAGATGACCTATGCAGCAGCATCATTGACGGCCGC---TTTCGGGAGCAGAAG agtattagtagttgcatgaaatccaaaacagactctctctcccattgcagAGCCTAGACCTGGGGAGTTAGTCCTAGATCACATTGTAGAACATAAGAGGATCGATGACCTGTGTAGCAGCATTATTGGTGGCCGCTTCTTCCGGGAGCAGAAAgtatacatatgacatagttaggattagctccttccgttttctagggcagt #### Mus81_ID1049_7 --> 1 - 2 Original Alignment gTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAA---cc tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagaTATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAGctgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from CESAR gTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAA---cc tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagaTATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAGctgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from Spaln_aa2Genome GTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAACC tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagATATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAgctgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from Spaln_nt2Genome GTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAAC--CT tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagATATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAGCTgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from Pairagon GTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAACC--- tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagATATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAGCTgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from Exonerate_protein2genome GTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAACC tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagATATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAgctgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from Exonerate_coding2genome GTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAACC tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagATATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAgctgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt Alignment from GeneWise GTATGCACTCACACCAGAGGGTCTGGAGCTGGCTCAGAAGCTGGCCGAGGCGGAAGGCCTGAGCACTCGGCACGCTGGCTTTAGGCCAGAGGAACATCACGGAGAGGACTCAGCAGTTCCAGAAGCCTTGTCAGAACCT-- tagatatgcagtggaaatatagtgatactgaatgtctgtctttgccatagATATGCTCTAACACCAGAGGGGCTAGAGCTCACTCAGAAGCTGTCGAAGGCAGAAGGCCTTAGCACAAGACATGCTGGCTTTAGACCAGAGGAACATCATGGGGAGGACTCAGCAGTGCCAGAGGCTCTGACAGAACAGCTgttagtatggtcaacttactatagcctccaaaaccgcgaccacttggtgt #### Mus81_ID1053_3 --> 2 - 0 Original Alignment gtGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA atgttgcaatttggagttccacactttcttttttcctcttttctttaaaggaGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCT------gtactagccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from CESAR CCACACGCGTTTCGTGTTTCAAA gtGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA CCATACACGATTTGTATTCCAGAagttcttttttcctcttttctttaaaggaGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCTGTACTAgccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from Spaln_aa2Genome GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA atgttgcaatttggagttccacactttcttttttcctcttttctttaaagGAGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCTGTACTAgccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from Spaln_nt2Genome GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA atgttgcaatttggagttccacactttcttttttcctcttttctttaaagGAGACCATGCCCCTA---CACCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCTGTACTAgccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from Pairagon GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA atgttgcaatttggagttccacactttcttttttcctcttttctttaaagGAGACCATGCCCCTA---CACCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCTGTACTAgccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from Exonerate_protein2genome GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCCATGCCA atgttgcaatttggagttccacactttcttttttcctcttttctttaaagGAGACCATGCCCCT---ACACCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCTGTACTAgccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from Exonerate_coding2genome atgttgcaatttggagttccacactttcttttttcctcttttctttaaaggagaccatgcccctacaccatctgggaaaaagggtgccagcaaagggccacctgagcaggtacaagaatcttctgtactagccagaaaatgaagaaaagctagatcacttaaagggaaacctat Alignment from GeneWise GTGACCATGCCCCCAGCTCACCATCTGGAAAGAAGGGAGCCAGCAAAGGGCCACCTGAGCAAGTCCAGGACTCTTCC atgttgcaatttggagttccacactttcttttttcctcttttctttaaagGAGACCATGCCCCTACA---CCATCTGGGAAAAAGGGTGCCAGCAAAGGGCCACCTGAGCAGGTACAAGAATCTTCTgtactagccagaaaatgaagaaaagctagatcacttaaagggaaacctat #### Myrf_ID2720_17 --> 0 - 2 Original Alignment TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCag atctcaagtctatatagggcaacacagctcagcacctccccctcccccag------TCTGCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCaggtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from CESAR TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCag atgggcatctcaagtctatatagggagctcagcacctccccctcccccagTCT------GCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCaggtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from Spaln_aa2Genome CCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCAG atctcaagtctatatagggcaacacagctcagcacctccccctcccccagTCTGCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCAGgtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from Spaln_nt2Genome TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCAG atctcaagtctatatagggcaacacagctcagcacctccccctcccccagT------CTGCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCAGgtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from Pairagon TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCAG atctcaagtctatatagggcaacacagctcagcacctccccctcccccagtctgcag-------------TCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCAGgtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from Exonerate_protein2genome TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCAG atctcaagtctatatagggcaacacagctcagcacctccccctcccccagTCT------GCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCAGgtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from Exonerate_coding2genome TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCAG atctcaagtctatatagggcaacacagctcagcacctccccctcccccagTCT------GCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCAGgtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca Alignment from GeneWise TCATCGCCAGCGGTCCCAGACCAGGCCTGCATCAGTCAGCGTTTTCTGCAGGGAACTATCATAGCTCTGGTGGTGGTCATGGCCTTCAG atctcaagtctatatagggcaacacagctcagcacctccccctcccccagTCT------GCAGTCCCAGACCAAGCCTGCATCAGTCAGCATTTTCTGCAGGGGACCATCATAGCTCTCGTAGTAGTGATGGCCTTCAGgtaggactcttaaccaggctgagtccctaaaagtgccatacaagctctca #### Myrf_ID2721_16 --> 1 - 0 Original Alignment cCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagcCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAG------------------------gtaggccagtccacagcagcgtacgctccccgggctgctttacagtgtac Alignment from CESAR cCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagcCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAA------------------------AAGgtaggccagtccacagcagcgtacgctccccgggctgctttacagtgtac Alignment from Spaln_aa2Genome CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAATAAG cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagCCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAGGTAGGCCAGTCCACAGCAGCGTACgctccccgggctgctttacagtgtac Alignment from Spaln_nt2Genome CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAG cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagCCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAGgtaggccagtccacagcagcgtacgctccccgggctgctttacagtgtac Alignment from Pairagon CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAG cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagCCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAGgtaggccagtccacagcagcgtacgctccccgggctgctttacagtgtac Alignment from Exonerate_protein2genome CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAA cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagCCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAGGTAGGCCAGTCCACAGCAGCgtacgctccccgggctgctttacagtgtac Alignment from Exonerate_coding2genome CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAGAGGCCCCCTAAACTGGCCAA cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagCCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAGGTAGGCCAGTCCACAGCAGCgtacgctccccgggctgctttacagtgtac Alignment from GeneWise CCATGCAGGGAGCCAGTTTAGCCGGGCAGGCAGTGTCCCCCACAAAAAG cgcaggtgtgttatgcattatccattttctaaaatgacaatgtgttttagCCATGCTGGTAGTGAATTTAGTAGGGCAGGCAGTGTCCCTCACAAAAAGgtaggccagtccacagcagcgtacgctccccgggctgctttacagtgtac #### Myrf_ID2722_15 --> 0 - 2 Original Alignment GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCag ggtggatacaaaatgagcagttccctcattatactttttggggactatag---CGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCaggtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from CESAR GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCag gtgggtggatacaaaatgagcagtttcattatactttttggggactatag---CGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCaggtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from Spaln_aa2Genome GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG ggtggatacaaaatgagcagttccctcattatactttttggggactatag---CGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCAGgtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from Spaln_nt2Genome GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG ggtggatacaaaatgagcagttccctcattatactttttggggactatag---CGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCAGgtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from Pairagon GAGCGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG ggtggatacaaaatgagcagttccctcattatactttttggggactatag---CGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCAGgtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from Exonerate_protein2genome CGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG ggtggatacaaaatgagcagttccctcattatactttttggggactatagCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCAGgtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from Exonerate_coding2genome CGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG ggtggatacaaaatgagcagttccctcattatactttttggggactatagCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCAGgtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa Alignment from GeneWise CGAATCTTCATGGAGAATGTGGGGGCTGTGAAGGAGTTATGCAAACTGACAGACAACCTAGAGACTCGCATTGATGAGTTGGAGCGATGGAGCCACAAGCTGGCCAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACTGGCAGCTCAGGGGCTTTCAG ggtggatacaaaatgagcagttccctcattatactttttggggactatagCGAATCTTCATGGAGAATGTGGGGGTTGTAAAGGAGTTATGCAAACTGAGAGACAACCTAGAGACTCGCATTGATGAGTTGGAACGATGGAGCCACAAGTTGGCTAAGCTGCGGCGCCTTGACAGCCTCAAGTCAACCGGCAGCTCAGGGGCTTTCAGgtaagacaaccaagaacatgggcaggagactaaggtaagaagaggaggaa #### Myrf_ID2732_6 --> 1 - 1 Original Alignment aCTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAg gc actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctaga---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTggttagtagaccccatgcagatttagtggctgatgtttctcttcaacaggg Alignment from CESAR aCTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAg gc actactgtagtgccgagggggaatgtttcgctgttgtttttcctccctaga---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTggttagtagaccccatgcagatttagttttcttttccattaaatcccaggg Alignment from Spaln_aa2Genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAG GC actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctagA---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTGgttagtagaccccatgcagatttagtggctgatgtttctcttcaacagGG Alignment from Spaln_nt2Genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAG GC actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctagA---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTGgttagtagaccccatgcagatttagtggctgatgtttctcttcaacagGG Alignment from Pairagon ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCC------------------------------------------------CAGGC actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctagA---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTGGTTAGTAGACCCCATGCAGATTTAGTGGCTGATGTTTCTCTTCAACAGGG Alignment from Exonerate_protein2genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAG GC actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctagA---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTGgttagtagaccccatgcagatttagtggctgatgtttctcttcaacagGG Alignment from Exonerate_coding2genome ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAG GC actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctagA---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTGgttagtagaccccatgcagatttagtggctgatgtttctcttcaacagGG Alignment from GeneWise ACTCCCTCCACACCCCTCTAAGAAGAGGAAGCACTCTGAATCACCCCCCAACACCCTCAATGCCCAAATGCTGAACGGAATGATCAAGCAGGAACCTGGGACTGTCACAGCCTTGCCTCCACACCCTGCCAGAGCCCCATCCCCTCCATGGCCTCCTCAAGGCCCACTGTCACCTGGCACTGGATCCTTGCCCCTCAGCATTGCCCGAGCCCAGACTCCACCCTGGCACCCGCCAGGTGCACCCTCCCCAG GC actgtagtgccgagggggaatgaagtttcgctgttgtttttcctccctagA---CCACCACACCCTTCCAAGAAGAGGAAGCACTCTGAAACACCCCCCAACACCCTCAATGCCCAAATGTTGAATGGGATGATTAAGCAGGAGCCTGGAACTGTAACAACCTTACCATTGCACCCTGCCAGAGTCCCTTCACCTCCATGGTTACCTAAAGGCCCACTCTCACCTGGTACTGGATCTTTGGCTCTCAGTACAGCCCGGGCTCAAACTCCACCTTGGCACCCACCAGGTGCACCCTCTCCTGgttagtagaccccatgcagatttagtggctgatgtttctcttcaacagGG #### Naa40_ID2074_6 --> 1 - 2 Original Alignment c---TATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACag ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagcAAGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATaggtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from CESAR c---TATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACag ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagcAAGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATaggtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from Spaln_aa2Genome C---TATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACAG ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagCAAGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATAGgtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from Spaln_nt2Genome C---TATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACAG ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagCAAGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATAGgtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from Pairagon C---TATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACAG ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagCAAGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATAGgtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from Exonerate_protein2genome CTATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACAG ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagcaaGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATAGgtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from Exonerate_coding2genome CTATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACAG ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagcaaGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATAGgtatttagcatcttggaagatttgaattgctggaggttggacctgagaat Alignment from GeneWise -TGCTATGAAGTGCAGCTGGAAAGCAAGGTACGGCGGAAAGGCCTAGGGAAGTTCCTCATTCAGATCCTGCAGCTCATGGCCAACAG ttacatgtctccattgtgtccaggtactcttttttaaacttgttttctagCAAGTACGAAGTACAGCTAGAAAGCAAGGTAAGGCAGAAAGGCCTAGAGAAGTTTCTCATTCAGATTCTCCAGCTAATGGCCAATAGgtatttagcatcttggaagatttgaattgctggaggttggacctgagaat #### Naaladl1_ID1447_6 --> 1 - 2 Original Alignment tAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGG---ag aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagtAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTaggtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from CESAR tAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGG---ag aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagtAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTaggtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from Spaln_aa2Genome TAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGGAGT-- aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagTAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTAGgtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from Spaln_nt2Genome TAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGGA---G aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagTAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTAGgtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from Pairagon TAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGG---AG aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagTAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTAGgtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from Exonerate_protein2genome TAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGG---AG aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagTAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTAGgtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from Exonerate_coding2genome aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagtaacctcacaggaacttctgcccctactttctggcagagagctctaggctgtgaatataagctaggtcctgggtttgagccaaatgaaagtttccctgatggaattaggtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc Alignment from GeneWise TAACCTCACCGGAACCTCTGCCCCTGCCTTCTGGCAGGGGGCCCTGGGCTGTGAGTACAAGCTGGGACCCGGCTTTGAGCCGAATGGAAGCTTCCCTGCTGGGAGT-- aattggagctaatcacaaatcctgtcatcacgattgtctcttgtctgcagTAACCTCACAGGAACTTCTGCCCCTACTTTCTGGCAGAGAGCTCTAGGCTGTGAATATAAGCTAGGTCCTGGGTTTGAGCCAAATGAAAGTTTCCCTGATGGAATTAGgtaagccacggagctgagtgcccttgagtgggcccccagaatcattgtcc #### Naaladl1_ID1448_7 --> 1 - 1 Original Alignment t---GAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTg ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagtCCAGACATCAGAGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTggtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from CESAR t---GAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTg ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagtCCAGACATCAGAGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTggtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from Spaln_aa2Genome T---GAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCT ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagTCCAGACATCAGAGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTGgtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from Spaln_nt2Genome T---GAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTG ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagTCCAGACATCAGAGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTGgtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from Pairagon TGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTG ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagtccagacatcag---------AGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTGgtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from Exonerate_protein2genome T---GAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTG ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagTCCAGACATCAGAGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTGgtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from Exonerate_coding2genome ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagtccagacatcagagtgcgtgttcacaacagattagaacttagaatttccactaacgtgcttggcatcatccaaggcagtgtagagcctggtgagcccattaatactccgccctgccctttggccctagcacctggccaa Alignment from GeneWise -AGTGAGGTGAAAGTGAGTGTCCACAACAGGCTGGAGCTGAGGACCTCTTCCAATGTCCTGGGCATCATCCAGGGGGCTGTGGAGCCTG ttgtattatcactagtcaataatagctcctgttcgttctttttggctcagTCCAGACATCAGAGTGCGTGTTCACAACAGATTAGAACTTAGAATTTCCACTAACGTGCTTGGCATCATCCAAGGCAGTGTAGAGCCTGgtgagcccattaatactccgccctgccctttggccctagcacctggccaa #### Naaladl1_ID1456_15 --> 2 - 1 Original Alignment gtTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGg gg aaacttggatttggcctctatcctgtgcagctgttttctttgtcccaaaggc---------CAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGggtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagga Alignment from CESAR gtTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGg gg atgaaggtgaaacttggatttggcctgcagctgttttctttgtcccaaaggc---------CAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGggtgagtcccaacatcttgagactgtggtttctgtgctcttccccgcagga Alignment from Spaln_aa2Genome GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGG GG aaacttggatttggcctctatcctgtgcagctgttttctttgtcccaaagGC---------CAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGGgtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagGA Alignment from Spaln_nt2Genome GCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGG GG aaacttggatttggcctctatcctgtgcagctgttttctttgtcccaaagGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGGgtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagGA Alignment from Pairagon GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGG GG aaacttggatttggcctctatcctgtgcagctgttttctttgtcccaaag---------GCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGGgtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagGA Alignment from Exonerate_protein2genome GTTTCAGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGG GG aaacttggatttggcctctatcctgtgcagctgttttctttGTCCCAAAGGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGGgtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagGA Alignment from Exonerate_coding2genome aaacttggatttggcctctatcctgtgcagctgttttctttgtcccaaaggccagcaggctgttgcccggactgctgggagtgtgcttctccagctcagtgatagcctcttcctgcccctaaatgttagtgactatagtgagaccttacaaagtttccttcaggcagcgcaagaagccctaggtacccaattagaaaagcagaatgtaagcttgggtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagga Alignment from GeneWise ----TTC---------AGCAGCCACCAAGCTGTGGCCCGGACTGCTGGGAGCGTGCTTCTCCGGCTCAGTGACAGCCTCTTCCTGCCCCTCAATGTCAGTGACTATAGTGAGACACTACAGAGTTTCCTGCAGGCTGCTCAAGAGGCCCTTGGCACCCAGTTAGAGAAACAGAACATCAGCCTGG GG aaacttggatttggcctctatcctgtgcagCTGTTTTCTTTGTCCCAAAGGCCAGCAGGCTGTTGCCCGGACTGCTGGGAGTGTGCTTCTCCAGCTCAGTGATAGCCTCTTCCTGCCCCTAAATGTTAGTGACTATAGTGAGACCTTACAAAGTTTCCTTCAGGCAGCGCAAGAAGCCCTAGGTACCCAATTAGAAAAGCAGAATGTAAGCTTGGgtgagtcccaacatcttgagactgtgctgttatgctaatggtatgcagGA #### Naaladl1_ID1457_16 --> 2 - 2 Original Alignment Gg gg---------CCTTTGGTGACTGCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTga GggtggaacccaacatcttgagactgtgctgctttctgtttattctctaggaTACTACAAGCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTgagtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from CESAR Gg gg---------CCTTTGGTGACTGCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTga GggtgagtcccaacatcttgagactgtgctgctttctgtttattctctaggaTACTACAAGCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTgagtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from Spaln_aa2Genome GG GGCCTTTGGTGACT---------GCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTGA GGgtggaacccaacatcttgagactgtgctgctttctgtttattctctagGATACTACAAGCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTGAgtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from Spaln_nt2Genome CAGCCTGGG-GCCTTTGGTGACTGCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTGA gggtggaacccaacatcttgagactgtgctgctttctgtttattctctagGATACTACAAGCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTGAgtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from Pairagon GGG---------------------------------------------------------GCCTTTGGTGACTGCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTGA GGGTGGAACCCAACATCTTGAGACTGTGCTGCTTTCTGTTTATTCTCTAGGATACTACAAGCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTGAgtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from Exonerate_protein2genome GGGG CCTTTGGTGACTGCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTGA GGGTggaacccaacatcttgagactgtgctgctttctgtttattctctaggatactacaagCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTGAgtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from Exonerate_coding2genome gggtggaacccaacatcttgagactgtgctgctttctgtttattctctaggatactacaagcctttggtaacggctgtggcaaactttaaggcttctgctgcctcgctgggagaagacatcctgaccctaggtcagagcagccctgagtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac Alignment from GeneWise GGGG---------------------------------------------------------CCTTTGGTGACTGCAGTGGCGAACTTTAAGGCTGCAGCTGCATCCTTGGGTGAGCACATCTTGACCCTGCAGAAGAGCAGCCCTGA GGGTGGAACCCAACATCTTGAGACTGTGCTGCTTTCTGTTTATTCTCTAGGATACTACAAGCCTTTGGTAACGGCTGTGGCAAACTTTAAGGCTTCTGCTGCCTCGCTGGGAGAAGACATCCTGACCCTAGGTCAGAGCAGCCCTGAgtaattgccagcagaggacatatctcaccaagtatacatgggggaggtac #### Ndufs8_ID193_3 --> 2 - 1 Original Alignment ag------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATT---CTGATGTGGACAGAACTCATCCGAg gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagagAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAGGCAGGT---GACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGggtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from CESAR ag------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTCTGATG---TGGACAGAACTCATCCGAg gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagagAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAG---GCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGggtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from Spaln_aa2Genome AG------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTCTGATGTGGACAGAACTCATCCGAG gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagAGAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAGGCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGGgtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from Spaln_nt2Genome AG------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTCTGATG---TGGACAGAACTCATCCGAG gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagAGAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAG---GCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGGgtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from Pairagon AG------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTC---TGATGTGGACAGAACTCATCCGAG gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagAGAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAG---GCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGGgtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from Exonerate_protein2genome AG------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTCTGATGTGGACAGAACTCATCCGAG gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagAGAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAGGCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGGgtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from Exonerate_coding2genome AG------TATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTCTGATGTGGACAGAACTCATCCGAG gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagAGAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAGGCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGGgtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg Alignment from GeneWise -----AAGTATGTGAATAAGAAGGAACAGGAGTCTGAGGTGGACATGAAGTCCGCAACTGACAATGCAGCTCGGATTCTGATG---TGGACAGAACTCATCCGAG gattctaacgattaatctccttgttgctaatgtgtgctctcttcatgcagAGAATACATATGTAAACAAAAAAGAGCAAGAGGCAGAAGTAGACATGAAG---GCAGGTGACAATGCTGCACAGATTCTGATGATGTGGACAGAAATAATCCGGGgtaaagtccaatgcaggatcgtaaggtgaaaatttaagactagtctggtg #### Ndufs8_ID194_2 --> 2 - 1 Original Alignment ga---------CATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACa ggggccctcttgaggaacagatctcctagttcttttcattttgtccacaggaAACAAAGTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACagtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from CESAR ga---------CATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACa ggggccctcttgaggaacagatctcctagttcttttcattttgtccacaggaAACAAAGTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACagtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from Spaln_aa2Genome GACATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACA ggggccctcttgaggaacagatctcctagttcttttcattttgtccacaggaaacaaagTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACAgtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from Spaln_nt2Genome GACATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACA ggggccctcttgaggaacagatctcctagttcttttcattttgtccacaggaaacaaagTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACAgtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from Pairagon GACATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACA ggggccctcttgaggaacagatctcctagttcttttcattttgtccacaggaaacaaagTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACAgtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from Exonerate_protein2genome GA---------CATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACA ggggccctcttgaggaacagatctcctagttcttttcattttgtccacagGAAACAAAGTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACAgtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from Exonerate_coding2genome GA---------CATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACA ggggccctcttgaggaacagatctcctagttcttttcattttgtccacagGAAACAAAGTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACAgtggttggctgaaattaagatctggctcacacgagctacagaaccatagg Alignment from GeneWise GACATCTTAATGGACAAAGCCTTCATAGCAGCGCAGTGGCGGCAACGTACA ggggccctcttgaggaacagatctcctagttcttttcattttgtccacaggaaacaaagTACATCTAAATGGACAGAGCCTACACAGCAGTGCTGTGGCATCAACGTACAgtggttggctgaaattaagatctggctcacacgagctacagaaccatagg #### Ndufv1_ID277_5 --> 0 - 1 Original Alignment GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGATGTG------g ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATGTGTGGGTGggtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from CESAR GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGAT------GTGg ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATGTGTGGGTGggtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from Spaln_aa2Genome GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGATGTG------G ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATGTGTGGGTGGgtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from Spaln_nt2Genome GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGATGTG--G ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATGTGTGGgtgggtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from Pairagon GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGATGT ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATGTgtgggtgggtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from Exonerate_protein2genome GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGAT ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATgtgtgggtgggtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from Exonerate_coding2genome GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGAT ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATgtgtgggtgggtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct Alignment from GeneWise GTAGCTATCCGAGAGGCCTATGAAGCAGGTCTGATTGGCAAGAATGCTTGTGGCTCCGACTATGATTTTGATGTGTTTGTGGTGCGTGGGGCTGGGGCCTACATCTGTGGAGAAGAGACGGCACTTATTGAATCCATTGAAGGCAAGCAGGGAAAGCCACGCCTGAAGCCGCCCTTTCCAGCAGATGTGGGAGTG- ctgtgtgactgagtaatgtagggctcggcgtcccgtgcctgggcccgcagGTAGCTATCCGAGGTGCCTATGAAGCAGTTCTGATTGGCAAGAATGCTTGTGGCTCTGACTATGATTTTGATGTGTTTCTGGTACGTGGTGCAGGTGCCTACATCTGTGGAGATGAGACAGCACTTATTGAATCAATTGAAGGCAAGCAGGGAAAGCCATGCCTGAAGCCGCCCTTCCCAGCAGATGTGTGGGTGGgtttgtcatctggtgtcctagttctcttctgacagcccctgcccccatct #### Nfkb2_ID9824_2 --> 0 - 1 Original Alignment GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAg tatcccttaataccactaccatcccctgtcatctttttcctttttccaag---------GGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAggtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from CESAR GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAg tcgccaatttatcccttaataccacctgtcatctttttcctttttccaag---------GGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAggtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from Spaln_aa2Genome GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAG tatcccttaataccactaccatcccctgtcatctttttcctttttccaag---------GGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAGgtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from Spaln_nt2Genome GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAG tatcccttaataccactaccatcccctgtcatctttttcctttttccaag---------GGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAGgtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from Pairagon GGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAG tatcccttaataccactaccatcccctgtcatctttttcctttttccaag---------GGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAGgtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from Exonerate_protein2genome CCAGGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAG tatcccttaataccactaccatcccctgtcatctttttCCTTTTTCCAAGGGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAGgtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from Exonerate_coding2genome CCAGGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAG tatcccttaataccactaccatcccctgtcatctttttCCTTTTTCCAAGGGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAGgtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact Alignment from GeneWise GACAATTGCTAC---GATCCAGGCCTGGATGGCATCCCCGAATATGATGATTTTGAATTCAGCCCCTCCATCGTGGAGCCTAAGGATCCAGCCCCTGAGACAG ttaataccactaccatcccc------TGTCATCTTTTTCCTTTTTCCAAGGGAATCCCAGATTATGAGGATTTTGAATTCAGCCCGACAATAGGTGAACCTAATGATCCAGCACCTGAAACAGgtaggagaatataaggaggcttttcagttgaggagtttgaggtgtccact #### Nfkb2_ID9825_3 --> 2 - 0 Original Alignment ctGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ttgggattaataaaagggggtactgtgttcccacgtctgctctaccttagct------CCCTATCTTGTGATTGTGGAACAAACGAAACAGgtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from CESAR ctGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ctgcttttgggattaataaaaggggtgttcccacgtctgctctaccttagct------CCCTATCTTGTGATTGTGGAACAAACGAAACAGgtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from Spaln_aa2Genome CTGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ttgggattaataaaagggggtactgtgttcccacgtctgctctaccttagCT------CCCTATCTTGTGATTGTGGAACAAACGAAACAGgtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from Spaln_nt2Genome GCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ttgggattaataaaagggggtactgtgttcccacgtctgctctaccttagCTCCCTATCTTGTGATTGTGGAACAAACGAAACAGgtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from Pairagon CTGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ttgggattaataaaagggggtactgtgttcccacgtctgctctaccttagCT------CCCTATCTTGTGATTGTGGAACAAACGAAACAGgtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from Exonerate_protein2genome CTGATGGCCCCTATCTGGTGATTGTGGAACAGCCCAAACAG ttgggattaataaaagggggtactgtgttcccacgtctgctctaCCTTAGCTCCCTATCTTGTGATTGTGGAACAAACGAAACAGgtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from Exonerate_coding2genome ttgggattaataaaagggggtactgtgttcccacgtctgctctaccttagctccctatcttgtgattgtggaacaaacgaaacaggtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg Alignment from GeneWise ttgggattaataaaagggggtactgtgttcccacgtctgctctaccttagctccctatcttgtgattgtggaacaaacgaaacaggtcagtgtacaataaaacaataagacaataaaacaataagaaaatgtgtg #### Nfkb2_ID9826_4 --> 0 - 0 Original Alignment CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCTACTGTCAAG gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCC---------gtaagaacagcctgagaaggtgccacagctgcttcatgcatagacctgtg Alignment from CESAR CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCTACTGTCAAG gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCC---------gtaagaacagcctgagaaggtgccacagctgcttcatgcat Alignment from Spaln_aa2Genome CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCTACTGTCAAG gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCCGTAAGAACAgcctgagaaggtgccacagctgcttcatgcatagacctgtg Alignment from Spaln_nt2Genome CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCC--TA--------CTGTCAAG gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCCGTAAGAACAGCCTGAGAAGgtgccacagctgcttcatgcatagacctgtg Alignment from Pairagon CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCT gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCCgtaagaacagcctgagaaggtgccacagctgcttcatgcatagacctgtg Alignment from Exonerate_protein2genome CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCTACTGTCAAG gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCCGTAAGAACAgcctgagaaggtgccacagctgcttcatgcatagacctgtg Alignment from Exonerate_coding2genome CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCTACTGTCAAG gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCCGTAAGAACAgcctgagaaggtgccacagctgcttcatgcatagacctgtg Alignment from GeneWise CGAGGCTTCAGATTTCGATATGGCTGTGAAGGCCCCTCCCATGGAGGTTTGCCAGGTGCCTCCAGTGAGAAGGGCCGGAAGACCTATCCT gggtagtttgcttcacctgctcattgtaaatgtgccttcctctttcacagAGAGGCTATAGATTCCGATATGGCTGTGAGGGCCCCTCCCATGGTGGCTTGCCAGGTGCATCCAGTGAGAAGGGCCGGAAGAGCTATCCCgtaagaacagcctgagaaggtgccacagctgcttcatgcatagacctgtg #### Nfkb2_ID9827_5 --> 0 - 2 Original Alignment ---------ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTca gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagTACCTGGTGATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTcagtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from CESAR ---------ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTca gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagTACCTGGTGATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTcagtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from Spaln_aa2Genome ATCTGTAACTAT---------GAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCA gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagTACCTGGTGATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTCAgtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from Spaln_nt2Genome --------GATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCA gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagTACCTGGTGATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTCAgtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from Pairagon ----------------------------------------------------------GATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCA GACCTGTGGGGCACTCAACAATATAGAAAATATCGTCATCATTTCTTCAGTACCTGGTGATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTCAgtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from Exonerate_protein2genome ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCA gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagtacctggtgATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTCAgtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from Exonerate_coding2genome ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCA gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagtacctggtgATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTCAgtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc Alignment from GeneWise ---------ATCTGTAACTATGAGGGACCGGCCAAGATTGAGGTGGACCTGGTGACACACAGTGACCCACCTCGTGCGCATGCCCACAGTCTGGTGGGCAAGCAGTGTTCAGAGTTGGGAGTGTGCGCTGTGTCTGTAGGACCCAAGGACATGACTGCTCA gacctgtggggcactcaacaatatagaaaatatcgtcatcatttcttcagTACCTGGTGATATGTAACTATGAGGGACCCACAAAGATTGTCGTTGACCTGGCAACACACAGTGACCCACCTCGTGCACATGCCCACAGTCTGGCGGGCAAGCAGTGTTCAGAACTCGGGGTATGTGCCATTTCTGTAGGCCCCAAGGACATGACTGCTCAgtgagtcacttatcagtcttggagttgatccaaaggatatctggatatcc #### Nfkb2_ID9829_7 --> 2 - 1 Original Alignment ag------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCa agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagagTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCagtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from CESAR ag------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCa agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagagTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCagtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from Spaln_aa2Genome AG------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCA agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagAGTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCAgtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from Spaln_nt2Genome AG------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCA agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagAGTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCAgtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from Pairagon AG------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCA agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagAGTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCAgtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from Exonerate_protein2genome AG------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCA agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagAGTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCAgtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from Exonerate_coding2genome AG------GCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCA agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagAGTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCAgtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt Alignment from GeneWise -----GAGGCTGAGCGGCGGGAGCTAGAGCAGGAGGCCAAGGAGCTGAAGAAAGTCATGGATCTGAGCATTGTACGGCTGCGCTTCTCAGCTTTCCTTCGAGCTAGCGATGGCTCCTTCTCCTTGCCCCTGAAGCCTGTGATCTCCCAGCCCATCCATGACAGCA agggcaatttattacttgccctacccatttaaccatatgtgtgcccacagAGTCCAATGCTGAGCGCCGAGAGCTTGAACAGGAGGCCAAGGAGCTGAAGAAAGTTATGGATTTGAGCATTGTACGGCTACGCTTCTCTGCTTTCCTTAGGGCCAGTGATGGTTCTTTCTCCTTACCCCTAAAGCCTGTAATCTCTCAACCAATCCATGATAGCAgtgagtctgcacaaacataagcgataagatttcaggtaaaagatcggttt #### Nfkb2_ID9837_15 --> 0 - 1 Original Alignment ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTGGCT------------------------------------------CTCCGGGCAGGT---GCTGCAGCCCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAG---------g ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACACGAA---TCTGCACTCCACCTGGCTCACACCTGTGAAAATTTCTTGCCATCTTGGACCTCTCAGGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGCTACACTCggtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from CESAR ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTGGCT------------------------------------------CTCCGGGCAGGTGCTGCA---GCCCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAG---------g ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACAC---GAATCTGCACTCCACCTGGCTCACACCTGTGAAAATTTCTTGCCATCTTGGACCTCTCAGGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGCTACACTCggtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from Spaln_aa2Genome ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTG GCTCTCCGGGCAGGT---GCTGCAGCCCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAG---------G ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACAC---GAATCTGCACTCCACCTGgctcacacctgtgaaaatttcttgccatcttggacctctcagGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGCTACACTCGgtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from Spaln_nt2Genome ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTG GCTCTCCGGGCAGGTGCTGCAGC---CCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAGG--------- ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACAC---GAATCTGCACTCCACCTGgctcacacctgtgaaaatttcttgccatcttggacctctcagGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGCTACACTCGgtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from Pairagon ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTGGCT------------------------------------------CTCCGGGCAGGTGCTGCA---GCCCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAGG--------- ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACACGAA---TCTGCACTCCACCTGGCTCACACCTGTGAAAATTTCTTGCCATCTTGGACCTCTCAGGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGCTACACTCGgtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from Exonerate_protein2genome ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTG GCTCTCCGGGCAGGT---GCTGCAGCCCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAGG ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACAC---GAATCTGCACTCCACCTGgctcacacctgtgaaaatttcttgccatcttggacctctcagGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGctacactcggtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from Exonerate_coding2genome ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTGGCTCTCCGGGCAGGTGCTGCAGCCCCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGA ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACAC---GAATCTGCACTCCACCTGGCTCACACCTGTGAAAATTTCTTGCCATCTTGGACCTCTCAGGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGtgaagcccatgctgtaccacatatacatatgcccgagtttgaggctacactcggtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag Alignment from GeneWise ACGCCTCTGCACCTGGCGGTAATCACTGGGCAGACAAGGGTGGTGAGCTTCCTGCTGCAGGTGGGTGCAGACCCCACGCTGCTGGATCGGCACGGAGACTCCGCCCTCCACTTGGCT------------------------------------------CTCCGGGCAGGTGCTGCAGCC---CCAGAGCTGTTGCAGGCACTGTTGCGCAGCGGAGCCCATGCTGTGCCCCAAATATTGCACATGCCTGATTTTGAG---------G ttgtaagcaaagagtgcaaggctatccctttttcttcttttcttctacagACCCCGCTGCACCTTGCTTTAATTACTGGGCAGAAAAGAGTGGTGAGCTTTCTGCTGCAGGTGGGTGTGGACCCCACACTACTGGAAAGACAC---GAATCTGCACTCCACCTGGCTCACACCTGTGAAAATTTCTTGCCATCTTGGACCTCTCAGGAGCTCAGGGCAGGAGCAGCAGCTGCCCCTGAGTTGTTGCAGGCTTTGTTACGCAGTGAAGCCCATGCTGTACCACATATA---CATATGCCCGAGTTTGAGGCTACACTCGgtgagtgctaaaagccatggcatgatgaatccagaagcctcagtagtcag #### Nfkb2_ID9840_18 --> 2 - 0 Original Alignment gtGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACCAAG cagttagagactataagtaatctttcaaaaactctattgtgtttttgcaggtGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACA---gttagtaggtacacggagtctgtgactgttccgaaaggactcaggtggtt Alignment from CESAR gtGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACCAAG cagttagagactataagtaatctttcaaaaactctattgtgtttttgcaggtGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACA---gttagtaggtacacggagtctgtgactgttccgaaaggactcaggtg Alignment from Spaln_aa2Genome GTGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACC cagttagagactataagtaatctttcaaaaactctattgtgtttttgcagGTGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACAgttagtaggtacacggagtctgtgactgttccgaaaggactcaggtggtt Alignment from Spaln_nt2Genome GTGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACC cagttagagactataagtaatctttcaaaaactctattgtgtttttgcagGTGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACAgttagtaggtacacggagtctgtgactgttccgaaaggactcaggtggtt Alignment from Pairagon GTGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACCAAGGTGAA cagttagagactataagtaatctttcaaaaactctattgtgtttttgcagGTGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTAC--------Agttagtaggtacacggagtctgtgactgttccgaaaggactcaggtggtt Alignment from Exonerate_protein2genome GTGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACC cagttagagactataagtaatctttcaaaaactctattgtgtttttgcagGTGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACAgttagtaggtacacggagtctgtgactgttccgaaaggactcaggtggtt Alignment from Exonerate_coding2genome GTGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACCAAGGTGAAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGA cagttagagactataagtaatctttcaaaaactctattgtgtttttgcagGTGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACAGTTAGTAGGTACACGGAGTCTGTGACTGTTCCGAAAGGACTCAGgtggtt Alignment from GeneWise GTGCTGACATCCATGCAGAGAATGAGGAGCCTCTGTGCCCGCTGCCCTCACCCTCGACCTCTGGGAGCGACTCCGACTCTGAAGGGCCTGAGAGGGATACCCAAAGAAACTTCCGAGGCCATACCCCTCTTGACCTCACTTGCAGTACC cagttagagactataagtaatctttcaaaaactctattgtgtttttgcagGTGCTGACACCCATACAGAGAATGAAGAGCCACTGTGTCCTTTGCCATCTCCCTCAACTTCTGGGAGTGACTCTGACTCTGAGGGGCCTGAAAGAGACACTCAAAGAACCTTCCACGGTCATACCCCTCTTGACCTCACTCGCAGTACAgttagtaggtacacggagtctgtgactgttccgaaaggactcaggtggtt #### Nfkb2_ID9841_19 --> 0 - 1 Original Alignment GTG---AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCA------g tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtagGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAggtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from CESAR GTGAAG---ACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCA------g tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtagGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAggtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from Spaln_aa2Genome GTGAAGACTCTGCTG---CTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAGGGCCAG tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtagGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAGgtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from Spaln_nt2Genome GTGAAGA---CTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTG------CAG tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtagGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAGgtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from Pairagon -------------------------------------------------------GAAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTG------CAG TGATAGTGACAGATACCTCCCCTTTAGGTACTCTGTTTTGTGAATTGTAGGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAGgtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from Exonerate_protein2genome GTG---AAGACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAGGGCCAG tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtagGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAGgtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from Exonerate_coding2genome tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtaggtaaaaaaaacactacttctaaacactgctcagaattccacagagccacccttggccccaccgaccccagtatcaccaggtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa Alignment from GeneWise GTGAAG---ACTCTGCTGCTAAATGCTGCTCAGAACACCACGGAGCCACCCCTGGCCCCACCCAGCCCTGCAGGGCCAG tgatagtgacagatacctcccctttaggtactctgttttgtgaattgtagGTAAAAAAAACACTACTTCTAAACACTGCTCAGAATTCCACAGAGCCACCCTTGGCCCCACCGACCCCAGTATCACCAGgtaaggctgcgtgccatggcctgcaggggagggattgagggcttttttaa #### Nfkb2_ID9842_20 --> 2 - 0 Original Alignment ggCCAGGGCTGTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG cttctgcacctaagcactgcccgtttctcttggtttctatgtgatgacagag---------TCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from CESAR ggCCAGGGCTGTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG aggtctaggcttctgcacctaagcatctcttggtttctatgtgatgacagag---------TCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from Spaln_aa2Genome TGTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG cttctgcacctaagcactgcccgtttctcttggtttctatgtgatgacagAGTCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from Spaln_nt2Genome -GTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG cttctgcacctaagcactgcccgtttctcttggtttctatgtgatgacagAGTCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from Pairagon GGCCAGGGCTGTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG cttctgcacctaagcactgcccgtttctcttggtttctatgtgatgacag---------AGTCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from Exonerate_protein2genome GGCCAGGGCTGTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG cttctgcacctaagcactgcccgtttctcttggtttctatgTGATGACAGAGTCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from Exonerate_coding2genome cttctgcacctaagcactgcccgtttctcttggtttctatgtgatgacagagtccctgggagatacagccctccaaaacttgcagcaactgttagatggtcctgaagcacaaggtagctgggcaaagctggctgagcgtctgggattgaggagcctggtggacacatacaggaaaactccatcttccagtggtagtctcctgcgtagctacaaggtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact Alignment from GeneWise GGCCAGGGCTGTCCCTGGGGGATGCAGCCCTGCAGAACCTGGAGCAACTGCTGGATGGTCCCGAAGCCCAGGGCAGCTGGGCAGAGCTGGCAGAGCGACTGGGGTTGAGAAGCCTGGTGGACACATACAGGAAGACCCCGTCTCCCAGCGGCAGTCTCCTTCGTAGTTACAAG cttctgcacctaagcactgcccgtttctcttggtttctatgtgatgacagAG---------TCCCTGGGAGATACAGCCCTCCAAAACTTGCAGCAACTGTTAGATGGTCCTGAAGCACAAGGTAGCTGGGCAAAGCTGGCTGAGCGTCTGGGATTGAGGAGCCTGGTGGACACATACAGGAAAACTCCATCTTCCAGTGGTAGTCTCCTGCGTAGCTACAAGgtgaggtaggtggactgctggggcctgaactactcttagtcttcagcact #### Npas4_ID776_5 --> 1 - 1 Original Alignment t------GTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGt gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagtAACGGCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGcgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from CESAR t------GTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGt gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagtAACGGCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGcgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from Spaln_aa2Genome T-------GTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGT gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagTAACGGCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGCgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from Spaln_nt2Genome T------GTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGT gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagTAACGGCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGCgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from Pairagon T------GTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGT gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagTAACGGCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGCgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from Exonerate_protein2genome TGTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGT gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagtaacggCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGCgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from Exonerate_coding2genome TGTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGT gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagtaacggCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGCgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata Alignment from GeneWise ----AGTGTCCTAATCTACCTGGGCTTTGAGCGCAGCGAACTGCTCTGTAAATCATGGTATGGACTGCTACACCCCGAGGACCTGGCCCAAGCTTCTTCTCAACACTACCGCCTGT gggagcaagaggctatatgcagtgtgaccagttttttaatctgtatttagTAACGGCGTCCTAATCTATCTTGGCTTTGAGCGCAGCAAACTGCTCTGTAAATCGTGGTATGGACTACTACACCCTGAGGACCTGGCCCAAGCATCTTCTCAACACTACCGCCTGCgtatgttttaatattgagtaggtcattgcagtaatctcataaattacata #### Npm3_ID9576_4 --> 0 - 1 Original Alignment CTCAGTGTGGATGATTTCCAACTCCAACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGCATCAGATCg gatacgtgtcttactaccgaccggtacttattattattttctcattgcag---------------------------CCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATC---------CATCACATTggtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca Alignment from CESAR CTCAGTGTGGATGATTTCCAACTCCAACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGCATCAGATCg tgatcgttgatacccattaaaaagtacttattattattttctcattgcag---------------------------CCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATC---------CATCACATTggtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca Alignment from Spaln_aa2Genome GTGTGGATGATTTCCAACTCCAACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGCATCAGATCG gatacgtgtcttactaccgaccggtacTTATTATTATTTTCTCATTGCAGCCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATC---------CATCACATTGgtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca Alignment from Spaln_nt2Genome AACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGCATCAGATCG gatacgtgtcttactaccgaccggtacttattattattttctcattgcag--CCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATC---------CATCACATTGgtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca Alignment from Pairagon CTCAGTGTGGATGATTTCCAACTCCAACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGCATCAGATCG gatacgtgtcttactaccgaccggtacttattattattttctcattgcag---------------------------CCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATC---------CATCACATTGgtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca Alignment from Exonerate_protein2genome CTCAGTGTGGATGATTTCCAACTCCAACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGC gatacgtgtcttactaccgaccgGTACTTATTATTATTTTCTCATTGCAGCCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATCCATCACATTGgtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCACTGGCCGGCATCAGATCG gatacgtgtcttactaccgaccggtacttattattattttctcattgcagCCACCAGTTTCCTTTCGATTGAGGTCAGGTTCAGGTCCAGTTCGAATC---------CATCACATTGgtaagtgggcagaattgtgtggactattatgcagtgagttgtcagcaaca #### Nrxn2_ID1761_12 --> 2 - 1 Original Alignment gtAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAG------g tgcatcagagacttcctgctgatttctctattttctcatttctttgtcaggtAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGTCAACggtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from CESAR gtAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAG------g tgcatcagagacttcctgctgatttctctattttctcatttctttgtcaggtAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGTCAACggtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from Spaln_aa2Genome GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAG------G tgcatcagagacttcctgctgatttctctattttctcatttctttgtcagGTAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGTCAACGgtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from Spaln_nt2Genome GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG------ tgcatcagagacttcctgctgatttctctattttctcatttctttgtcagGTAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGTCAACGgtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from Pairagon GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG------ tgcatcagagacttcctgctgatttctctattttctcatttctttgtcagGTAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGTCAACGgtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from Exonerate_protein2genome GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG tgcatcagagacttcctgctgatttctctattttctcatttctttgtcagGTAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGtcaacggtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from Exonerate_coding2genome GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAGG tgcatcagagacttcctgctgatttctctattttctcatttctttgtcagGTAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGtcaacggtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa Alignment from GeneWise GTAAAGGCCCCGAGACACTGTTTGCGGGGCACAAGCTGAATGACAATGAATGGCACACGGTGAGGGTGGTCCGGCGTGGCAAGAGCCTGCAGCTGTCCGTGGACAACGTGACTGTGGAG------G tgcatcagagacttcctgctgatttctctattttctcatttctttgtcagGTAAAGGTCCTGAAACACTGTTTGCAGGGCACAAACTAAATGACAATGAGTGGCACATGGTGAGGGTGGTCCAGCATGGCAAGAGCCTCCAGCTATTTGTTGACAATGTGACTGTGGAGGTCAACGgtgagaggctgagactgttcctgcctgggagtgctccaaagtctcattaa #### Nudt22_ID1971_4 --> 1 - 0 Original Alignment gTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcaggTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAA------gtatctcttagtgagcttagctctagttggcacctggattatttaaggct Alignment from CESAR gTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcaggTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAA------gtatctcttagtgagcttagctctagttggcacctggattattt Alignment from Spaln_aa2Genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcagGTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAAgtatctcttagtgagcttagctctagttggcacctggattatttaaggct Alignment from Spaln_nt2Genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcagGTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAAgtatctcttagtgagcttagctctagttggcacctggattatttaaggct Alignment from Pairagon GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcagGTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAAgtatctcttagtgagcttagctctagttggcacctggattatttaaggct Alignment from Exonerate_protein2genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcagGTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAAGTATCTcttagtgagcttagctctagttggcacctggattatttaaggct Alignment from Exonerate_coding2genome GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcagGTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTGGAAGTATCTcttagtgagcttagctctagttggcacctggattatttaaggct Alignment from GeneWise GTGCAGCTTGACTTCAGAGGAGGTCAGGAGTTATTACCTGAGTGGGGGACCTGAGGCCCACGAGTCTACAGGAATCATCTTTGTGGAGACACAG gattatgagaacgcaacactatcctagcggtcaaggtgcgcggtctgcagGTGCAGCTTGACTTCAGAGGAGGTCAGGAGCTATTACCTGAGTGGGGGACCTGAGGCCCACGAATCTACAGGAATCATCTTTGTG------GAAgtatctcttagtgagcttagctctagttggcacctggattatttaaggct #### Nudt8_ID268_3 --> 0 - 0 Original Alignment GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAG--------- attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGgtgagtggagcactttttggactaggggacttaggagtggatgcgtgtcc Alignment from CESAR GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAG--------- attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGgtgagtggagcactttttggactaggggacttaggagtggatgcgtgtcc Alignment from Spaln_aa2Genome GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAG--------- attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGgtgagtggagcactttttggactaggggacttaggagtggatgcgtgtcc Alignment from Spaln_nt2Genome GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAG--------- attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGgtgagtggagcactttttggactaggggacttaggagtggatgcgtgtcc Alignment from Pairagon GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAG--------- attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGgtgagtggagcactttttggactaggggacttaggagtggatgcgtgtcc Alignment from Exonerate_protein2genome GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAGGTGGATGAA attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGgtgagtggagcactttttggactaggggacttaggagtggatgcgtgtcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAAAAGGCAACCATAGTCCCAGTACTTGCCAACGTGGGCCCACTGGATCTGCAGAGCCTTAGGCCCAACCTTGAGGAG----------------------------------------------------------- attggcaacagacatctggacttgattgtaagaaacactttcttttccagGACAAGGCAAGCTTAGTCCCTGTTCTTGCAAATGTGGGCCCTTTGGATTTACAGAGCCTGAGGCCCAACCTTGAGGAGAGCCTGCTGGTGAGTGGAGCACTTTTTGGACTAGGGGACTTAGGAGTGGATGCGTGTCC #### Nxf1_ID2344_4 --> 0 - 0 Original Alignment ATTCCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttag---CCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc Alignment from CESAR ATTCCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG agcaaggaatctgaaaaaatagcatggttgggtctttggcttccttttag---CCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatg Alignment from Spaln_aa2Genome ATTCCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttag---CCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc Alignment from Spaln_nt2Genome CCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttagCCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc Alignment from Pairagon ATTCCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttag---CCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc Alignment from Exonerate_protein2genome CCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttagCCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc Alignment from Exonerate_coding2genome CCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttagCCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc Alignment from GeneWise CCTTATGGTAGAAAGTATGACAAAACGTGGCTTCTGAGCATGATTCAGAGCAAATGCAGTGTCCCCTTCAATCCCATCGAG aaggaatctgaaaaaatagcatcccggttgggtctttggcttccttttagCCCTATGGTAAAAAGCATGACAAAACTTGGCTTCTCAGCATGATTCAGAGTAAATGTAGTGTACCTTTCAACCCCATTGAGgtaagaacaatagagccagatttgagtagcttcgttcagtgaggagtatc #### Nxf1_ID2345_5 --> 0 - 0 Original Alignment TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATC---CAGGATCGAGAAAACAGAAGG--- ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGTTCgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from CESAR TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATC---CAGGATCGAGAAAACAGAAGG--- ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGTTCgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from Spaln_aa2Genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGAAGG--- ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGTTCgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from Spaln_nt2Genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGAAG ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGgttcgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from Pairagon TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGAAGG--- ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGTTCgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from Exonerate_protein2genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGAAGG ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGttcgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from Exonerate_coding2genome TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAG---ATCCAGGATCGAGAAAACAGAAGG ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGttcgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac Alignment from GeneWise TTTCACTATGAAAATACACGGGCCCATTTTTTTGTGGAGGATGCCACTACTGCTTCTGCATTAAAGGGTGTCAACCATAAGATC---CAGGATCGAGAAAACAGAAGGATA ttgagtagcttcgttcagtgaggagtatgtgttctttttccttcctctagTTTCACCATGAAAATACACGCAATCATTTCTTTGTAGAGGATGCAACTACTGGTTCCACATTAAAAGGTGTGAACCATCAGATCATCCAGGATCGAGAGAACAGACGGTTCgtaggcgcagccaaaattaaagaatggactggtcgtatcaacttttctac #### Nxf1_ID2352_12 --> 0 - 0 Original Alignment GATGGCCATGAGCTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaggtcattacaagttcactctgaatttagggggaatcgctttttcag---------CAGCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from CESAR GATGGCCATGAGCTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaagatgcccaggtcattacaagaatttagggggaatcgctttttcag---------CAGCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from Spaln_aa2Genome GATGGC---------CATGAGCTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaggtcattacaagttcactctgaatttagGGGGAATCGCTTTTTCAGCAGCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from Spaln_nt2Genome GCCAT GAGCTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG CCCAGgtcattacaagttcactctgaatttagggggaatcgctttttcagCAGCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from Pairagon GATGGCCATGAGCTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaggtcattacaagttcactctgaatttagggggaatcgctttttcag---------CAGCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from Exonerate_protein2genome GATGGCCATGAGCTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaggtcattacaagttcactctgaatttagggggaatcgCTTTTTCAGCAGCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from Exonerate_coding2genome CTACCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaggtcattacaagttcactctgaatttagggggaatcgctttttcagcagCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat Alignment from GeneWise ---CCCCCTCCAATTTCCTTTGATGTCGAAGCCCCTACAATGTTACCACCCTGCAAG cccaggtcattacaagttcactctgaatttagggggaatcgctttttcagcagCTACCCCCCCCAATTTCTTTTGATGTTGAAGCTCCTACAATGTTACCACCCTGTAAGgtaagtgttgggtgcactttagtaactcatgagaagagattgcagaacat #### Nxf1_ID2353_13 --> 0 - 2 Original Alignment GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAG------------ca atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACATATTTTTACcagtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat Alignment from CESAR GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAG------------ca atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACATATTTTTACcagtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat Alignment from Spaln_aa2Genome GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAGCAG----------- atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACATATTTTTACCAgtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat Alignment from Spaln_nt2Genome GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAG------------CA atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACATATTTTTACCAgtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat Alignment from Pairagon GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAG------------CA atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACATATTTTTACCAgtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat Alignment from Exonerate_protein2genome GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAGCA atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACatatttttaccagtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat Alignment from Exonerate_coding2genome GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCT atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagggatgcttctttggggccaagaatttgaaaagtctggtcatacacttcttgcaaacatatttttaccagtaagtgccccacatGATAGTCATTGCGGTAACAATGGGTTTATACATAT Alignment from GeneWise GGAAGCTATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAGCAGTACTATGTA-- atgagaagagattgcagaacatatgacttattcatatgagtttctcgtagGGATGCTTCTTTGGGGCCAAGAATTTGAAAAGTCTGGTCATACACTTCTTGCAAACATATTTTTACCAgtaagtgccccacatgatagtcattgcggtaacaatgggtttatacatat #### Nxf1_ID2354_14 --> 1 - 2 Original Alignment gTACTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCcg cggtaacaatgggtttatacatatcccctcaatgccgtttttatttccagg---TTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCaggtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from CESAR gTACTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCcg ttgcggtaacaatgggtttatacatccctcaatgccgtttttatttccagg---TTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCaggtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from Spaln_aa2Genome GTACTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCCG cggtaacaatgggtttatacatatcccctcaatgccgtttttatttccagG---TTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCAGgtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from Spaln_nt2Genome GTACTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCCG cggtaacaatgggtttatacatatcccctcaatgccgtttttatttccagG---TTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCAGgtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from Pairagon --------------------------------------------------CTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCCG CGGTAACAATGGGTTTATACATATCCCCTCAATGCCGTTTTTATTTCCAGGTTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCAGgtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from Exonerate_protein2genome GTACTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCCG cggtaacaatgggtttatacatatcccctcaatgccgtttttatttccagG---TTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCAGgtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from Exonerate_coding2genome TATTTTGGAACCGAGAACCTAAAGAGTCTGGTCCTGCGCTTCTTGCAGCAGTACTATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCCG CGGTAACAATGGGTTTATACATATCCCCTCAATGCCGTTTTTATTTCCAGG---TTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCAGgtgagagcacatctattactctatttggtattgtaaaactacctgcaatc Alignment from GeneWise ---------------------------------------------------TATGTAATTTATGACTCAGGAGACCGCCAGGGTCTCCTGTATGCCTACCATGATGGCGCCTGTTGCTCGCTAAGCATTCCTTACAACCCTCAGAATCCTGTCCG GTAACAATGG--GTTTATACATATCCCCTCAATGCCGTTTTTATTTCCAGGTTTGTCATTTGTGACCTGGGAGACCGTCAGGGTCTCCAGCATGCCTACCATGATGGTGCTTGTTGCTCTCTAAGCATCCCATACAACCCTCAAAACCCTGTCAGgtgagagcacatctattactctatttggtattgtaaaactacctgcaatc #### Nxf1_ID2358_18 --> 2 - 2 Original Alignment tgGATGGGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAgg ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagta------AAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGgggtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from CESAR tgGATGGGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAgg ccgtaactcttttgcacctcaaggctgttgccatcttttcttcctttcagta------AAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGgggtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from Spaln_aa2Genome TGGATGGGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAGG ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagTA------AAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGGGgtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from Spaln_nt2Genome GGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAGG ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagTAAAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGGGgtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from Pairagon TGGATGGGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAGG ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagT------AAAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGGGgtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from Exonerate_protein2genome GGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAGG ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagTAAAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGGGgtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from Exonerate_coding2genome GGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAGG ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagTAAAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGGGgtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt Alignment from GeneWise GGAAGTCTCGAGATTCTTTACGTGCTTTCACAAGAACGTTCATTGCTGTTCCTGCCAGCAATTCAGG ctcttttgcacctcaaggcactgtgtgttgccatcttttcttcctttcagTAAAGTTTCGAGATTCTTTACATGCCTATGCCAGGACATTCATTGCAGTTCCTGCAAGTAATACGGGgtaaggagatctgattgattaacaatgagaggaatggaggacagaacagt #### Opalin_ID8090_5 --> 0 - 0 Original Alignment GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG--------- atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCCA---ATATCTGAGCACAACCTTgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata Alignment from CESAR GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG--------- atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCCA---ATATCTGAGCACAACCTTgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata Alignment from Spaln_aa2Genome GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG--------- atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCCA---ATATCTGAGCACAACCTTgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata Alignment from Spaln_nt2Genome GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGA atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCC---AATATCTGAgcacaaccttgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata Alignment from Pairagon GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG----------------------------- atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCC---AATATCTGAGCACAACCTTGTAATAGTATGTGACAGCTTgtaagtactgatatgcctgtgagacaaata Alignment from Exonerate_protein2genome GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAGAAT atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCCAATATCTGAGCACAACcttgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata Alignment from Exonerate_coding2genome GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAGAAT atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCCAATATCTGAGCACAACcttgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata Alignment from GeneWise GAGACTGAGATACCATGTGAAATTTCAGAACTCTATGACAATCCCAAAATATCTGAG--------- atacatatgagtatcactcttttggatatgaaattcccttccctccgcagGAGACTGAGATACCATGTGAAATTTCAGAGCTCTTTGACAATCCA---ATATCTGAGCACAACCTTgtaatagtatgtgacagcttgtaagtactgatatgcctgtgagacaaata #### Osbp_ID3347_6 --> 1 - 0 Original Alignment aCGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAACAG gacctagaatcctgggtatagttcttattctgccctctgctttccttcagaCGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAG---gtatagagactacatcctcccgaggtgtgttatgtcctggtaacccttta Alignment from CESAR aCGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAACAG gacctagaatcctgggtatagttcttattctgccctctgctttccttcagaCGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAG---gtatagagactacatcctcccgaggtgtgttatgtcctggtaaccct Alignment from Spaln_aa2Genome ACGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAA gacctagaatcctgggtatagttcttattctgccctctgctttccttcagACGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAGgtatagagactacatcctcccgaggtgtgttatgtcctggtaacccttta Alignment from Spaln_nt2Genome ACGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGA------------ACAGTACA---AG gacctagaatcctgggtatagttcttattctgccctctgctttccttcagACGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAGGTATAGAGACTACATCCTCCCGAGgtgtgttatgtcctggtaacccttta Alignment from Pairagon ACGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAA gacctagaatcctgggtatagttcttattctgccctctgctttccttcagACGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAGgtatagagactacatcctcccgaggtgtgttatgtcctggtaacccttta Alignment from Exonerate_protein2genome ACGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAA gacctagaatcctgggtatagttcttattctgccctctgctttccttcagACGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAGgtatagagactacatcctcccgaggtgtgttatgtcctggtaacccttta Alignment from Exonerate_coding2genome ACGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAA gacctagaatcctgggtatagttcttattctgccctctgctttccttcagACGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGATGAGgtatagagactacatcctcccgaggtgtgttatgtcctggtaacccttta Alignment from GeneWise ACGTACTGGCAGCAATATCAGTGGGGCCAGCAGTGATGTCAGCCTTGATGAACAG gacctagaatcctgggtatagttcttattctgccctctgctttccttcagACGTACTGGCAGCAATATCAGTGGGCCCAGCAGTGATGTCAGCCTTGAT---GAGgtatagagactacatcctcccgaggtgtgttatgtcctggtaacccttta #### Otub1_ID2060_6 --> 0 - 0 Original Alignment TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG ttgtcataccatgcaaggctcagtgacgagctgacagcatgtgtgctcag---------------GAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAA---------------AGTCAGGAGgtatttcctcccccagcacctgtactgaggccccccttttttttcttggt Alignment from CESAR TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG gaccatctccatactttgtcataccacgagctgacagcatgtgtgctcag---------------GAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGT---------------CAGGAGgtatttcctcccccagcacctgtactgaggccccccttttttttcttggt Alignment from Spaln_aa2Genome TGGACCTTATC---------GAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG ttgtcataccatgcaaggctcagtgacgagCTGACAGCATGTGTGCTCAGGAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTATTTCCTCCCCCAgcacctgtactgaggccccccttttttttcttggt Alignment from Spaln_nt2Genome TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAG gtcataccatgcaaggctcagtgacgagctgacag--CATGTGTGCTCAGGAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAA---GTCAGGAGgtatttcctcccccagcacctgtactgaggccccccttttttttcttggt Alignment from Pairagon TTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTG ttgtcataccatgcaaggctcagtgacgagctgacagcatgtgtgctcag---------------GAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGgtcaaagtcaggaggtatttcctcccccagcacctgtactgaggccccccttttttttcttggt Alignment from Exonerate_protein2genome GAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG ttgtcataccatgcaaggctcagtgacgagctgacagcatgtgtgctcagGAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTATTTCCTCCCCCAgcacctgtactgaggccccccttttttttcttggt Alignment from Exonerate_coding2genome GAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG ttgtcataccatgcaaggctcagtgacgagctgacagcatgtgtgctcagGAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGTCAGGAGGTATTTCCTCCCCCAgcacctgtactgaggccccccttttttttcttggt Alignment from GeneWise --------ATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTACAGCGGGAGAGCAAGTTCTTCGAGCACTTCATCGAGGGTGGCCGGACTGTTAAGGAGTTCTGCCAGCAG ttgtcataccatgcaaggctcagtgacgagCTGACAGCATGTGTGCTCAGGAGCGTGTGGAGAAGAAGACCTCTGTCACTGACCTGCTAGCTTCCTTCAATGACCAAAGTACATCAGACTACCTGGTGGTCTACCTGCAGCTGTTAACCTCAGGCTATGTACAACGAAAAAGCAAGTTCTTTGAACACTACATTGAGGGTGGTCAAAGT---------------CAGGAGgtatttcctcccccagcacctgtactgaggccccccttttttttcttggt #### Pacs1_ID881_13 --> 1 - 0 Original Alignment cAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG gttggcttctgtctgcttcccttatctcagtgttttttgttcttcctcagt------GAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc Alignment from CESAR cAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG tttgtagttggcttctgtctgcttcctcagtgttttttgttcttcctcagt------GAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc Alignment from Spaln_aa2Genome CAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG gttggcttctgtctgcttcccttatctcagtgttttttgttcttcctcagT------GAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc Alignment from Spaln_nt2Genome CAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG gttggcttctgtctgcttcccttatctcagtgttttttgttcttcctcag------TGAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc Alignment from Pairagon ---------------------------------------------------GAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG GTTGGCTTCTGTCTGCTTCCCTTATCTCAGTGTTTTTTGTTCTTCCTCAGTGAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc Alignment from Exonerate_protein2genome GGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG gttggcttctgtctgcttcccttatctcagtgttttttgttcttcctcagTGAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CAAGGTGGAAGGGACACACACACCTCGGCAGAAGAGGAGCACTCCCCTGAAGGAGCGACAGCTCTCCAAGCCCCTGAGTGAGAGAACCAACAGCTCTGACAGTGAGCGATCTCCTGATCTGGGCCACAGCACACAG gttggcttctgtctgcttcccttatctcagtgttttttgttcttcctcagT------GAAGGGACACACACACCTCCACAGAAAAGAAGCACACCCCTTAAGGAGCGACAACTTCTAAAACCCCTGAGTGAGCGAACTAATAGTGCTGACAGTGAGAAGTCACCTGATCTGGGCCACAGCATACAGgtgggggtgtctcatctgtatggtaaggaccagggaggaggggttgatgc #### Patl1_ID3327_12 --> 2 - 0 Original Alignment tgCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagtg---------GGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from CESAR tgCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT gatggacccagatcaaaggttaggagtgaacactaaacaccttgtttcagtg---------GGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from Spaln_aa2Genome TGCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagTG---------GGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from Spaln_nt2Genome AGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagTGGGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from Pairagon TGCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagT---------GGGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from Exonerate_protein2genome AGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagTGGGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from Exonerate_coding2genome AGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagTGGGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc Alignment from GeneWise TGCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGAT agatcaaaggttaggagtttgacctgtgaacactaaacaccttgtttcagTG---------GGCTCATTGGGGAAACTTACTGTCTCCAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTAGAAGCGAGGATGATgtgtgtttgagggcagtgtttacgggcagttactatagcaaaatccatcc #### Pcgf6_ID10083_4 --> 1 - 1 Original Alignment gTTGGACCGGCAGTTACAAGACATAGTATACAAATTAGTGATCAATCTAGAGGAAa tgccatacatgctcaataccgagtcctaactttgttcatctctctaacagg------------------GACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGagtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from CESAR gTTGGACCGGCAGTTACAAGACATAGTATACAAATTAGTGATCAATCTAGAGGAAa gtgccaaaagaaacagcttgccatactaactttgttcatctctctaacagg------------------GACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGagtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from Spaln_aa2Genome ACAAGACATAGTATACAAATTAGTGATCAATCTAGAGGAAA tgccatacatgctcaataccgagtcctaactttgttcatctctctaacagG---GACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGAgtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from Spaln_nt2Genome AGACATAGTATACAAATTAGTGATCAATCTAGAGGAAA tgccatacatgctcaataccgagtcctaactttgttcatctctctaacagGGACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGAgtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from Pairagon GTTGGACCGGCAGTTACAAGACATAGTATACAAATTAGTGATCAATCTAGAGGAAA tgccatacatgctcaataccgagtcctaactttgttcatctctctaacagG------------------GACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGAgtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from Exonerate_protein2genome GTTGGACCGGCAGTTACAAGACATAGTATACAAATTAGTGATCAATCTAGAGGAAA tgccatacatgctcaataccgagtcctaacttTGTTCATCTCTCTAACAGGGACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGAgtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from Exonerate_coding2genome GTTGGACCGGCAGTTACAAGACATAGTATACAAATTAGTGATCAATCTAGAGGAAA tgccatacatgctcaataccgagtcctaacttTGTTCATCTCTCTAACAGGGACATAGTATACAAGTTAGTGATTGTTCTAGAGGAGAgtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc Alignment from GeneWise tgccatacatgctcaataccgagtcctaactttgttcatctctctaacagggacatagtatacaagttagtgattgttctagaggagagtgtgtatgagttatcccacagctgtcagtccaaaagactgaatacaccc #### Pcnxl3_ID1161_32 --> 0 - 2 Original Alignment ---GTAAACCGAGAGTGTGTGCGTGGGCTGTGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGag acctaagatgtattgatgtccctcctcatgttctcattttcattacccagACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTCC---GATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAAcagtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from CESAR ---GTAAACCGAGAGTGTGTGCGTGGGCTGTGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGag acctaagatgtattgatgtccctcctcatgttctcattttcattacccagACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTCC---GATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAAcagtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from Spaln_aa2Genome ---GTAAACCGAGAGTGTGTGCGTGGGCTGTGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGA acctaagatgtattgatgtccctcctcatgttctcattttcattacccagACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTCC---GATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAACAgtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from Spaln_nt2Genome GTAAACCGAGAGTGTGTGCGTGGGCTG---TGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGAG acctaagatgtattgatgtccctcctcatgttctcattttcattacccagACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTC---CGATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAACAgtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from Pairagon -----------------------------------------------------GTAAACCGAGAGTGTGTGCGTGGGCTGTGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGAG ACCTAAGATGTATTGATGTCCCTCCTCATGTTCTCATTTTCATTACCCAGACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTC---CGATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAACAgtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from Exonerate_protein2genome ---GTAAACCGAGAGTGTGTGCGTGGGCTGTGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGAG acctaagatgtattgatgtccctcctcatgttctcattttcattacccagACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTCC---GATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAACAgtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from Exonerate_coding2genome acctaagatgtattgatgtccctcctcatgttctcattttcattacccagactgtaaactgggaatgtgtacaaggtctgtgggctgggcagcaacaagagctagtctttttgtgcaatcgcaaccctgagcggggtagtgtccagaatgcccagcaggcaatctgcaacaagattaattcttccgatcgaccactaggatatccaacctttgtctcacctttgactacacctttgcctgggacacatccccaactacaagcactgtggggtggacctgttagcttgggtgccattgcacgatggcttttacatcactgggaacagtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa Alignment from GeneWise ---GTAAACCGAGAGTGTGTGCGTGGGCTGTGGGCTGGGCAGCAACAAGAGCTGGTGTTCCTGCGCAACCGCAACCCTGAGCGCGGCAGCATCCAGAATGCCAAGCAGGCACTCCGCAACATGATCAATTCCTCCTGCGACCAGCCACTGGGATATCCCATCTACGTGTCACCTCTTACCACATCTCTGGCTGGTAGCCACCCCCAACTGCGGGCGCTGTGGGGTGGTCCTGTCAGCCTGGGTGCCATTGCCCGATGGCTCTTGCGCAGCTGGGAGAG acctaagatgtattgatgtccctcctcatgttctcattttcattacccagACTGTAAACTGGGAATGTGTACAAGGTCTGTGGGCTGGGCAGCAACAAGAGCTAGTCTTTTTGTGCAATCGCAACCCTGAGCGGGGTAGTGTCCAGAATGCCCAGCAGGCAATCTGCAACAAGATTAATTCTTCC---GATCGACCACTAGGATATCCAACCTTTGTCTCACCTTTGACTACACCTTTGCCTGGGACACATCCCCAACTACAAGCACTGTGGGGTGGACCTGTTAGCTTGGGTGCCATTGCACGATGGCTTTTACATCACTGGGAACAgtaagttctaatagggctggctttggttcacatagtccccaaactgtaaa #### Pcnxl3_ID1163_30 --> 1 - 0 Original Alignment c---------------------------CTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT------CACCAG cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagcGCTCCCTGTGATCCCACCTTCATCCTTTTAGAGCCCTTCCTCTATGACCTACGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCCCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATCAGgtaagtataattaatgcagtgtaggagcaggtgtttcctttaccttggac Alignment from CESAR agcctggttaccaggcttcatactaccaatgaccaaccctgcatcaaaaga Alignment from Spaln_aa2Genome AGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT------CACCAG cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagcgctccctgtgatcccaccttcatccttttagAGCCCTTCCTCTATGACCTACGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCCCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATCAGgtaagtataattaatgcagtgtaggagcaggtgtttcctttaccttggac Alignment from Spaln_nt2Genome CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTTCACCA------G cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagcgctccctgtgatcccaccttcatccttttag-----AGCCCTTCCTCTATGACCTACGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCCCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATCAGgtaagtataattaatgcagtgtaggagcaggtgtttcctttaccttggac Alignment from Pairagon CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTTCAC----------------------------------------------------------- cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagcgctccctgtgatcccaccttcatccttttag-----AGCCCTTCCTCTATGACCTACGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCCCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATCAGGTAAGTATAATTAATGCAGTGTAGGAGCAGGTGTTTCCTTTACCTTGGAC Alignment from Exonerate_protein2genome CCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT------CACCAG cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagcgctccctgtgatcccaccttcatcctTTTAGAGCCCTTCCTCTATGACCTACGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCCCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATCAGgtaagtataattaatgcagtgtaggagcaggtgtttcctttaccttggac Alignment from Exonerate_coding2genome cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagcgctccctgtgatcccaccttcatccttttagagcccttcctctatgacctacgagctctgtttaagggagatttcaggatcacctccccccgtgatgagtgggacatagatttattgcaccaggttgtggcaccaggggtacgtatggccctaaagcttcatcatcatcaggtaagtataattaatgcagtgtaggagcaggtgtttcctttaccttggac Alignment from GeneWise -------------------------AGCCTGGAGCCCTTCCTCTATGGCCTGCACGCCCTGTTCAAGGGGGACTTCCGCATCACCTCTCCCCGTGACGAGTGGGTCTTTGCCGACATGGATCTGCTTCACCGAGTGGTAGCCCCTGGGGTTCGCATGGCCCTCAAGCTT------CACCAG cctcaatgatcctttgaaatggagaagctgacttgtcttcatcataacagCGCTCCCTGTGATCCCACCTTCATCCTTTTAGAGCCCTTCCTCTATGACCTACGAGCTCTGTTTAAGGGAGATTTCAGGATCACCTCCCCCCGTGATGAGTGG---------GACATAGATTTATTGCACCAGGTTGTGGCACCAGGGGTACGTATGGCCCTAAAGCTTCATCATCATCAGgtaagtataattaatgcagtgtaggagcaggtgtttcctttaccttggac #### Pcnxl3_ID1164_29 --> 0 - 2 Original Alignment CCCGTGGACCAGGACTGGAATTCACCGTTGGTTACACTGTGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCag tctgtggtgctcctgggctctttagtaatcctttttccacctcttactag---------------------------------------TGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCaggtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from CESAR CCCGTGGACCAGGACTGGAATTCACCGTTGGTTACACTGTGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCag agggatgttaccctgggctctttagtaatcctttttccacctcttactag---------------------------------------TGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCaggtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from Spaln_aa2Genome TGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCAG tctgtggtgctcctgggctctttagtaatcctttttccacctcttactagTGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCAGgtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from Spaln_nt2Genome TGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCAG tctgtggtgctcctgggctctttagtaatcctttttccacctcttactagTGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCAGgtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from Pairagon CCCGTGGACCAGGACTGGAATTCACCGTTGGTTACACTGTGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCAG tctgtggtgctcctgggctctttagtaatcctttttccacctcttactag---------------------------------------TGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCAGgtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from Exonerate_protein2genome GTGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCAG tctgtggtgctcctgggctctttagtaatcctttttccacctcttactaGTGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCAGgtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from Exonerate_coding2genome tctgtggtgctcctgggctctttagtaatcctttttccacctcttactagtgctttggcttgtgtgtgttgggtcgccgggctctgggcacagcagcgcacagcatgtcagccaggtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact Alignment from GeneWise TGCTTTGGCCTGTGTGTGCTGGGTCGCCGGGCCCTGGGAACAGCGTCACACAGTATGTCTGCCAG tctgtggtgctcctgggctctttagtaatcctttttccacctcttactagTGCTTTGGCTTGTGTGTGTTGGGTCGCCGGGCTCTGGGCACAGCAGCGCACAGCATGTCAGCCAGgtgagagcctgcaggcagctaaagaagacccaacaacccattagtagact #### Pcnxl3_ID1179_14 --> 0 - 1 Original Alignment ------GGCCACAACTGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTg tgTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagCTCCTTGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTggtgggtcacctcaagatattttgatttgttcttatgacagtaTTCACCTT Alignment from CESAR ------GGCCACAACTGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTg tgTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagCTCCTTGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTggtgggtcacctcaagataccaagcacttgtgcatacccagtaTTCACCTT Alignment from Spaln_aa2Genome GGCCACAAC------TGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTG TGTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagCTCCTTGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTGgtgggtcacctcaagatattttgatttgttcttatgacagTATTCACCTT Alignment from Spaln_nt2Genome ------GGCCACAACTGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTG TGTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagCTCCTTGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTGgtgggtcacctcaagatattttgatttgttcttatgacagTATTCACCTT Alignment from Pairagon ------GGCCACAACTGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTG TGTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagCTCCTTGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTGgtgggtcacctcaagatattttgatttgttcttatgacagTATTCACCTT Alignment from Exonerate_protein2genome GGCCACAACTGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTG TGTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagctccttGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTGgtgggtcacctcaagatattttgatttgttcttatgacagTATTCACCTT Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ------GGCCACAACTGGGTGATTGCATACAGCCGGCCTGTCTACTTCTGTATCTGCTGTCTACTCATCTGGCTGCTGGATGCCCTGGGGACCGCTCAGCCCTTCCCACCTGTCTCTCTGTACGGCCTCACACTCTTCTCTGCCTCTTTCTTCTTTTGTGCCCGAGATGTGGCCACTG TGTTCACCTT caataacttatagttgcttggcctatgaatgaaaaatctcttccctttagCTCCTTGGTCACAACTGGGTGATTGCATACAGCCGTCCTGTTTACTTTTGTATTTGTTGCCTGCTCATCTGGTTGCTGGATGCACTTGGGACAACTCAACCCTTCCCACCTGTCTCTCTGTATGGTCTAACCCTCTTTTCTGCCTCGTTCTTCTTTTGTGCACGAGATGTGGCAACTGgtgggtcacctcaagatattttgatttgttcttatgacagTATTCACCTT #### Pcnxl3_ID1181_12 --> 1 - 0 Original Alignment gACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTCAAG ttctataggcattttaggaaacatagtacatatttgtccttcctctgcaggACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTC---gtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc Alignment from CESAR gACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTCAAG ttctataggcattttaggaaacatagtacatatttgtccttcctctgcaggACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTC---gtatgtcctactgggttctcagttttagaacagtagcctgcttgcta Alignment from Spaln_aa2Genome GACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTC ttctataggcattttaggaaacatagtacatatttgtccttcctctgcagGACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTCgtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc Alignment from Spaln_nt2Genome GACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTC ttctataggcattttaggaaacatagtacatatttgtccttcctctgcagGACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGAT---TATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTCgtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc Alignment from Pairagon GACACGTGG---GGTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTC ttctataggcattttaggaaacatagtacatatttgtccttcctctgcagGACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTCgtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc Alignment from Exonerate_protein2genome GACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTC ttctataggcattttaggaaacatagtacatatttgtccttcctctgcagGACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTCgtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc Alignment from Exonerate_coding2genome GACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTC ttctataggcattttaggaaacatagtacatatttgtccttcctctgcagGACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTCgtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc Alignment from GeneWise GACACGTGGG---GTAATGGAGAACATTTTCGGTGTTGGATTGAGCAGCCTGGTTGCCTTCCTGGGATACCTGTTGCTGCTCAAGGGCTTCTTCACTGACATCTGGGTCTTCCAGTTCTGTCTGGTCATCGCCTCCTGTCAGTACTCCCTGCTC ttctataggcattttaggaaacatagtacatatttgtccttcctctgcagGACACGTGGTCTAGTAATGGAGAATATTTTTGGTGTAGGGGTGAGTACCCTACTTGCTATCCTTGGGTACCTGTTGCTCCTAAAGGGATTCATCACAGAGATT---ATCTTTCAGTTTTGTCTGGTCATTGCTTCTTGTCAGTATTTTCTGCTCgtatgtcctactgggttctcagttttagaacagtagcctgcttgctatcc #### Pcx_ID553_3 --> 2 - 0 Original Alignment gtGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggaggggggttgcttcttctgtctccccaggtGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATC---------------gtacttaccaattacttcaaacctttgaacctttacaggatagagttttt Alignment from CESAR gtGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggaggggggttgcttcttctgtctccccaggtGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATC---------------gtacttaccaattacttcaaacctttgaaccttta Alignment from Spaln_aa2Genome GTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATC tggtggttcctatccccaggggaggggggttgcttcttctgtctccccagGTGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATCgtacttaccaattacttcaaacctttgaacctttacaggatagagttttt Alignment from Spaln_nt2Genome GTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATC ATCAAGG tggtggttcctatccccaggggaggggggttgcttcttctgtctccccagGTGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATCgtacttaccaattacttcaaacctttgaacctttacaggatagAGTTTTT Alignment from Pairagon GTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATC tggtggttcctatccccaggggaggggggttgcttcttctgtctccccagGTGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATCgtacttaccaattacttcaaacctttgaacctttacaggatagagttttt Alignment from Exonerate_protein2genome GTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggaggggggttgcttcttctgtctccccagGTGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATCGTACTTACCAATTACttcaaacctttgaacctttacaggatagagttttt Alignment from Exonerate_coding2genome GTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATCATCAAGGTGGCCAAG tggtggttcctatccccaggggaggggggttgcttcttctgtctccccagGTGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATCGTACTTACCAATTACttcaaacctttgaacctttacaggatagagttttt Alignment from GeneWise GTGAGATTGCCATCCGAGTGTTTCGTGCGTGCACAGAGCTGGGTATCCGCACAGTGGCTGTCTACTCGGAGCAGGACACAGGGCAGATGCACAGGCAGAAAGCTGATGAAGCCTACCTTATTGGCCGTGGCCTGGCACCTGTGCAGGCCTACCTGCACATTCCAGACATC tggtggttcctatccccaggggaggggggttgcttcttctgtctccccagGTGAGATTGCTATCCGCGTCTTTCGTGCATGCAGAGAACTTGGCATCCGCACAGTAGCTGTGTATTCGGAACAGGATACAGGGCTAACGCACAGGCAGAAAACAGATGAGGGTTACCTTCTTGGTCGTGGCCTGGCACCTGTCCAAACCTATTTGCACATTCCAGACATCgtacttaccaattacttcaaacctttgaacctttacaggatagagttttt #### Pcx_ID555_5 --> 2 - 0 Original Alignment gcGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG--- aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctaggtGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from CESAR gcGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG--- aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctaggtGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from Spaln_aa2Genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGAG aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from Spaln_nt2Genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGA- aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from Pairagon GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAG--- aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from Exonerate_protein2genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGAG aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from Exonerate_coding2genome GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGAG aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag Alignment from GeneWise GCGTTCCAGTGGTCCCCGGCACGGACTCCCCCATCAGCTCCCTGCACGAGGCGCATGAGTTCTCCAACACCTACGGCTTCCCTATTATCTTCAAGGCCGCCTACGGAGGTGGGGGCCGCGGCATGCGGGTCGTGCATAGCTATGAGGAG aacttgaaccagaagtacaggtgttttggtctctgtttgcttttccctagGTGCCCCGGTAGTTCCTGGAACAGAGTCCCCCATCAGCTCCCTATATGAAGCCCATGAGTTCTCCAACACCTATGATCCTCCCTTTATTTTCAATGCAGCTTATGGAGATGGAGGTCATGATATGAGGGTTGTGCAGAGCTATGAGGATgtgtgtggggcagcatagggtaaggtggtcatggcagggccagtctttag #### Pcx_ID567_16 --> 2 - 0 Original Alignment ag---GTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagctCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTAT------TTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGT------AGACTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttttc Alignment from CESAR ag---GTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagctCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTAT------TTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGTAGA------CTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttgct Alignment from Spaln_aa2Genome AG---GTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagCTCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTAT------TTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGT------AGACTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttttc Alignment from Spaln_nt2Genome A---GGTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagCTCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTA------TTTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGTA------GACTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttttc Alignment from Pairagon ---AGGTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCAT------------------------------------------------------ ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagCTCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTA------TTTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGTA------GACTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAGTAGGATAAATTGCCAGGTACTTCTCTGGTGCACTTGCAGAAGCCTTTTC Alignment from Exonerate_protein2genome AG---GTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagCTCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTAT------TTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGTAGA------CTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttttc Alignment from Exonerate_coding2genome AG---GTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagCTCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTAT------TTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGTAGA------CTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttttc Alignment from GeneWise --GAGGTACCCCTGGAGCGTGTGTTTGACTACAGTGAGTACTGGGAAGGGGCTCGGGGACTGTACGCAGCCTTCGATTGCACGGCTACCATGAAGTCTGGCAACTCCGACGTGTATGAGAATGAGATTCCAGGGGGCCAGTACACCAACCTGCACTTCCAGGCCCATAGCATGGGGCTTGGCTCCAAGTTCAAGGAGGTCAAGAAGGCCTATGTGGAGGCTAACCAGATGCTGGGGGACCTCATCAAG ttgttcccctttcaactacttttgtacagtgctttgtgctgtatctccagCTCTGTTGCCGCTGGAACGAGTATTTGACTATAGTGGGTACTGGGAAGGTTCTAGGGGGTTGTAT------TTTGATTGCATTGCCTCTATGAAAGCTGGTAACTTGGATCTATACAAGAATGAGGTACCAGGTGGACAATACACCAATCAGCATTTCCCAGCCCGTAGA------CTTGGTTCAAAGTTCAAAGCAGTTAAGAAAGCTTATGTGGAGGCTAATCAAATGCTGGGGGACCTTATTGAAgtaggataaattgccaggtacttctctggtgcacttgcagaagccttttc #### Pcx_ID569_18 --> 0 - 0 Original Alignment GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAGTTTGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCCATAT------ACCCAATTCAAAGACTTCACAGCTACTTTCAGC---CTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAAGAA------gtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from CESAR GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAGTTTGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCCA------TATACCCAATTCAAAGACTTCACAGCTACTTTCAGC---CTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAA------GAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from Spaln_aa2Genome GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCCA------TATACCCAATTCAAAGACTTCACAGCTACTTTC---AGCCTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAAGAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from Spaln_nt2Genome GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCC------ATATACCCAATTCAAAGACTTCACAGCTACTTTCAG---CCTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAAGAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from Pairagon GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCC------ATATACCCAATTCAAAGACTTCACAGCTACTTTCAGCCTTC---ATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAAGAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from Exonerate_protein2genome GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCCA------TATACCCAATTCAAAGACTTCACAGCTACTTTCAGC---CTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAAGAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from Exonerate_coding2genome GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCCA------TATACCCAATTCAAAGACTTCACAGCTACTTTCAGC---CTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAAGAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta Alignment from GeneWise GTGCTAAAGGACCTGCCAAGAATAGAGGGGCGGCCTGGAGCCTCCCTCCCTCCCCTGAACCTGAAGGAGCTGGAGAAGGACCTGATTGATAGGCATGGGGAGGAGGTGACCCCAGAGGACGTCCTCTCTGCAGCCATGTACCCTGATGTCTTTGCTCAATTCAAAGACTTCACGGCTACCTTCGGCCCCCTGGATAGCCTTAATACTCGTCTCTTTCTTCAAGGACCCAAAATTGCAGAGGAGTTTGAG aggttgatgtgggtgtaaatcagtctttctgtggtggatgtgtttttcagGTGCTAAAGGACCTCCCAAGAATTGAAGGAAGGCCAGGAGCCTCGTTACCTCCCTTGAACCTGGAGGAGTTGGATAAGGGTCTGATTGATAGACATGGTGAAGATGTTTCACAAGAGGAAGTGCTCTCTGCAGCTATGTACCCA------TATACCCAATTCAAAGACTTCACAGCTACTTTCAGC---CTTCATAGCCTAAATACAAGTCTATTTCTTCAAGGACCCAAAATTGCAGAA------GAAgtaagtcctagcggtttctatgcctatgtctacactctccatggggctta #### Pcx_ID570_19 --> 0 - 0 Original Alignment GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATGAAG GAGATGCA gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATG---gtacatagaccaagtttgattctgtttgaaactctcttacagGAAATGCA Alignment from CESAR GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATGAAG GAGAT gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATG---gtacatagaccaagtttttgatccccctaccactccccgcagGAAAT Alignment from Spaln_aa2Genome GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATG AAGGAGAT gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATGgtacatagaccaagtttgattctgtttgaaactctcttacag---GAAAT Alignment from Spaln_nt2Genome GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATG AAGGAGATGC gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATGgtacatagaccaagtttgattctgtttgaaactctcttacAGGAAATGCA Alignment from Pairagon GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATGA---------------------------------------AGGAGATGCA gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATGGTACATAGACCAAGTTTGATTCTGTTTGAAACTCTCTTACAGGAAATGCA Alignment from Exonerate_protein2genome GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATGAAG GAGAT gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATG---gtacatagaccaagtttgattctgtttgaaactctcttacagGAAAT Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTTGAGCTGGAACGGGGCAAGACCCTGCACATCAAAGCCCTGGCTGTAAGCGACCTGAACCGTGCTGGCCAGAGGCAGGTGTTCTTTGAACTCAATGGGCAGCTTCGATCCATTCTGGTTAAAGACACCCAGGCCATG---------------------------------------AAGGAGATGCA gaacatcatgcacccaattttgaaggagagctcaactgtatttctcccagGTTAAGCTAGAACAAGGAAAAACACTGCACATTAAAGCATTAGCTATAAGTGACCTGAACCGCACTGGCCAGAGACAGGTGTTTTTTGAACTCAATGGCCAGCTTCGATCAATTTTGGTCAAAGACACGCAGGCCATGGTACATAGACCAAGTTTGATTCTGTTTGAAACTCTCTTACAGGAAATGCA #### Pdcd11_ID10111_5 --> 0 - 1 Original Alignment CTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAg catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagCTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAAC---ggtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from CESAR CTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAg catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagCTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAAC---ggtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from Spaln_aa2Genome CTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAAC- catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagCTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAACGgtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from Spaln_nt2Genome CATGCTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAG catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccag----CTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAAC---Ggtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from Pairagon CTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAG catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagCTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAAC---Ggtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from Exonerate_protein2genome CTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAACAAAG catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagCTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAAC---Ggtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from Exonerate_coding2genome catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagctcctgacaggaacagtttctagcctcgaagaccatggctaccttgtgggcattggtgttggcgcaactagagcctttctattactgaagaaggcacaagagtacactcgacagaagaacggtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt Alignment from GeneWise CTGCTGACAGGCACAGTGTCAAGCCTGGAAGACCATGGCTACCTAGTGGACATTGGCGTTGGTGGGACCAGAGCTTTTCTGTCACTTAAGAAGGCACAAGAGTACATCCGGCAGAAGAAC- catgtcttctgttagaaacatccaaaagtccctttctcctctgtctccagCTCCTGACAGGAACAGTTTCTAGCCTCGAAGACCATGGCTACCTTGTGGGCATTGGTGTTGGCGCAACTAGAGCCTTTCTATTACTGAAGAAGGCACAAGAGTACACTCGACAGAAGAACGgtaaagtggcatcataaccttagtccttgtgtttcgggttagtagttctt #### Pdcd11_ID10115_9 --> 0 - 2 Original Alignment ---GTCAGCCATCTCTCTGATTCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGaa caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGaagtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from CESAR ---GTCAGCCATCTCTCTGATTCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGaa caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGaagtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from Spaln_aa2Genome GTCAGCCATCTCTCTGAT---TCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGAA caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGAAgtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from Spaln_nt2Genome GGTCAGCCATCTCTC--TGATTCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGAA caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGAAgtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from Pairagon -------GCCATCTCTCTGATTCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGAA caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGAAgtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from Exonerate_protein2genome ---GTCAGCCATCTCTCTGATTCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGAA caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGAAgtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from Exonerate_coding2genome caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacaggaagtaagccatctctctgattctaaaaaagcattcaatgccgaggccctgaaaccagggagcactcatgagtgtaggatcattgactttagccagatggatgagctggccctgctctcactgcggaagtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa Alignment from GeneWise ---GTCAGCCATCTCTCTGATTCTAAGAAAGCATTCAACGCTGAGGCCTTCAAACCGGGGAGCACTCACAAGTGTAGAATCATTGACTACAGCCAGATGGATGAGCTGGCCTTGCTCTCTCTGCGGAA caaatgaaccaaatgaacagctttactccaaaatccttttctttcaacagGAAGTAAGCCATCTCTCTGATTCTAAAAAAGCATTCAATGCCGAGGCCCTGAAACCAGGGAGCACTCATGAGTGTAGGATCATTGACTTTAGCCAGATGGATGAGCTGGCCCTGCTCTCACTGCGGAAgtaagtgccatctaccacacatgtgcatgtgctagttgcagtgtctttaa #### Pdcd11_ID10138_32 --> 1 - 0 Original Alignment aGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctagg---GAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from CESAR aGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG tatgtgaatggtttccatgtaggtatcttgaccttccttgtatattctagg---GAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from Spaln_aa2Genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctagG---GAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from Spaln_nt2Genome GGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctagGGAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from Pairagon AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctag---GGAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from Exonerate_protein2genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctagG---GAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from Exonerate_coding2genome AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctagG---GAACAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt Alignment from GeneWise AGAGGAGCAGGAGAAGCTGAACGTGTGGGTGGCCCTGCTGAACCTGGAAAACATGTACGGCTCTCAGGAGTCCCTGACTAAGGTCTTCGAGCGAGCTGTGCAGTACAACGAGCCTCTCAAGGTTTTCCTGCATCTGGCTGACATCTACACCAAGTCCGAGAAATACAAG gtgaatggtttccatgtaggtagattcttgaccttccttgtatattctagGGAA---CAAGAGAAGCTAAATATATGGGTAGCCCTATTAAATCTGGAAAACATGTACGGCTCCCAGGCATCACTGACAAATGTTTTTGATCAAGCTGTCCAATACAATGAATCTCTTAAGGTTTTTCTGCACTTGGATGATATATACACCAAGTCCAAGAGATACAAGgtaagatgttggccacattatcaatgcagtttatcctgcacccttgcctt #### Pde6c_ID7533_3 --> 0 - 0 Original Alignment GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG--------- agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAATACCGTCATgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from CESAR GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG--------- agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAATACCGTCATgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from Spaln_aa2Genome GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG--------- agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAATACCGTCATgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from Spaln_nt2Genome GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG---- agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAATACCgtcatgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from Pairagon GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG--------- agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAATACCGTCATgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from Exonerate_protein2genome GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAAtaccgtcatgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from Exonerate_coding2genome GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAAtaccgtcatgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta Alignment from GeneWise GTCTTTTCTAAGTACCTCAGCTTTGTTGCTGTCGCACTAAGGCTGCAGCACACCAGTTACCTGTACAGTGTGGAGTCCCGGAGAAGCCAG--------- agccatgggtgcaccattaaaattacctgggcccttacttaatattttagGTCATCTCAAGATACCTCAGCTTTGTTGCTGTTGCACTACGGCTGAAGCACACGAGTTATCTGTACAGTTTAGAGTCCCGGAGGAGTCAATACCGTCATgtaagtgaatactactgaaagcctggcatttccacaactacacatcgtta #### Pde6c_ID7536_6 --> 0 - 2 Original Alignment GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATT---------cc ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTTCGAATTccgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from CESAR GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTG---------ATTcc ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTTCGAATTccgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from Spaln_aa2Genome GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTG---------ATTCC ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTTCGAATTCCgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from Spaln_nt2Genome GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATT---------CC ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTTCGAATTCCgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from Pairagon GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTG---------ATTCC ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTTCGAATTCCgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from Exonerate_protein2genome GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCC ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTtcgaattccgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from Exonerate_coding2genome GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATTCC ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTtcgaattccgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca Alignment from GeneWise GAAATCATCTTCTATAAAATCATCGATTACATTTTACATGGAAAAGAAGAGATCAACGTGATT---------CC ttcagtcaggttacccttggctatctagcttatttttttcttaaacctagGAAATCATATTCTACAAAATTACTGACTACATTTTGCATGGGAAGGAGGAACTCAATGTGATTTTTCGAATTCCgtaagaagtcaactgaaggcagtctaccctcccatgccatgataacacca #### Peo1_ID9266_3 --> 1 - 2 Original Alignment g------TCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACag catctgttaaggactttatctatatgatctttttaaccaatttctttcaggACGGGGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACaggtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from CESAR g------TCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACag catctgttaaggactttatctatatgatctttttaaccaatttctttcaggACGGGGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACaggtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from Spaln_aa2Genome GTCCGTCATAGACACAATG------CAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAG catctgttaaggactttatctatatgatctttttaaccaatttctttcagGACGGGGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACAGgtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from Spaln_nt2Genome G------TCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAG catctgttaaggactttatctatatgatctttttaaccaatttctttcagGACGGGGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACAGgtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from Pairagon ------GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAG catctgttaaggactttatctatatgatctttttaaccaatttctttcagGACGGGGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACAGgtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from Exonerate_protein2genome GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAG catctgttaaggactttatctatatgatctttttaaccaatttctttcaggacgggGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACAGgtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from Exonerate_coding2genome GTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAG catctgttaaggactttatctatatgatctttttaaccaatttctttcaggacgggGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACAGgtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct Alignment from GeneWise ----AGGTCCGTCATAGACACAATGCAACATGCTGTCTACGTCTATGACGTCTGTCATGTAGTCATTGACAACTTGCAGTTCATGATGGGTCACGAGCAGCTCTCCTCTGACAG catctgttaaggactttatctatatgatctttttaaccaatttctttcagGACGGGGTCTGTCATAGACACAATGCAACATGCAGTATATGTTTATGATATATGTCATGTGGTCATTGACAACTTACCATTCATGATGGGTCATGAGCAGCTTTCTTCAGACAGgtaagtatcagagatgagcttgagtggactggtaatgactccgagggtct #### Pitpnm1_ID306_3 --> 1 - 1 Original Alignment gTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGg gattatactgcagaccctcaagcctgaacggaattctacctgccgtgtagg------------------------------------------------TACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTggtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from CESAR gTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGg ccttatactgcagaccctcaagcctgaacggaattctacctgccgtgtaggTAC------------------------------------------------TTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTggtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from Spaln_aa2Genome GTACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG gattatactgcagaccctcaagcctgaacggaattctacctgccgtgtagG------------------------------------------------TACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGgtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from Spaln_nt2Genome CCCCTTTGTGGAGAAGTTCTCCATTGA---GATAGAGACCTAC--------TACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG GATTATACTGCAGACCCTCAAGCCTGAACGGAATTCTACCTGCCGTGTAGGTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGgtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from Pairagon -------------------------------CACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG TACTGCAGACCCTCAAGCCTGAACGGAATTCTACCTGCC-----GTGTAG--------------------------GTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGgtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from Exonerate_protein2genome ---TACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG GATTATACTGCAGACCCTCAAGCCTGAACGGAATTCTACCTGCCGTGTAGGTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGgtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from Exonerate_coding2genome ---TACACCTGCCCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTACTACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTGG GATTATACTGCAGACCCTCAAGCCTGAACGGAATTCTACCTGCCGTGTAGGTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGgtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat Alignment from GeneWise CCCTTTGTGGAGAAGTTCTCCATTGAGATAGAGACCTAC------------TACTTGCCTGATGGGGGGCAGCAACCTAACGTCTTCAACCTGAGTGGGGCTGAGAGAAGACAGAGAATCGTG- TTATACTGCAGACCCTCAAGCCTGAACG--GAATTCTACCTGCCGTGTAGGTACTTGTCTGATGGGGGTCAGCAACTTAATGTCCTCAAC---AGTGGGGCTGAGAGAAGACAGCAAATTGTTGgtgaggtcttacatgctatgtcttgtatgatttaagctgaggtctttcat #### Pitpnm1_ID309_6 --> 2 - 1 Original Alignment gc---GGCGTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATg aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcaggtGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATggtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from CESAR gcGGC---GTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATg aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcaggtGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATggtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from Spaln_aa2Genome GCGGC---GTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATG aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcagGTGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATGgtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from Spaln_nt2Genome GCG---GCGTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATG aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcagGTGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATGgtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from Pairagon --------------------------------------------------------GCGTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATG AATATGGGGGTGAGCATCTTTTTAACATCAGCTTCTCCTTCCTGTTGCAGGTGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATGgtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from Exonerate_protein2genome GAGGCGGCGTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATG aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcagGTGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATGgtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from Exonerate_coding2genome GAGGCGGCGTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATG aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcagGTGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATGgtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat Alignment from GeneWise --GGCGGCGTGTCTCCACAGAGCTTGTCTGAGTGGCGCATGCAGAACATTGCCCGAGACTCTGAGAACAGCTCCGAGGAAGAATTCTTTGATGCCCATG aatatgggggtgagcatctttttaacatcagcttctccttcctgttgcagGTGATTGTGTATCTCCACAGAGTTTGTCCGAATGGCACATGCAGAATATTGCCCGAGACACCAAAAACAGCTCTGAGGAAGACTTCTTTGATCCCCATGgtaggaaagaaaggtaaaatgtaaagaatgatgtgattgatgggtgacat #### Pitpnm1_ID312_9 --> 0 - 2 Original Alignment GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCTCTTGTCTCCaa attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCA---------aagtcggtgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from CESAR GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCTCTTGTCTCCaa attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCA---------aagtcggtgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from Spaln_aa2Genome GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCTCTTGTCTCCAA attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCA---AAGTCGGTgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from Spaln_nt2Genome GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCT-- attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCAAAgtcggtgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from Pairagon GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCC attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCgtcctgtgcagcagcttatgcaaagtcggtgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from Exonerate_protein2genome GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCTCTTGTC attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCAAAGTCGgtgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from Exonerate_coding2genome GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCTCTTGTC attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCAAAGTCGgtgcacctttccctgagaggaatagtaaatacacataaataaagca Alignment from GeneWise GGCCTAGATGGAGCGGGGGATCTAGTGGTCGAGGCGTGCTCTGTGCATGCCCTCTTCCTCATCCTGCACAGCGGCAGCATCCTGGACTCTGGCCCTGGAGACACCAACTCCAAGCAGGCCGACGTGCAAACGCTGAGCACAGCCTTTGAGGCCGTCACCCGAGTCCATTTCCCCGAGGCCCTGGGTCACGTGGCACTGCGGCTGGTGCCCTGTCCACCCATTTGCGCGGCTGCCTATGCTCT attaggtggggtcaacatatgctcttgttttgatgttctcttccttgcagGGACTAGATGGGGCTGGGGACCTAGTTGTTGAAGCATGCTCTGTGCATGATCTTTTCCTCATACTGCACAGTGGTAGCATTCCAGACCCTGGCCCTGGGGACACCAATTCTAAGCAAGCTGACGTCCAAACTCTGAGCACTGCTTTTGAGGCTGTCTTTCGAGTTCATTCTCCCAAGGCCCTTGGACATGTAGCACTGCGGTTGATACCCTGTCCGTCC---TGTGCAGCAGCTTATGCAAAgtcggtgcacctttccctgagaggaatagtaaatacacataaataaagca #### Pitpnm1_ID314_11 --> 0 - 0 Original Alignment GTGGTGCTGATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccag---------ATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from CESAR GTGGTGCTGATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG cacacacaggtagaaaaaccagcatcccttttggcaccttctgtccccag---------ATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from Spaln_aa2Genome ATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccagATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from Spaln_nt2Genome ATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccagATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from Pairagon GTGGTGCTGATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccag---------ATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from Exonerate_protein2genome ATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccagATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from Exonerate_coding2genome ATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccagATTGGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt Alignment from GeneWise GTGGTGCTGATCGGAGATGGTGTTGGTGGCATCCTGGGCTTTGATGCGCTCTGCCACAGTGCCAGTGCAGGCCCAGGGAGTCGGGGCAGCAGCCGCCGTGGGAGCATG gtagaaaaaccagcatatttctcgccccttttggcaccttctgtccccagATT---------GGAGATGGAGTTGGTGGCATTCTTGGTTTTGACGCTCTCTGTCGCAGTGCCAGTGCAGGCCCAGGGAGCCAGGGCAGCAGCCACCATGGGAGCATGgtactgttccatttcagggagtcaccagctaagggagccagggctgcagt #### Pitpnm1_ID316_13 --> 1 - 1 Original Alignment cCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGg tttgaatataaaaacctggacctatttttctgtctcctctggtcaaacagc---CAGTTAGCAACAACAGCAACTTCC---------------------TGCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGggtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from CESAR cCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGg cactttgaatataaaaacctggaccttttctgtctcctctggtcaaacagc---CAGTTAGCAACAACAGCAACTTCC---------------------TGCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGggtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from Spaln_aa2Genome CCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGG tttgaatataaaaacctggacctatttttctgtctcctctggtcaaacagC---CAGTTAGCAACAACAGCAACTTCC---------------------TGCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGGgtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from Spaln_nt2Genome CCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGG tttgaatataaaaacctggacctatttttctgtctcctctggtcaaacag---CCAGTTAGCAACAACAGCAACTTCCT---------------------GCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGGgtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from Pairagon CCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGG tttgaatataaaaacctggacctatttttctgtctcctctggtcaaacag---CCAGTTAGCAACAACAGCAACTTCCT---------------------GCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGGgtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from Exonerate_protein2genome CCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGG tttgaatataaaaacctggacctatttttctgTCTCCTCTGGTCAAACAGCCAGTTAGCAACA------ACAGCAACTTCCTGCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGGgtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from Exonerate_coding2genome CCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGG tttgaatataaaaacctggacctatttttctgTCTCCTCTGGTCAAACAGCCAGTTAGCAACA------ACAGCAACTTCCTGCACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGGgtgaataccaatgctcttattcttcttatcatctacctcggacaattgct Alignment from GeneWise CCTCCAGGTAGCCTCCACAGCTACCTCCTCTGGGGAGCCCCGCCGTGCAAGCACAGCCTCCTGTCCACCTGCCAGTTCTGAGGCTCCTGACGGCCCCACGAACGCTGCTCGCCTGGACTTCAAGGTCTCAGGCTTCTTCCTCTTTGGCTCCCCACTGGGCCTGGTGCTGGCTCTTCGCAAAACCGTGATGCCCGCCTTGGAGG tttgaatataaaaacctggacctatttttctgtctcctctggtcaaacagC---CAGTTAGCAACAACAGCAACTTCCTGC---------------------ACATCCTCCTGTCCACCAGCAAGCTCTGAAGCGCATGATGGGCCAACAAATGCTGCTCACCTTGACTTCAGAGTGTTGGGTTTCTTCCTCTTTGGTTCCCCAGTAGGCTTAGTGCTGGCTCTTCGAAAAACTGTGATGTCTGCCTTGGAGGgtgaataccaatgctcttattcttcttatcatctacctcggacaattgct #### Pitpnm1_ID320_17 --> 0 - 0 Original Alignment GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from CESAR GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from Spaln_aa2Genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from Spaln_nt2Genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from Pairagon GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from Exonerate_protein2genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from Exonerate_coding2genome GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCG ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGgcgattggtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac Alignment from GeneWise GTCATTGAGAAGGAGCGGCCACAGCTGACAGAGTGTGAGGAGCCATCCATCTATAGCCCCGCCTTCCCCAGGGAGAAGTGGCAGCGCAAACGCACACAGGTCAAGATCCGG------ ccattgtagtatgggtgtatcttgtatgaagctttttgggttctttgcagATTATGGAGAAAGAATGGCCACAATTAACTGAGTGTCAAGAACCATCCATCTACAGCCCTGCCTTCCCTAAGGAAAAGTGGCAGTGCAAGCAAACACAGGTCAAGATTCGGCGATTGgtaaggatcctagtttgtttctcccttggctgtttacagttgtttgaaac #### Pkd2l1_ID8954_14 --> 1 - 0 Original Alignment gCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATG--- actctaaaacccttccttgattgccttgtaacttatgaccttaaacccaggCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from CESAR gCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATG--- actctaaaacccttccttgattgccttgtaacttatgaccttaaacccaggCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from Spaln_aa2Genome GCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATG--- actctaaaacccttccttgattgccttgtaacttatgaccttaaacccagGCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from Spaln_nt2Genome GCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATG--- actctaaaacccttccttgattgccttgtaacttatgaccttaaacccagGCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from Pairagon GCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATG--- actctaaaacccttccttgattgccttgtaacttatgaccttaaacccagGCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from Exonerate_protein2genome GCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATG--- actctaaaacccttccttgattgccttgtaacttatgaccttaaacccagGCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from Exonerate_coding2genome actctaaaacccttccttgattgccttgtaacttatgaccttaaacccaggcttacaaggagggtattgcagctacaatgcgttttagggggagttgtctcccagattgatgccattggctctaagctaaaaatgctggagagaaaaggggagttggctccttaccctggtatgcgagtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt Alignment from GeneWise GCTCACAAGGAGAGTTCTGCAGCTGCAGTGTGTTCTGGAAGGAGTTGTGTCCCAGATTGATGCTGTAGGCTCAAAGCTGAAGATGCTGGAGAGGAAAGGGGAGCTGGCTCCCTCCCCAGGAATGGGG actctaaaacccttccttgattgccttgtaacttatgaccttaaacccagGCTTACAAGGAGGGTATTGCAGCTACAATGCGTTTTAGGGGGAGTTGTCTCCCAGATTGATGCCATTGGCTCTAAGCTAAAAATGCTGGAGAGAAAAGGGGAGTTGGCTCCTTACCCTGGTATGCGAgtgagtactatctgggggcacgcagagggaagcactactggcaatcatgt #### Pkd2l1_ID8957_11 --> 0 - 2 Original Alignment AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG------ga tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCgagtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta Alignment from CESAR AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG------ga tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCgagtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta Alignment from Spaln_aa2Genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGAA----- tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCGAgtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta Alignment from Spaln_nt2Genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGG------A tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCGAgtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta Alignment from Pairagon AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG------GA tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCGAgtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta Alignment from Exonerate_protein2genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGG------GA tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCGAgtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta Alignment from Exonerate_coding2genome AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGA--ACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGAACTGGGGCACGAGGAGCACGAGATCACCGCTGCCTTCACCAGGTTTGATCAGGATG tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGT--GGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCGAGTAAGTAAGTCCATGCCTGCCAGATGTTCTGATCACACTGGGCTAAGGTA Alignment from GeneWise AGCTACAACAAGACCCTACTAAGGCTGCGCCTGAGGAAAGAGCGGGTTTCTGATGTGCAGAAGGTCCTGAAGGGTGGGGAACCAGAGATCCAGTTTGAAGATTTCACCAGCACCTTGAGGGAACTG-- tggtaccaacaccacatctatcatattcgctcctttctgttccactctagAGCTATAACAAGACCCTATTACGGTTGCGCCTGAGAGAGGAGCGGGTTTCAGATGTGCAAAAGGTCCTTAAGGGTGGAGAACCAGAGATCAAGTTTGAAGATTCCACAAGCACATTGAGAGTACTCGAgtaagtaagtccatgcctgccagatgttctgatcacactgggctaaggta #### Plcb3_ID1901_30 --> 0 - 0 Original Alignment CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccaag---------GCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from CESAR CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG ttcctcatcattgctcagacttccactttgaatttttttttcctcccaag---------GCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from Spaln_aa2Genome CTGGAAGAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccaag---------GCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from Spaln_nt2Genome GCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccaagGCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from Pairagon GCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccaagGCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from Exonerate_protein2genome GAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccAAGGCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from Exonerate_coding2genome GAGGCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccAAGGCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc Alignment from GeneWise GCCCAGAAGCAGCGCCATGAACGCCTGGTGGCAGGGCAACAGCAAGTCCTCCAGCAGCTAGAGGAAGAGGAACCCAAG attgctcagacttccaaccctttctctttgaatttttttttcctcccaagGCCCAAAAACAGCAACATGAGCGGCTAGTGGCAGGACAACAGCAAGTCCTCCAGCAACTAGAGGAAGAGAAACCAAAAgtaagactctgtagggttgcatgtacacactaataggggaactggtcagc #### Plcb3_ID1902_29 --> 1 - 0 Original Alignment t gGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagaGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCC---------gtaagagggtgcgaggcgacttgtctttgtcaataacttcctttgtcacc Alignment from CESAR gGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG tgtaggcaccctgagaagcaggccaatatggttgtgctaactttttacagaGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCC---------gtaagagggtgcgaggcgacttgtctttgtcaataacttcc Alignment from Spaln_aa2Genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG------ tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagAGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCGTAAGAGGGTGCGAGgcgacttgtctttgtcaataacttcctttgtcacc Alignment from Spaln_nt2Genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGG tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagAGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCGTAAGA-GGgtgcgaggcgacttgtctttgtcaataacttcctttgtcac Alignment from Pairagon GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCC tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagAGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCgtaagagggtgcgaggcgacttgtctttgtcaataacttcctttgtcacc Alignment from Exonerate_protein2genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACG tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagAGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCGTAAGAGGgtgcgaggcgacttgtctttgtcaataacttcctttgtcacc Alignment from Exonerate_coding2genome GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACG tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagAGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCGTAAGAGGgtgcgaggcgacttgtctttgtcaataacttcctttgtcacc Alignment from GeneWise GGAACTGACAGAGATTAATCGGCGGCACATCACTGAGTCGGTAAACTCCATCAGACGGCTGGAAGAGGCC- tgtaagaaccctgagaagcaggccaatatggttgtgctaactttttacagAGAATTGACAGAGATTATCCGGCAACACATCACTGAGTCAATAAATTCCGTAAGAGGGTGCGAGGCGACTTgtctttgtcaataacttcctttgtcacc #### Plcb3_ID1904_27 --> 0 - 2 Original Alignment GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAag GACAGgtgagttgtgggatggtatcaccgtttttattaaaatggctttag------CAGTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAaggtactgataagcaggaattcaatttggtatgattccttacatacaattca Alignment from CESAR GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAag GACAGgtaagtgatcaatgtgggataccgtttttattaaaatggctttag------CAGTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAaggtactgataagcaggaattcaatttggtatgattccttacatacaattca Alignment from Spaln_aa2Genome GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAAG GACAGgtgagttgtgggatggtatcaccgtttttattaaaatggctttag------CAGTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAAGgtactgataagcaggaattcaatttggtatgattccttacatacaattca Alignment from Spaln_nt2Genome GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAAG GACAGgtgagttgtgggatggtatcaccgtttttattaaaatggctttag------CAGTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAAGgtactgataagcaggaattcaatttggtatgattccttacatacaattca Alignment from Pairagon GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAAG GACAGgtgagttgtgggatggtatcaccgtttttattaaaatggctttag------CAGTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAAGgtactgataagcaggaattcaatttggtatgattccttacatacaattca Alignment from Exonerate_protein2genome GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAAG GACAGgtgagttgtgggatggtatcaccgtttttattaaaatggCTTTAGCAGTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAAGgtactgataagcaggaattcaatttggtatgattccttacatacaattca Alignment from Exonerate_coding2genome GACAG GCTCATCAGCGGCTCAAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAG GACAGgtgagttgtgggatggtatcaccgtttttattaaaatggctttagcagtgggttaaggaggttgtactggacacacacacaatccaatttaagaggctaagggaacttaaagAAAGGTACTGATAAGCAGGAATTCAATTTGGTATGATTCCTTACATACAATTCA Alignment from GeneWise GACAGGCTCATCAGCGGCTC ------AAGGAGGTTGTCCTGGATACACACACAACACAGTTCAAGAGGCTGAAGGAGCTGAATGAAAG GACAGGTGAGTTGTGGGATGgtatcaccgtttttattaaaatggctttagcagTGGGTTAAGGAGGTTGTACTGGACACACACACAATCCAATTTAAGAGGCTAAGGGAACTTAAAGAAAGgtactgataagcaggaattcaatttggtatgattccttacatacaattca #### Plcb3_ID1905_26 --> 1 - 0 Original Alignment gGGCAAGGCCACCAACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG GCTCA gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagg---------TCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggttgagcctttactctcacatcagGCACA Alignment from CESAR gGGCAAGGCCACCAACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG GCTCA tctcatttggttgtatcagttagaggtgaaaatcttctctccccttccagg---------TCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggtatcaccctgcgtggctttccagGCACA Alignment from Spaln_aa2Genome GGGCAAGGCCACCAACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG GCTCA gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagG---------TCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggttgagcctttactctcacatcagGCACA Alignment from Spaln_nt2Genome CACCAACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG GCTCA gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagGTCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggttgagcctttactctcacatcagGCACA Alignment from Pairagon GGGCAAGGCCACCAACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG GCTCA gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagG---------TCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggttgagcctttactctcacatcagGCACA Alignment from Exonerate_protein2genome C---AACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG GCTCA gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagGTCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggttgagcctttactctcacatcagGCACA Alignment from Exonerate_coding2genome C---AACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGACAG gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagGTCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGgtaagtgatcaatgtgggatggttgagcctttactctcacatcaggcaca Alignment from GeneWise GGGCAAGGCCACCAACTCGGAGGACGTGAAGGAGGAAGAGGAGGCCAAACAGTATCGAGAGTTCCAGAACCGACAAGTACAGAGCCTGTTGGAGCTGAGGGAAGCCCAGGCAGATGTGGAGACCAAGCGGAAGCTGGAGCATCTACGA---------------------------------------------CAGGCTCA gttgtatcagttagagagttcacgggtgaaaatcttctctccccttccagG---------TCCAACTCAGAGGATGTGAAGGATGAAGAAGAATCCAAGCAGTATAGGGACTTGCAAAATCAAAAAGCACAAAGCTTGTTGGAATTGAGAGAAGCCCAGGGTGATGTGGAGACCAACTGCAAGCTGGAACATCTACGACAGGTAAGTGATCAATGTGGGATGGTTGAGCCTTTACTCTCACATCAGGCACA #### Plcb3_ID1912_19 --> 0 - 0 Original Alignment GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG--------------------- cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGATTTGGTTGACCTTCTTTGGGgtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac Alignment from CESAR GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGatttggttgaccttctttggggtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac Alignment from Spaln_aa2Genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGatttggttgaccttctttggggtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac Alignment from Spaln_nt2Genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG----- cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGATTTGgttgaccttctttggggtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac Alignment from Pairagon GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG----------------------------------------------------- cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGATTTGGTTGACCTTCTTTGGGGTGCCTTCCAGCAGTTGTGCCCTCCATTTCATgtaggacagcaagaccac Alignment from Exonerate_protein2genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGatttggttgaccttctttggggtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac Alignment from Exonerate_coding2genome GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAG cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGatttggttgaccttctttggggtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac Alignment from GeneWise GTGATTTCGGGGCAGTTCCTGTCTGACAAGAAGGTGGGCATCTACGTCGAGGTGGACATGTTTGGCCTCCCAGTTGACACAAGACGCAAATATCGTACCCGGACATCCCAGGGGAACTCATTCAACCCTGTGTGGGACGAGGAACCCTTTGACTTCCCCAAGGTT------------------ cacacgaaaattctctcatcaactttcatgactcctttctctctcattagGTGATCCCAGGGCAATTCCTTTCTCATAAGAAAGTCGGTATCTACGTTGAGGTGGATATGTTTGGTCTCCCACTAGATACTAGATGTAAATATCGTACCCGGACATCTCAGGGAAACTCATTCAACCCTGTATGGGAAGAAGAACCGTTTGACTTCCCCAAGATTTGGTTGACCTTCTTTGGGgtgccttccagcagttgtgccctccatttcatgtaggacagcaagaccac #### Plcb3_ID1913_18 --> 2 - 0 Original Alignment atTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGGGTCAAG catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagatCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGG------gtatgtgattgggcataatagttaaccttattttacaacaatgtattgtg Alignment from CESAR atTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGGGTCAAG catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagatCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGG------gtatgtgattgggcataatagttaaccttattttacaacaatgt Alignment from Spaln_aa2Genome ATTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGG catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagATCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGGgtatgtgattgggcataatagttaaccttattttacaacaatgtattgtg Alignment from Spaln_nt2Genome ATTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGG catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagATCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGGgtatgtgattgggcataatagttaaccttattttacaacaatgtattgtg Alignment from Pairagon ATTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGG catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagATCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGGgtatgtgattgggcataatagttaaccttattttacaacaatgtattgtg Alignment from Exonerate_protein2genome ATTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGGGTCA catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagATCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGGGTATgtgattgggcataatagttaaccttattttacaacaatgtattgtg Alignment from Exonerate_coding2genome ATTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGGGTCA catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagATCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGGGTATgtgattgggcataatagttaaccttattttacaacaatgtattgtg Alignment from GeneWise ATTTGCCAATGCAGCTCAACGCAGGCGTGTTTGAGTACAATGGGCGCAGCGGGTACTTGCTCAAGCCCGAGTTTATGCGGCGGCCGGACAAGTCTTTTGATCCCTTCACTGAGGTCATCGTAGATGGCATAGTGGCCAACGCCTTGCGG catgcaatgttttctgatctcactctgcatgttcttgtcttttcttgcagATCTGCCAATGCAGCTCAATGCAGGTGTTGTTGAGTACAATGGGCGCAGTGGGTACTTGCTCAAGCCTGAGTTTATGCGACGGCCGGACAAATCTTTTGAACCTTTCACTGAGGTCATCGTAGATGCTCTAGTGGCCAATGCATTGAGGgtatgtgattgggcataatagttaaccttattttacaacaatgtattgtg #### Plcb3_ID1923_8 --> 1 - 2 Original Alignment tGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAG------at tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagtGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCatgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa Alignment from CESAR tGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAG------at tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagtGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCatgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa Alignment from Spaln_aa2Genome TGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAGATA----- tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagTGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCATgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa Alignment from Spaln_nt2Genome TGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAG------AT tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagTGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCATgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa Alignment from Pairagon TGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAG------AT tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagTGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCATgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa Alignment from Exonerate_protein2genome TGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAGATAGGTGCCAAGGGCAAGCCGTACCT tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagTGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCATGTATTTAAGTCATCCCAGgtcatgggtggctgtgaaatcccattgaaaaa Alignment from Exonerate_coding2genome tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagtgaatccattcgccctgatgaatttcctttggaagtttttgaacggttcttgaataaactgtgtctgcgagcagatattgacaagattgtgctggaggatatcatgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa Alignment from GeneWise TGAGTCCATTCGCCCTGATGAGTTTCCCTTGGAAATTTTTGAGCGGTTCTTGAATAAACTGTGTCTGCGCCCGGATATTGACAAGATCCTGCTGGAG---ATA-- tgttgggtcaatattctcatcctgccatacccccaatgtcttcggtgcagTGAATCCATTCGCCCTGATGAATTTCCTTTGGAAGTTTTTGAACGGTTCTTGAATAAACTGTGTCTGCGAGCAGATATTGACAAGATTGTGCTGGAGGATATCATgtatttaagtcatcccaggtcatgggtggctgtgaaatcccattgaaaaa #### Plcb3_ID1928_3 --> 0 - 0 Original Alignment GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCCAAG taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCC---gtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga Alignment from CESAR GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCCAAG taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCC---gtaaggagtcactggctttgcacatgtaaataccacaccacttttgg Alignment from Spaln_aa2Genome GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCC taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCCgtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga Alignment from Spaln_nt2Genome GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCC taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCCgtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga Alignment from Pairagon GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCC taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCCgtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga Alignment from Exonerate_protein2genome GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCC taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCCgtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga Alignment from Exonerate_coding2genome taaatcggtggacaaccttgttccttgatctctgttttggtgcctcataggaggtggacacactggatatcagctcgatcagaggtacaaggacaggtcgttatgcccacctgcccgtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga Alignment from GeneWise GAGGTGGACACACTGGACATCAGCTCCATCAGGGACACAAGGACAGGTCGTTATGCCCGCCTGCCC taaatcggtggacaaccttgttccttgatctctgttttggtgcctcatagGAGGTGGACACACTGGATATCAGCTCGATCAGAGGTACAAGGACAGGTCGTTATGCCCACCTGCCCgtaaggagtcactggctttgcacatgtaaataccacaccacttttgggga #### Pnlip_ID12748_7 --> 2 - 1 Original Alignment gaTTTGGAATGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAg ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagga---------AGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAggtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from CESAR gaTTTGGAATGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAg gtctgggctttgaataatctacggggtcactggttccactctcttcccagga---------AGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAggtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from Spaln_aa2Genome TGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAG ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagGAAGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAGgtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from Spaln_nt2Genome GAATGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAG ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagGA---AGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAGgtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from Pairagon GATTTGGAATGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAG ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagGA---------AGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAGgtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from Exonerate_protein2genome TGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAG ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagGAAGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAGgtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from Exonerate_coding2genome TGAGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAG ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagGAAGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAGgtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga Alignment from GeneWise --AGCCAGACTGTGGGTCACTTAGATTTCTTTCCAAACGGAGGAATCGAAATGCCAGGATGCCAGAAGAATATTCTTTCCCAAATTGTTGACATCGACGGGATCTGGGAAG ttgaataatctacgggccttcgtgtgtcactggttccactctcttcccagGAAGCCAGACTGTGGGTCACTTAGACTTCTTCCCCAATGAAGGAATTGAAATGCCAGGATGCCAGAAAAATACTCTTTCCCAGATTGTTGATATTGATGGGATCTGGGAAGgtgagtgcttgtgtagctgaaataaactataatgcaattaattctcttga #### Pnlip_ID12752_11 --> 1 - 2 Original Alignment gGGCTCTCTGCAGCCAGGTACTTCTCACGTCAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA---gt caccagggactaaacaaatggctcaagtctttcttttcttctttttccagg------------------------GATGGCAATGAATTTGAGTCTGAA------GTTGGAGATTTGCAGAGGGTCAAATTTATTGGC---AACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTgtgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from CESAR gGGCTCTCTGCAGCCAGGTACTTCTCACGTCAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA---gt caccagggactaaacaaatggctcaagtctttcttttcttctttttccaggGAT------------------------GGCAATGAATTTGAGTCT------GAAGTTGGAGATTTGCAGAGGGTCAAATTTATT---GGCAACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTgtgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from Spaln_aa2Genome CAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGAGTG-- caccagggactaaacaaatggctcaagtctttcttttcttctttttccagGGATGGCAATGAATTTGAGTCTGAAGTTGGAGATTTGCAGAGGGTCAAATTTATTGGC---AACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTGTgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from Spaln_nt2Genome TCACGTCAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA---GT caccagggactaaacaaatggctcaagtctttcttttcttctttttccagGGATGGCAATGAATTTGAGTCT------GAAGTTGGAGATTTGCAGAGGGTCAAATTTATTGG---CAACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTGTgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from Pairagon GGGCTCTCTGCAGCCAGGTACTTCTCACGTCAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA---GT caccagggactaaacaaatggctcaagtctttcttttcttctttttccagGG------------------------ATGGCAATGAATTTGAGTCT------GAAGTTGGAGATTTGCAGAGGGTCAAATTTATTGG---CAACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTGTgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from Exonerate_protein2genome CAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA---GT caccagggactaaacaaatggctcaagtctttcttttcttctttttccagGGATGGCAATGAATTTGAGTCTGAAGTTGGAGATTTGCAGAGGGTCAAATTTATTGGC---AACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTGTgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from Exonerate_coding2genome CAATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA---GT caccagggactaaacaaatggctcaagtctttcttttcttctttttccagGGATGGCAATGAATTTGAGTCTGAAGTTGGAGATTTGCAGAGGGTCAAATTTATTGGC---AACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGATCTGTgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat Alignment from GeneWise -------AATGAATTCGACTCTGATGTGGATGTTGGAGATTTGCAGAAGGTTAAATTTATTTGGTACAACAATGTGATCAACCCAACTCTACCCAAAGTGGGAGCATCAAGGATCACAGTGGAAAGAAATGATGGCAGA caccagggactaaacaaatggctcaagtctttcttttcttctttttccagGGATGGCAATGAATTTGAGTCTGAAGTT------GGAGATTTGCAGAGGGTCAAATTTATTGGC---AACAATGTAATTAACCCAACACTTCCGAGAGTGGGGGCATCAGGGATTACTGTAGAAAGAAATGATGGGAGAtctgtgtaacttacttgtgtaccaaaagacagcagggcgtagcttaaagtcacat #### Pnliprp1_ID12769_6 --> 2 - 1 Original Alignment gaCTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCATTCTTGg aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccaggaCTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCA------ggtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from CESAR gaCTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCATTCTTGg aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccaggaCTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCA------ggtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from Spaln_aa2Genome GACTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCA- aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccagGACTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCAGgtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from Spaln_nt2Genome GACTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCATTCTTGG aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccagGACTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCA------Ggtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from Pairagon GACTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCATTCTTGG aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccagGACTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCA------Ggtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from Exonerate_protein2genome GACTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCATTCTTGG aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccagGACTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCA------Ggtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from Exonerate_coding2genome GACTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCATTCTTGG aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccagGACTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCA------Ggtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac Alignment from GeneWise GACTGGATCCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGGTCCGGCTCGACCCCTCGGATGCTGACTTTGTTGATGTGATTCACACAGATGCAGCTCCCTTGATCCCAT aactctgtactctcatgctgctacatttgctgcttttcctcaatgaccagGACTGGATTCTGTAGAAGCAAATTTTGAGGGAACCCCTGAAGAGATTCGGCTGGACCCCTCAGATGCTGACTTTGTCGATGTGATTCACACAGATGCAGCTGCCTTGGTCCCAGgtaagtggcgttcctggtaccctgtaatcatctaccaggtattgcaagac #### Pola2_ID1325_15 --> 0 - 2 Original Alignment ---CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTag ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagTGCCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATG---TACTCAACTACTGCAGACTTACTCTATCACCTTGGGGCTGAGGAACTGTTTaggtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag Alignment from CESAR ---CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTag ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagTGCCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTAC---TCAACTACTGCAGACTTACTCTATCACCTTGGGGCTGAGGAACTGTTTaggtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag Alignment from Spaln_aa2Genome CGAGTGCAGTTT---GTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagTGCCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCA---ACTACTGCAGACTTACTCTATCACCTTGGGGCTGAGGAACTGTTTAGgtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag Alignment from Spaln_nt2Genome CGAGTGCAG---TTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagTGCCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGT---ACTCAACTACTGCAGACTTACTCTATCACCTTGGGGCTGAGGAACTGTTTAGgtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag Alignment from Pairagon ---CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGT------------------------------TTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagTGCCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCAACTACTGCAGACTTACTCTATCACCTT---------------------------------GGGGCTGAGGAACTGTTTAGgtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag Alignment from Exonerate_protein2genome ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagtgccgagtgcagtttgtatcagagccctgcagcctacagataaatggagtaatgtactcaactactgcagacttactctatcaccttggggctgaggaactgtttaggtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---CGAGTGCAGTTTGTGTCAGAGCCCTGCAGCCTCTCCATAAATGGAGTGATGTTTGGTTTGACATCCACGGACCTGCTGTTCCACATCGGGGCTGAGGAGATCTTTAG ggctcactgtaggttttattgcaaggaggggatggggtctgtttactcagTGCCGAGTGCAGTTTGTATCAGAGCCCTGCAGCCTACAGATAAATGGAGTAATGTACTCA---ACTACTGCAGACTTACTCTATCACCTTGGGGCTGAGGAACTGTTTAGgtaagcccattcgacccaataaagggtgttacttaacatggttcttgaag #### Pold4_ID437_2 --> 2 - 1 Original Alignment ggGAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAg agacagatcataatcggactacagcctggacatcccttgtgttggaccaggg------------------AGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAggtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from CESAR ggGAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAg taggcagatcagaggattagacagactggacatcccttgtgttggaccaggg------------------AGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAggtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from Spaln_aa2Genome GACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG atcggactacagcctggacatcccttgtgttggacca gGGAGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from Spaln_nt2Genome GTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG agacagatcataatcggactacagcctggacatcccttgtgttggaccagG-----GAGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from Pairagon GGGAAGACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG agacagatcataatcggactacagcctggacatcccttgtgttggaccagGG------------------AGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from Exonerate_protein2genome CAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG agacagatcataatcggactacagcctggacatcccttgtgttggaccaggGAGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from Exonerate_coding2genome CAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG agacagatcataatcggactacagcctggacatcccttgtgttggaccaggGAGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta Alignment from GeneWise ACACCCAGTCCCTCAGCCAGGAGGAAACAGAGCTGGAGCTGCTGAGGCAGTTTGACCTGGCCTGGCAGTATGGGCCTTGTACAG agacagatcataatcggactacagcctggacatcccttgtgttggaccagGG------------AGCCAAGAGGAGACTGAGCTGGAGTTTCTACGGCAATCTGACTTGACATGGCAATATGGGCCTTGTACAGgtaagtaacccagcttctgcacagcgaaagaaaactaccgtcagagtgta #### Poll_ID9484_3 --> 1 - 0 Original Alignment gTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACCCAAGCCCAG gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcaggTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACT---------gtaaccttgatattgggtcgcgccattcaagattgttagtgatagaacac Alignment from CESAR gTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACCCAAGCCCAG gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcaggTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACT---------gtaaccttgatattgggtcgcgccattcaagattgttagtg Alignment from Spaln_aa2Genome GTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACC gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcagGTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACTgtaaccttgatattgggtcgcgccattcaagattgttagtgatagaacac Alignment from Spaln_nt2Genome GTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACC gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcagGTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACTgtaaccttgatattgggtcgcgccattcaagattgttagtgatagaacac Alignment from Pairagon GTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACC gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcagGTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGA---TTCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACTgtaaccttgatattgggtcgcgccattcaagattgttagtgatagaacac Alignment from Exonerate_protein2genome GTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACCCAAGCCCAG gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcagGTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACTGTAACCTTGatattgggtcgcgccattcaagattgttagtgatagaacac Alignment from Exonerate_coding2genome GTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACCCAAGCCCAG gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcagGTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGAACTGTAACCTTGatattgggtcgcgccattcaagattgttagtgatagaacac Alignment from GeneWise GTCCTTGGATGAACCACAGCCCAGCAAGTCAGGCCAAGATGCTTCTGCTCCTGGCACCCAGCGGGATTTACCCAGGACCACCCTTTCTCTTTCCCCTCCTCACACCAGAGCTGTATCTCCTCCCCCAACGGCAGAAAAGCCATCAAGAACCCAAGCCCAG gaccattcatactctttaaatagctcctaacgccaccttcctgtctgcagGTCCTTGGATGAGCCACAGCCCAGCAAGTCCGGCCAAGAT---TCTGCTCCTGGTATACAGTGGGACTTGCCTAGAACCACACTCTCCCTTTCCCCTCCCCATCCTCGAGCAGTATCACCACCTCCAACAGCAGAAAAACCATCCAGA---------ACTgtaaccttgatattgggtcgcgccattcaagattgttagtgatagaacac #### Polr2g_ID2378_5 --> 0 - 0 Original Alignment TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAG------ ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTgtaagccagcatgcactgggggatgagatgacaagagaggacagcaattc Alignment from CESAR TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAG------ ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTgtaagccagcatgcactgggggatgagatgacaagagaggacagcaattc Alignment from Spaln_aa2Genome TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAGGACATTGTGATTCAGCAG ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTGTAAGCCAGCATgcactgggggatgagatgacaagagaggacagcaattc Alignment from Spaln_nt2Genome TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAGGA ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAgtttgtaagccagcatgcactgggggatgagatgacaagagaggacagcaattc Alignment from Pairagon TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAGGACATT ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTgtaagccagcatgcactgggggatgagatgacaagagaggacagcaattc Alignment from Exonerate_protein2genome TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAGGACATT ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTgtaagccagcatgcactgggggatgagatgacaagagaggacagcaattc Alignment from Exonerate_coding2genome TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAGGACATTGTGATTCAG ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTGTAAGCCAGcatgcactgggggatgagatgacaagagaggacagcaattc Alignment from GeneWise TCCATCCCTTCAGAGATGGAGTTTGATCCAAATTCAAACCCCCCTTGCTATAAGACCATGGACGAGGACATTGTGATTCAGCAG------GACGATGAGATACGCTTGAAGATTGTAGGCAC ttcagtttctcatcttggaagtatgtcacaacatggcttttctcttctagTCCATACCATCTGAAATGGAATTTGACTCAAACTCAAACCCCCCCTGCTATAAGACCATGGATGAAGAGTTTGTAAGCCAGCATGCACTGGGGGATGAGATG------------------AC #### Polr2g_ID2381_2 --> 0 - 2 Original Alignment ATTTCCCTGGAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGaa tggtcaagccagttaaagttcctccgttcttttcctttctctaccgtcag---------GAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGaagtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from CESAR ATTTCCCTGGAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGaa tcctgaccctggtcaagccagttaagttcttttcctttctctaccgtcag---------GAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGaagtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from Spaln_aa2Genome ATTTCCCTGGAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGAA tggtcaagccagttaaagttcctccgttcttttcctttctctaccgtcag---------GAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGAAgtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from Spaln_nt2Genome GAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGAA tggtcaagccagttaaagttcctccgttcttttcctttctctaccgtcagGAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGAAgtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from Pairagon GGAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGAA tggtcaagccagttaaagttcctccgttcttttcctttctctaccgtcaGGAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGAAgtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from Exonerate_protein2genome GAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGAA tggtcaagccagttaaagttcctccgttcttttcctttctctaccgtcagGAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGAAgtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from Exonerate_coding2genome GAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGAA tggtcaagccagttaaagttcctccgttcttttcctttctctaccgtcagGAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGAAgtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa Alignment from GeneWise TTTTATCACATTTCCCTGGAGCACGAGATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACACGGTGAAGCAGAAGCTGTTTACCGAGGTGGAGGGGACCTGCACTGGGAA tggtcaagccagttaaagttcctccgttctttTCCTTTCTCTACCGTCAGGAGCGCGAAATCCTCCTGCACCCACGATACTTCGGTCCAAACTTGCTCAACATGGTGAAGCAGAAGCCATTTACTGAAGTGGAGGGGACCTGCACTGGGAAgtatgcctcttctttacaggagcaagaccttttgaatgcattggcagcaa #### Ppp1ca_ID412_6 --> 0 - 0 Original Alignment GTTGTAGAAGATGGCTATGAGTTCTTTGCCAAG---AGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCC------TTCCAG atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTATT---GGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACATTC---TCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTGCAGGGCTTTC---gtgagtagtagaaggaatagccagtagggaataatatatctttggatctt Alignment from CESAR GTTGTAGAAGATGGCTATGAGTTCTTTGCC---AAGAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGT------TCCTTCCAG atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTATT---GGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACA---TTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTGCAGGGCTTTC---gtgagtagtagaaggaatagccagtagggaataatatatctttggat Alignment from Spaln_aa2Genome GTTGTAGAAGATGGCTATGAGTTCTTTGCCAAGAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCCTTCCAG--- atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTATTGGTGGATATGATTTC---TTTGCAAAAAAGAAAAAACTAGTAACATTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTGCAGGGCTTTCgtgagtagtagaaggaatagccagtagggaataatatatctttggatctt Alignment from Spaln_nt2Genome GTTGTAGAAGATGGCTATGAGTTCTTTGCCAA---GAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCC-----TTCC atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTAT---TGGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACA---TTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTGCAGGGCTTTCgtgagtagtagaaggaatagccagtagggaataatatatctttggatctt Alignment from Pairagon --------------------------------------------------------------TATGAGTTCTTTGC--------------------CAAGAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCCTTCC-------------------------------------------------------------- ATGATCTAAGGTCGAACTTAATAATATAAGCTACTTCCCTCCCCTGCCAGGTTATTGGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACA--------------------TTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATG-------CTGCAGGGCTTTCGTGAGTAGTAGAAGGAATAGCCAGTAGGGAATAATATATCTTTGGATCTT Alignment from Exonerate_protein2genome GTTGTAGAAGATGGCTATGAGTTCTTTGCCAAGAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTT atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTATT---GGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACATTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTgcagggctttcgtgagtagtagaaggaatagccagtagggaataatatatctttggatctt Alignment from Exonerate_coding2genome GTTGTAGAAGATGGCTATGAGTTCTTTGCCAAGAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTT atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTATT---GGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACATTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTgcagggctttcgtgagtagtagaaggaatagccagtagggaataatatatctttggatctt Alignment from GeneWise GTTGTAGAAGATGGCTATGAGTTCTTTGCCAAGAGACAGTTGGTGACACTCTTCTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCCTTCCAGATC atgatctaaggtcgaacttaataatataagctacttccctcccctgccagGTTATT---GGTGGATATGATTTCTTTGCAAAAAAGAAAAAACTAGTAACATTCTCAGCTCCTAATTACTGTGGTGAATTTGAAAACGCTGGTGCCATGACCAGTGTAGACAAGACCCTCATATGCTGCAGGGCTTTCgtgagtagtagaaggaatagccagtagggaataatatatctttggatctt #### Ppp1r32_ID2841_10 --> 0 - 2 Original Alignment GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAA---------gg catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACGCTCGTTgggtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from CESAR GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAA---------gg catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACGCTCGTTgggtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from Spaln_aa2Genome GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAAGG catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACgctcgttgggtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from Spaln_nt2Genome GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAAGG catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACgctcgttgggtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from Pairagon GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAA---------GG catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACGCTCGTTGGgtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from Exonerate_protein2genome GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAAGG catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACgctcgttgggtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from Exonerate_coding2genome catcccaaattatgagatactatactatctccacatatgtctgactctaggaaccaacgggatttaatttgaacaaccccagtcatgttcagacttcttatcaggaagatagagagcagaggtacctaagcacctataatcagacgctcgttgggtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt Alignment from GeneWise GAGCCCACAGGGTTCACTCTTAACAACCCCAGCTATGTTCGGAGTTCCTATGAACAGGACAGAGATCAGCGGTACCTGACCACCTACAACCAA---------GG catcccaaattatgagatactatactatctccacatatgtctgactctagGAACCAACGGGATTTAATTTGAACAACCCCAGTCATGTTCAGACTTCTTATCAGGAAGATAGAGAGCAGAGGTACCTAAGCACCTATAATCAGACGCTCGTTGGgtgagtatgtaaaaattgaatctgggagagtgtagtcacttgatttatgt #### Ppp1r32_ID2844_7 --> 0 - 0 Original Alignment GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACAC------gtttgtcaaactattgcagtctgtcggaacaatatgtatgcaccaggtgt Alignment from CESAR GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCAG gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACAC------gtttgtcaaactattgcagtctgtcggaacaatatgtatgcacc Alignment from Spaln_aa2Genome GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCAC gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACACgtttgtcaaactattgcagtctgtcggaacaatatgtatgcaccaggtgt Alignment from Spaln_nt2Genome GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCACCCTCA gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACACGTTT-gtcaaactattgcagtctgtcggaacaatatgtatgcaccaggtg Alignment from Pairagon GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAA------------------------------------------------------- gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACACGTTTGTCAAACTATTGCAGTCTGTCGGAACAATATGTATGCACCAGGTGT Alignment from Exonerate_protein2genome GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCAC gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACACgtttgtcaaactattgcagtctgtcggaacaatatgtatgcaccaggtgt Alignment from Exonerate_coding2genome gctacaacacatgttcaccattaaatgttctcccttttttctttccccaggttctgcatccaggtcgaagtatcagcaagtcatactacctccctctaacacacgtttgtcaaactattgcagtctgtcggaacaatatgtatgcaccaggtgt Alignment from GeneWise GTCCTCCATCCAGGACGGAGTATCACCAAGTCAGACTACCTCCCTGTAACTCAC-------------------------------------------------- gctacaacacatgttcaccattaaatgttctcccttttttctttccccagGTTCTGCATCCAGGTCGAAGTATCAGCAAGTCATACTACCTCCCTCTAACACACGTTTGTCAAACTATTGCAGTCTGTCGGAACAATATGTATGCACCAGGTGT #### Pprc1_ID9724_12 --> 0 - 2 Original Alignment GAAGAGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAgg tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatag------AGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAgggtaagacatatgagtcaacagtgatgtgt Alignment from CESAR GAAGAGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAgg aatctgtgcctgctatataacaggtccaattgtgaacagtgtgggactcgtgtttttgttctgtcttatag------AGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAgggtaagacatatgagtcaacagtgatgtgt Alignment from Spaln_aa2Genome GAAGAGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAGG tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatag------AGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAGGgtaagacatatgagtcaacagtgatgtgt Alignment from Spaln_nt2Genome GAAGAGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAGG tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatag------AGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAGGgtaagacatatgagtcaacagtgatgtgt Alignment from Pairagon GAAGAGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAGG tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatag------AGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAGGgtaagacatatgagtcaacagtgatgtgt Alignment from Exonerate_protein2genome AGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAGG tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatAGAGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAGGgtaagacatatgagtcaacagtgatgtgt Alignment from Exonerate_coding2genome AGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAGG tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatAGAGACGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAGGgtaagacatatgagtcaacagtgatgtgt Alignment from GeneWise GAAGAGAGAAGGGTGGTCTTCATTGGGAAAATACCTGGCCGAATGACTCGGTCGGAGCTGAAACAGAGGTTCTCTGTTTTTGGAGAAATTGAGGAGTGTACCATTCATTTTCGTGTCCAAGG tgcctgctatataacaggtccaattgtgaacagtgtgggaatccttctcgtgtttttgttctgtcttatagAGA------CGGGTGGTCTTCATTGGTAAAACACCTGGACGGATGACTCGGTCAGAACTTAAACAGAGGTTCTCTGTTTTTGGCGAAATTGAGGAGTGTACCATCCACTTTAGGGTGCAAGGgtaagacatatgagtcaacagtgatgtgt #### Prdx5_ID1853_4 --> 0 - 0 Original Alignment ---GTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagTCTGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from CESAR ---GTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagTCTGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from Spaln_aa2Genome GTTCGGCTCCTGGCT---GACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagTCTGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from Spaln_nt2Genome GCAAGGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagTC--TGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from Pairagon ---GTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagTCTGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from Exonerate_protein2genome GTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagtctGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from Exonerate_coding2genome GTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAG ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagtctGTTCGGCTCCTGGCTGACCCCACTGGAGCCTTTGGGAAGgtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca Alignment from GeneWise ggtgccgcccataggaggtaatacaaagctcttgtcaatgtttcttatagtctgttcggctcctggctgaccccactggagcctttgggaaggtaaggtaagagcttctgcacagcaaaaaaatctacaaacagagcaaaca #### Prdx5_ID1854_3 --> 0 - 0 Original Alignment ---ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagATGGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from CESAR ---ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagATGGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from Spaln_aa2Genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagATGGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from Spaln_nt2Genome A---CCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagATGGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from Pairagon AAGACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagATGGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from Exonerate_protein2genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagatgGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from Exonerate_coding2genome ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagatgGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt Alignment from GeneWise ---ACCCACCTGCCTGGGTTTGTGGAGCAAGCTGGAGCTCTGAAGGCCAAGGGAGCGCAGGTGGTGGCCTGTCTGAGCGTTAATGACGTCTTTGTGATTGAAGAGTGGGGTCGAGCCCACCAGGCAGAAGGCAAG agtagccccagggcatgcactgatagtgattttgggtcttgtgttcccagATGGCCCACCTGCCTGGCTTGGTAGAACAGGCTGGAGCTCGGAAAGCCAAAGGTGCACAGGTAGTGGCATGTTTAAGTGTAAATGATGTCTTTGTGGTTGAGGAGTGGGGACGAGCCCATGAAGCAGAAGGTAAAgtgagagatccttctgctagttgtgatagcctaggaccagattgcgattt #### Prpf19_ID3044_3 --> 2 - 0 Original Alignment ttGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAGGATGAGTGG GATGCAGTCATGCTGCA atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagttGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAA---------gtaagaaaatttaagtaattttctcttactcagGATGCAGTCATGCTGCA Alignment from CESAR ttGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAGGATGAGTGG GATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagttGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAA---------gtaagaaaacttcgatgttccctctccccacagGATGCAGT Alignment from Spaln_aa2Genome TTGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAG GATGAGTGGGATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagTTGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAAgtaagaaaatttaagtaattttctcttactcag---------GATGCAGT Alignment from Spaln_nt2Genome TTGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAG GATGAGTGGGATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagTTGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAAgtaagaaaatttaagtaattttctcttactcag---------GATGCAGT Alignment from Pairagon TTGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAG GATGAGTGGGATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagTTGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAAgtaagaaaatttaagtaattttctcttactcag---------GATGCAGT Alignment from Exonerate_protein2genome TTGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAG GATGAGTGGGATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagTTGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAAgtaagaaaatttaagtaattttctcttactcag---------GATGCAGT Alignment from Exonerate_coding2genome TTGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAG GATGAGTGGGATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagTTGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAAgtaagaaaatttaagtaattttctcttactcag---------GATGCAGT Alignment from GeneWise TTGCTCACCCAATCCGACCCAAGCCTCCCTCCGCCACCAGCATCCCAGCCATTCTGAAAGCCTTGCAG GATGAGTGGGATGCAGT atgtgagaggttgcatgcaaggaatatgttttattatgttttcttcttagTTGCACACCCAATTCGACCCAAGCCTCCCTCTGCGACCAGTATTCCAGCTATCCTAAAGGCCTTACAAgtaagaaaatttaagtaattttctcttactcagGAT---------GCAGT #### Prpf19_ID3046_5 --> 2 - 0 Original Alignment CTCGAGAAg ctCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG--------- CTCGAGAAggtgagactcattccactgtcttgttaacttgctgtttctagccTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTGTAATAAACCAGTGCgtgaggtgtgcacccccccactagcagtacctcatgggaactatacagtt Alignment from CESAR CTCGAGAAg ctCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG--------- CTCGAGAAggtgagtctcattccactgtcttgttaacttgctgtttctagccTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTGTAATAAACCAGTGCgtgaggtgtgcacccccccactagcagtacctcatgggaactatacagtt Alignment from Spaln_aa2Genome CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG--------- CTCGAGAAGgtgagactcattccactgtcttgttaacttgctgtttctagCCTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTGTAATAAACCAGTGCgtgaggtgtgcacccccccactagcagtacctcatgggaactatacagtt Alignment from Spaln_nt2Genome CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGT GT CTCGAGAAGgtgagactcattccactgtcttgttaacttgctgtttctagCCTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTgtaataaaccagtgcgtgaggtgtgcacccccccactagcagtacctcatgggaactatacag-T Alignment from Pairagon CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAG------------------------------------------------------------------ CTCGAGAAGgtgagactcattccactgtcttgttaacttgctgtttctagCCTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTGTAATAAACCAGTGCGTGAGGTGTGCACCCCCCCACTAGCAGTACCTCATGGGAACTATACAGTT Alignment from Exonerate_protein2genome CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTT CTCGAGAAGgtgagactcattccactgtcttgttaacttgctgtttctagCCTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTGTAataaaccagtgcgtgaggtgtgcacccccccactagcagtacctcatgggaactatacagtt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTCGAGAAG CTCTGGCTACTCTGAAACCACAGGCTGGGCTTATTGTACCTCAGGCTGTGCCAAGCTCACAGCCCAGTGTTGTG--------- CTCGAGAAGgtgagactcattccactgtcttgttaacttgctgtttctagCCTTGGCCACCCTAAAACCACAGGCTGGCCTGATAGTACCTCAAGCTGTGCCAAGTTCACCACCCAGTGTAATAAACCAGTGCgtgaggtgtgcacccccccactagcagtacctcatgggaactatacagtt #### Prpf19_ID3047_6 --> 0 - 0 Original Alignment GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATGACCCCTGAGATTATCCAGAAG ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGGGAAATG---------------------gtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from CESAR GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGAATGACCCCTGAGATTATCCAGAAG ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGG------------------GAAATGgtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from Spaln_aa2Genome GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGA---ATG ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGGGAAATGgtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from Spaln_nt2Genome GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGG-TGGG--AATG ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGGGAAATGgtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from Pairagon GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGG---------TGGGAAT ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGGGAAATGGTAATgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from Exonerate_protein2genome GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGAATGACC ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGGGAAATGgtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from Exonerate_coding2genome ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagggggctggagatgcaatggatttgggtgagcttgctggggaaatggtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg Alignment from GeneWise GGTGCAGGAGAGCCCATGGATTTGGGTGAGCTGGTGGGAATGACCCCTGAGATTATCCAGAAGCTTCAAGACAAGGCTACTGTGCTAACCACGGAGCGTAAGAAG ggtttttgttgtgggtgtctgtcatgtgatgaaatattctgtcccctcagGGGGCTGGAGATGCAATGGATTTGGGTGAGCTTGCTGGG------------------------------------------------------------GAAATGgtaatgtgagatccatccacatcctccgtttacaaaacaggagcaagctg #### Prpf19_ID3048_7 --> 0 - 0 Original Alignment CTTCAAGACAAGGCTACTGTGCTAACCACGGAG------CGTAAGAAG actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcag---CAA---GAGGCCACTGTGTTAACCACAGACACAGGACAGAAGAAAgtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from CESAR CTTCAAGACAAGGCTACTGTGCTAACCACGGAG------CGTAAGAAG ctaactaattagtgatgcccacttctctgctgtgttttgctttgtttcag---CAAGAG---GCCACTGTGTTAACCACAGACACAGGACAGAAGAAAgtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from Spaln_aa2Genome CCACGGAGCGTAAGAAG actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcagcaagaggccactgtgttaaccacagACACAGGACAGAAGAAAgtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from Spaln_nt2Genome CTTCAAGACAAGGCTACTGTGCTAACCACGGAG------CGTAAGAAG actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcag---CAAG---AGGCCACTGTGTTAACCACAGACACAGGACAGAAGAAAgtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from Pairagon actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcagcaagaggccactgtgttaaccacagacacaggacagaagaaagtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from Exonerate_protein2genome CTTCAAGACAAGGCTACTGTGCTAACCACGGAGCGTAAGAAG actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcagCAAGAGGCCACTGTGTTAACCACAGACACAGGACAGAAGAAAgtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from Exonerate_coding2genome actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcagcaagaggccactgtgttaaccacagacacaggacagaagaaagtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca Alignment from GeneWise actaattagtgatgcccacttcatttctgctgtgttttgctttgtttcagcaagaggccactgtgttaaccacagacacaggacagaagaaagtaagtctggccaatgtggaaaactgcatctttagtgtgaagtgtgtgca #### Prpf19_ID3049_8 --> 0 - 0 Original Alignment ------AGAGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttaccttgactgttcactttgcagCCTGATAGAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from CESAR ------AGAGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttaccttgactgttcactttgcagCCTGATAGAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from Spaln_aa2Genome ----AGAGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttaccttgactgttcactttgcagCCTGATAGAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from Spaln_nt2Genome -GGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttaccttgactgttcactttgcagcctgatagAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from Pairagon --------------------------------------------------------AGAGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG GAAGTGTGTGCACAACTACTTCTGCTTTACCTTGACTGTTCACTTTGCAGCCTGATAGAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from Exonerate_protein2genome AGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttaccttgactgttcactttgcagcctgatagAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from Exonerate_coding2genome GTGCTAACCACGGAGCGTAAGAAGAGAGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttacctTGACTGTTCACTTTGCAGCCTGATAGAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg Alignment from GeneWise CTTCAAGACAAGGCTACTGTGCTAACCACGGAGCGTAAGAAGAGAGGAAAGACTGTCCCCGAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTG gaagtgtgtgcacaactacttctgctttaccttgactgttcactttgcagCCTGAT------------------------------------AGAGGAAAGACCGTCCCCAAGGAGCTGGTGAAACCTGAAGAGCTCAGCAAGTACCGGCAGGTGGCATCCCATGTGgtgagtgctgtgtgttaagtggctctcactgttctgactaatgtggattg #### Pygm_ID1679_3 --> 0 - 1 Original Alignment CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGACGCCTGGCAg tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGGA---------ggtaatgcctgcgagatgttacagaaaagtatttgtagtcttcaagattgt Alignment from CESAR CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGACGCCTGGCAg tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGGAGGTAATGCCtgcgagatgttacagaaaagtatttgtagtcttccaaatggt Alignment from Spaln_aa2Genome CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGACGCCTGGCAG tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGGAGGTAATGCCTgcgagatgttacagaaaagtatttgtagtcttcaagattgt Alignment from Spaln_nt2Genome CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGACGCCTGGCAG tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGGAGGTAATGCCTgcgagatgttacagaaaagtatttgtagtcttcaagattgt Alignment from Pairagon CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGACGCCTGGCAG tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGG---------AGgtaatgcctgcgagatgttacagaaaagtatttgtagtcttcaagattgt Alignment from Exonerate_protein2genome CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGAC tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGGAGgtaatgcctgcgagatgttacagaaaagtatttgtagtcttcaagattgt Alignment from Exonerate_coding2genome tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagctgggcttagacatggaggagttggaggagattgaggaggatgcagggttgggaaatggtggcctgggaggtaatgcctgcgagatgttacagaaaagtatttgtagtcttcaagattgt Alignment from GeneWise CTGGGCTTGGACATGGAGGAGTTGGAGGAGATCGAGGAGGATGCAGGGTTGGGCAATGGGGGCCTGGGA- ------------- tgtgagcatttgagctttacagatgccagtctttgtgatttaaattgtagCTGGGCTTAGACATGGAGGAGTTGGAGGAGATTGAGGAGGATGCAGGGTTGGGAAATGGTGGCCTGGGAGgtaatgcctgcgagatgttacagaaaagtatttgtagTCTTCAAGATTGT #### Pygm_ID1684_8 --> 0 - 0 Original Alignment TTCTTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctag---TTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from CESAR TTCTTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG agttgtgaccatctgacatgatatgcattaatgaatgtcatttttgctag---TTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from Spaln_aa2Genome TTCTTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctag---TTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from Spaln_nt2Genome TTCTTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctag---TTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from Pairagon TTCTTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctag---TTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from Exonerate_protein2genome TTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctagTTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from Exonerate_coding2genome TTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctagTTTGAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt Alignment from GeneWise TTCTTTGAAGGGAAGGAGCTGCGGCTGAAGCAGGAGTACTTTGTGGTGGCTGCCACCCTCCAGGACATCATCCGACGTTTCAAGTCCTCCAAGTTTGGCAGCCGTGATCCTGTGCGCACAAACTTCGATGCCTTCCCTGATAAG tgtgaccatctgacatgatatgatgcattaatgaatgtcatttttgctagTTT---GAAGGGAAGGAGCTGCGGCTTAAACAGGAGTACTTGGTGGTGGCTGCCAGCCTTCAAGACATCATCCGATGTTTCAAGTCCTCTAAGTTAGGCAGCCGTGATCCTGTGCGCACAAACTTTGATGCCTTCCCTGATAAGgtaccttctggttcaagttgttactttacccaccatctcacaatgtattt #### Pygm_ID1686_10 --> 0 - 0 Original Alignment GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--------- acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATGACTCTgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from CESAR GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--------- acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATGACTCTgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from Spaln_aa2Genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--------- acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATGACTCTgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from Spaln_nt2Genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--------- acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATGACTCTgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from Pairagon GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--------- acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATGACTCTgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from Exonerate_protein2genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATgactctgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from Exonerate_coding2genome GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAACCGG acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATgactctgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat Alignment from GeneWise GCCTGGGACGTAACAGTGAAGACCTGTGCCTACACCAACCACACGGTGCTGCCTGAAGCCCTGGAGCGCTGGCCAGTGCACCTCATGGAGACACTGCTGCCCCGCCACTTGCAGATCATTTACGAGATCAACCAGCGTTTCCTTAAC--------- acaaagatgggtggagggtgactaatgctgttcaccgttgtcttctacagGCCTGGGATGTTACAGTAAAGACCTGCGTCTACACTAACCACACAGTGCTGCCTGAAGCTCTAGAGCGATGGCCTGTGCATCTCATGGAGTCACTGCTACCCCGTCACTTGCAGATAATTTACGAGATTAATCAGTGTTTCCTGAATAATGACTCTgtatcaacagaatgatgaggaggagcctgaggagcttgagtatgatgtat #### Pygm_ID1687_11 --> 0 - 2 Original Alignment CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCat gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAG---atgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from CESAR CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCat gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAG---atgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from Spaln_aa2Genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAAC gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAGATgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from Spaln_nt2Genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTC---AAAAAGATgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from Pairagon CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAAC gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAGATgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from Exonerate_protein2genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAG---ATgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from Exonerate_coding2genome CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAACCAT gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAG---ATgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc Alignment from GeneWise CGGGTGGCGGCTGCATTCCCTGGGGACGTAGATAGGCTGCGGCGCATGTCACTCGTGGAGGAAGGAGCAGTGAAACGCATCAACATGGCACACCTGTGCATTGCTGGCTCGCACGCTGTCAACGGCGTGGCTCGCATCCATTCGGAGATCCTCAAGAAAAC gagagggaagagttctgaaccagggatcactataaccctctgctccctagCGGGTGGCAGCTGCATCCCCAGGGGATGTAGACAGGCTGTGGCGCATGTCACTTGTCAAGGATGGAGCAGTAAGGCGCATCAACATGTCACATCTGTGCATTACAGGCTCACATGCTGTCAACAGTCTGGCCCGAATCCTTTCAGAGATCCTCAAAAAGATgtaagtagtattgagattgaggtaggcaacagggccccaagatagaaagc #### Pygm_ID1690_14 --> 0 - 1 Original Alignment GAAAACAAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACc cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcag------AAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAGAGC---CCTGAGTGC------CAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACcgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from CESAR GAAAACAAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACc ccagagcattgtttgccctttcaccctttaccatcaccctctctcctcag------AAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAGAGC---CCTGAGTGC------CAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACcgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from Spaln_aa2Genome GAAAACAAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACC cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcag------AAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAGAGCCCT---------GAGTGCCAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACCgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from Spaln_nt2Genome AAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACC cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcagAAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGT---AAAGAGCCCTGAGT------GCCAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACCgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from Pairagon TGAAACAGGAAAACAAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACC cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcag--------------AAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAGAG---CCCTGAGTGC------CAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACCgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from Exonerate_protein2genome AAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACC cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcagAAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAG---------AGCCCTGAGTGCCAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACCgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from Exonerate_coding2genome AAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACC cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcagAAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAG---------AGCCCTGAGTGCCAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACCgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag Alignment from GeneWise AAGTTGAAGTTCTCTGCATACCTCGAGAGGGAATACAAAGTCCACATCAACCCCAACTCGCTCTTTGACGTCCAGGTGAAAAGGATTCATGAGTACAAGCGGCAGCTCCTCAACTGCCTGCACATCATCACCTTGTATAACC cattgtttgccctttcaccccaaacctttaccatcaccctctctcctcagAAGTTAAAGTTCTCTGCATACCTTGAAAGTGAGTATAAAGTCCACATTAACCCCAATTCTCTCTTTGATGTCCAAGTAAAG---------AGCCCTGAGTGCCAACTGCTCAATTGCCTGCAAATTATTACTTTGTATAACCgtaagatgcttagaattgccaacaacctgccattgtatggtgtagaaaag #### Pygm_ID1691_15 --> 2 - 0 Original Alignment gcATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaaggaATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGG---gtactcagtacagactgatgcatgaaaaaaggagattgatgcatgagaat Alignment from CESAR gcATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaaggaATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGG---gtactcagtacagactgatgcatgaaaaaaggagattgatgcatgag Alignment from Spaln_aa2Genome GCATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAGGCTG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaagGAATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGGGTACTCAgtacagactgatgcatgaaaaaaggagattgatgcatgagaat Alignment from Spaln_nt2Genome GCATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaagGAATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGG---Ggtactcagtacagactgatgcatgaaaaaaggagattgatgcatgagaat Alignment from Pairagon GCATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCA------------------------------------------------- tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaagGAATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGGGTACTCAGTACAGACTGATGCATGAAAAAAGGAGATTGATGCATGAGAAT Alignment from Exonerate_protein2genome GCATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaagGAATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGGGTActcagtacagactgatgcatgaaaaaaggagattgatgcatgagaat Alignment from Exonerate_coding2genome GCATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaagGAATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGGGTActcagtacagactgatgcatgaaaaaaggagattgatgcatgagaat Alignment from GeneWise GCATCAAAAGGGAGCCCAATAGGTTTATGGTGCCGAGGACTATCATGATTGGAGGCAAGGCTG tccgagcattttcagagcaagagtaactaattgtgttctttgtttctaagGAATAAAAAGGGAGCTCAATCGGTTCATGGTGCCAAAGACTATCATGATTGGAGGGGTACTCAgtacagactgatgcatgaaaaaaggagattgatgcatgagaat #### Rab1b_ID845_3 --> 0 - 0 Original Alignment GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaagtggacttattttgtcatcacag------------------------ATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct Alignment from CESAR GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT gccagatgttggtttgtttcccactaagtggacttattttgtcatcacag------------------------ATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgctccctctgcatttc Alignment from Spaln_aa2Genome CACTTACACA---GAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaagTGGACTTATTTTGTCATCACAGATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct Alignment from Spaln_nt2Genome ATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaagtggacttattttgtcatcacagATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct Alignment from Pairagon GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaagtggacttattttgtcatcacag------------------------ATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct Alignment from Exonerate_protein2genome GATGACACTTACACAGAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaAGTGGACTTATTTTGTCATCACAGATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct Alignment from Exonerate_coding2genome GAGAGCTACATCAGCACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaagtggacttattttgTCATCACAGATCAGCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct Alignment from GeneWise CACCATCGGTGTGGATTTCAAGATTCGAACCATTGAGCTGGACGGCAAAACCATCAAACTGCAGATT tcggggctcctgttatccctgtggaaagtggacttattttgtcatcacagatcagCACCATTGGTGTTGATTTTAAGATACGGACAATTAAGCTGGATGGCAAAACCATCAAACTGCAGATTgtgagctctaatctgatcctgttttctcgtggctgcttatcttttggcct #### Rab3il1_ID2652_7 --> 0 - 2 Original Alignment CTCTCAGCTCTGGTTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCaa aatcttgtagcttcataagttggtctcttaactttttctgtttttaacag---------TTAGTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCaagtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from CESAR CTCTCAGCTCTGGTTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCaa gcaatctgcaatcttgtagcttcattcttaactttttctgtttttaacag---------TTAGTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCaagtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from Spaln_aa2Genome TTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCAA aatcttgtagcttcataagttggtctcttaactttttctgtttttaacagttagTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCAAgtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from Spaln_nt2Genome CTCTCAGCT CTGGTTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCAA atcttgtagCT-TCATAAgttggtctcttaactttttctgtttttaacagTTAGTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCAAgtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from Pairagon CTCTCAGCTCTGGTTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCAA aatcttgtagcttcataagttggtctcttaactttttctgtttttaacag---------TTAGTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCAAgtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from Exonerate_protein2genome CTCTCAGCTCTGGTTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCAA aatcttgtagcttcataagttggtctcttaactttttctgtTTTTAACAGTTAGTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCAAgtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from Exonerate_coding2genome CTCTCAGCTCTGGTTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCAA aatcttgtagcttcataagttggtctcttaactttttctgtTTTTAACAGTTAGTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCAAgtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa Alignment from GeneWise TTCGGACTGCTGTGGAGGACAACACACTCACCATTGAGCCTGTGGCTTCACAGACACTGCCCGCTGTGAAGGTGCCCACTGTTGAGTGTAACAACACCAA aatcttgtagcttcataagttggtctcttaactttttctgtttttaacagttagTTCAAACTGCTGTAGAAGACAATACACTCACCATTGAGCCCGTTGCTTCACAGACACTGCCGGCAGTAAAGGTACCTAGTATTGAGTGTAACAACACCAAgtgagctcatacatgcctctgaaaggctcaaaatttctagatttagctaa #### Rasgrp2_ID1711_10 --> 0 - 0 Original Alignment CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCAGAGCACATTGAGAAGATGGTGGAG atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCGACCT---GTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAA------------------------------------gttagtccatgctaatttttctgagactctaccccgctcgcgaccgaacc Alignment from CESAR CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGGCAGAGCACATTGAGAAGATGGTGGAG atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCGA---CCTGTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAA------------------------------------gttagtccatgcta Alignment from Spaln_aa2Genome CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCCTTGGTGG atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCGA---CCTGTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAAGTTAGTCCATgctaatttttctgagactctaccccgctcgcgaccgaacc Alignment from Spaln_nt2Genome CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAA atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCG---ACCTGTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAAgttagtccatgctaatttttctgagactctaccccgctcgcgaccgaacc Alignment from Pairagon CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAA atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCGA---CCTGTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAAgttagtccatgctaatttttctgagactctaccccgctcgcgaccgaacc Alignment from Exonerate_protein2genome CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAG atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCGA---CCTGTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAAGttagtccatgctaatttttctgagactctaccccgctcgcgaccgaacc Alignment from Exonerate_coding2genome ---CCCACCAGCTGCACCCCGCCT ATACCCACTTCTACTACAACCCCTcaggaacatcgtggccctgctttcagcctaccagtccaacaagttgtatgtcacctcctcgacctgtgtttgaagagtggacatcagctgctaaacctaatcttgatcaagttagtccatgctaatttttctgagactctaccccgctcgcgaccgaacc Alignment from GeneWise CCAACCAGCCCCACCAGCTGCACCCCGCCTCCCCGGCCCCCTGTGTTGGAAGAGTGGACCTCAGTTGCCAAGCCTAAGCTGGACCAAGCC- atacccacttctactacaacccctcaggaacatcgtggccctgctttcagCCTACCAGTCCAACAAGTTGTATGTCACCTCCTCGACCT---GTGTTTGAAGAGTGGACATCAGCTGCTAAACCTAATCTTGATCAAGTTAgtccatgctaatttttctgagactctaccccgctcgcgaccgaacc #### Rce1_ID576_6 --> 2 - 1 Original Alignment CTTTTTTGGAGTCg ccCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAg CTTTCTTGGGGTTggtgcgtttgtgtagtttcctgtgttttgctggatagct---TTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAggtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from CESAR CTTTTTTGGAGTCg ccCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAg CTTTCTTGGGGTTggtacgtttatttagtttcctgtgttttgctggatagct---TTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAggtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from Spaln_aa2Genome CTTTTTTGGAGTCG CCCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAG CTTTCTTGGGGTTGgtgcgtttgtgtagtttcctgtgttttgctggatagCT---TTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAGgtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from Spaln_nt2Genome CTTTTTTGGAGTCG CCCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAG CTTTCTTGGGGTTGgtgcgtttgtgtagtttcctgtgttttgctggatagC---TTTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAGgtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from Pairagon CTTTTTTGGAGTCG CCCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAG CTTTCTTGGGGTTGgtgcgtttgtgtagtttcctgtgttttgctggatagcttttcag-----------CACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAGgtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from Exonerate_protein2genome CTTTTTTGGAGTCG CCCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAG CTTTCTTGGGGTTGgtgcgtttgtgtagtttcctgtgttttgctggatagCT---TTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAGgtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from Exonerate_coding2genome CTTTTTTGGAGTCG CCCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAG CTTTCTTGGGGTTGgtgcgtttgtgtagtttcctgtgttttgctggatagCT---TTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAGgtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag Alignment from GeneWise CTTTTTTGGAGTCG CCCATTTTCACCACATTATTGAGCAGCTGCGCTTCCGCCAGAGCAGTGTGGGAAGTATCTTCGTGTCTGCAG CTTTCTTGGGGTTGgtgcgtttgtgtagtttcctgtgttttgctggatagCT---TTTCAGCACATTATAGAGCAGTTACGCTTCCGCCAGAGCAGTGTGGGGAGCATCTTTGTGTCTACAGgtaagagggaaaagtagtaatgaagagaaaaaagggctggctctttatag #### Rce1_ID577_5 --> 2 - 1 Original Alignment ccCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTTTTTGGAGTCg ccCATTTTCACCAC gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagcaCCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTCTTT---------ggtgaggttagtggtggctgtctcctctaacctccagctCATTTTCAGCAC Alignment from CESAR ccCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTTTTTGGAGTCg ccCATTTTCACCAC gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagcaCCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTCTTTGGTGAGGTTagtgtgtagttctcctttttaattttagctCATTTTCAGCAC Alignment from Spaln_aa2Genome CCCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTT- TTTGGAGTCGCCCAT gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagCACCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTCTTTGgtgaggttagtggtggctgtctcctctaacctcca gCTCAT Alignment from Spaln_nt2Genome CCCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTTTTTGGAGTCG-------------------------------CCCATTTTCA gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagCACCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTCTTTGGTG----AGGTTAGTGGTGGCTGTCTCCTCTAACCTCCAGCTCATTTTCA Alignment from Pairagon CCCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTTTTTGGAGTCG CCCATTTTCACCAC gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagCACCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTCTTT---------GgtgaggttagtggtggctgtctcctctaacctccagCTCATTTTCAGCAC Alignment from Exonerate_protein2genome CCCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTTTTTGGAGTC GCCCATTTTCACCAC gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagCACCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTC---TTTGGTGAGgttagtggtggctgtctcctctaacctccaGCTCATTTTCAGCAC Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCCCTCGTTCTTGGGCCCGCTGCCTCACAGACATGCGCTGGCTACGAAACCAAGTTATTGCACCGCTGACAGAGGAGCTGGTGTTCCGGGCTTGCATGCTGCCCATGCTAGCGCCGTGCACGGGTCTGGGCCCTGCTGTGTTCACCTGCCCACTCTTTTTTGGAGTCG CCCATTTTCACCAC gtcataggctagcaagtaggtacatgagtaaccgtccctctatcacccagCACCCTGTTCATGGGCTCAATGTCTGACTGAAATGCGCTGGCTGAGTAACAAAGTTATTGCACCATTGACTGGGGAGTTGGTGTTCCGGGCATGCATGCTGCCCATGCTAGCACCATGTACTGGTCTCAGTCCAGCGGTGTTTGCATGCCCACTCTTTGGTGAGGTTAgtggtggctgtctcctctaacctccagCTCATTTTCAGCAC #### Rce1_ID578_4 --> 0 - 1 Original Alignment ---------ATCCTTTTCCTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGg aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagAAACTGCTGATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGggtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from CESAR ---------ATCCTTTTCCTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGg aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagAAACTGCTGATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGggtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from Spaln_aa2Genome ATCCTTTTCCTGGGTCCA---------CTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGG aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagAAACTGCTGATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGGgtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from Spaln_nt2Genome TGATCCTTTTCCTGGGT-------CCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGG aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagAAACTGCTGATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGGgtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from Pairagon ---------ATCCTTTTCCTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGG aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagAAACTGCTGATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGGgtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from Exonerate_protein2genome ATCCTTTTCCTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGG aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagaaactgctgATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGGgtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from Exonerate_coding2genome ATCCTTTTCCTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGG aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagaaactgctgATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGGgtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag Alignment from GeneWise ---------ATCCTTTTCCTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCTTGTGACCTGACAGATGGGCTGAAGGTTGTCCTGG aaatgtgagaagtactgcaccttatgctggctgtttgtgctcctgtctagAAACTGCTGATCCTTTTCCCAGGTCCACTGACACAGCTTTCTATGGACTGTCCCTGTGACTTGACAGATGGATTGAAAGTTGTTCTGGgtacgttccacgtcttgcgaggagagaagaatacaaaagcagtgcaaaag #### Rce1_ID579_3 --> 0 - 0 Original Alignment CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATG--------------------- cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGGATCAAATTCCCATGATCAGTgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc Alignment from CESAR CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATG--------------------- cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGGATCAAATTCCCATGATCAGTgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc Alignment from Spaln_aa2Genome CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATG------ATCCTTTTCCTGG cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGGATCAAATTCCCATGATCAgtgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc Alignment from Spaln_nt2Genome CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATGA-------TCC-------- cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGGATCAAATTCCCATGATCAgtgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc Alignment from Pairagon CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATG--------------------- cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGGATCAAATTCCCATGATCAGTgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc Alignment from Exonerate_protein2genome CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATG cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGgatcaaattcccatgatcagtgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CCAGGCACATCACTGCTTACCTTGATGGGCTTCAGGCTGGAGGGCATTTTCCCAGCAGCGCTGCTGCCCCTGCTGCTAACTATG--------------------- cataccgaggaatcttttatctgcaacatcttaaacttttaatatttcagCCTGGAACATCACTCCTCATCTTGATGGGTTTCAGGCTAGAGGGCATTTTCCCTGCAGCATTGCTGCCACTGCTATTAACTATGGATCAAATTCCCATGATCAGTgtaagccatgcttggtatttttacaacattattatagtcacttaatggcc #### Rcor2_ID2095_6 --> 1 - 0 Original Alignment tGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagtGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCC---------gtaagggccgtatcggtcatgccacattggatcccataccataccaaccc Alignment from CESAR tGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagtGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCC---------gtaagggccgtatcggtcatgccacattggatcccatacca Alignment from Spaln_aa2Genome TGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagTGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCCGTAAGGGCCgtatcggtcatgccacattggatcccataccataccaaccc Alignment from Spaln_nt2Genome TGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagTGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCCGTAAGGGCCgtatcggtcatgccacattggatcccataccataccaaccc Alignment from Pairagon TGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCC tgtgacttgggggaatgataatggagtggatgagatatattgatttttagTGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCCgtaagggccgtatcggtcatgccacattggatcccataccataccaaccc Alignment from Exonerate_protein2genome TGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagTGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCCGTAAGGGCCgtatcggtcatgccacattggatcccataccataccaaccc Alignment from Exonerate_coding2genome TGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagTGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCCGTAAGGGCCgtatcggtcatgccacattggatcccataccataccaaccc Alignment from GeneWise TGATGAACTAGAAGAGGGACGAGGAGCTGTGAGTGAGGGGGAACCGGATACTGGAGACCCCAAGCGAGAG tgtgacttgggggaatgataatggagtggatgagatatattgatttttagTGATGAAGTAGATGAGGGGCAGCGGGCCATCAGTGAGGGGGATCCAGATACTGGGGATCCCGTAAGGGCCgtatcggtcatgccacattggatcccataccataccaaccc #### Rcor2_ID2098_9 --> 0 - 1 Original Alignment GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAA---g cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGATggtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from CESAR GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAA---g cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGATggtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from Spaln_aa2Genome GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAA---G cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGATGgtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from Spaln_nt2Genome GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAAGCT- cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGATGgtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from Pairagon GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAAG--- cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGATGgtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from Exonerate_protein2genome GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAAG cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGatggtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from Exonerate_coding2genome GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAAG cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGatggtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc Alignment from GeneWise GCTAATACCAAGTTCAACTCCCGCTGGACCACTGATGAGCAACTTCTAGCTGTTCAAGCT- cctcccttctcccattttttcattgatatggggtggtgcctgttttccagGCTAATACCAAATTCAACTCCCGCTGGACCACTGATGAGGAACTTTTAGCAGTTCAAGATGgtaagctacgctactgtgggtttccaagaatctcggagatgattgagacc #### Rela_ID1126_3 --> 2 - 0 Original Alignment agCCAGCCCAGGCTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG agggcacaccatactgcctttttggcctccccaccactgtcccatcccagaa---------GCAGCTGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from CESAR agCCAGCCCAGGCTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG ctggaggcaagggcacaccatactgcctccccaccactgtcccatcccagaa---------GCAGCTGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from Spaln_aa2Genome CTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG agggcacaccatactgcctttttggcctccccaccactgtcccatcccagaagCAGCTGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from Spaln_nt2Genome AGCCAGCCCAGGCTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG agggcacaccatactgcctttttggcctccccaccactgtcccatcccagAAGCAG---------CTGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from Pairagon AGCCAGCCCAGGCTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG agggcacaccatactgcctttttggcctccccaccactgtcccatcccagAAGCAGC---------TGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from Exonerate_protein2genome TCAGAGCCAGCCCAGGCTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG agggcacaccatactgcctttttggcctccccaccacTGTCCCATCCCAGAAGCAGCTGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from Exonerate_coding2genome agggcacaccatactgcctttttggcctccccaccactgtcccatcccagaagcagctggtccttatgtagacatcatcaaacaaccaaaccaacaaggccatttccactataaatctgatgggcactccgaaggtggtatccctggtgagaggagcatggatactaaaaaaacacatcccactataaaggtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc Alignment from GeneWise GACGATCTGTTTCCCCTCATCTTTCCCTCAGAG---CCAGCC---CAGGCTTCTGGGCCTTATGTGGAGATCATCGAACAGCCGAAGCAACGGGGCATGCGATTCCGCTATAAATGCGAGGGGCGCTCAGCGGGCAGTATTCCTGGCGAGAGAAGCACAGATACCACCAAGACACACCCCACCATCAAG agggCACACCATACTGCCTTTTTGGCCTCCCCACCACTGTCCCATCCCAGAAGCAGCTGGTCCTTATGTAGACATCATCAAACAACCAAACCAACAAGGC---CATTTCCACTATAAATCTGATGGGCACTCCGAAGGTGGTATCCCTGGTGAGAGGAGCATGGATACTAAAAAAACACATCCCACTATAAAGgtacctaataaagtccttgtatggcaaacaaggaaagaagtcttggtatc #### Rela_ID1128_5 --> 1 - 1 Original Alignment cTTCCAGAACCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACg ctttccttagcaaatctaacaaatctttatataattattttcttttctagt---------TTAGGCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACggtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from CESAR cTTCCAGAACCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACg agaacatgactttccttagcaaatctttatataattattttcttttctagt---------TTAGGCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACggtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from Spaln_aa2Genome CTTCCAGAACCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACG ctttccttagcaaatctaacaaatctttatataattattttcttttctagT---------TTAGGCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACGgtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from Spaln_nt2Genome CCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACG ctttccttagcaaatctaacaaatctttatataattattttcttttctagTTTAGGCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACGgtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from Pairagon CTTCCAGAACCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACG ctttccttagcaaatctaacaaatctttatataattattttcttttctagtttag--------------GCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACGgtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from Exonerate_protein2genome CTTCCAGAACCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACG ctttccttagcaaatctaacaaatctttatataattattttCTTTTCTAGTTTAGGCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACGgtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from Exonerate_coding2genome ctttccttagcaaatctaacaaatctttatataattattttcttttctagtttaggcatacagtgtgtgaaaaagcgcgacctggcacaagcaataagtcagcgaattcagactaccaataactcatttcacggtaattagcagggcagaaaggaattccatctctatatggaccattaatct Alignment from GeneWise CTTCCAGAACCTGGGGATCCAGTGTGTGAAGAAGCGAGACCTGGAGCAAGCCATTAGCCAGCGAATCCAGACCAACAATAACCCCTTTCACG ctttccttagcaaatctaacaaatctttatataattattttcttttctagT---------TTAGGCATACAGTGTGTGAAAAAGCGCGACCTGGCACAAGCAATAAGTCAGCGAATTCAGACTACCAATAACTCATTTCACGgtaattagcagggcagaaaggaattccatctctatatggaccattaatct #### Rin1_ID810_5 --> 1 - 1 Original Alignment aGCCATTCATCAGGCAGCCACCCACAAAGAGCTGGAGGCCATCTCCCATCTGGGCATGg ttcctccctgatggcttttcccccaggcctggaagccattcttcccacaggGCGATTCATCAGGCAGCCACCCACAAAGAG---------------------------ggtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa Alignment from CESAR aGCCATTCATCAGGCAGCCACCCACAAAGAGCTGGAGGCCATCTCCCATCTGGGCATGg ttcctccctgatggcttttcccccaggcctggaagccattcttcccacaggGCGATTCATCAGGCAGCCACCCACAAAGAG---------------------------ggtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa Alignment from Spaln_aa2Genome AGCCATTCATCAGGCAGCCACCCACAAAGAGCTGGAGGCCATCTCCCATCTGGGCATG------G ttcctccctgatggcttttcccccaggcctggaagccattcttcccacagGGCGATTCATCAGGCAGCCACCCACAAAGAGGGTAAGTATCCCCAGCAGTTACACAAAACCGACAgcgccgccttttcacaa Alignment from Spaln_nt2Genome AGCCATTCATCAGGCAGCCACCCACAAAGAGC ttcctccctgatggcttttcccccaggcctggaagccattcttcccacagGGCGATTCATCAGGCAGCCACCCACAAAGAGGgtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa Alignment from Pairagon AGCCATTCATCAGGCAGCCACCCACAAAGAGCTGGAGGCCATCTCCCATCTGGGCATGG ttcctccctgatggcttttcccccaggcctggaagccattcttcccacagGGCGATTCATCAGGCAGCCACCCACAAAGA---------------------------GGgtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa Alignment from Exonerate_protein2genome AGCCATTCATCAGGCAGCCACCCACAAAGAGC ttcctccctgatggcttttcccccaggcctggaagccattcttcccacagGGCGATTCATCAGGCAGCCACCCACAAAGAGGgtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa Alignment from Exonerate_coding2genome AGCCATTCATCAGGCAGCCACCCACAAAGAGC ttcctccctgatggcttttcccccaggcctggaagccattcttcccacagGGCGATTCATCAGGCAGCCACCCACAAAGAGGgtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa Alignment from GeneWise ttcctccctgatggcttttcccccaggcctggaagccattcttcccacagggcgattcatcaggcagccacccacaaagagggtaagtatccccagcagttacacaaaaccgacagcgccgccttttcacaa #### Rnaseh2c_ID1103_2 --> 2 - 0 Original Alignment ggCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC------------------------------------------------ cataggtcttgaggtccatgggtttgactgactttgggcatggactgcaggaTTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGGTCACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTGGAGAGAGTCTTACACCGGGTTGATCTGGGCAATGCACGGCTCAGCTGCTTTATAGCTATGgtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from CESAR ggCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC cataggtcttgaggtccatgggtttgactgactttgggcatggactgcaggaTTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGGTCACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTGGAGAGA------gtcttacaccgggttgatctgggcaatgcacggctcagctgctttatagctatggtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from Spaln_aa2Genome GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC------ cataggtcttgaggtccatgggtttgactgactttgggcatggactgcagGATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGGTCACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTGGAGAGAGTCTTACACCGGgttgatctgggcaatgcacggctcagctgctttatagctatggtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from Spaln_nt2Genome GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGGGACTTC cataggtcttgaggtccatgggtttgactgactttgggcatggactgcagGATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGGTCACAGAAGATGATGCCCAGGAACCATTGGAGAGAGT---CTTACACCGGGTTGATCTGGGCAATGC--AC--GGCTC---AGCTGCTTTATAGCTA--TGgtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from Pairagon GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATG cataggtcttgaggtccatgggtttgactgactttgggcatggactgcagGATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGgtcacagaagatgatgcccaggaaccattggagagagtcttacaccgggttgatctgggcaatgcacggctcagctgctttatagctatggtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from Exonerate_protein2genome GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAG cataggtcttgaggtccatgggtttgactgactttgggcatggactgcagGATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGGTCACAGAAGATGATGCCCAGgaaccattggagagagtcttacaccgggttgatctgggcaatgcacggctcagctgctttatagctatggtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from Exonerate_coding2genome cataggtcttgaggtccatgggtttgactgactttgggcatggactgcaggattacaggtaccatttcatggctgtggcttgtggggtgaggaggtagctgtgcctccagagtttgcaggatttgtaatggtcacagaagatgatgcccaggaaccattggagagagtcttacaccgggttgatctgggcaatgcacggctcagctgctttatagctatggtgggtatttagagagagtactagtgggcatgaagagattatacaagtga Alignment from GeneWise GGCTACAGGCGTCGTTTCGCGGTCGCGGCCTGCGGGGCGAGGAGGTAGCTGTGCCGCCAGGGTTTGCGGGATTCGTGATGGTGACGGAGGAGAAGGGAGAGGGGTTGATAGGGAAACTGAACTTCTCCGGGGACGCGGAGGACAAAGCGGACGAGGCGCAGGAGCCGCTGGAGCGG cataggtcttgaggtccatgggtttgactgactttgggcatggactgcagGATTACAGGTACCATTTCATGGCTGTGGCTTGTGGGGTGAGGAGGTAGCTGTGCCTCCAGAGTTTGCAGGATTTGTAATGGTCACAGAA------------------------------------------------------------GATGATGCCCAGGAACCATTGGAGAGAgtcttacaccgggttgatctgggcaatgcacggctcagctgctttatagctatggtgggtatttagagagagtactagtgggcatgaagagattatacaagtga #### Rom1_ID2497_2 --> 1 - 0 Original Alignment cCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAG------ ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagtCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCACGA------TGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGATATGCgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from CESAR cCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAG------ ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagtCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCA---CGA---TGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGATATGCgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from Spaln_aa2Genome CCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAG------ ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagTCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCA------CGATGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGATATGCgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from Spaln_nt2Genome CCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAGAT---- ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagTCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCA------CGATGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGATATGCgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from Pairagon CCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAG------ ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagtcacattcccag------------CAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCACGA------TGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGATATGCgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from Exonerate_protein2genome CCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAG ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagTCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCA------CGATGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGatatgcgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from Exonerate_coding2genome CCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAG ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagTCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCA------CGATGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGatatgcgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag Alignment from GeneWise CCGGATCCAGAGCAATGTGGAAGGCTTATATCTGATTGATGGCGTCCCCTTCTCCTGTTGTAATCCCCACTCACCCCGGCCTTGCCTGCAAAGCCAACTCTCGGACCCCTATGCCCATCCACTCTTCGATCCTCGGCAGCCCAACCTAAACCTCTGGGCCCAAGGGTGCCATGAAGTGCTGCTGGAACACCTGCAGGGTTTATCAGGCACACTGGGAAGTATTCTGGCTGTCACCTTATTGCTGCAGATTCTA ttgtataactgctgacaagatcttattggaacaagtgccttgctccttagTCACATTCCCAGCAATATAGAAGGATTATACCTGATTGATGGTGTTCCGTTCTCCTGCTGTAATCCCCACTCACGA------TGCTTGCAAAGCCAACTCTCAGACCCCTATGCTCATCCCCTTCTC---CCTCAGCAGCCAAATCTAAACCTGTGGTCCCAGGGATGCCACAAAGTGCTGTTCGAACGCCTGCAAGGATTATCTGGAACATTGGGGACAATTCTGGTGATTACTTTATTGTTGCAGATATGCgtgaggcatcaaaattccatgttcctcatcaagatctctaacctctgtag #### Rpp30_ID7088_8 --> 0 - 0 Original Alignment AATGTAATTCTGTCCAGTGCTGCAGAAAGG tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcag---GTTATTCTGTCAAGTACAGCAGCAAGAgtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from CESAR AATGTAATTCTGTCCAGTGCTGCAGAAAGG cagtatgaaactgctcattggtttctcaagtaagtgtttgttttcttcag---GTTATTCTGTCAAGTACAGCAGCAAGAgtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from Spaln_aa2Genome AATGTAATTCTGTCCAGTGCTGCAGAAAGG tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcag---GTTATTCTGTCAAGTACAGCAGCAAGAgtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from Spaln_nt2Genome GTAATTCTGTCCAGTGCTGCAGAAAGG tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcagGTTATTCTGTCAAGTACAGCAGCAAGAgtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from Pairagon GAAAGAATGTAATTCTGTCCAGTGCTGCAGAAAGG tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcag--------GTTATTCTGTCAAGTACAGCAGCAAGAgtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from Exonerate_protein2genome tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcaggttattctgtcaagtacagcagcaagagtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from Exonerate_coding2genome tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcaggttattctgtcaagtacagcagcaagagtatgcttagactggcagtggttaagacacttaacataggcaactctctt Alignment from GeneWise tatgaaactgctcattggtttctcttcaagtaagtgtttgttttcttcaggttattctgtcaagtacagcagcaagagtatgcttagactggcagtggttaagacacttaacataggcaactctctt #### Rps6ka4_ID1804_16 --> 2 - 0 Original Alignment ggCTACTGACAGTCGACCCCGCCAAGCGGCTGAAGCTGGAGGGGCTGCGTAGCAGCTCGTGGCTTCAGGACGGCAGCGCGCGCTCCTCGCCCCCGCTCCGCACGCCGGATGTGCTGGAGTCCTCTGGGCCAGCTGTGCGTTCCGGGCTCAATGCCACTTTCATG ctcttgaacacctatcattcccgctttgttttatttcaacttttctccaggg------------------------------------GAGGGGCTGCGTAGCAGCTCGTGGCTACAGGATGGTAGTGCACGCTCCTCACCACCACTATGCACCCCAGATGTGCTGGAGTTCTCTGGACCAGCTGTGCGTTCTGGGCTGAATGCCACATTTATGgtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag Alignment from CESAR ggCTACTGACAGTCGACCCCGCCAAGCGGCTGAAGCTGGAGGGGCTGCGTAGCAGCTCGTGGCTTCAGGACGGCAGCGCGCGCTCCTCGCCCCCGCTCCGCACGCCGGATGTGCTGGAGTCCTCTGGGCCAGCTGTGCGTTCCGGGCTCAATGCCACTTTCATG gattttagtcacattcattcccgctttgttttatttcaacttttctccaggg------------------------------------GAGGGGCTGCGTAGCAGCTCGTGGCTACAGGATGGTAGTGCACGCTCCTCACCACCACTATGCACCCCAGATGTGCTGGAGTTCTCTGGACCAGCTGTGCGTTCTGGGCTGAATGCCACATTTATGgtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag Alignment from Spaln_aa2Genome CCAAGCGGCTGAAGCTGGAGGGGCTGCGTAGCAGCTCGTGGCTTCAGGACGGCAGCGCGCGCTCCTCGCCCCCGCTCCGCACGCCGGATGTGCTGGAGTCCTCTGGGCCAGCTGTGCGTTCCGGGCTCAATGCCACTTTCATG ctcttgaacacctatcattcccgctttgttttatttcaacttttctccagGG---------------GAGGGGCTGCGTAGCAGCTCGTGGCTACAGGATGGTAGTGCACGCTCCTCACCACCACTATGCACCCCAGATGTGCTGGAGTTCTCTGGACCAGCTGTGCGTTCTGGGCTGAATGCCACATTTATGgtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag Alignment from Spaln_nt2Genome GCTGGAGGGGCTGCGTAGCAGCTCGTGGCTTCAGGACGGCAGCGCGCGCTCCTCGCCCCCGCTCCGCACGCCGGATGTGCTGGAGTCCTCTGGGCCAGCTGTGCGTTCCGGGCTCAATGCCACTTTCATG ctcttgaacacctatcattcccgctttgttttatttcaacttttctccagG--GGAGGGGCTGCGTAGCAGCTCGTGGCTACAGGATGGTAGTGCACGCTCCTCACCACCACTATGCACCCCAGATGTGCTGGAGTTCTCTGGACCAGCTGTGCGTTCTGGGCTGAATGCCACATTTATGgtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag Alignment from Pairagon GTCCGAGGGCTACTGACAGTCGACCCCGCCAAGCGGCTGAAGCTGGAGGGGCTGCGTAGCAGCTCGTGGCTTCAGGACGGCAGCGCGCGCTCCTCGCCCCCGCTCCGCACGCCGGATGTGCTGGAGTCCTCTGGGCCAGCTGTGCGTTCCGGGCTCAATGCCACTTTCATG ctcttgaacacctatcattcccgctttgttttatttcaacttttctccagG-------------------------------------------GGAGGGGCTGCGTAGCAGCTCGTGGCTACAGGATGGTAGTGCACGCTCCTCACCACCACTATGCACCCCAGATGTGCTGGAGTTCTCTGGACCAGCTGTGCGTTCTGGGCTGAATGCCACATTTATGgtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag Alignment from Exonerate_protein2genome ctcttgaacacctatcattcccgctttgttttatttcaacttttctccaggggaggggctgcgtagcagctcgtggctacaggatggtagtgcacgctcctcaccaccactatgcaccccagatgtgctggagttctctggaccagctgtgcgttctgggctgaatgccacatttatggtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise TGGAGGGGCTGCGTAGCAGCTCGTGGCTTCAGGACGGCAGCGCGCGCTCCTCGCCCCCGCTCCGCACGCCGGATGTGCTGGAGTCCTCTGGGCCAGCTGTGCGTTCCGGGCTCAATGCCACTTTCATG ctcttgaacacctatcattcccgctttgttttatttcaacttttctccagGGGAGGGGCTGCGTAGCAGCTCGTGGCTACAGGATGGTAGTGCACGCTCCTCACCACCACTATGCACCCCAGATGTGCTGGAGTTCTCTGGACCAGCTGTGCGTTCTGGGCTGAATGCCACATTTATGgtatgtgtaatatggccattaggtagatgatcctgtatttcccaatacag #### Rps6ka4_ID1807_13 --> 0 - 0 Original Alignment CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG gggcctgtatacactttgcagattcctccttctctttcttcctccctcag------ACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc Alignment from CESAR CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG tggtgagggcctgtatacactttgcctccttctctttcttcctccctcag------ACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc Alignment from Spaln_aa2Genome CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG gggcctgtatacactttgcagattcctccttctctttcttcctccctcag------ACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc Alignment from Spaln_nt2Genome ACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG gggcctgtatacactttgcagattcctccttctctttcttcctccctcagACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc Alignment from Pairagon CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG gggcctgtatacactttgcagattcctccttctctttcttcctccctcag------ACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc Alignment from Exonerate_protein2genome CTACACACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG gggcctgtatacactttgcagattcctccttctctttcttcctcCCTCAGACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ACTTACCTGGTCCTGGAGTTGCTGCGAGGCGGAGAGCTATTGGAACACATCCGCAAGAAGCGGCTCTTCAGCGAGTCGGAGGCCAGCCAGATCCTTCGGAGCCTGGTTTCGGCCGTGAGCTTCATGCACGAGGAGGCAGGCGTGGTGCACCGCGACCTGAAACCCGAG gggcctgtatacactttgcagattcctccttctctttcttcctccctcagACTTACCTGGTCCTGGAGTTGCTACGAGGTGGAGAACTATTGGAACACATTCACAAGAAACGGCTATTCAGTGAATCAGAGGCCAGCCAGATCCTACGGAGTCTAGTTTCAGCCGTGAGCTTCATGTATGAGGAGGCCGGTGTAGTGCACCGCGACCTGAAACCTGAGgtgagttgagcaaaggacatggagtttagtataattaatgggcctgggcc #### Rps6ka4_ID1808_12 --> 1 - 0 Original Alignment gCTGGAGGAGAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG acaatctactttactactttaggctgttaatcatagtctttgctttgtagg---------AACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga Alignment from CESAR gCTGGAGGAGAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG tgtgacagcacaatctactttactagttaatcatagtctttgctttgtagg---------AACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga Alignment from Spaln_aa2Genome GCTGGAGGAGAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG acaatctactttactactttaggctgttaatcatagtctttgctttgtagG---------AACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga Alignment from Spaln_nt2Genome GAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG acaatctactttactactttaggctgttaatcatagtctttgctttgtagGAACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga Alignment from Pairagon GCTGGAGGAGAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG acaatctactttactactttaggctgttaatcatagtctttgctttgtag---------GAACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga Alignment from Exonerate_protein2genome GCTGGAGGAGAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG acaatctactttactactttaggctgttaatcatagtctttGCTTTGTAGGAACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAACACTCAGCGAGAGGTGGCTGCTCTTCGCCTGTGCCAGTCACACCCCAACGTGGTGAATCTGCATGAGGTGCTTCATGACCAG acaatctactttactactttaggctgttaatcatagtctttgctttgtagGAACACACAGCAAGAGGTGGCTGCTCTTCGCCTTTGTCAGTCACACCCCAATGTAGTGAATCTTCATGAGGTGCTTTATGATCAGgtaagaaaagcttgttattggccacccatgtagagagctagaaggtggga #### Rps6ka4_ID1809_11 --> 0 - 2 Original Alignment GACTCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCag aattctggtttcaggaagcaaactatgtattgcctctatctgattgccag---TCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCaggtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag Alignment from CESAR GACTCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCag tccaattctggtttcaggaagcaaatgtattgcctctatctgattgccag---TCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCaggtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag Alignment from Spaln_aa2Genome GACTCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCAG aattctggtttcaggaagcaaactatgtattgcctctatctgattgccag---TCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCAGgtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag Alignment from Spaln_nt2Genome GACTCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCAG aattctggtttcaggaagcaaactatgtattgcctctatctgattgccag---TCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCAGgtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag Alignment from Pairagon ------------------------------------------------ACTCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCAG AATTCTGGTTTCAGGAAGCAAACTATGTATTGCCTCTATCTGATTGCCAGTCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCAGgtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag Alignment from Exonerate_protein2genome TCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCAG aattctggtttcaggaagcaaactatgtattgcctctatctgattgccagTCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCAGgtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise -----------------------------------------------GACTCGCCTTTCTTCCAGCAGTACGAACTGGACCTTCGGGAGCCAGCGCTGGGGCAGGGCAGCTTCTCTGTGTGTCGGAGATGTAGGCAGCGCCAGAGCGGCCAGGAGTTTGCTGTCAAGATCCTCAGCCGCAG AATTCTGGTTTCAGGAAGCAAACTATGTATTGCCTCTATCTGATTGCCAGTCACCCTTATTACAACAGTATGAGCTTGACCTTTGGGAACCAGCACTGGGGCAGGGCAGTTTCACTGTGTGCCGAAGATGTAGACGACGCCAGACTGGCCAGGAGTTTGCTGTCAAGATTCGCAGTTGCAGgtgagagctctatgagcataggtttaacaaaaggaaacctgtgcagacag #### Rps6ka4_ID1814_6 --> 0 - 0 Original Alignment AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGGCAAG--- gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACgtaagttactttggtggactgagggtgtgaatgtttttttttctttttaa Alignment from CESAR AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGGCAAG--- gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACgtaagttactttggtggactgagggtgtgtctctcccatctacccaccca Alignment from Spaln_aa2Genome AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGGCAAG--- gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACgtaagttactttggtggactgagggtgtgaatgtttttttttctttttaa Alignment from Spaln_nt2Genome AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGGCAAG--- gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACgtaagttactttggtggactgagggtgtgaatgtttttttttctttttaa Alignment from Pairagon AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGG------------------------------------------------------CAA gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACGTAAGTTACTTTGGTGGACTGAGGGTGTGAATGTTTTTTTTTCTTTTTAA Alignment from Exonerate_protein2genome AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGGCAAG--- gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACgtaagttactttggtggactgagggtgtgaatgtttttttttctttttaa Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise AAAGAGCGGACCTTCTCCTTCTGTGGCACAATCGAGTACATGGCTCCCGAAATCATCCGAAGCAAGGCTGGACATGGCAAGGCT gtgggggcaaaaactgactgcctttgataagcccatgtgctctatcatagGAAGAGTGGACTTTTTCTTTCTGTGGTACAGTTGAATACATGGCTCCTGAGATCTTCCGTAGCAAAGCTGGGCGTGGTAAGAACgtaagttactttggtggactgagggtgtgaatgtttttttttctttttaa #### Rps6kb2_ID368_14 --> 0 - 2 Original Alignment GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATC---------------------------ag agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCGTCATTCCTCGGCTTTGCAGATGTAaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from CESAR GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATCag agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCgcgtcattcctcggctttgcagatgtaaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from Spaln_aa2Genome GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATCAG agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCgtcattcctcggctttgcagatgtaaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from Spaln_nt2Genome GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATCAG agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCgtcattcctcggctttgcagatgtaaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from Pairagon GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATC---------------------------AG agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCGTCATTCCTCGGCTTTGCAGATGTAAGgtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from Exonerate_protein2genome GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATCAG agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCgtcattcctcggctttgcagatgtaaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from Exonerate_coding2genome GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATCAG agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCgtcattcctcggctttgcagatgtaaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga Alignment from GeneWise GGCTTTACATATGTGGCACCTTCTGTCCTGGACAGCATCAAAGAGGGCTTCTCCTTCCAGCCCAAGCTGCGTTCTCCCAGACGCCTTAACAGCAGTCCCCGCACCCCCATCAG agacggggtcgtgccacctggctttactctaactctctcttcctctctagAGTTTTATGTATGTGGCACCTTTTGTCCTAGACAGCATCAAAGAAGGTTTTTCATTCCAGCCCAAGCTGCGTTCCCCACGATGCCTTAACAGTAGTCCCCGCACACCCATCGCgtcattcctcggctttgcagatgtaaggtaagaggcagggcagataattccaaacatgcaccactactcagcagaga #### Rps6kb2_ID369_13 --> 0 - 0 Original Alignment CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTG------ tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAGGTCCAgtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac Alignment from CESAR CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTG------ tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAGGTCCAgtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac Alignment from Spaln_aa2Genome CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTGGGC--- tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAGGTCCAgtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac Alignment from Spaln_nt2Genome CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTGG tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAGgtccagtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac Alignment from Pairagon CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCT--------------------------------------------------------- tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAGGTCCAGTTTGTTGCTGGGTTACGAGAAAAGACGGGGTCGTGCCACCTGGCTTTAC Alignment from Exonerate_protein2genome CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTG tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAggtccagtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac Alignment from Exonerate_coding2genome CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTG tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAggtccagtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac Alignment from GeneWise CAATCAGAAGAGGATGTGAGCCAGTTTGATGCACGATTCACACGGCAGACGCCGGTAGATAGTCCAGATGACACAGCCCTCAGTGAGAGTGCCAACCAAGCCTTCCTGGGC--- tattggggtcagcagtatgctagatcagtttactatctggcctcctctagCAATCTGAGGAGGATGTGAGCCAGTTTGATGCACGCTTCATGCGACAAACTCCAGTTAGTACCCCAGATGACACACCACTAACTGAGTGCGCCAACCAAGCCGTCTTAGGTCCAgtttgttgctgggttacgagaaaagacggggtcgtgccacctggctttac #### Rps6kb2_ID371_11 --> 0 - 0 Original Alignment TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTC---gtaagaagaagatccgttgcttaacctgctggagaatacagagatcaaga Alignment from CESAR TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAG tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTC---gtaagaagaagatccgttgcttaacctgctggagaatacagagatca Alignment from Spaln_aa2Genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTC tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCgtaagaagaagatccgttgcttaacctgctggagaatacagagatcaaga Alignment from Spaln_nt2Genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCC--------AGA--- tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCGTAAGAAGAAGATCCgttgcttaacctgctggagaatacagagatcaaga Alignment from Pairagon TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTC tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCgtaagaagaagatccgttgcttaacctgctggagaatacagagatcaaga Alignment from Exonerate_protein2genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTC tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCgtaagaagaagatccgttgcttaacctgctggagaatacagagatcaaga Alignment from Exonerate_coding2genome TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTC tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCgtaagaagaagatccgttgcttaacctgctggagaatacagagatcaaga Alignment from GeneWise TTTCTGAAGCGGAACCCCACTCAGCGAATTGGGGGTGGCCTGGGAGATGCTGCTGATGTCCAGAGG--------- tcttgaccaccttcattcatttttgcccgtctcctcttcctgctttctagTTACTGAAGCGAAATCCAACGCAACAAATTGGGGATGATTTAGGAGATGCTGCTGATGTCGTAAGAAGAAGATCCgttgcttaacctgctggagaatacagagatcaaga #### Rps6kb2_ID376_6 --> 2 - 2 Original Alignment gtGGTGAGCTCTTCACACATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCtg atgaagtcatgcgcctctcctgcttaaaatttcttgaatcttccaaacagtt---------------CATCTAGAACGGGAAGGTGTGTTTCTGGAAGACACAGCTtggtagggaaagtctgcaggatacctactgtagcgggtagcttattttcttt Alignment from CESAR gtGGTGAGCTCTTCACACATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCtg agtcgaagtttgctgatgaagtcataaaatttcttgaatcttccaaacagtt---------------CATCTAGAACGGGAAGGTGTGTTTCTGGAAGACACAGCTtggtagggaaagtctgcaggatacctactgtagcgggtatcacagagccatt Alignment from Spaln_aa2Genome CACATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCTG atgaagtcatgcgcctctcctgcttaaaatttcttgaatcttccaaacagTTCATCTAGAACGGGAAGGTGTGTTTCTGGAAGACACAGCTTGgtagggaaagtctgcaggatacctactgtagcgggtagcttattttcttt Alignment from Spaln_nt2Genome --CATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCTG atgaagtcatgcgcctctcctgcttaaaatttcttgaatcttccaaacagTTCATCTAGAACGGGAAGGTGTGTTTCTGGAAGACACAGCTTGgtagggaaagtctgcaggatacctactgtagcgggtagcttattttcttt Alignment from Pairagon GTGGTGAGCTCTTCACACATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCTG atgaagtcatgcgcctctcctgcttaaaatttcttgaatcttccaaacagttcatctag------------------------AACGGGAAGGTGTGTTTCTGGAAGACACAGCTTGgtagggaaagtctgcaggatacctactgtagcgggtagcttattttcttt Alignment from Exonerate_protein2genome GTGGTGAGCTCTTCACACATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCTG atgaagtcatgcgcctctcctgcttaaaatttcttGAATCTTCCAAACAGTTCATCTAGAACGGGAAGGTGTGTTTCTGGAAGACACAGCTTGgtagggaaagtctgcaggatacctactgtagcgggtagcttattttcttt Alignment from Exonerate_coding2genome GTGGTGAGCTCTTCACACATCTTGAGCGAGAAGGCATCTTCCTGGAAGACACAGCCTG atgaagtcatgcgcctctcctgcttaaaatttcttGAATCTTCCAAACAGTTCATCTAGAACGGGAAGGTGTGTTTCTGGAAGACACAGCTTGgtagggaaagtctgcaggatacctactgtagcgggtagcttattttcttt Alignment from GeneWise GTGGTGAGCTCTTCACACA atgaagtcatgcgcctctcctgcttaaaatttcttgaatcttccaaacagttcatctagaacgggaaggtgtgtttctggaagacacagcttggtagggaaagtctgcaggatacctactgtagCGGGTAGCTTATTTTCT-- #### Rps6kb2_ID379_3 --> 1 - 0 Original Alignment g------ACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacaggATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAGA------AATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from CESAR g------ACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacaggATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAGA------AATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from Spaln_aa2Genome GACAGTGGGACAC------TATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacagGATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAGA------AATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from Spaln_nt2Genome GCCTGGAGACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacagG-ATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAG------AAATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from Pairagon ------GACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacagGATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAG------AAATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from Exonerate_protein2genome CCTGGAGACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacagGATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAGA------AATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from Exonerate_coding2genome CCTGGAGACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacagGATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAGA------AATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta Alignment from GeneWise ----GAGACAGTGGGACACTATGAAGAAGTAGAGCTGACAGAGAGCAGCGTGAACCTGGGTCCTGAGCGCATCGGGCCCCACTGCTTTGAGCTACTGAGTGTACTGGGCAAGGGGGGCTATGGCAAG gtgtgtatacttccctaaattgtctcccgaccatgtccccctttccacagGATTGCGACAGTGGGCCACTATGATGAAGTCGAACTAACAGAGAGA------AATCTTGACCCTGAACGCATTGGGCCCCACTGCTTTGAGTTACTCAGTGTCCTGGTGAAAGGAGGTTATGGAAAGgtaagctatctcccgtcccaatgacatcagctctagtacaactgtaggta #### Rrp12_ID8295_28 --> 1 - 1 Original Alignment cATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTT---g gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagcATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA------TTGGTC------AGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCCAGGCCggtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from CESAR cATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTT---g gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagcATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA------TTGGTC------AGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCCAGGCCggtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from Spaln_aa2Genome CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTT---G gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagCATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA------TTGGTC------AGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCCAGGCCGgtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from Spaln_nt2Genome CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagCATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGC------AATTGG------TCAGGAGCCGATCATG---GAAGGATGGAGGTGG---TGCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCC-AGgccggtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from Pairagon CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTG gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagCATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA-------------------------------------------------------------------------------------------------TTGgtcaggagccgatcatggaaggatggaggtggtgcacctctcaatttcccaaaagtagcacatcgtatccaggccggtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from Exonerate_protein2genome CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTGCCA gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagCATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA------------TTGGTCAGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCCAGGCCGgtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from Exonerate_coding2genome CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTGCCA gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagCATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA------------TTGGTCAGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCCAGGCCGgtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg Alignment from GeneWise CATTGAGGAGATTTTGGCTGACTCTGAGGATGAGGATGAGGAAGAAGAAAGAGGCCGGGGCAAGGAGCAGCGGAAGCTGGCACGACAGAGGAGCCGGGCATGGCTGAAGGAAGGTGGTGGCGATGAGCCCCTCAACTTCCTGGATCCCAAGGTGGCCCATCGAGTCCTTGCC- gtaagttagggcagggttgcgtcctattctcacacgaccctcggccacagCATTGAGGAAATTTCAGCTGACTCAAAGGATGAGTTTGAGGAAGAACAAAGAGGCCGAGGCAAAGAGCAA------------TTGGTCAGGAGCCGATCATGG---AAGGATGGAGGTGGT---GCACCTCTCAATTTC------CCAAAAGTAGCACATCGTATCCAGGCCGgtgatgaggggtaaggatgccctactttgctcggggggtcaagggttagg #### Rrp12_ID8296_27 --> 1 - 2 Original Alignment aTTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGACag atgctatgcagacatccacccttggtgactgccggctctcttcctctcaggTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGT---aggtgagccggccaattcgcacctcagcaattagtaagttagggcagggttg Alignment from CESAR aTTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGACag atgctatgcagacatccacccttggtgactgccggctctcttcctctcaggTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGT---aggtgagccggccaattcgcacctcagcaattagtaagttagggcagggttg Alignment from Spaln_aa2Genome ATTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGA atgctatgcagacatccacccttggtgactgccggctctcttcctctcagGTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGTAGgtgagccggccaattcgcacctcagcaattagtaagttagggcagggttg Alignment from Spaln_nt2Genome ATTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGACAG- atgctatgcagacatccacccttggtgactgccggctctcttcctctcagGTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGTAGGTGAgccggccaattcgcacctcagcaattagtaagttagggcagggttg Alignment from Pairagon ATTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTG--------------------------------------------------- atgctatgcagacatccacccttggtgactgccggctctcttcctctcagGTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGTAGGTGAGCCGGCCAATTCGCACCTCAGCAATTAGTAAGTTAGGGCAGGGTTG Alignment from Exonerate_protein2genome ATTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGACAG atgctatgcagacatccacccttggtgactgccggctctcttcctctcagGTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGT---AGgtgagccggccaattcgcacctcagcaattagtaagttagggcagggttg Alignment from Exonerate_coding2genome ATTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGACAG atgctatgcagacatccacccttggtgactgccggctctcttcctctcagGTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGT---AGgtgagccggccaattcgcacctcagcaattagtaagttagggcagggttg Alignment from GeneWise ATTCGAGTTGGTGAAGGGTCTGCTACCCGCAGAATACCACAAAGTCCTGATAAACATCAGGAAAGCTGAGACCCGAGCCAAGAAGCATCGTGCCCTGAGCCAGGCTGCTGTAGAGGAGGAGGAAGAGGAGGAAGAGGAAGAGGAGCCTGTCCAGAGCAAAGGTGA atgctatgcagacatccacccttggtgactgccggctctcttcctctcagGTATGAATCAGTCAAGGGACTGTTACCTGCAGAGTACCACAAAGTACTAATAAATATGAGGAAAGCAGAGACCCGGGCAAAGAAATATAAGGCCTTGAGTCAAGCTGCTGTAGAGGAGGAAGAAGTGGAAGAAGAGGAACAGGAGCCTTTGCAAAGCAAAGGTAGgtgagccggccaattcgcacctcagcaattagtaagttagggcagggttg #### Rrp12_ID8297_26 --> 0 - 2 Original Alignment ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCGCAAGTTTgg taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACA---------gggtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from CESAR ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCGCAAGTTTgg taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACA---------gggtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from Spaln_aa2Genome ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCG taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACAGGgtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from Spaln_nt2Genome ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCG taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACAGGgtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from Pairagon ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCGCAAGTTTGGATTCGAGTTGG taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACA--------------------GGgtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from Exonerate_protein2genome ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCG taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACAGGgtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from Exonerate_coding2genome ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCG taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACAGGgtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg Alignment from GeneWise ATGGAAGCCATTGGGAAGTTGTCAGATGACATGCGACGGCACTTCCGGATGAAGCTTCGGAACCTGTTCATCAAGTTCACCCG taatgatggatgacctaggtggataatgaaaaacatctgcttttttccagATGGAAGCAATAGGGAAACTGTCAGATGACATGCAACGGCACTTCCGGATGAAACTCCAGAATCTGTTCATCAAGTTCACAGGgtgggccaatcgccccccaagtagagggagaatggaacatggtgtatttg #### Rrp12_ID8298_25 --> 2 - 0 Original Alignment ggCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctaggc---ATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from CESAR ggCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG actaggtactgggtcaatatgtcattcgccatgagctctctgtcccctaggc---ATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from Spaln_aa2Genome GGCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctagGC---ATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from Spaln_nt2Genome GGCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctagG---CATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from Pairagon GGCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctagG---CATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from Exonerate_protein2genome GGCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctagGC---ATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from Exonerate_coding2genome GGCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctagGC---ATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac Alignment from GeneWise GGCTGATGGGGACCAGCACAGTGGAGCAGCTCCTGGAGAACGTGTGCCTGCTGCTGGCCTCTCGAACCCGTGATGTGGTCAAGTCCGCGCTAGGCTTCATCAAGGTTGCTGTGGTGGTCATGGACGTGGTGCACCTTGCTAAGCATGTGCAGCTAGTG aggtactgggtcaatatgtcatatttcgccatgagctctctgtcccctagGC---ATGGGGACCAGCACAGCAGAACAACTCTTAGGGAATGTGTGCTTCCTGTTAGCCTCTAGAACATGGGATGTAGTAAAAGCCGCACTAGGCTTCATTAAGGTTACTGTGGTGGTCATGGATGTAGTTCATCTTGCTAAGCACGTACACCTAGTGgtgactccttccagtgtacatgggggggaacaacactagtggacgccaac #### Rrp12_ID8302_21 --> 0 - 0 Original Alignment AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAGG--------- gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGGCAACCTCAAgtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc Alignment from CESAR AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAGG--------- gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGGCAACCTCAAgtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc Alignment from Spaln_aa2Genome AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAGG------CCC gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGGCAACCTCAAgtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc Alignment from Spaln_nt2Genome AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAG gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGgcaacctcaagtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc Alignment from Pairagon AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAGG----------------------------------------- gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGGCAACCTCAAGTACTCGCTCTAACTTGATCCACCAAGTACGGgtgaggttgtgtgcaagc Alignment from Exonerate_protein2genome AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAG gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGgcaacctcaagtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc Alignment from Exonerate_coding2genome ATGAAGCTGCCATCAGTAAGCTATACTCTACCATCCGGCCCTACCTTGAGAGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAG GATTAACACTTGAGCCTGATATTACATGACAGCTTTCTGTCTTCCTATAGAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGgcaacctcaagtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc Alignment from GeneWise AGCAAGGTCCACGGTGTACAGAAGAAGGCCTACCGCGTGCTGGAGGAGGTGTGTGCCAGTTCTCAGGGCCCGGCAGCCCGCTTCGTGCAGAGCCACCTGGATGATCTGAAGAAGACTCTGCTGGACTCGCTTCGGACCACATCCTCGCCTGCTAAAAGG---CCCCGT gattaacacttgagcctgatattacatgacagctttctgtcttcctatagAGTAAAGTGCATGGAATACAGAAAAAGGCTTTTCGGGTTCTGGAAGAAGTTTGTGACAGCTCTCAGGGCCCAGCAGCTCACTTATTGCAAAGCCATCGTGATGATCTGAAGAAAACCCTCCTGGACTCACTTCGGACAACATCATCCCCAGCAAAAAGGCAACCTCAAgtactcgctctaacttgatccaccaagtacgggtgaggttgtgtgcaagc #### Rrp12_ID8304_19 --> 0 - 2 Original Alignment TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACC------ag atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCCTGGAAaggtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from CESAR TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACC------ag atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCCTGGAAaggtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from Spaln_aa2Genome TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTCTGT atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACC---CTGGAAAGgtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from Spaln_nt2Genome TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCA--GATTG atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCCTGGAAAGgtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from Pairagon TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACC------AG atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCCTGGAAAGgtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from Exonerate_protein2genome TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTC atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACCCTGGAAAGgtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from Exonerate_coding2genome atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagctggtgaatagcttcctagagaaagccattgaaaaggttcttgacccccccagttcagatttcaccctggaaaggtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac Alignment from GeneWise TTGGTGAATAGCTTCCTGGAAAAAGCCACCGAGAAGGTTCTCGATCCTGCCAGCTCTGATTTCACCAGATTGTCTGT atcataggtaatggatgggtcttttaggtgccatttcctcttcctcacagCTGGTGAATAGCTTCCTAGAGAAAGCCATTGAAAAGGTTCTTGACCCCCCCAGTTCAGATTTCACC---CTGGAAAGgtgagtctgagcttttcaggtgccttggtgtacaatgcatggtacatgac #### Rrp12_ID8307_16 --> 2 - 0 Original Alignment caATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTCCAGTGGCAG taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagcaATGGATCTAGCTCAAGCC------ACAGTGGAGTCCAAGATT---GATACACTC---------gtattggccataggatcgaattgggaactgagggctgagcacatttgact Alignment from CESAR caATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTCCAGTGGCAG taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagcaATGGATCTAGCTCAAGCC------ACAGTGGAGTCCAAGATT---GATACACTC---------gtattggccataggatcgaattgggaactgagggctgagca Alignment from Spaln_aa2Genome CAATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTC taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagCAATGGATCTAGCTCAAGCC------ACAGTGGAGTCCAAGATT---GATACACTCgtattggccataggatcgaattgggaactgagggctgagcacatttgact Alignment from Spaln_nt2Genome CAATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTC taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagCAATGGATCTAGCTCAAGC------CACAGTGGAGTCCAAGAT---TGATACACTCgtattggccataggatcgaattgggaactgagggctgagcacatttgact Alignment from Pairagon CAATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTC-CAGTGGC------------------------------------------ taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagCAATGGATCTAGCTCAAGC------CACAGTGGAGTCCAAGAT---TGATACACTCGTATTGGCCATAGGATCGAATTGGGAACTGAGGGCTGAGCACATTTGACT Alignment from Exonerate_protein2genome CAATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTCCAGTGGCAG taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagCAATGGATCTAGCTCAAGCC------ACAGTGGAGTCCAAGATT---GATACACTCGTATTGGCCataggatcgaattgggaactgagggctgagcacatttgact Alignment from Exonerate_coding2genome CAATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTA taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagcaatggatctagctcaagccacagtggagtccaagattgatacactcgtatTGGCCATAGGATCGAATTGGGAACTGAGGGCTGAGCACATTTGACT Alignment from GeneWise CAATGGACCTGGCTCAGGCAGGCAGCACAGTGGAGTCGAAGATTTATGATACACTCCAGTGGCAG taataaaaagtggcatggcatgacctatgttccttcctcttgttctgcagCAATGGATCTAGCTCAAGCC------ACAGTGGAGTCCAAGATT---GATACA---------CTCgtattggccataggatcgaattgggaactgagggctgagcacatttgact #### Sart1_ID956_19 --> 0 - 2 Original Alignment CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAAT---gc ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATCGAgcgtactcaggtaggagttgtcagcttggactggtatgctgaacacaattat Alignment from CESAR CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAAT---gc ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATCGAgcgtactcaggtaggagttgtcagcttggactggtatgctgaacacaattat Alignment from Spaln_aa2Genome CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAATGCG-- ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATCGAGCgtactcaggtaggagttgtcagcttggactggtatgctgaacacaattat Alignment from Spaln_nt2Genome CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAAT---GC ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATCGAGCgtactcaggtaggagttgtcagcttggactggtatgctgaacacaattat Alignment from Pairagon CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAAT---GC ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATCGAGCgtactcaggtaggagttgtcagcttggactggtatgctgaacacaattat Alignment from Exonerate_protein2genome CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAAT ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATcgagcgtactcaggtaggagttgtcagcttggactggtatgctgaacacaattat Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise CTCCTGAAGAAAATGAGCTCCAGTGACACGCCCCTGGGCACCGTGGCACTGCTCCAGGAGAAGCAGAAGGCCCAGAAGACACCGTATATCGTGCTCAGTGGCAGTGGCAAGAGCATGAATGCGAACACCATCACCAAA ctgatatgccaaaattggcagcactgacaatgtaatttccatttttatagCTTCGTAAGAAGATGAGCTCTAGTGATACACCCCTGGGAACAGTGGCATTGCTCCAGGAGAAGCAGAAGGCCCAAAAGACACCTCAGATTGTACTCAGTGGCAGTGGCAAGAGCATGAATCGAGCGTACTCAGGTAGGagttgtcagcttggactggtatgctgaacacaattat #### Sart1_ID961_14 --> 0 - 0 Original Alignment ------GACTTTGAAAGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCATCAGGAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagTCCATCGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGAC------GAACAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt Alignment from CESAR ------GACTTTGAAAGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCATCAGGAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagTCCATCGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGACGAA------CAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt Alignment from Spaln_aa2Genome GACTTTGAA------AGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCATCAGGAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagTCCATCGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGACGAA------CAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt Alignment from Spaln_nt2Genome ------GACTTTGAAAGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCATCAGGAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagTCCATCGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGACG------AACAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt Alignment from Pairagon ------GACTTTGAAAGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCATCAGGAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagTCCATCGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGACG------AACAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt Alignment from Exonerate_protein2genome GACTTTGAAAGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagtccatcGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGACGAACAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ------GACTTTGAAAGGGATGAGGAGCGCTCGGCCAACGGTGGCTCTGAATCAGATGGGGAAGAGAACATTGGCTGGAGCACCGTCAACCTGGATGAGGAGAAGCAGCATCAGGAT tgtgagatacaggtagaatctgtgcatttatgataaatactgctttttagTCCATCGACTTTGAGAGGGATGAGGAGCACTCAGCTAACGGAGGATCTGAATCAGATGGGGAAGAGAACATTGGTTGGAGCACAATCAACCTCGACGAA------CAGCCTCAGGATgtaagtcctcatgtctataggtggagggcagtgggcatcccccataggtt #### Sart1_ID965_10 --> 0 - 2 Original Alignment GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTTGGATCCag aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGG------------aggtgggtacagtgatcccaagcgtagtaagcacaagatggagaaattcaaa Alignment from CESAR GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTTGGATCCag aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGG------------aggtgggtacagtgatcccaagcgtagtaagcacaagatggagaaattcaat Alignment from Spaln_aa2Genome GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTTGGATCCAG aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGGAGGTGG---GTACAgtgatcccaagcgtagtaagcacaagatggagaaattc Alignment from Spaln_nt2Genome GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTTGGATCCA aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGG--AGGTGGGTACAgtgatcccaagcgtagtaagcacaagatggagaaattcaaa Alignment from Pairagon GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTTGGATCCAG aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGG------------AGgtgggtacagtgatcccaagcgtagtaagcacaagatggagaaattcaaa Alignment from Exonerate_protein2genome GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTT aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGGAGGTGGgtacagtgatcccaagcgtagtaagcacaagatggagaaattcaaa Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTGACCTTCAAGAAGACCAAACGGAGAGTGAAGAAAATCCGAAAGAAGGAGAAGGAGGTGATAATGCGGGCAGATGACTTGCTGCCCCTGGGCGACCAGACTCAGGATGGGGACTTT aggggatgctaacatcttgggaggctcgtcgcgggtttgtcatccaacagGTGACCTTCAAAAAGTCCAAGTGGAGGGTCAAAAAAACCAGGAAGAAGGAGCAGGAGGTGATAATGCAGGCTGATGATTTACTGCCTCTGGGAGATCAGACACAGGATGGGAGGTGGgtacagtgatcccaagcgtagtaagcacaagatggagaaattcaaa #### Sart1_ID969_6 --> 0 - 0 Original Alignment ------------------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagCGAGGCAATGACAACTGGGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt Alignment from CESAR ------------------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagCGAGGCAATGACAACTGGGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt Alignment from Spaln_aa2Genome GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagcgaggcaatgacaactgggctaag------CTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt Alignment from Spaln_nt2Genome ------------------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagCGAGGCAATGACAACTGGGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt Alignment from Pairagon ------------------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagCGAGGCAATGACAACTGGGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt Alignment from Exonerate_protein2genome GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagcgaggcaatgacaactggGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ------------------GCTAAGCTACTAGAGGAGATGGACCAAGAGTTTGGTGTGAGCACTTTAGTGGAGGAGGAGTTTGAGCAGAGGCGACAG agctatctgttaagtcccaaaccttttcttaatgaatttgtatcttacagCGAGGCAATGACAACTGGGCTAAGCTGTTGGAGGAAATGGGTCAAAAGTTTGGTGTGAGCACATTAGTTGAGGAAGAGTTTGAGCAGAAGCGACAGgtgaggatccaattgcagcaatgacaattactatgttgagtaccacaatt #### Sart1_ID970_5 --> 1 - 0 Original Alignment gAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagtAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCAAAGAAG---gtaagttgtacacatggttattcaaaagctatctgttaagtcccaaacct Alignment from CESAR gAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagtAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCA---AAGAAGgtaagttgtacacatggttattcaaaagctatctgttaagtcccaaactt Alignment from Spaln_aa2Genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCA---AAGAAGgtaagttgtacacatggttattcaaaagctatctgttaagtcccaaacct Alignment from Spaln_nt2Genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCAAAGAAGgtaagttgtacacatggttattcaaaagctatctgttaagtcccaaacct Alignment from Pairagon GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCAAAGAAGgtaagttgtacacatggttattcaaaagctatctgttaagtcccaaacct Alignment from Exonerate_protein2genome GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCA---AAGAAGgtaagttgtacacatggttattcaaaagctatctgttaagtcccaaacct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GAAAATAAAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGG tcttcacctgcccagggttcaggaaaacttatttggttgtctgggcttagTAAAGTTAAAACTCTGGGAGAAGATGACCCCTGGCTGGACGATACAGCAGCATGGATAGAGAGGAGC------CTCCAGAAAGAGAAGGATTTGGCA---AAGAAGgtaagttgtacacatggttattcaaaagctatctgttaagtcccaaacct #### Sec31b_ID9028_24 --> 0 - 0 Original Alignment ---AAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagCACAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from CESAR ---AAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagCACAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from Spaln_aa2Genome CTTAAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagCACAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from Spaln_nt2Genome CTTAAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagCACAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from Pairagon CACTGACCTTAAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagCAC-------AAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from Exonerate_protein2genome AAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagcacAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from Exonerate_coding2genome AAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagcacAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc Alignment from GeneWise CTTAAAACAAAAAGGAAGCTGGAGGAGGCAGCCCGCCGCCTAGAATGTCTGTATGAGAAGCTTTGCGAGGGGACA ctcctatttatacccaaattcaggatgtctactttcccgacaccccccagCACAAAACTAAAAAAGAACTAGAGGAGGCAGCATGGCACCTTGAATGCCTATATGAGAAGCTTTGTGAGGGAACAgtaagtcctttgtactgtgaacccacacttatgcctaggacagttagccc #### Sec31b_ID9030_22 --> 0 - 0 Original Alignment CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAG cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGT---------gtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga Alignment from CESAR CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGCAGCCTGCAG cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGT---------gtaagtgaacattggggtagtctgcacttgccctagtcaag Alignment from Spaln_aa2Genome CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGC cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGTgtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga Alignment from Spaln_nt2Genome CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGC cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGTgtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga Alignment from Pairagon CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGC cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGTgtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga Alignment from Exonerate_protein2genome CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGC cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGTgtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga Alignment from Exonerate_coding2genome CTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGC cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagctgcctgaagcattcatgacgcctgcaccgactacagCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGTgtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga Alignment from GeneWise CTGCCTGAGACATTCATGCCTCCAGCACCAATTACAGCTCCGCTTAGGAGCCTTGGCCCTGAGCCACAACAGGCCCTGCTACCTCAGCCCCTAGTCTCCAGTGCGACCCTGCCTCCTCCTGGAGCCCCAAGAGAATGC cagatgctgagttggtgtgaacttatgagtaattctaaccttcatttcagCTGCCTGAAGCATTCATGACGCCTGCACCGACTACAGCCCCACTTCGAAGCCCTGGACCGGATTCACAACAAGCCTTGCTTCCAAAACCATTAGTCTCCAGTGCAATCTTACCCCCTCCCGGAGCCCCCAGAGAGTGTgtaagtgaacattggggtagtctgcacttgccctagtcaaggcaacctga #### Sec31b_ID9031_21 --> 2 - 0 Original Alignment gaCCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG gtaaccacctgcctatgctctacgatggtgacctttggctctgattataggg---------------------ACACCTGCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from CESAR gaCCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG tgttaaagttgtcagtgatgagtaatggtgacctttggctctgattataggg---------------------ACACCTGCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from Spaln_aa2Genome TTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG gtaaccacctgcctatgctctacgatggtgacctttggctctgattatagGGACACCTGCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from Spaln_nt2Genome TTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG gtaaccacctgcctatgctctacgatggtgacctttggctctgattatagGGACACCTGCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from Pairagon GACCCCAGGACTCCTGGAAAGTTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG gtaaccacctgcctatgctctacgatggtgacctttggctctgattatag-------GGACACCT--------------GCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from Exonerate_protein2genome TTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG gtaaccacctgcctatgctctacgatggtgacctttggctctgattatagGGACACCTGCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from Exonerate_coding2genome gtaaccacctgcctatgctctacgatggtgacctttggctctgattatagggacacctgcctctgagggcaatcttcaaaggaagaaagtaagtgcctttccataaccattagcctagtccatccctatgttcttact Alignment from GeneWise TTTCTCCAGCCTCCCAGGGAAACCTCCAAAGGAAAAAG gtaaccacctgcctatgctctacgatggtgacctttggctctgattatagGGACACCTGCCTCTGAGGGCAATCTTCAAAGGAAGAAAgtaagtgcctttccataaccattagcctagtccatccctatgttcttact #### Sec31b_ID9038_14 --> 2 - 0 Original Alignment acACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagtgtctctcaaaaatcaatttttatcaacagat------GGGCTCCTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from CESAR acACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG atacagtaaagcattgactgagtgactcaaaaatcaatttttatcaacagat------GGGCTCCTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Spaln_aa2Genome ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagtgtctctcaaaaatcaatttttatcaacagAT------GGGCTCCTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Spaln_nt2Genome ATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagtgtctctcaaaaatcaatttttatcaacagATGGGCTCCTAAGCC---CTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCA---TGGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Pairagon ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagtgtctctcaaaaatcaatttttatcaacag------ATGGGCTCCTAAGCC---CTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCA---TGGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Exonerate_protein2genome ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagtgtctctcaaaaatcaatttttatCAACAGATGGGCTCCTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from Exonerate_coding2genome ACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagtgtctctcaaaaatcaatttttatCAACAGATGGGCTCCTAAGC---CCTTTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca Alignment from GeneWise -----------------------GACACTGATGGACTCCTGAGCCAGGCTCTGCTGCTCGGGGAACTGCGGTCTGCTGTGGAGCTGTGTTTGAAGGAGGAACGCTTTGCTGATGCCATCATCCTGGCTCAGGCTGGGGATGCAGAGCTGCTCAAGTGGACACAAGAACGCTACCTAGCCAAGAGGAGAACCAAAACCTCCTCG taaagcattgactgagtgagTGTCTCTCAAAAATCAATTTTTATCAACAGATGGGCTCCTAAGCCCT---TTGTTAATTGGGGAACTGCACTCTGCTGTAGATTTGTGTTTGAAGGAGGAGCGATTTGCAGATGCTGTTATTTTGGCTCAT---GGGGATGCAGAGTGGCTTAAGTGGACCCAAGAGCATTATCTGGCCAAGAGGAGAACAAAAACATCCTCTgtaagtcctgttgtccataattgtgttgctcacagccatgtcattcaaca #### Sec31b_ID9040_12 --> 0 - 0 Original Alignment GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttgtgcag------ACCTGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from CESAR GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG tgcaggcaaccttggtggtccacctacgcacccccttctcatttgtgcag------ACCTGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from Spaln_aa2Genome GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttgtgcag------ACCTGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from Spaln_nt2Genome TGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttgtgcagacctgcctaaaaagTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from Pairagon GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttgtgcag------ACCTGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from Exonerate_protein2genome GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttGTGCAGACCTGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from Exonerate_coding2genome GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttGTGCAGACCTGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta Alignment from GeneWise GTGGACACTTGCCTGAAGAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCGGTTGACCTCAAAAGTGACAGAGCACACAGCCCTTGCGCCCAG caaccttggtggtccacctggtttgacgcacccccttctcatttgtgcagACC------TGCCTAAAAAGTGACTCAAAATCACAGGAAAGCCCTCAGCTTGAGGCAGTTGACCTCAAAAGTGATAGAGCACATAGCCCTTGTGCTCAGgtatcatgaaagtcttggctacttgccttttggggccaacatgtccccta #### Sema4g_ID9244_2 --> 2 - 0 Original Alignment agCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagactgtgtgtctaatggactctccttagaa------CAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTC------AGTGAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from CESAR agCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG cttgctcatgccttatccatcataatgtgtgtctaatggactctccttagaa------CAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCAGT------GAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from Spaln_aa2Genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagactgtgtgtctaatggactctccttagAA------CAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCAGT------GAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from Spaln_nt2Genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagactgtgtgtctaatggactctccttagA------ACAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCA------GTGAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from Pairagon AGAGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagactgtgtgtctaatggactctccttagaacaagtacaacgctttagGGAGCAGGCCCAAATTC---------------------------ATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCA------GTGAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from Exonerate_protein2genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagactgtgtgtctaatggactctccttagAA------CAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCAGT------GAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from Exonerate_coding2genome AGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagactgtgtgtctaatggactctccttagAA------CAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCAGT------GAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct Alignment from GeneWise --------------------GAGCTCTCCCAGATTCGGCACTTCAAGGGCCAAACCCAGAACTATTCAACACTGCTGCTGGAGGAGGCTTCTGAGAGGCTGCTGGTGGGGGCTCGAGGCGCCCTGTTCTCTCTCAGTGCCCGTGACATAAGAGATAGGACTCACAAAGAG catgccttatccatcataactagACTGTGTGTCTAATGGACTCTCCTTAGAACAAGTACAACGCTTTAGGGAGCAGGCCCAAATTCATTCGACATTGCTGTTGGAGGAGGCTTCTGAAAAGCTGTCAGCAGGCGCGCGGGGTCCATTGTTCTCCCTCAGT------GAAATCAGAGAGAGAACACATAAAGAGgtaccttgctgatactgggtttacaggaccccacattttgcgtctggtct #### Sema4g_ID9247_5 --> 0 - 1 Original Alignment ------GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTg ggtcctaaacctgctctcacctaacctgtttttttttttttccttttaagCCCCGAGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTggtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from CESAR ------GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTg agccctaaacctgctctcacctaacctgtttttttttttttccttttaagCCCCGAGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTggtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from Spaln_aa2Genome ------GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATT ggtcctaaacctgctctcacctaacctgtttttttttttttccttttaagCCCCGAGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from Spaln_nt2Genome ------GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG ggtcctaaacctgctctcacctaacctgtttttttttttttccttttaagCCCCGAGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from Pairagon --------------------------------------------------------GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG GGTCCTAAACCTGCTCTCACCTAACCTGTTTTTTTTTTTTTCCTTTTAAGCCCCGAGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from Exonerate_protein2genome GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG ggtcctaaacctgctctcacctaacctgtttttttttttttccttttaagccccgaGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from Exonerate_coding2genome GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG ggtcctaaacctgctctcacctaacctgtttttttttttttccttttaagccccgaGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt Alignment from GeneWise ------GATGCTGAAACCTTCATCTTGCCTACTAGTTTCGAGGAGGGAAAGGAGAAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCCTTATCATTG ggtcctaaacctgctctcacctaacctgtttttttttttttccttttaagCCCCGAGATTCTGAAACCTTCATCTTGCCTACTAGTTTTGAGGAGGGAAAAGAGGAATGTCCTTATGACCCGGCCCGGGGCTTCACAGGCATTATTATTGgtgagaaaaatgtaaccaatccatcacaattctaagccctgaacattgtt #### Sema4g_ID9248_6 --> 2 - 1 Original Alignment atGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATg ctttcgcggcgaaatactcgcgatcacctgtgggtttttttcttttctagat------------------------TACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATggtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from CESAR atGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATg tcctagtagggcagcatgtcctatcacctgtgggtttttttcttttctagat------------------------TACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATggtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from Spaln_aa2Genome ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG ctttcgcggcgaaatactcgcgatcacctgtgggtttttttcttttctagAT------------------------TACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATGgtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from Spaln_nt2Genome GGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG ctttcgcggcgaaatactcgcgatcacctgtgggtttttttcttttctagATTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATGgtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from Pairagon ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG ctttcgcggcgaaatactcgcgatcacctgtgggtttttttcttttctagAT------------------------TACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATGgtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from Exonerate_protein2genome CCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG ctttcgcggcgaaatactcgcgatcacctgtggGTTTTTTTCTTTTCTAGATTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATGgtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from Exonerate_coding2genome CCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG ctttcgcggcgaaatactcgcgatcacctgtggGTTTTTTTCTTTTCTAGATTACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATGgtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt Alignment from GeneWise ATGGAGGCCTCTACACAGCCACCCGGTATGAATTCCGGAGCATTCCTGATATCCGCCGGAGCCGCCACCCACACTCTCTGAGAACTGAGGAGGCACCCATGCACTGGCTCAATG ctttcgcggcgaaatactcgcgatcacctgtgggtttttttcttttctagAT------------------------TACGAATTCCGGAGCATTCCTGATATTAGGAGGAGCCGACACCCACACTCTCTGAGAACTGAGGAAGCACCGATGCACTGGCTCAATGgtgagcatcaggtgctttcaaggggttggttaaggggacagctctagtgt #### Sema4g_ID9250_8 --> 0 - 2 Original Alignment ------------------------------GGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGtg ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcagGACAACTTTACGTTGGAACTGGCAGCAGTGGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGtggtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from CESAR ------------------------------GGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGtg ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcagGACAACTTTACGTTGGAACTGGCAGCAGTGGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGtggtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from Spaln_aa2Genome GCAAGGGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGTG ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcaggacaactttacgttggaactggcagCAGTGGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGTGgtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from Spaln_nt2Genome --GGAGATCTGGGAGG-GAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGTG ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcaggacaactttacgttggaactggcagcagTGGGAGATCTAGCTGGAGAAGAA-ATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGTGgtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from Pairagon --GGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGTG ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcaggacaactttacgttggaactggcagcagTGGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGTGgtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from Exonerate_protein2genome GGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGTG ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcaggacaactttacgttggaactggcagcagtgGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGTGgtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from Exonerate_coding2genome GGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGTG ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcaggacaactttacgttggaactggcagcagtgGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGTGgtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc Alignment from GeneWise ------------------------------GGAGATCTGGGAGGGAAGAAGATCCTACAGAAGAAGTGGACATCCTTCCTGAAGGCTCGTCTCATCTGCCACATCCCACAGTATGAGACACTACGTGGGGTCTGCAGCCTGAATGCTGATACATCATCCCACACACATTTCTATGCCGTCTTCACACTGACAACACAGTG ttagttctaccccctagttttatggactagtggtgtttcctgtcttgcagGACAACTTTACGTTGGAACTGGCAGCAGTGGGAGATCTAGCTGGAGAAGAAATTTTACAGAAGAAGTGGGAATCCTTCCTGAAGGCACGACTAATCTGCCATGTTCCTAAGTATGACACATTACGGGGAGTCTGCAGTCTTAATGCTGATACATCTTCTCACACACATTTCTATTCTGTCTTTATGCTATCAACCCAGTGgtgtgtatggagaatgggtatatatagcaggtaagcacaagagagtcagc #### Sema4g_ID9252_10 --> 0 - 1 Original Alignment TGCATCACAGATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCAT---CCCCTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAg aaatatagcagcagtgtccttacataccttagatccttttttctttttag---------GATTCTCTGCGGAGCCAAGGATACAACTCC---CAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAggtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from CESAR TGCATCACAGATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCAT---CCCCTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAg gttatgtgaaaatatagcagcagtgaccttagatccttttttctttttag---------GATTCTCTGCGGAGCCAAGGATACAAC---TCCCAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAggtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from Spaln_aa2Genome GATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCATCCCCTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAG aaatatagcagcagtgtccttacataccttagatccttttttctttttagGATTCTCTGCGGAGCCAAGGATACAACTCCCAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAGgtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from Spaln_nt2Genome GATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCATCCCC---TGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAG aaatatagcagcagtgtccttacataccttagatccttttttctttttagGATTCTCTGCGGAGCCAAGGATACAAC---TCCCAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAGgtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from Pairagon GATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCAT---CCCCTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAG aaatatagcagcagtgtccttacataccttagatccttttttctttttagGATTCTCTGCGGAGCCAAGGATACAAC---TCCCAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAGgtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from Exonerate_protein2genome GATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCAT---CCCCTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAG aaatatagcagcagtgtccttacataccttagatccttttttctttttagGATTCTCTGCGGAGCCAAGGATACAAC---TCCCAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAGgtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from Exonerate_coding2genome GATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCAT---CCCCTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAG aaatatagcagcagtgtccttacataccttagatccttttttctttttagGATTCTCTGCGGAGCCAAGGATACAAC---TCCCAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAGgtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc Alignment from GeneWise GATTCATTGCGCAGCCGAGGCTACAACTCATCCCAAGACTTGCCATCCCTGGTTCTGGACTTTGTGAAGTTGCATCCC---CTGATGGCTCGGCCTGTGGTGCCCACACGTGGGCGGCCCTTGCTGCTGAAGCGCAATGTACGCTACACACATCTCACAGGAACACACGTCAGCACACCTGCTGGACCCACCTATGACCTGCTCTTTCTGGGCACAG aaatatagcagcagtgtccttacataccttagatccttttttctttttagGATTCTCTGCGGAGCCAAGGATACAACTCC---CAAGATTTGCCTTCACTTGTCCTTGATTCCGTGAAGCTACATCCACCACTGATGGCTCATCCTGTAGTTCCCACACGGGGGCAGCCTCTACTGCTGAAGCACAATGTACACTACACACATGTCACAGGTACACATGTCAGTCCACCTGCAGGACCTACCTACGAGTTGCTATTTCTAGGCACAGgtaatgtaaccccgccctgcacatgcctccacctagtggggatacaatgc #### Sema4g_ID9254_12 --> 0 - 2 Original Alignment CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAAC---------ag tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAATT---CAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGCGCAAGCaggtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat Alignment from CESAR CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAAC---------ag tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAATT---CAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGCGCAAGCaggtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat Alignment from Spaln_aa2Genome CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAACAGG-------- tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAATT---CAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGCGCAAGCAGgtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat Alignment from Spaln_nt2Genome CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAACAGG tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGA---ATTCAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGCgcaagcaggtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat Alignment from Pairagon CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGC----------------------------------------------------------------- tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAA---TTCAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGCGCAAGCAGGTATGGAGACAAAATATAACAGCGCCCTGTTCACCAACTGGTAGTAGTAT Alignment from Exonerate_protein2genome CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAACAG tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAATT---CAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGcgcaagcaggtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat Alignment from Exonerate_coding2genome CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAACAG tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAATT---CAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGcgcaagcaggtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat Alignment from GeneWise CACAGCCTCTACGTGGGGGCTGCAAGTGGAGTCCTCCAGTTTCCTCTGTCCAGCTGCTCACGCTACCAGTCCTGCTATGACTGCATCCTGGCACGGGACCCCTACTGTGGCTGGGACTCCAGCATCCATGCCTGCATGGTGGCCACCACCGTAGCCAAC---------AG tgacatgggaggactaatactgctcatctgcatttttgcctacatcatagCACAGCCTATATGTGGGGGCTGCAAGTGGAATT---CAGTTTCCTCTTTCTAGCTGCTCACGCTACCAGTCTTGTTATGACTGCATTCTAGCACGAGACCCCTACTGTGGCTGGGATTCTAGTATCCATGTGTGCATGGTGGCCACTACGGTAGCAAACAGCGCAAGCAGgtatggagacaaaatataacagcgccctgttcaccaactggtagtagtat #### Sema4g_ID9255_13 --> 1 - 1 Original Alignment gACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGGGATGCAg ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagaACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGG------ggtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from CESAR gACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGGGATGCAg ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagaACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGG------ggtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from Spaln_aa2Genome GACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGG- ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagAACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGGGgtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from Spaln_nt2Genome GACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGGG ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagAACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGGGgtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from Pairagon GACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGGG ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagAACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGGGgtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from Exonerate_protein2genome GACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGGG ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagAACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGGGgtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from Exonerate_coding2genome ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagaacagaactaatacaagacattgaaagaggaaatctaggctgtgaggacagccggggtaggaaacgacagaactgacacctaacttggattctaggccatttaacc Alignment from GeneWise GACAGAATTGATACAGGACATAGAGAGAGGAAATCGAGGCTGTGAGGGCAGCAGGG ttcaccaactggtagtagtattgtaatactcacgacttcttcctctctagAACAGAACTAATACAAGACATTGAAAGAGGAAATCTAGGCTGTGAGGACAGCCGGGgtaggaaacgacagaactgacacctaacttggattctaggccatttaacc #### Sf1_ID1665_6 --> 1 - 0 Original Alignment aGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG------ caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagaGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGGAGAAAgtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from CESAR aGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG------ caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagaGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGGAGAAAgtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from Spaln_aa2Genome AGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG------ caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagAGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGGAGAAAgtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from Spaln_nt2Genome AGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG------ caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagAGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGGAGAAAgtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from Pairagon AGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG------ caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagAGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGGAGAAAgtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from Exonerate_protein2genome AGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagAGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGgagaaagtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from Exonerate_coding2genome AGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagAGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGgagaaagtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg Alignment from GeneWise AGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAG------ caatcagatcaactgaacaggggtgaccaacctctccctgcttcctacagAGGGAACACACTGAAGAACATTGATAAGGACTGCAATGCAAAGATCATGATTCGGGGGAAAGGATCCGTGAAAGAGGGGAAGGTTGGACGTAAAGATGGACAGATGTTGCCAGGTGAAGATGAGCCTCTTCATGCTCTAGTTACAGCCAATACAATGGAGAATGTCAAAAAGGCAGTAGAACAGGAGAAAgtaagagttcagcctaggaaaggaagcctggcaatcaactcacagtaggg #### Sf1_ID1666_7 --> 0 - 2 Original Alignment ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAAT---------ag agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAA---GCGAGAACCTTAcagtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg Alignment from CESAR ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAAT------ag agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACCTTAcagtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg Alignment from Spaln_aa2Genome ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAGG----- agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACCTTACAgtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg Alignment from Spaln_nt2Genome ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATG--ATAA---TAGG agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACCTTACAgtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg Alignment from Pairagon ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATA------------------------------------------------------------ agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACCTTACAGTGAGTTTGAATGTTGAAGAAAAGGCATGGGCAGGTATCAGTTTTAACGG Alignment from Exonerate_protein2genome ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAG agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACcttacagtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg Alignment from Exonerate_coding2genome ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAG agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACcttacagtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg Alignment from GeneWise ATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAGGATC-- agccaaactgccatgtttttgaataaggacactacatgtcttcattccagATCCGAAATATGCTAAAGCAAGGTATTAAAACCCCTAAAGGCCAAAATGATCTACACAAGATGCAGCTTCGGGAGCTGGCTCACCTAAATGGCACTCTACGGGAGGAAGCGAGAACCTTACAgtgagtttgaatgttgaagaaaaggcatgggcaggtatcagttttaacgg #### Sf1_ID1669_10 --> 0 - 1 Original Alignment TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGg gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCA---ggtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from CESAR TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGg gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCA---ggtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from Spaln_aa2Genome TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCA- gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAGgtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from Spaln_nt2Genome TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCA---Ggtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from Pairagon TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCA---Ggtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from Exonerate_protein2genome TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCA---Ggtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from Exonerate_coding2genome TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAATGG gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCA---Ggtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc Alignment from GeneWise TCTCTCATGTCTACAACTCAGAGCCGCCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGTCCTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGTGGGCATCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCACCACCACCGATGAACCAGGGCCCCCACCCACCTGGGCACCATGGCCCTCCTCCAA gggtcagactttgtctatgctaaactagttgtgggttttccatcccgcagTCTCTCATGTCTACAACTCAGAGCCACCCACCCTGGATGAATTCTGGTCCTTCAGAGAATCGGCCCTACCATGGCATGCATGGAGGTGGTCCTGGTGGGCCTGGTGGAGGCCCCCACAGTTTTCCACACCCATTACCCAGTCTCACAGGTGGCCATGGTGGTCACCCCATGCAGCACAACCCAAATGGACCACCACCACCTTGGATGCAGCCACCTCCACCACCAATGAACCAAGGCCCACACCCATCTGGGCACCATGCCCCTCCGCCAGgtgagaaaaaaccaagagcatttagggcttgagcaaatggcagacacccc #### Sipa1_ID1138_14 --> 1 - 0 Original Alignment gCCAGAACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG aattttctgttgggtgtggcatcctccactactctccttctcctctgtagg------CCTGGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from CESAR gCCAGAACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG cttaattttctgttgggtgtggcatccactactctccttctcctctgtagg------CCTGGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from Spaln_aa2Genome GCCAGAACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG aattttctgttgggtgtggcatcctccactactctccttctcctctgtagG------CCTGGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from Spaln_nt2Genome GAACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG aattttctgttgggtgtggcatcctccactactctccttctcctctgtagG--CCTGGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from Pairagon GCCAGAACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG aattttctgttgggtgtggcatcctccactactctccttctcctctgtagG------CCTGGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from Exonerate_protein2genome ACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG aattttctgttgggtgtggcatcctccactactctccttctcctctgtagGCCTGGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from Exonerate_coding2genome aattttctgttgggtgtggcatcctccactactctccttctcctctgtaggcctgggagcctatcaggaaaggtgtctcatctagagtccatgctctggaaattgcaagaggatctgcagcgagtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg Alignment from GeneWise GCCAGAACCCGGGAGCCTGTCAGAAAAGGTCTCTCACCTAGAGTCCATGCTCTGGAAGCTCCAGGAGGACCTGCAGAGG aattttctgttgggtgtggcatcctccactactctccttctcctctgtagGCCT------GGGAGCCTATCAGGAAAGGTGTCTCATCTAGAGTCCATGCTCTGGAAATTGCAAGAGGATCTGCAGCGAgtatgttgccaacctggaggaaagggtttacaaggctgccatgggacatg #### Sipa1_ID1139_13 --> 2 - 2 Original Alignment ga------------------CAACCCATCTCAGAGAGCGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTga ggtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagggCTTTGGGGTATTATTGCACAATCAATCTCTGAAAGTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTgagtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from CESAR ga------------------CAACCCATCTCAGAGAGCGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTga ggtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagggCTTTGGGGTATTATTGCACAATCAATCTCTGAAAGTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTgagtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from Spaln_aa2Genome G CGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTGA GgtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagggctttggggtattattgcacaatcaatctctgaaagTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTGAgtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from Spaln_nt2Genome G------------------ACAACCCATCTCAGAGAGCGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTGA ggtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagGGCTTTGGGGTATTATTGCACAATCAATCTCTGAAAGTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTGAgtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from Pairagon ---------------------------------------------------------------------ACAACCCATCTCAGAGAGCGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTGA GGTGATGCTGTTCATTGGGCTTTCGCAAAACCCAACTCCCTGCTCTGCAGGGCTTTGGGGTATTATTGCACAATCAATCTCTGAAAGTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTGAgtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from Exonerate_protein2genome GACAACCCATCTCAGAGAGCGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTGA ggtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagggctttggggtattattgCACAATCAATCTCTGAAAGTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTGAgtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from Exonerate_coding2genome ggtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagggctttggggtattattgcacaatcaatctctgaaagtggtgatctcaaggaggcttcaaagtgtgattctgagtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc Alignment from GeneWise -----------------GGACAACCCATCTCAGAGAGCGGAGACCCCAAGGAAGCTTTAAAGTGTGATTCTGA ggtgatgctgttcattgggctttcgcaaaacccaactccctgctctgcagGGCTTTGGGGTATTATTGCACAATCAATCTCTGAAAGTGGTGATCTCAAGGAGGCTTCAAAGTGTGATTCTGAgtaagtctcttgtgatcatgttgcttaattttctgttgggtgtggcatcc #### Sipa1_ID1140_12 --> 2 - 1 Original Alignment ttATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTGTCCCGGGAGg taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagttATGCCAGAAGCTGCCACTGAAACATTGGAT---GAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCTG---------ggtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc Alignment from CESAR ttATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTGTCCCGGGAGg taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagttATGCCAGAAGCTGCCACTGAAACATTG---GATGAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCTG---------ggtgagctcccggtactctctgtcttgggaaggtgatgctgttcattcaat Alignment from Spaln_aa2Genome TTATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTG- taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagTTATGCCAGAAGCTGCCACTGAAACATTG---GATGAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCTGGgtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc Alignment from Spaln_nt2Genome TTATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTGTCCCGGGAGG taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagTTATGCCAGAAGCTGCCACTGAAACATT---GGATGAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCT---------GGgtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc Alignment from Pairagon TTATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTGTCCCGGGAGG taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagTTATGCCAGAAGCTGCCACTGAAACATT---GGATGAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCT---------GGgtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc Alignment from Exonerate_protein2genome TTATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTGT taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagTTATGCCAGAAGCTGCCACTGAAACATTG---GATGAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCTGGgtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc Alignment from Exonerate_coding2genome taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagttatgccagaagctgccactgaaacattggatgaatggcagtccatatctgcaatttcctccacttgcaacacaatcctggagtccctgggtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc Alignment from GeneWise TTATGTCGGAAGCTGGCAGTGAGACCCTGGAGGATGAGTGGCAGTCCATCTCAGAGATCGCCTCCACTTGCAACACAATTCTGGAGTCACTGT taggttgacaccattgtgttcgctcttgacctttgctttctttcttccagTTATGCCAGAAGCTGCCACTGAAACATTG---GATGAATGGCAGTCCATATCTGCAATTTCCTCCACTTGCAACACAATCCTGGAGTCCCTGGgtgagctcccggtactctctgtcttgggaaggtgatgctgttcattgggc #### Sipa1_ID1142_10 --> 1 - 0 Original Alignment cTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagcTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGAA---------------gttcgtagggaggtggagtccaggtattgataggctctactaacacatag Alignment from CESAR cTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagcTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGAA---------------gttcgtagggaggtggagtccaggtattgataggc Alignment from Spaln_aa2Genome CTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagCTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGAAGTT---CGTAGGGAGgtggagtccaggtattgataggctctactaacaca Alignment from Spaln_nt2Genome CTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagCTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGA---AGTTCGTAGGGAGgtggagtccaggtattgataggctctactaacacatag Alignment from Pairagon CTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAA ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagCTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGAAgttcgtagggaggtggagtccaggtattgataggctctactaacacatag Alignment from Exonerate_protein2genome CTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCC ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagCTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGAAGTTCGTAGGGAGgtggagtccaggtattgataggctctactaacacatag Alignment from Exonerate_coding2genome ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagctccctgactgatgaggtccctgtcctacccaagattacaccagacctcctactgattacaacagctaacacttccgcccctgatactgatagagaagttcgtagggaggtggagtccaggtattgataggctctactaacacatag Alignment from GeneWise CTCCCTGTCCGATGAGGCTCCAGTCCTGCCCAACACCACTCCAGACCTCCTCCTTGTCACCACTGCCAACCCATCTGCACCTGGTACTGACAGAGAAACACCCCCTTCCCAG ggagaggtgcttatgcaggagaatagtccgtttaccctctgcttctccagCTCCCTGACTGATGAGGTCCCTGTCCTACCCAAGATTACACCAGACCTCCTACTGATTACAACAGCTAACACTTCCGCCCCTGATACTGATAGAGAAGTTCGT---AGGGAGgtggagtccaggtattgataggctctactaacaca #### Sipa1_ID1145_7 --> 1 - 0 Original Alignment gGTGGCAGTGAGCCGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagattgcaaatttccttgttcaccttttgcctctttaagg---------------------------------TTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCAC------CCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from CESAR gGTGGCAGTGAGCCGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG actcttggctgggcactcaaatttccttgttcaccttttgcctctttaagg---------------------------------TTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCAC------CCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from Spaln_aa2Genome GGTGGCAGTGAGC----CGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagATTGCAAATTTCCTTGtTCACCTTTTGCCTCTTTAAGGTTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCAC------CCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from Spaln_nt2Genome GGTGGCAGTGAGCCG---CACCCAG-GACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagATTGCAAATTTCCTTGTTCACCTTTTGCCTCTTTAAGGTTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACC------ACCCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from Pairagon GGTGGCAGTGAGCCGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagattgcaaatttccttgttcaccttttgcctctttaagG---------------------------------TTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCA------CCCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from Exonerate_protein2genome GGTGGCAGTGAGC----CGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagATTGCAAATTTCCTTGTTCACCTTTTGCCTCTTTAAGGTTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCAC------CCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from Exonerate_coding2genome GGTGGCAGTGAGC----CGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagATTGCAAATTTCCTTGTTCACCTTTTGCCTCTTTAAGGTTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCAC------CCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga Alignment from GeneWise GGTGGCAGTGAGCCGCACCCAGGACACTCCTGCCTTCGGTCCTGCGCTGCCAGAAGGCGGAGGCCCCTTTGCAGCCAATGCCGATTTCCGGGCCTTTCTGTTGGCTAAGGCACTCAATGGTGAGCAAGCGGCTGGTCATGCACGCCAGTTCCACGCCATGGCTACACGCACACGCCAACAGTACCTGCAGGACCTGGCTACTAATGAAGTGACCACTACTTCGCTGGACTCGGCTTCGCGGTTTGGCCTGCCATCTCTGGGGGGTAGGCGCCGGGCAACCCCTCGGAGCCCAGGCGCGGAGCTACAGGCGGCGGGTGCGCTGATGTGGGGCGTACGCGCGGCTCCAGGGGCGCGGGTCGCAGCGGGAGCTGAAACGAGCGGTCCGGAGGACGCCGAGGTGCCCTGCTTGTTGGGCATCTCAGCAGAGACACTGGTGCTGGTGGCACCTCGCGACGGCCGCGTGGTCTTCAATTGTGCCTGTCGCGACGTATTGGCCTGGACCTTCTCAGAGCACCAACTCGATCTGTACCACGGGCGCGGGGAGGCGATCACGCTGCGGCTCGACGGGGCCCCAGGGCAAGCCGTGGGCGAAGTCGTGGCACGTCTGCAG gttgacgaggcagattgcaaatttccttgttcaccttttgcctctttaagG---------------------------------TTCAGTCCTGCACTACCAGAAGGCGGAGGTCCCTTTGCAGCCAATACTGACTTCCAAGCATTCCCATGGGCGAAGGCACTAAATGGTGAGCAAGCAGCTGGGCACACAAGGCAGTTCCATGCCATGACTACATGTACACGGCAACAG---CTGCAAGAGTTGGCAACAAATGAGGTGAGTACTACTTTGCTAGACTTGGCCTCCCGATCTGGGTTACCATCCCTAGGCGGTAGACACCAC------CCACAGAGTTCTGGAGCAAAGCTACAAGCAACTGATGCATTGATGTGGGGTGTACATGCAGCTCCTGGGGCACGGGTTGCAGCAGGGGCTGAAACAAAAGGGCCAGAAGATACTGAAGTACCTTGTTTATTGGGTATTTCTGCTGAAACACTAGTGCTGGTCACACCTTCTGATAGTCATGTGGCCTTTAACTGTACATGTCGAGATGTATTGGCCTGGACCTTTTCAGAGCACCAACTTGACCTATACCATGGGCGTGGGAAAGCAATCACATTGCAATTGGATGGTCCACCAGGTCAAGCTGTTGGTGATGTTGTGGCACGTCTGCAAgtaaggtgcaattacgggagtaaggtacaatgcaattactggagtaagga #### Sipa1_ID1147_5 --> 2 - 0 Original Alignment cgGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAG--------- tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagcaGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGTTGGATGGCgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from CESAR cgGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAG--------- tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagcaGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGTTGGATGGCgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from Spaln_aa2Genome CGGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAG--------- tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagCAGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGTTGGATGGCgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from Spaln_nt2Genome CGGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACA tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagCAGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAgttggatggcgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from Pairagon CGGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAG--------- tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagCAGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGTTGGATGGCgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from Exonerate_protein2genome CGGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAG tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagCAGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGttggatggcgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from Exonerate_coding2genome CGGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAG tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagCAGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGttggatggcgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc Alignment from GeneWise CGGATTCCACGGGCACACACTCACTCTACACCACCTACCAAGACCATGAGATCATGTTTCACGTGTCCACGATGCTGCCTTACACGCCTAATAACCAGCAACAGCTC------ tggagccttccacagcacacttgccaatgacgtgaacatctttccaacagCAGATTCCACGGGCACCCACTCACTCTACACCACCTACCAAGATCATGAGATCATGTTTCATGTGTCCACGATGTTGCCTTACACACCTAATAACCAGCAACAGTTGGATGGCgtcagctaagtatttgccaaaactaggaaaaactactgggaatcagtctc #### Sipa1_ID1150_2 --> 2 - 0 Original Alignment aaCACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAG--- caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagaaCATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGGAGgtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from CESAR aaCACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAG--- caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagaaCATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGGAGgtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from Spaln_aa2Genome AACACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAG--- caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagAACATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGGAGgtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from Spaln_nt2Genome AACACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAG--- caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagAACATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGGAGgtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from Pairagon AACACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAG--- caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagAACATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGGAGgtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from Exonerate_protein2genome AACACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAG caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagAACATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGgaggtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from Exonerate_coding2genome caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagaacatcaaaacttctttggactagatgaggcactaggtccagtggctttgagtctccaacgggaggaaaagcagggcagtcgaggggcccccttacacagctttcaagtcattgtgcgaacaatgcaggaggtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa Alignment from GeneWise AACACCAGAACTTCTTTGGGCTGGATGAGGCGCTGGGTCCGGTGGCCGTGAGCCTGCGACGGGAGGAGAAAGAGGGCAGCGGAGGGGGCACCCTACACAGCTACCGGGTCATCGTGCGGACCACGCAGCTC caagagggattacaacaaaccaggaacagatatgtgccttctttgtgcagAACATCAAAACTTCTTTGGACTAGATGAGGCACTAGGTCCAGTGGCTTTGAGTCTCCAACGGGAGGAAAAGCAGGGCAGTCGAGGGGCCCCCTTACACAGCTTTCAAGTCATTGTGCGAACAATGCAGGAGgtagggacatagtgaacaggcaatctgcaaaatgagaagatatacaagaa #### Slc22a20_ID1345_8 --> 2 - 2 Original Alignment at---CTGCAGACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATCag ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacaggtCCTCAGCAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCCA------ATCaggttagtccaggacttaatcatctctagaccaggtcctttgacattctgtt Alignment from CESAR at---CTGCAGACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATCag ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacaggtCCTCAGCAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCCA------ATCaggttagtccaggacttaatcatctctagaccaggtccttcatctctgctgt Alignment from Spaln_aa2Genome ATCTG---CAGACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATCAG ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacagGTCCTCAGCAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCCA------ATCAGgttagtccaggacttaatcatctctagaccaggtcctttgacattctgtt Alignment from Spaln_nt2Genome ATCTGCAG---ACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATCAG ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacagGTCCTCAGCAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCC------AATCAGgttagtccaggacttaatcatctctagaccaggtcctttgacattctgtt Alignment from Pairagon ATCTGCAGACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATCAG ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacaggtcctcag-----CAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCC------AATCAGgttagtccaggacttaatcatctctagaccaggtcctttgacattctgtt Alignment from Exonerate_protein2genome AGGATCTGCAGACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATCAG ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacagGTCCTCAGCAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCCA------ATCAGgttagtccaggacttaatcatctctagaccaggtcctttgacattctgtt Alignment from Exonerate_coding2genome ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacaggtcctcagcaaatgttgcgaactgtgccagctgaactagggaagggctgtctgttgagttcatttatctgtgtgtacctttttatagggggactatatccaatcaggttagtccaggacttaatcatctctagaccaggtcctttgacattctgtt Alignment from GeneWise --GATCTGCAGACCTTGCGGACAGTGCAGGCAGCGCTGGGCAAAGGCTGCCTGGCCAGCTCCTTCATCTGCGTGTATCTGTTCACGGGAGAACTCTATCCCACAGAGATC---------------------------------------------- ataccagtacatgtaagtccagcctagatactgccttgcaatttgcacagGTCCTCAGCAAATGTTGCGAACTGTGCCAGCTGAACTAGGGAAGGGCTGTCTGTTGAGTTCATTTATCTGTGTGTACCTTTTTATAGGGGGACTATATCCAATCAGGTTAGTCCAGGACTTAATCATCTCTAGACCAGGTCCTTTGACATTCTGTT #### Slc22a6_ID2281_2 --> 0 - 2 Original Alignment TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATG---ATGTTTGGCTACCTGGCGGACag gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTG---TTTGGTGCCATGATGTTGTTTGGTTACCTT------aggtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from CESAR TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATGATG---TTTGGCTACCTGGCGGACag gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTGTTT---GGTGCCATGATGTTGTTTGGTTACCTT------aggtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from Spaln_aa2Genome TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATGATGTTTGGCTACCTGGC gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTGTTTGGTGCCATGATGTTGTTTGGTTACCTTAGgtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from Spaln_nt2Genome TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATGATGTT---TGGCTACCTGGCGG gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTGT---TTGGTGCCATGATGTTGTTTGGTTACCT--TAGgtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from Pairagon TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATGA---TGTTTGGCTACCTGGCGGACAG gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTGT---TTGGTGCCATGATGTTGTTTGGTTACCT------TAGgtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from Exonerate_protein2genome TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATGATGTTTGGCTACCTGGC gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTGTTTGGTGCCATGATGTTGTTTGGTTACCTTAGgtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from Exonerate_coding2genome gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagtggaacctttgctcccatagagcctttcaccgattggcccagtcactgttcatggtaggagtgtttggtgccatgatgttgtttggttaccttaggtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat Alignment from GeneWise TGGAACCTTGTGTGCTCTCATCGGGCCTTCCGCCAGCTGGCCCAGTCCCTGTTCATGGTGGGAGTGTTACTGGGAGCCATGATGTTTGGCTACCTGGC gctactaaaattgacatatttcagtgcagagttatgtttgttctgcccagTGGAACCTT---TGCTCCCATAGAGCCTTTCACCGATTGGCCCAGTCACTGTTCATGGTAGGAGTGTTTGGTGCCATGATGTTGTTTGGTTACCTTAGgtgagtagtctttaacaagtattcatgcacggggtagatgaacccattat #### Slc22a8_ID2270_3 --> 1 - 1 Original Alignment gTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCC---AGCCTCACTGTC---TATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTG---AGCACCATTATCTTG------a gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagaTTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGGTGTACAACTACTCTACCTTACagtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from CESAR gTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCC---AGCCTCACTGTC---TATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTG---AGCACCATTATCTTG------a gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagaTTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGGTGTACAACTACTCTACCTTACagtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from Spaln_aa2Genome GTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCC---AGCCTCACTGTC---TATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTG---------AGCACCATTATCTTGA gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagATTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGGTGTACAACTACTCTACCTTACAgtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from Spaln_nt2Genome GTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCCA---GCCTCAC---TGTCTATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTGAGCA gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagATTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGGTgtacaactactctaccttacagtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from Pairagon GTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCC---AGCCT---CACTGTCTATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTGAG gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagATTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGgtgtacaactactctaccttacagtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from Exonerate_protein2genome GTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCC---AGCCTCACTGTC---TATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTGAG gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagATTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGgtgtacaactactctaccttacagtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from Exonerate_coding2genome gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagatttggtcaccagcccattcttacctggagttatttgttgctaactgcaagtgcttgcagtggtgtttttagccccactagccttaccattttttatattcttttccaagttctatgcagttgcagcatctcaggcatttctttgaggtgtacaactactctaccttacagtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg Alignment from GeneWise GTTTGGCCGCAAGCCCATCCTGACCTGGAGCTATCTCTTGCTGGCAGCCAGTGGCTCCAGTGCTGCCTTCAGCCCC---AGCCTCACTGTC---TATATGATCTTCCGATTCCTGTGTGGCTGCAGCATCTCGGGCATTTCTCTG---------AGCACCATTATCTTGA gatggccccaaaagcatgttgtcaagccacctcctcctccttctcctcagATTTGGTCACCAGCCCATTCTTACCTGGAGTTATTTGTTGCTAACTGCAAGTGCTTGCAGTGGTGTTTTTAGCCCCACTAGCCTTACCATTTTTTATATTCTTTTCCAAGTTCTATGCAGTTGCAGCATCTCAGGCATTTCTTTGAGGTGTACAACTACTCTACCTTACAgtgagcccatagtattgctagagcaggcactttatgtggccttgggtagg #### Slc25a45_ID1293_4 --> 0 - 0 Original Alignment GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGTCTCCGG---gtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from CESAR GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGTCTC---CGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from Spaln_aa2Genome GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGT---CTCCGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from Spaln_nt2Genome GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGTCTCCGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from Pairagon GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGTCTCCGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from Exonerate_protein2genome GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGT---CTCCGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from Exonerate_coding2genome CGTACCAGGGCATTGTGGACTGCGTAGTCAAGACTTACCGCCATGAGTCAGTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG CATTCCACTACCAAAGTTTTGCTAATGACTCTCTGTCTCCTCTCTCCCAGGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGT---CTCCGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa Alignment from GeneWise GTCCTGGGTTTCTTCAAGGGAATGAGTTTCCCCATCGCCAGTGTAGCCCTGGTCAACTCCGTCCTGTTCGGAGTGTACAGCAACACGCTCCTGGCGCTAACAGCCACCTCCCATCAGGAGCGACGGGCCCAGCCACCCAGCTACACAAACATCTTTATAGCAGGTTGTACTGGGGGCCTCCTGCAG cattccactaccaaagttttgctaatgactctctgtctcctctctcccagGTTCTAGGGTTCTTTAAAGGAATGAGTTTCCCAATAGCTACTGTAGCTCTGGTTAATTCTGTCTTGTTTGGAGTGTATAGCAACACACTCCTGGCATTAACAGCCACATCCCATCAGGAACACCAGGTTCAGCCTCCAAGCCACACAAATACCTTTATAGCAGGTTGTACAGGGGGTCTC---CGGgtaagcagtatatcatggttgaaggataactcacataccctgagtttgaa #### Slc29a2_ID792_6 --> 2 - 0 Original Alignment gtGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG--------- gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccaggtGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGCGCCATGAAgtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag Alignment from CESAR gtGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG--------- gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccaggtGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGCGCCATGAAgtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag Alignment from Spaln_aa2Genome GTGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG--------- gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccagGTGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGCGCCATGAAgtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag Alignment from Spaln_nt2Genome GTGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG--------- gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccagGTGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGCGCCATGAAgtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag Alignment from Pairagon GTGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG--------- gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccagGTGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGCGCCATGAAgtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag Alignment from Exonerate_protein2genome GTGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccagGTGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGcgccatgaagtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GTGGCGTGGATGCCCAGACCTCTGCTCTTGGATACTTCATCACACCCTGTGTGGGCATCCTCCTCTCCATCGTATGTTACCTCAGCCTGCCTCATCTG--------- gtacaaacaaagctggaatgggagacttgtggtctgtttgtgttttccagGTGACGTGGATGCCCAAACCTCTGCTCTGGGATACTTCATCACACCTTGTGTGGGCATCCTACTCCCCATTGTATGTTACCTTAGCTTGCCACACCTGCGCCATGAAgtgagtcgcttcatagtttatgttatgcatgcactgcttaaatataaaag #### Slc29a2_ID794_8 --> 2 - 0 Original Alignment atGAGAAGAATGGGGTTCCCATCAGCCCCCAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTGTCTTCCGGAAG tgtgggcccggtatggtagagacaatgtgtaacaatttctttttccaaagat---------------------------CAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAgtaagctgtaatgtacagacagggctgggagcagtgggttgtttgacctg Alignment from CESAR atGAGAAGAATGGGGTTCCCATCAGCCCCCAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTGTCTTCCGGAAG ctaatgatagtttttagggccataatgtgtaacaatttctttttccaaagat---------------------------CAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAgtaagctgtaatgtacagacagggctgggagcagtgggttgtttgacctg Alignment from Spaln_aa2Genome CCCAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTGTCTTCCGGAAG tgtgggcccggtatggtagagacaatgtgtaacaatttctttttccaaagATCAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAgtaagctgtaatgtacagacagggctgggagcagtgggttgtttgacctg Alignment from Spaln_nt2Genome AGCCCCCAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTGTCTTCCGGAAG tgtgggcccggtatggtagagacaatgtgtaacaatttctttttccaaagA----TCAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAgtaagctgtaatgtacagacagggctgggagcagtgggttgtttgacctg Alignment from Pairagon ATGAGAAGAATGGGGTTCCCATCAGCCCCCAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTG------------------------------------------------------------- tgtgggcccggtatggtagagacaatgtgtaacaatttctttttccaaagAT---------------------------CAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAGTAAGCTGTAATGTACAGACAGGGCTGGGAGCAGTGGGTTGTTTGACCTG Alignment from Exonerate_protein2genome ATGAGAAGAATGGGGTTCCCATCAGCCCCCAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTGTCTTCCGGAAG tgtgggcccggtatggtagagacAATGTGTAACAATTTCTTTTTCCAAAGATCAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAgtaagctgtaatgtacagacagggctgggagcagtgggttgtttgacctg Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise -GAGAAGAATGGGGTTCCCATCAGCCCC---CAACAGGCCAGCCCAACTCTGGATCTTGACCCTGAGAAGGAGCCAGAGCCGGAGGAGCCACAGAAGCCAGGAAAACCTTCAGTCTTTGTTGTCTTCCGGAAG tgtgggcccggtatggtagagACAATGTGTAACAATTTCTTTTTCCAAAGATCAGCAGGCAAGCCCAACTCTTGAGCTGGACCCTGAAACGGAGCCAGAACCAGAGCAGCCACAAAAGCCAGGCAAACCCTCAGTCTTTGTGGTTCTCAAGAAAgtaagctgtaatgtacagacagggctgggagcagtgggttgtttgacctg #### Slc29a2_ID795_9 --> 0 - 1 Original Alignment ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGAAGTGGg tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTGGG------ggtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc Alignment from CESAR ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGAAGTGGg tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTGGG------ggtcagtccatttacttgtaatagttcacagtatggaccagcagccctttg Alignment from Spaln_aa2Genome ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGG- tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTGGGGgtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc Alignment from Spaln_nt2Genome ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGAAGTGGG tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTG------GGGgtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc Alignment from Pairagon ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGAAGTGGG tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTG------GGGgtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc Alignment from Exonerate_protein2genome ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGA tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTGGGGgtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc Alignment from Exonerate_coding2genome ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGA tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTGGGGgtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc Alignment from GeneWise ATCTGGCTGACGGCGCTGTGCCTTGTGTTGGTCTTCACAGTCACCCTGTCGGTCTTTCCTGCCATCACAGCCATGGTGACCACCAGCTCCAATAGCCCCGGGA tgacctgaatacttcagtgactatccagtgatggggtgtgtgtctttcagATCTGGCTGACAGCGCTGTGCCTTGTGTTAGTCTTCACAGTTACCCTATCTGTTTTTCCTGCTATCACAGCCATGGTGACCACCAGCTCCAATAGCCCTGGGGgtcagtccatttacttgtaatagttcacagtatggaccagaggtgcttcc #### Slit1_ID8222_17 --> 1 - 2 Original Alignment a------CGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAat tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagtACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAatgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from CESAR a------CGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAat tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagtACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAatgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from Spaln_aa2Genome -GAGCTACGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAAT tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagTACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAATgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from Spaln_nt2Genome A------CGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAAT tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagTACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAATgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from Pairagon ------ACGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAAT tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagTACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAATgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from Exonerate_protein2genome TGAGCTACGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAAT tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagTACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAATgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from Exonerate_coding2genome TGAGCTACGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAAT tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagTACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAATgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact Alignment from GeneWise ----CTACGACTGAACAACAATGAGATTTCTATCCTAGAGGCCACTGGGTTGTTTAAGAAGCTCTCACATCTGAAGAAAAT tgagatggaggggggagctaggggttgacttgttttgtcctttgttttagTACATTTCGGCTGAACAACAATGAGATCTCTATCCTAGAGGCCACTGGTTTATTTAGGAAGCTCACACATCTGGAGAAAATgtactaacagatttgattctgaacagtggttgtatgaagcaggactaact #### Slit1_ID8233_6 --> 1 - 2 Original Alignment aCAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTT---ct tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagaCAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTGctgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from CESAR aCAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTT---ct tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagaCAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTGctgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from Spaln_aa2Genome ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCT tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTgctgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from Spaln_nt2Genome ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCTGAC tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTGCTgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from Pairagon ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCTGAC tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTGCTgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from Exonerate_protein2genome ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTT---CT tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTGCTgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from Exonerate_coding2genome tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagacagctggacaagaaccgcattagctgcatcaaggaaggggccctccgtgccctacgtggattggatgttttgctgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg Alignment from GeneWise ACAGCTGGACAAGAACCGGATCAGCTGCATCGAGGAAGGGGCCTTCCGTGCCCTACGGGGACTGGAGGTTCTG-- tgccaaaactgttcttatggtcactttccgtgtctgttgtttccccacagACAGCTGGACAAGAACCGCATTAGCTGCATCAAGGAAGGGGCCCTCCGTGCCCTACGTGGATTGGATGTTTTGCTgtaagaggagtatgaagattaaattagtgcatcaatactgttattcaatg #### Slk_ID10265_17 --> 0 - 0 Original Alignment TTTGCTGCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatag------GCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from CESAR TTTGCTGCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG atcagtagagggaagatatatctctttgatggcggcctcttcttttatag------GCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from Spaln_aa2Genome TTTGCTGCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatag------GCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from Spaln_nt2Genome GCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatagGCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from Pairagon TTTGCTGCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatag------GCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from Exonerate_protein2genome GCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatagGCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from Exonerate_coding2genome GCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatagGCACAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac Alignment from GeneWise TTTGCTGCACAAGAAGAAAAGAGACAGAAAAATGAGAGAATGGCTCAGCATCAAAAACATGAGAGCCAAATGCGGGATCTTCAGTTGCAGTGTGAAGCCAATGTTCGGGAACTGCACCAGCTGCAG agagggaagatatatctctgtatttttgatggcggcctcttcttttatagGCA------CAAGACAAAAAGCGAAAAAAAAATAAAAGGATGTCTCAACATCAAAAACATGAAAGCCATATGCAGGACCTTCAGCTGCAATGTGAAGCTAATGTGCAGGAATTACATCAGTTGCCAgtaatttttctaaaactggagtgacaggaagtgcatttgtattgtttaac #### Smc3_ID11322_10 --> 0 - 0 Original Alignment CTTTCTGCTAAGCGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacag---------AAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from CESAR CTTTCTGCTAAGCGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG gtttttatccaatgttcagattagagtgcgtggctgaccgcggactacag---------AAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from Spaln_aa2Genome CTTTCTGCTAAGCGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacag---------AAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from Spaln_nt2Genome GAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacagaagcagGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from Pairagon CTTTCTGCTAAGCGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacag---------AAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from Exonerate_protein2genome AAGCGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacagAAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from Exonerate_coding2genome AAGCGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacagAAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct Alignment from GeneWise ---CGAGAAACGAGTGGAGAGAAATCCAGACAACTAAGGGATGCCCAGCAGGATGCAAGAGACAAAATGGAG caatgttcagattagatagccctgtgtgcgtggctgaccgcggactacagAAGCAGGAAACAAGTGGAGAGAAATCAAGACAACTAAGGGATGCACAGCAGGATACAAGAGATAAAATGGAAgtaaggtgaagcctaaggtaatacctagatgttacttttactgataatct #### Smc3_ID11338_26 --> 0 - 0 Original Alignment GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacag---TCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac Alignment from CESAR GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tcgtttataaaagaagcatgccaccatgcgggtttctctcttccgtacag---TCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac Alignment from Spaln_aa2Genome GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacagTCTAAGAACTTT---AGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac Alignment from Spaln_nt2Genome TCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacagTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac Alignment from Pairagon TCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAG--------------------------------------------------- tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacagTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTGTACGGGACTTATTATACTTAGTTTCTCATGTACCTTTTTACTTTAAAAC Alignment from Exonerate_protein2genome TCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacagTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac Alignment from Exonerate_coding2genome TCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacagTCTAAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac Alignment from GeneWise GTATCTAAGAACTTCAGTGAAGTTTTCCAGAAGTTGGTACCTGGTGGCAAAGCGACTTTGGTGATGAAGAAAGGAGATGTGGAGGGCAGCCAGTCTCAGGACGAAGGAGAAGGGAGTGGCGAGAGTGAGCGGGGCTCTGGGTCACAGAGCAGTGTTCCATCAGTTGACCAGTTCACAGGAGTTGGGATCAGG tttataaaagaagcatgccacctagatgcgggtttctctcttccgtacagTCT---AAGAACTTTAGTGAAATCTTCCAGAAATTGGTACCTGGTGGCAAATCAACTTTGGTGATGAAGAAAGGTGATGTGGAGAGCAGTGAATCTAAGGACAAAGGAGAGGGGAGTGGCGAGAGTGAGCGAGGATCTGGGTCACAGTGCAGTGTTCCATCAGTTGACCAATTCACAGGAGTTGGGATCAGTgtacgggacttattatacttagtttctcatgtacctttttactttaaaac #### Snx15_ID1467_5 --> 0 - 1 Original Alignment GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCA---g tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAggtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from CESAR GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCA---g tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAggtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from Spaln_aa2Genome GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCAGTGG tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAGgtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from Spaln_nt2Genome GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCAGTGG tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAGgtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from Pairagon GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCAG--- tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAGgtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from Exonerate_protein2genome GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCAGTGG tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAGgtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from Exonerate_coding2genome GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCAGTGG tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAGgtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc Alignment from GeneWise GGCGGGGAGGTGACACGGCCCTCTGAGGTGTCCAGGGACCTGCGAATCCTGCCACCCCCTCTCATCCCCACACCACCTCCGGATGAGGCCCGGCTACTTCAGCCGCTGCCTGCGGAAAGGAGGGGCCAGGAGGAGTTGGAGGTGCCAGTG- tgatggtcagccatattattctgccctcgttcttgttgggctttcaacagGGTGGGGAGATAACACGCCCCTTTGAGGTGTCTAGAGACCTGCGGATCCCACTCCCTCCTCTTATTCCAACAATGCCTCCAGTTGAAGCTCGTTTATTTCAGGCTTTGCTGGCTGAAAGAAGGGGCCAGGAGGAGCTGGAGGTCCCAGAAGgtgagtccggtttcaggaggtgggctgatactgccaatagtagccctttc #### Snx15_ID1468_4 --> 2 - 0 Original Alignment ggCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacagga---TTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from CESAR ggCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caccaacactgaaacattcatgctgtaacactggggtcttgtgaccacagga---TTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from Spaln_aa2Genome GGCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacagGA---TTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from Spaln_nt2Genome GGCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacag---GATTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from Pairagon GGCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacag---GATTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from Exonerate_protein2genome GGCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacagGA---TTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from Exonerate_coding2genome GGCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacagGA---TTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt Alignment from GeneWise GGCGGTTTGAAGCCTCTGTGATCGAGGAGCGGCGCAAGGGCGCGGAGGACCTGCTGCGCTTCACGGTGCCCATCCCTGCACTCAACAACAGCCCCCAACTCAAGGAGTTTTTCCGG caacactgaaacattcatgctggcataacactggggtcttgtgaccacagGA---TTCGAAGCTTCTGTTATTGAGGAACATCAGAAAGGTGCAGATGACCTGCTGCGCTTCACAGTGCCAATCCCAGCCCTCAACAACAGCCCTCAAGTTAAAGAATTCTTCCGCgtaagtgcctgtactaacagggtccccttctagtcaaatcacccagcctt #### Snx32_ID1066_12 --> 2 - 0 Original Alignment AACAAg ag---------CTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAggtgagtcctgcaggattgtaactgttacccatgttcttctgcagaaTGCCCAGGCCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from CESAR ACTCCGCCAAACAAg agCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG ACTCTACCAAACAAggtgagtcctgcaggattgtccatgttcttctgcagaatgcccaggcCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from Spaln_aa2Genome AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagtcctgcaggattgtaactgttacccatgttcttctgcagaatgcccagGCCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from Spaln_nt2Genome AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagtcctgcaggattgtaactgttacccatgttcttctgcagaatgcccagGCCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from Pairagon AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagtcctgcaggattgtaactgttacccatgttcttctgcagaatgcccagGCCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from Exonerate_protein2genome AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagtcctgcaggattgtaactgttacccatgttcttctgcagaatgcccagGCCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from Exonerate_coding2genome aacaaggtgagtcctgcaggattgtaactgttacccatgttcttctgcagaatgcccaggccttatggacttcaaatctcacagggtctcctctttccgtaagaacctcatcgagttgactgagctggagctcaagcaggccaaggtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta Alignment from GeneWise AACAAG AGCTCATGGACTTCAAGTCTCGCAGGGTCTCCTCTTTCCGTAAGAATCTCATTGAGCTGGCCGAACTGGAGCTCAAGCACGCCAAG AACAAGgtgagtcctgcaggattgtaactgttacccatgttcttctgcagaatgcccagGCCTTATGGACTTCAAATCTCACAGGGTCTCCTCTTTCCGTAAGAACCTCATCGAGTTGACTGAGCTGGAGCTCAAGCAGGCCAAGgtctgttgctattccagttacatcaaaaagaactcaatctgctcattcta #### Snx32_ID1073_5 --> 1 - 0 Original Alignment gGAATACTTGGCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aatggcattctagtagacctctaattattgtgtttctgaccctactttagg---------GCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from CESAR gGAATACTTGGCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aacaagcaaaatggcattctagtagtattgtgtttctgaccctactttagg---------GCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from Spaln_aa2Genome GGAATACTTGGCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aatggcattctagtagacctctaattattgtgtttctgaccctactttagG---------GCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from Spaln_nt2Genome CTTGGCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aatggcattctagtagacctctaattattgtgtttctgaccctactttag---GGCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from Pairagon GGAATACTTGGCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aatggcattctagtagacctctaattattgtgtttctgaccctactttag---------GGCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from Exonerate_protein2genome GGAATACTTG---GCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aatggcattctagtagacctctaattattgtgtttctgACCCTACTTTAGGGCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from Exonerate_coding2genome GGAATACTTG---GCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGATCTG aatggcattctagtagacctctaattattgtgtttctgACCCTACTTTAGGGCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATGTAaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg Alignment from GeneWise GGAATACTTGGCCATCTTTAAGAAGACTGTTGCGATGCATGAAGTCTTCCTGCAGCGCCTGGCAGCCCATCCCACCCTGCGTCGGGACCACAACTTCTCCGTCTTCTTGGAATACAGCCAGGAT aatggcattctagtagacctctaattattgtgtttctgaccctactttagG---------GCCATTTTTAAGAAGACTGTTGCTATGCATGAAGTCTTTCTCCAACGCCTGGCAGCCCATCCCACCCTGCGTCGGGATCACAACTTCTCCATCTTCTTGGAATATAGCCAGGATgtaaggttgttgaatcattacaacaaaatgagaggctgatgggcatgtgg #### Snx32_ID1074_4 --> 0 - 2 Original Alignment ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAA---------gc tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGATATGCTGgcgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from CESAR ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAA---------gc tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGATATGCTGgcgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from Spaln_aa2Genome ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAGCG-------- tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGATATGCTGGCgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from Spaln_nt2Genome ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAG---------C tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGATATGCTGGCgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from Pairagon GTACGCCGGCCTCATCATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAA---------GC tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccag----------------CTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGATATGCTGGCgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from Exonerate_protein2genome ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAG tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGatatgctggcgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from Exonerate_coding2genome ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAAG tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGatatgctggcgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc Alignment from GeneWise ATTCCCCCAGCCCCTCCCAGGCCAGACTTTGAGGCTTCAAGGGAAAAGCTGCAGAAGTTGGGTGAGGGCAACAGCTCCATCACCCGGGAAGAATTCTCCAAGATGAAGCAGGAGCTAGAA---------GC tctagctggaaatgttgtgttaatttgggaaaatcaggctctgattccagCTTCCCCCAGCCCCCCCCAGGTCAGACTTTGAAGCCTCAAGGGAAAAACTGCAGAGGTTAGGTGAAGGTAATAGTTCAATCACCCGGGAAGAGTTCTCCAAGATGAAACCAGAGTTAGAAGATATGCTGGCgtaagaatttccctccatctccttgattctagtagagttttcaaagtctc #### Sptbn2_ID610_5 --> 1 - 2 Original Alignment GATGAAGACTGCAgg aTACCCCAATGTCAATGTGCACAACTTTACCACCAGTTGGAGAGATGGGCTGGCCTTTAATGCCATTGTGCACAAACAC---cg GATGAAAACAGCTgggtacttgatgtgaaggttgccccctttcccctcaggTACCCCAATGTCAATGTGCATAACTTCACCACCAGCTGGAGAGATGGGCTAGCCTTCAATGCCATCATACATAAACACCTAcggtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from CESAR GATGAAGACTGCAgg aTACCCCAATGTCAATGTGCACAACTTTACCACCAGTTGGAGAGATGGGCTGGCCTTTAATGCCATTGTGCACAAACAC---cg GATGAAAACAGCTgggtaagagatgtgaaggttgccccctttcccctcaggTACCCCAATGTCAATGTGCATAACTTCACCACCAGCTGGAGAGATGGGCTAGCCTTCAATGCCATCATACATAAACACCTAcggtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from Spaln_aa2Genome GATGAAGACTGCAGG ATACCCCAATGTCAATGTGCACAACTTTACCACCAGTTGGAGAGATGGGCTGGCCTTTAATGCCATTGTGCACAAACACCGG-- GATGAAAACAGCTGGgtacttgatgtgaaggttgccccctttcccctcagGTACCCCAATGTCAATGTGCATAACTTCACCACCAGCTGGAGAGATGGGCTAGCCTTCAATGCCATCATACATAAACACCTACGgtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from Spaln_nt2Genome GATGAAGACTGCAGG ATACCCCAATGTCAATGTGCACAACTTTACCACCAGTTGGAGAGATGGGCTGGCCTTTAATGCCATTGTGCACAAACACC---G GATGAAAACAGCTGGgtacttgatgtgaaggttgccccctttcccctcagGTACCCCAATGTCAATGTGCATAACTTCACCACCAGCTGGAGAGATGGGCTAGCCTTCAATGCCATCATACATAAACACCTACGgtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from Pairagon GATGAAGACTGCAGG ATACCCCAATGTCAATGTGCACAACTTTACCACCAGTTGGAGAGATGGGCTGGCCTTTAATGCCATTGTGCACAAACAC---CG GATGAAAACAGCTGGgtacttgatgtgaaggttgccccctttcccctcagGTACCCCAATGTCAATGTGCATAACTTCACCACCAGCTGGAGAGATGGGCTAGCCTTCAATGCCATCATACATAAACACCTACGgtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from Exonerate_protein2genome gatgaaaacagctgggtacttgatgtgaaggttgccccctttcccctcaggtaccccaatgtcaatgtgcataacttcaccaccagctggagagatgggctagccttcaatgccatcatacataaacacctacggtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from Exonerate_coding2genome gatgaaaacagctgggtacttgatgtgaaggttgccccctttcccctcaggtaccccaatgtcaatgtgcataacttcaccaccagctggagagatgggctagccttcaatgccatcatacataaacacctacggtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat Alignment from GeneWise GATGAAGACTGCAGG ATACCCCAATGTCAATGTGCACAACTTTACCACCAGTTGGAGAGATGGGCTGGCCTTTAATGCCATTGTGCACAAACACCGG-- GATGAAAACAGCTGGgtacttgatgtgaaggttgccccctttcccctcagGTACCCCAATGTCAATGTGCATAACTTCACCACCAGCTGGAGAGATGGGCTAGCCTTCAATGCCATCATACATAAACACCTACGgtgagagtgtgaggtcctagctcctgacttacctatttgttcggatgtat #### Sptbn2_ID611_6 --> 1 - 1 Original Alignment gCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGGATCCTGAAg cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagtCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAGTGTAATGTCCACTACAATTTGCAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTG---------ggtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac Alignment from CESAR gCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGGATCCTGAAg cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagtCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAGTGTAATGTCCACTACAATTTGCAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTG---------ggtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac Alignment from Spaln_aa2Genome GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTG- cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAGTGTAATGTCCACTACAATTTGCAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac Alignment from Spaln_nt2Genome GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGGATC--CTGAAG cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAGTGTAATGTCCACTACAATTTGCAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGGTGAGCTGGCGgtaattcgttaagccagctgatagcaagatagaggctac Alignment from Pairagon GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGG cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAGTGTAATGTCCACTACAATTTGCAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac Alignment from Exonerate_protein2genome cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagtccagatctgttggattttgagtccctaaaaaagtgtaatgtccactacaatttgcagaatgctttcaatcttgctgaaaaggaacttggccttagaagaatcctgggtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac Alignment from Exonerate_coding2genome cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagtccagatctgttggattttgagtccctaaaaaagtgtaatgtccactacaatttgcagaatgctttcaatcttgctgaaaaggaacttggccttagaagaatcctgggtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac Alignment from GeneWise GCCAGACCTGTTGGATTTTGAGTCCCTGAAGAAGTGTAATGCACACTACAATCTGCAGAATGCTTTCAATCTGGCTGAAAAGGAACTTGGCCTGACGAAGCTCCTGG cagtcaaaatggcaatagcacaacaggatgatgatttgctccacatttagTCCAGATCTGTTGGATTTTGAGTCCCTAAAAAAGTGTAATGTCCACTACAATTTGCAGAATGCTTTCAATCTTGCTGAAAAGGAACTTGGCCTTAGAAGAATCCTGGgtgagctggcggtaattcgttaagccagctgatagcaagatagaggctac #### Sptbn2_ID615_10 --> 0 - 0 Original Alignment GCCTGGGAGCGGCTGGAGAAAGCCGAACATGAGCGAGAGCTAGCGCTGCGCACAGAGCTGATCCGCCAGGAGAAGCTGGAGCAACTGGCTGCTCGCTTCGACCGCAAGGCTGCCATGCGGGAGACCTGGCTCAGTGAGAACCAGCGACTTGTGTCCCAG--- ctaacccattctgccactacccccactttccttgtgccttgttcctgcagGCCTGGGAGCGATTGGAGAAATCCGAACATGAGAGAGAGCTAGCATTGCGCACAGAGCTCATTCGTCAGAAAAAGCTAGAGAAATTAGCTGCTCGATTTGACCACAAGGCTTCTATGCGGAAGACTTGGCTCAGAGAGAATCAGCGTCTTGTTTCTCAAGCTgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from CESAR GCCTGGGAGCGGCTGGAGAAAGCCGAACATGAGCGAGAGCTAGCGCTGCGCACAGAGCTGATCCGCCAGGAGAAGCTGGAGCAACTGGCTGCTCGCTTCGACCGCAAGGCTGCCATGCGGGAGACCTGGCTCAGTGAGAACCAGCGACTTGTGTCCCAG--- ctaacccattctgccactacccccactttccttgtgccttgttcctgcagGCCTGGGAGCGATTGGAGAAATCCGAACATGAGAGAGAGCTAGCATTGCGCACAGAGCTCATTCGTCAGAAAAAGCTAGAGAAATTAGCTGCTCGATTTGACCACAAGGCTTCTATGCGGAAGACTTGGCTCAGAGAGAATCAGCGTCTTGTTTCTCAAGCTgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from Spaln_aa2Genome GCCTGGGAGCGGCTGGAGAAAGCCGAACATGAGCGAGAGCTAGCGCTGCGCACAGAGCTGATCCGCCAGGAGAAGCTGGAGCAACTGGCTGCTCGCTTCGACCGCAAGGCTGCCATGCGGGAGACCTGGCTCAGTGAGAACCAGCGACTTGTGTCCCAG ctaacccattctgccactacccccactttccttgtgccttgttcctgcagGCCTGGGAGCGATTGGAGAAATCCGAACATGAGAGAGAGCTAGCATTGCGCACAGAGCTCATTCGTCAGAAAAAGCTAGAGAAATTAGCTGCTCGATTTGACCACAAGGCTTCTATGCGGAAGACTTGGCTCAGAGAGAATCAGCGTCTTGTTTCTCAAgctgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from Spaln_nt2Genome GCCTGGGAGCGGCTGGAGAAAGCCGAACATGAGCGAGAGCTAGCGCTGCGCACAGAGCTGATCCGCCAGGAGAAGCTGGAGCAACTGGCTGCTCGCTTCGACCGCAAGGCTGCCATGCGGGAGACCTGGCTCAGTGAGAACCAGCGACTTGTGTCCCAGG-- ctaacccattctgccactacccccactttccttgtgccttgttcctgcagGCCTGGGAGCGATTGGAGAAATCCGAACATGAGAGAGAGCTAGCATTGCGCACAGAGCTCATTCGTCAGAAAAAGCTAGAGAAATTAGCTGCTCGATTTGACCACAAGGCTTCTATGCGGAAGACTTGGCTCAGAGAGAATCAGCGTCTTGTTTCTCAAGCTgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from Pairagon GCCTGGGAGCGGCTGGAGAAAGCCGAACATGAGCGAGAGCTAGCGCTGCGCACAGAGCTGATCCGCCAGGAGAAGCTGGAGCAACTGGCTGCTCGCTTCGACCGCAAGGCTGCCATGCGGGAGACCTGGCTCAGTGAGAACCAGCGACTTGTGTCCCAG--- ctaacccattctgccactacccccactttccttgtgccttgttcctgcagGCCTGGGAGCGATTGGAGAAATCCGAACATGAGAGAGAGCTAGCATTGCGCACAGAGCTCATTCGTCAGAAAAAGCTAGAGAAATTAGCTGCTCGATTTGACCACAAGGCTTCTATGCGGAAGACTTGGCTCAGAGAGAATCAGCGTCTTGTTTCTCAAGCTgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from Exonerate_protein2genome ctaacccattctgccactacccccactttccttgtgccttgttcctgcaggcctgggagcgattggagaaatccgaacatgagagagagctagcattgcgcacagagctcattcgtcagaaaaagctagagaaattagctgctcgatttgaccacaaggcttctatgcggaagacttggctcagagagaatcagcgtcttgtttctcaagctgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from Exonerate_coding2genome ctaacccattctgccactacccccactttccttgtgccttgttcctgcaggcctgggagcgattggagaaatccgaacatgagagagagctagcattgcgcacagagctcattcgtcagaaaaagctagagaaattagctgctcgatttgaccacaaggcttctatgcggaagacttggctcagagagaatcagcgtcttgtttctcaagctgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca Alignment from GeneWise GCCTGGGAGCGGCTGGAGAAAGCCGAACATGAGCGAGAGCTAGCGCTGCGCACAGAGCTGATCCGCCAGGAGAAGCTGGAGCAACTGGCTGCTCGCTTCGACCGCAAGGCTGCCATGCGGGAGACCTGGCTCAGTGAGAACCAGCGACTTGTGTCCCAGGAC ctaacccattctgccactacccccactttccttgtgccttgttcctgcagGCCTGGGAGCGATTGGAGAAATCCGAACATGAGAGAGAGCTAGCATTGCGCACAGAGCTCATTCGTCAGAAAAAGCTAGAGAAATTAGCTGCTCGATTTGACCACAAGGCTTCTATGCGGAAGACTTGGCTCAGAGAGAATCAGCGTCTTGTTTCTCAAGCTgtgagttttctccaccagcctaaaaggtgtatattaatgagatctgtgca #### Sptbn2_ID634_29 --> 2 - 0 Original Alignment ttTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG--------- aatgaacctttaaagtctctatataaccctcatagctgctctccctttagtaTTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAGGAAAAAACgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from CESAR ttTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG--------- aatgaacctttaaagtctctatataaccctcatagctgctctccctttagtaTTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAGGAAAAAACgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from Spaln_aa2Genome TTTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG--------- aatgaacctttaaagtctctatataaccctcatagctgctctccctttagTATTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAGGAAAAAACgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from Spaln_nt2Genome TTTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG--------- aatgaacctttaaagtctctatataaccctcatagctgctctccctttagTATTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAGGAAAAAACgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from Pairagon TTTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG--------- aatgaacctttaaagtctctatataaccctcatagctgctctccctttagTATTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAGGAAAAAACgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from Exonerate_protein2genome TTTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG aatgaacctttaaagtctctatataaccctcatagctgctctccctttagTATTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAggaaaaaacgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from Exonerate_coding2genome TTTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG aatgaacctttaaagtctctatataaccctcatagctgctctccctttagTATTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAggaaaaaacgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct Alignment from GeneWise TTTTGGAGGTGCTTGTGTTTGGGAGAGATGCAGGGATGGCGGAGGCCTGGCTGTGCAGTCAGGAGCCATTGGTGCGAAGTGCAGAACTGGGTTGCACTGTGGACGAAGTAGAGAGCCTCATCAAGCGACACGAAGCCTTTCAGAAGTCGGCCGTGGCCTGGGAAGAGCGTTTCAGTGCGCTGGAGAAGCTCACTGCG--------- aatgaacctttaaagtctctatataaccctcatagctgctctccctttagTATTAGAGGTACTTGTATTTGGGAAAGATGCGGGGATGTCAGAGGCATGGCTGTGCAGCCAGGCACCAGTGGTGCGAAGTCCAGAATTGGGTTGTACTGTGGATGAAGTAGAGGCTCTCATGAAGCGGCATGAGGCCTATCAGAAATCAGCTGTAGCATGGGAAGAGCGATTTGGTGCATTAGATAAGCTCACTGCAGGAAAAAACgtgagcctaccggtacatgttcatagacccttgattgttgtgcttcatct #### Ssh3_ID447_9 --> 0 - 0 Original Alignment ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC agtccacttagacattcagccttaactaattcttgttgttactgttgtag---------GCCTTAGAACTACACCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcactttgtctattttatttgcagGGC Alignment from CESAR ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC tagaccttcagtccacttagacattctaattcttgttgttactgttgtag---------GCCTTAGAACTACACCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcaatgatctcttccctctgacagGGC Alignment from Spaln_aa2Genome CAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC agtccacttagacattcagccttaactaattcttgttgttactgttgtag---GCCTTAGAACTACACCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcactttgtctattttatttgcagGGC Alignment from Spaln_nt2Genome CAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC agtccacttagacattcagccttaactaattcttgttgttactgttgtag---GCCTTAGAACTACACCTTGGATGTCCTTT------ATATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcactttgtctattttatttgcagGGC Alignment from Pairagon ATCCGTCAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC agtccacttagacattcagccttaactaattcttgttgttactgttgtag---------GCCTTAGAACTACACCTTGGATGTCCTTT------ATATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcactttgtctattttatttgcagGGC Alignment from Exonerate_protein2genome CAGGCCCTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC agtccacttagacattcagccttaactaattcttgttgttactgttgTAGGCCTTAGAACTACACCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcactttgtctattttatttgcagGGC Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise ---CTGGAGCTGCGTCTGGGATGTCCTCTCCAGCAGTACCGTGACTTTATTGACAACCAGATGTTGCTGCTCATGGCCCAGCAAGACCGGGCCTCTCGCATCTTCCCCCACCTCTACTTG GGC agtccacttagacattcagccttaactaattcttgttgttactgttgtagGCCTTAGAACTACACCTTGGATGTCCTTTA------TATCGTGTCTTTATTGATAACCAGATGTTGCTTCTTATGGCCCATCAGGATCAGACATCTCGAATCTACCCATACCTCTACTTAgtaaacggtcttctattcattcttcactttgtctattttatttgcagGGC #### Ssh3_ID449_7 --> 1 - 2 Original Alignment gGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGA---ca tatctggttggtcatctagggccaaggtctctgactcatcccattgccaggGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAGcagttagtggcaggacagggcaaagcagaaaaataatgtggagggtgtttac Alignment from CESAR gGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGA---ca tatctggttggtcatctagggccaaggtctctgactcatcccattgccaggGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAGcagttagtggcaggacagggcaaagcagaaaaataatgtggagggtgtttac Alignment from Spaln_aa2Genome GGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGACA tatctggttggtcatctagggccaaggtctctgactcatcccattgccagGGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAgcagttagtggcaggacagggcaaagcagaaaaataatgtggagggtgtttac Alignment from Spaln_nt2Genome GGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGACAGGCTTCAGAG-CAGGAAAAG tatctggttggtcatctagggccaaggtctctgactcatcccattgccagGGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAGCAGTTAGTGGCAGGACAGGgcaaagcagaaaaataatgtggagggtgtttac Alignment from Pairagon GGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGACA tatctggttggtcatctagggccaaggtctctgactcatcccattgccagGGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAgcagttagtggcaggacagggcaaagcagaaaaataatgtggagggtgtttac Alignment from Exonerate_protein2genome GGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGACAGGCTTCAGAGCAGGA tatctggttggtcatctagggccaaggtctctgactcatcccattgccagGGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAGCAGTTAGTGGCAGGacagggcaaagcagaaaaataatgtggagggtgtttac Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GGCCACACTGCAGGTATTGCACCAGGCATGTGAGGTAGCTCTAGGCAGTGGCCTTGTGCCTGGTGGCAGTGCCCTTGCCTGGGCTACTTACTACCAGGAGAAACTCAACTCTGACCAGGGTTGCCTCAATGAGTGGATGGCCATGTCTGACCTGGAGTCCTTTCGACCACCTAATGCTGAGCCTGGACAG-- tatctggttggtcatctagggccaaggtctctgactcatcccattgccagGGCCACATTGCAAGTATTGCATCAGGCATGTGAGGTAGCTCTTGGTAGTGGCCTTGTGCCTGGTGGGAGTGCTCTAGCATGGGCTACTTACTATCAGGTGAAGCTTAACTCTGATCAGGGCTGCCTAAATGAATGGATGGCAATGTCTGACCTGGAAACATTTCGACCACCCAATGCTGAGCCCACACAGCAgttagtggcaggacagggcaaagcagaaaaataatgtggagggtgtttac #### Ssh3_ID450_6 --> 1 - 2 Original Alignment gGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGtg tattgattacctgctctcaaagtctgactccctttgtcttcctgctgcagt---TTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGtggtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta Alignment from CESAR gGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGtg gcctattgattacctgctctcaaaggactccctttgtcttcctgctgcagt---TTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGtggtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta Alignment from Spaln_aa2Genome GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG tattgattacctgctctcaaagtctgactccctttgtcttcctgctgcagT---TTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGTGgtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta Alignment from Spaln_nt2Genome CTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG tattgattacctgctctcaaagtctgactccctttgtcttcctgctgcagTTTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGTGgtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta Alignment from Pairagon GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG tattgattacctgctctcaaagtctgactccctttgtcttcctgctgcag---TTTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGTGgtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta Alignment from Exonerate_protein2genome GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG tattgattacctgctctcaaagtctgactccctttgtcttcctgctgCAGTTTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGTGgtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise GGGCTTCAGTGTGACATCTGGTGGTCAAAGCCGAATCTTCAAGCCTGTCTCTATCCAGACCATGTG tattgattacctgctctcaaagtctgactccctttgtcttcctgctgcagT---TTGAGTGTGACACCTGGTGGCAAAAGCCGAATCTTCAAGCCTCTCTCTATCCAGACCATGTGgtaagtggtccaaacaataaggtttccaagcatacttggctgaccatcta #### Ssh3_ID451_5 --> 1 - 2 Original Alignment tTCCCAC---------AGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGAT------gg ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagtTGTCATAGCTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGgggtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from CESAR tTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGAT------gg aacaggctgctattgacattatgcggggagacaactgcatctcattccagttgtcatagcTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGgggtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from Spaln_aa2Genome TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGAT---GGGGG ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagttgtcatagCTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGGGgtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from Spaln_nt2Genome TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGAT---GGGGG ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagttgtcatagCTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGGGgtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from Pairagon TTCCCACAGC---------TGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGA---TGGGGG ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagTTGTCATAGCTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGGGgtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from Exonerate_protein2genome TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGAT---GGGGG ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagttgtcatagCTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGGGgtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from Exonerate_coding2genome ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagttgtcatagctgcacaagttgcacgcttggacttgttgtgcccctttggagtgttactcatgtatacctatacggagattttggggggtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc Alignment from GeneWise TTCCCACAGCTGCACCCTGGGCCTGGTCTTGCCCCTCTGGAGTGATACCCAGGTGTACCTGGACGGCGATGGGGGC-- ctattgacattatgcggggagacaaattgcaagtctgcatctcattccagttgtcatagCTGCACAAGTTGCACGCTTGGACTTGTTGTGCCCCTTTGGAGTGTTACTCATGTATACCTATACGGAGATTTTGGGGGgtaagcgggtctccgtcggggaaacaagatagggctgagaaaattgggcc #### Stip1_ID1988_13 --> 0 - 2 Original Alignment GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCT------------GAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGC------ga caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACA------------------CTTGAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGCCACgagtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from CESAR GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGA------------CATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGC------ga caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACA------------------CTTGAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGCCACgagtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from Spaln_aa2Genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGCGAA----- caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACA------CTTGAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGCCACGAgtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from Spaln_nt2Genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAG------CGA caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGA----CAGCCCTGAGGAA--GTTACACTTGAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGCCACGAgtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from Pairagon GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAG------------ACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAG------CGA caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGT------------------TACACTTGAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGCCACGAgtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from Exonerate_protein2genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGCGA caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACACTT------GAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGccacgagtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from Exonerate_coding2genome GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGCGA caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACACTT------GAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGccacgagtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc Alignment from GeneWise GAAGCAGCAGATGGTTACCAACGCTGTATGATGGCACAGTACAACAGACATGATAGCCCTGAGGATGTGAAGCGGCGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCAGCCATGAGACTCATCCTGGAGCAGATGCAAAAGGACCCCCAGGCTCTGAGCGAACAC-- caaacacaaattagggctaaagtcctccgaattgtctttttttctcctagCAAGCAGCAGACAAATACCAGCGATGCATGATGGCACAGTACAACAGACATGACAGGTCACATGACAGCCCTGAGGAAGTTACACTT------GAGGTTCAGCAAATAATGAGTGACCCATCCATGAGACTCATACTGGAGCAAATGCAAAAAGACCCCCAGGCTTTGAGTGGCCACGAgtatgctaaacaacaatggaagaatggatgggatagaaatttttgtttgc #### Stx3_ID3299_7 --> 2 - 0 Original Alignment ctGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG--------- agtaaaccagactctccttcttactaaaccccccctttccttcctctcagctGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGTTTCTCCAGgttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from CESAR ctGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG--------- agtaaaccagactctccttcttactaaaccccccctttccttcctctcagctGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGTTTCTCCAGgttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from Spaln_aa2Genome CTGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG--------- agtaaaccagactctccttcttactaaaccccccctttccttcctctcagCTGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGTTTCTCCAGgttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from Spaln_nt2Genome CTGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGG agtaaaccagactctccttcttactaaaccccccctttccttcctctcagCTGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGgtttctccaggttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from Pairagon CTGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG--------- agtaaaccagactctccttcttactaaaccccccctttccttcctctcagCTGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGTTTCTCCAGgttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from Exonerate_protein2genome CTGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG agtaaaccagactctccttcttactaaaccccccctttccttcctctcagCTGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGtttctccaggttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from Exonerate_coding2genome CTGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG agtaaaccagactctccttcttactaaaccccccctttccttcctctcagCTGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGtttctccaggttggttacatacatgcttggttatagtccaggtatcaagcatattgcca Alignment from GeneWise CTGGCAAGAAGACAACAGATGAGGAGCTGGAAGAGATGTTGGAGAGTGGCAACCCAGCCATCTTCACTTCTGGG--------- agtaaaccagactctccttcttactaaaccccccctttccttcctctcagCTGGCAAAAAAACAACAGATGAAGAGCTAGAGGAGATGTTGGAGAGTAGTAACCCAGCTATCTTTACTTCTGGGTTTCTCCAGgttggttacatacatgcttggttatagtccaggtatcaagcatattgcca #### Stx3_ID3300_6 --> 0 - 1 Original Alignment CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTa aatatggtttgataggtgacagcccaggtttttgtgattaaaaattatag---------CTCTCACAGAAA---GTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTagtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from CESAR CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTa gactacaacaatatggtttgataggaggtttttgtgattaaaaattatag---------CTCTCACAGAAA---GTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTagtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from Spaln_aa2Genome CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA aatatggtttgataggtgacagcccaggtttttgtgattaaaaattatag---------CTCTCACAGAAA---GTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTAgtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from Spaln_nt2Genome CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA aatatggtttgataggtgacagcccaggtttttgtgattaaaaattatag---------CTCTCACAGAA---AGTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTAgtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from Pairagon CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA aatatggtttgataggtgacagcccaggtttttgtgattaaaaattatag---------CTCTCACAGAAA---GTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTAgtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from Exonerate_protein2genome CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA aatatggtttgataggtgacagcccaggtttttgtgattaaAAATTATAGCTCTCACAGAAA---GTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTAgtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from Exonerate_coding2genome CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA aatatggtttgataggtgacagcccaggtttttgtgattaaAAATTATAGCTCTCACAGAAA---GTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTAgtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta Alignment from GeneWise CACTCCGTCCTCTCCCGGAAGTTTGTGGAGGTGATGACAAAGTACAATGAGGCTCAGGTGGACTTCCGTGAACGCAGCAAAGGGCGCATCCAACGGCAGCTTGAAATTA aatatggtttgataggtgacagcccaggtttttgtgattaaaaattatagCTCTCA------------CAGAAAGTGGAGGTGATGACCAAGTACAATGATGCCCAGGTAGATTTTCGAGAACGGAGCAAAGGCCGCATCCAATATCAACTTGAAATTAgtaagttttgagtaccagtggatatcgtgccatgtagctggccaccctta #### Stx5a_ID2330_2 --> 0 - 2 Original Alignment AATGGAATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCag caaagatgactgaccctatcaaccctcagtcatctctcctctttccacag------ATCCCAACAACCAAA---CCTCTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTcggtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from CESAR AATGGAATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCag ggggtacaaagatgactgaccctattcagtcatctctcctctttccacag------ATCCCAACAACCAAACCT---CTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTcggtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from Spaln_aa2Genome ATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCAG caaagatgactgaccctatcaaccctcagtcatctctcctctttccacagATCCCAACAACCAAACCT---CTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTCGgtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from Spaln_nt2Genome ATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCAG caaagatgactgaccctatcaaccctcagtcatctctcctctttccacagATCCCAACAACCAAAC---CTCTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTCGgtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from Pairagon AATGGAATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCAG caaagatgactgaccctatcaaccctcagtcatctctcctctttccacag------ATCCCAACAACCAAAC---CTCTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTCGgtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from Exonerate_protein2genome ATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCAG caaagatgactgaccctatcaaccctcagtcatctctcctctttccacagATCCCAACAACCAAACCT---CTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTCGgtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from Exonerate_coding2genome ATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCAG caaagatgactgaccctatcaaccctcagtcatctctcctctttccacagATCCCAACAACCAAACCT---CTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTCGgtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca Alignment from GeneWise ATCCAAACAAGCAAACCGGCTCTGCACGCAGCCCGACAGTGCAGTGAATTTACCCTCATGGCCAG caaagatgactgaccctatcaaccctcagtcatctctcctctttccacagATCCCAACAACCAAACCT---CTTCATGCAGCCCGTCAGTGCAGTGAACTTACCCTTATGGCTCGgtatgatgtagctgtcttaatgggctgactttttgtaatatgtagagtca #### Stx5a_ID2336_8 --> 2 - 0 Original Alignment ga---------GGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctaggaAGTCGCGAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from CESAR ga---------GGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctaggaAGTCGCGAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from Spaln_aa2Genome GA---------GGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctagGAAGTCGCGAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from Spaln_nt2Genome GAGGT---------GGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctagGAAGTCGCGAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from Pairagon GA---------GGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctagGAAGTCGCGAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from Exonerate_protein2genome GAGGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctaggaagtcgcgAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from Exonerate_coding2genome GAGGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctaggaagtcgcgAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg Alignment from GeneWise -------GGTGGTCCCATAATTTTGGGAGCAGAGTCCCGAGCTTCCAGGGACGTGGCTATTGACATGATGGACCCTAGAACAAGCCAGCAGCTTCAGCTCATTGATGAGCAG aatgtcaaacttccacaaagtgccagaagacccctgactcgtgcctctaggaagTCGCGAGGGGGGTACCATAATCCTGGGGGCAGAATCACAAGCATCCAGAGATGTAGCAATTGATATGATGGACCCTAGAACAAGCCAACAGCTGCAGGTCATTGATGAGCAGgtaaggtacaccacattgtgaagctgacctataaccagggttcccttagg #### Syvn1_ID1383_2 --> 0 - 0 Original Alignment GTCCTGTACATCCAGGCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatgtctgcag---------------GCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from CESAR GTCCTGTACATCCAGGCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG agacagaaattggcagtacccttaagggtctcctgctgccatgtctgcag---------------GCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from Spaln_aa2Genome GCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatgtctgcagGCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from Spaln_nt2Genome GCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatgtctgcagGCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from Pairagon GTCCTGTACATCCAGGCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatgtctgcag---------------GCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from Exonerate_protein2genome ACATCCAGGCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatGTCTGCAGGCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from Exonerate_coding2genome ACATCCAGGCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatGTCTGCAGGCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc Alignment from GeneWise GCCTTTGTCCTTGTCTTCCTCTTGGGCAAGGTGATGGGCAAGGTGTTCTTCGGGCAGCTGAGGGCAGCAGAGATGGAG gtacccttaaatgataatatgatgcgggtctcctgctgccatgtctgcagGCCTTTGTTCTTGTCTTCCTCTTGGGGAAGGTGATGGGGAAGGTGTTCTTTGGGCAGCTGAGGGCACCAGAGATGGAAgtgagaagggtccagcagttagggcaaggcttctaaattgccatgctggc #### Syvn1_ID1384_3 --> 0 - 0 Original Alignment CACCTTCTGGAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT ctggctgtcttgcagcttcatgcccatgaattctaaaaattgtatattag---------GAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from CESAR CACCTTCTGGAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT attgccatgctggctgtcttgcagcatgaattctaaaaattgtatattag---------GAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from Spaln_aa2Genome CACCTTCTGGAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT ctggctgtcttgcagcttcatgcccatgaattctaaaaattgtatattag---------GAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from Spaln_nt2Genome GGAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT ctggctgtcttgcagcttcatgcccatgaattctaaaaattgtatattag-GAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from Pairagon -----------GCACCTTC-----------------------------TGGAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT CTGGCTGTCTTGCAGCTTCATGCCCATGAATTCTAAAAATTGTATATTAGGAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from Exonerate_protein2genome GAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT ctggctgtcttgcagcttcatgcccatgaattctaaaaattgtatattagGAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from Exonerate_coding2genome GAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT ctggctgtcttgcagcttcatgcccatgaattctaaaaattgtatattagGAACAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag Alignment from GeneWise CACCTTCTGGAACGGTCCTGGTACGCTGTTACTGAGACTTGTTTGGCCTTCACCGTTTTTCGGGATGACTTCAGCCCTCGCTTTGTGGCGCTCTTTACGCTGCTCCTCTTCCTCAAATGTTTCCATTGGTTGGCTGAAGACCGTGTGGACTTT ctggctgtcttgcagcttcatgcccatgaattctaaaaattgtatattagGAA---------CAGTCTTGGTATGCTGTCACAGAAATCTGTTTGACCTTTACAGTTATTGGCGATGACTCAAGTCCCCAATTTGTGGCACTCTTCATGCTTCTTCTCTTCCTCAAGTGCTTCCAGTGGTTAGCTGCAGATCATGTTGATTCTgtaagttcaaatctcctgatgaatatgcaggtgctcttgtagtttcacag #### Syvn1_ID1387_6 --> 0 - 1 Original Alignment TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------g gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTggtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from CESAR TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------g gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTggtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from Spaln_aa2Genome TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------G gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTGgtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from Spaln_nt2Genome TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------G gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTGgtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from Pairagon TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------G gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTGgtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from Exonerate_protein2genome TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------G gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTGgtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from Exonerate_coding2genome TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------G gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTGgtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag Alignment from GeneWise TACGCCATTCTGATGACCATGGTGCTTACCATCTTCATCAAGTATGTGCTGCACTCCGTGGACCTCCAGAGCGAGAACCCCTGGGACAACAAGGCTGTATACATGCTCTACACGGAGCTGTTTACA------G gctctcttggtccattatggttcagatcctttttcttcaatgttttctagTATGCCATTCTGATGACGATGGCACTCACTATTTTCATCAAGTATGTGCTGCATTCTGTTGACCTCCAGAGTAAAAATCCCTGGGATAATAAGGCTGTATACATGCTCTACACAGAGCTATTTACGCTGTCTGgtgagtactcccagacaatctagaggtggttcatggttaatctgcaggag #### Syvn1_ID1388_7 --> 2 - 2 Original Alignment gcTTCATCAAGGTCCTGCTGTACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGag cagttggcgtcggtacgcggtaacaaattgcttcctttttgattttgcaggc---------------------ATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGaggtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from CESAR gcTTCATCAAGGTCCTGCTGTACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGag ttggtgcatcttccatccttgcagtaattgcttcctttttgattttgcaggc---------------------ATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGaggtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from Spaln_aa2Genome ATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGAG cagttggcgtcggtacgcggtaacaaattgcttcctttttgattttgcagGCATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGAGgtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from Spaln_nt2Genome GCTTCATCAAGGTCCTGCT-------------------------------GTACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGAG TTGGCGTC--GGTAC-GCGGTAACAAATTGCTTCCTTTTTGATTTTGCAGG--CATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGAGgtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from Pairagon GCTTCATCAAGGTCCTGCTGTACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGAG cagttggcgtcggtacgcggtaacaaattgcttcctttttgattttgcagG---------------------CATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGAGgtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from Exonerate_protein2genome CTGCTGTACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGAG cagttggcgtcggtacgcggtaacaaattgcttcctttttgatTTTGCAGGCATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGAGgtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from Exonerate_coding2genome CTGCTGTACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGAG cagttggcgtcggtacgcggtaacaaattgcttcctttttgatTTTGCAGGCATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGAGgtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc Alignment from GeneWise ACATGGCCTTCATGACCATCATGATCAAGGTGCACACATTCCCACTCTTTGCCATTAGGCCCATGTACCTGGCCATGAG cagttggcgtcggtacgcggtaacaaattgcttcctttttgattttgcagGCATGGCCTTCATGACCATCATGATCAAGGTGCACACTTTTCCACTGTTTGCCATTAAGCCCATGTACCTGGCTATGAGgtagagtaggcctcacatctgctattttgtcaccttgatttttgtcttcc #### Syvn1_ID1393_12 --> 2 - 1 Original Alignment ccGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------g gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagctGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCggtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac Alignment from CESAR ccGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------g gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagctGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCggtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac Alignment from Spaln_aa2Genome CCGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------G gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagCTGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCGgtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac Alignment from Spaln_nt2Genome CCGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------G gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagCTGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCGgtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac Alignment from Pairagon CCGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT--------------------------------------------------------- gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagCTGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCGGTGAGTTACCTGTCACCCTACTCTCTTTGGAAAGATGCGCAATACTAAAC Alignment from Exonerate_protein2genome CCGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------G gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagCTGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCGgtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac Alignment from Exonerate_coding2genome CCGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------G gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagCTGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCGgtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac Alignment from GeneWise CCGTTTCTCGGCCTAGTGGAGCAGCCACCACCACAGCTGCTGGCACCAGTACTTCTGCCCCAGCACCTGGGTCTGTACCTGGCCCAGAGGCTGGTCCTGCCCCCGGCTTCCCTTTCCCTCCTCCTTGGATGGGTATGCCTCTGCCTCCACCTTTT------G gaaattgactcacttccaatttaccttgagtagcatttacctcctcttagCTGTCTCTCAGTATAGTGGAGCAGCAACCACTCCAGCTTCTAGCACAGGTCCCTCTGCCCCAGCACCTGGATCTGTACCAAGCGCAGAGTCTGGTCCTGGCCCTGATTCCCCTTTCCCCCCTCCCTGGATGGGGATGCCTCTACCTCCACCATTTATAAGCGgtgagttacctgtcaccctactctctttggaaagatgcgcaatactaaac #### Taf5_ID10102_10 --> 0 - 1 Original Alignment GGACCAATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAg atgccaatacactacaaatccaattaatgacattctctctctttccttag------ATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAggtacagccagtagtgacctcataacagggcctactcccactctccatctc Alignment from CESAR GGACCAATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAg atccgcatgccaatacactacaaataatgacattctctctctttccttag------ATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAggtacagccagtagtgacctcataacagggcctacaatagtgtctgtgccc Alignment from Spaln_aa2Genome GGACCAATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAG atgccaatacactacaaatccaattaatgacattctctctctttccttag------ATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAGgtacagccagtagtgacctcataacagggcctactcccactctccatctc Alignment from Spaln_nt2Genome GGACCAATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAG atgccaatacactacaaatccaattaatgacattctctctctttccttag------ATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAGgtacagccagtagtgacctcataacagggcctactcccactctccatctc Alignment from Pairagon GGACCAATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAGGT------------------------------------------------ atgccaatacactacaaatccaattaatgacattctctctctttccttag------ATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAGGTACAGCCAGTAGTGACCTCATAACAGGGCCTACTCCCACTCTCCATCTC Alignment from Exonerate_protein2genome ATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAG atgccaatacactacaaatccaattaatgacattctctctctttccttagATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAGgtacagccagtagtgacctcataacagggcctactcccactctccatctc Alignment from Exonerate_coding2genome ATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAG atgccaatacactacaaatccaattaatgacattctctctctttccttagATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAGgtacagccagtagtgacctcataacagggcctactcccactctccatctc Alignment from GeneWise ATTCATTCCTTGACATTTTCTCCCAATGGGAGATTCCTGGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACACGGCTTGATGGTTGGAGAATTAAAAGGCCACACTGATACAGTGTGTTCACTTAGGTTTAGTAGAGATGGTGAAATTTTGGCATCAG atgccaatacactacaaatccaattaatgacattctctctctttccttagATTCATTCTTTGACATTTTCTCCCAATGGGAGGTTCCTAGCTACAGGAGCAACAGATGGCAGAGTACTTCTTTGGGATATTGGACATGGCCTAATGGTTGGAGAATTAAAAGGCCACACAGATACAGTGTGTTCACTTAGATTTAGTAGAGATGGTGGAATTTTGGCGTCAGgtacagccagtagtgacctcataacagggcctactcccactctccatctc #### Tbc1d10c_ID399_5 --> 1 - 0 Original Alignment g---CAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGATAC------TGCCAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagaGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa Alignment from CESAR g---CAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGATAC------TGCCAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagaGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa Alignment from Spaln_aa2Genome G----CAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGATAC------TGCCAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagAGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa Alignment from Spaln_nt2Genome G---CAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGATA------CTGCCAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagAGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa Alignment from Pairagon ---GCAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGAT------ACTGCCAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagAGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa Alignment from Exonerate_protein2genome G---CAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGATAC------TGCCAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagAGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise -GGGCAGCAGGGGCTGCTGCAGGTTCTCAAGGCCTACACCCTGTACCGGCCAGAGCAGGGATACTGC------CAGGCTCAGGGACCTGTAGCTGCTGTGCTGCTCATGCATCTACCCCCAGAG tgaacagggaagatcatatgggagggtgtttgatgttttcaattttacagAGTACAGCAAGGGTTTCTGCAGGTTATGAAAGCCTATAATCTTCACCACCCAGAACAAGGATATTGTCACTGTCAAGCACAGGGACCTGTAGCTGCAGTACTTCTCATGCATCTCCCTCCAGAGgtgaggtccctagatagaaacagtaaggtatatatactatggcgactgaa #### Tbc1d10c_ID400_4 --> 0 - 2 Original Alignment CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACAC---------gg ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCCTGgggtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from CESAR CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACAC---------gg ATATCAGgtagacaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCCTGgggtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from Spaln_aa2Genome CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACACGGG-------- ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCCTGGGgtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from Spaln_nt2Genome CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACAC---------GG ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCCTGGGgtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from Pairagon CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACAC---------GG ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCCTGGGgtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from Exonerate_protein2genome CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACACGGGCAG ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCctggggtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from Exonerate_coding2genome CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACACGGGCAG ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCctggggtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg Alignment from GeneWise CTACCAG GAGCTGGCAGCAGCCCCCGGGGACCCGCAGTGGATGGAGACCATTGGCAGAGACTTGCACCGTCAGTTTCCTCTGCATGAGATGTTTGTGTCACCCCAGGGACAC---------GG ATATCAGgtgtggaggccaggaatgccctcttgttccccttgcattacagGAGCTGGCATCAGCACCCGGAGACCCCCAGTGGATGGAAGCCACCGGCAGAGACTTACACCAACAATTTCCTTTGCATGAGATACTTGTCCTGCCTCAGGGACATAATCTCCTGGGgtgaatgttgaggaaatagggtccatctgttgtccacagaaaggggaggg #### Tcirg1_ID173_14 --> 1 - 0 Original Alignment gCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG--------- tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccaggCACTTCGGTGAGGCCCACAGGCTGCTGCTT------GTGTCAGAGCTTATTTTCCTCCTGGGCCTC------TATCTGGTGCTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCC------ATTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACCCG---AATCATCTGCTGTTCCATGGGCAGTGTTACTGTgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from CESAR gCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG--------- tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccaggCACTTCGGTGAGGCCCACAGGCTGCTGCTT------GTGTCAGAGCTTATTTTCCTCCTGGGCCTC------TATCTGGTGCTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCC------ATTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACCCG---AATCATCTGCTGTTCCATGGGCAGTGTTACTGTgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from Spaln_aa2Genome GCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG--------- tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccagGCACTTCGGTGAGGCCCACAGGCTGCTGCTTGTGTCA------GAGCTTATTTTCCTCCTGGGCCTCTATCTGGTG------CTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCC------ATTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACCCG---AATCATCTGCTGTTCCATGGGCAGTGTTACTGTgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from Spaln_nt2Genome GCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG- tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccagGCACTTCGGTGAGGCCCACAGGCTGCTGCTTG------TGTCAGAGCTTATTTTCCTCCTGGGCCT------CTATCTGGTGCTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCCA------TTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACC---CGAATCATCTGCTGTTCCATGGGCAGTgttactgtgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from Pairagon GCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG---------------- tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccagGCACTTCGGTGAGGCCCACAGGCTGCTGCTTG------TGTCAGAGCTTATTTTCCTCCTGGGCCT------CTATCTGGTGCTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCCA------TTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACC---CGAATCATCTGCTGTTCCATGGGCAGTGTTACTGTGTAACAAgtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from Exonerate_protein2genome GCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccagGCACTTCGGTGAGGCCCACAGGCTGCTGCTT------GTGTCAGAGCTTATTTTCCTCCTGGGCCTC------TATCTGGTGCTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCC------ATTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACCCG---AATCATCTGCTGTTCCATGGGCAGtgttactgtgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from Exonerate_coding2genome tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccaggcacttcggtgaggcccacaggctgctgcttgtgtcagagcttattttcctcctgggcctctatctggtgctcctaattctctataaatgggtaaacatctcagcaactagttctgcctcagcccccattattcacttcatcaatttcctcttctcccagaacccgaatcatctgctgttccatgggcagtgttactgtgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc Alignment from GeneWise GCACTTTGGCCAGGCCCACCGGCTACTGCTGGAGACCTTGCCTGAGCTCATCTTCCTGCTGGGTCTCTTTGGCTACCTTGTGTTCCTCATTGTCTACAAGTGGGTGAATGTCTCAGCTGCTAGCGCCTCCTCGGCCCCCAGTATCCTCATTCACTTCATCAATATGTTCCTCTTCTCTCAAAACCCCACCAATCATCTGCTCTTCCATGGGCAG--------- tgagtcttgcctcatcctgatgagaatactcacaccctgttttcttccagGCACTTCGGTGAGGCCCACAGGCTGCTGCTT------GTGTCAGAGCTTATTTTCCTCCTGGGCCTC------TATCTGGTGCTCCTAATTCTCTATAAATGGGTAAACATCTCAGCAACTAGTTCTGCCTCAGCCCCC------ATTATTCACTTCATCAAT---TTCCTCTTCTCCCAGAACCCG---AATCATCTGCTGTTCCATGGGCAGTGTTACTGTgtaacaagtgtgtgacaggtgattctaatgtcatatagcataatctgacc #### Tcirg1_ID174_13 --> 0 - 2 Original Alignment ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATCTTCAACCACgt accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATC---------gtgtgatacattgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from CESAR ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATCTTCAACCACgt accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATC---------gtgtgatacattgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from Spaln_aa2Genome ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATCTT accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATCGTgtgatacattgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from Spaln_nt2Genome ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATCTTCAACCACGT- accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATCGTGTGATACATTgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from Pairagon ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATC accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATCgtgtgatacattgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from Exonerate_protein2genome ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATCTTCAACCACGTG accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATCGTGTGATACATTgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from Exonerate_coding2genome ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATC accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATCgtgtgatacattgtttgagcttgatttgggcatgggtagtatgtgctgagtc Alignment from GeneWise ATCTGGAGCCTGGCCACGAACCACCTGAGCTTTCTCAACTCCTTCAAGATGAAGATGTCTGTCATCCTTGGGGTCACGCACATGGCCTTTGGGGTGTTCCTCAGCATCTT accactgaagtgcatgttgcaaagtgttctttatgtggcatcttcttcagCTCTGCAGTCTGGCCACAAACCACCTGAGCTTTCTCAACTCTTTTAAGATGAAGACATCAGTCATCCTAGGAGTCATACACATGGCATTTGGGGTCTTCCTCAGCATCGTgtgatacattgtttgagcttgatttgggcatgggtagtatgtgctgagtc #### Tcirg1_ID175_12 --> 1 - 0 Original Alignment tGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCCG--- gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagtGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTCTGgtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from CESAR tGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCCG--- gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagtGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTCTGgtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from Spaln_aa2Genome TGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCCG--- gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagTGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTCTGgtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from Spaln_nt2Genome TGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCC---G gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagTGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTCTGgtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from Pairagon ------------------------------------------------AGTGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCC---G GAGCAGTTCTGATACGAAGTATTGGTTAAGCTCTCTGACTGCGCCTTCAGTGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTCTGgtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from Exonerate_protein2genome TGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCCG gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagTGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTctggtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from Exonerate_coding2genome TGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCCG gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagTGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTctggtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag Alignment from GeneWise TGACGAGTATCTGTCCCAGCACTCCATGCTCACCCTGAACCCTAACATCACTGGTGTCTTCCTTGGACCATATCCCTTTGGCATTGACCCGATC gagcagttctgatacgaagtattggttaagctctctgactgcgccttcagTGAGGAGTATTTATCTTGGCATTCCATGTTCACCTTGAACCCTAACATAACTGGGGTCTTTCTTGGCCCATACCCATTTGGCATTGAGCCTCTGgtactggcatacgagtgtaggataaatagatacatgagaaggtagtccag #### Tcirg1_ID181_6 --> 0 - 2 Original Alignment CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGAC------tg CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGtggtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from CESAR CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGAC------tg CAGTGGCAgtaaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGtggtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from Spaln_aa2Genome CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGACTGC----- CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGTGgtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from Spaln_nt2Genome CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGAC------TG CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGTGgtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from Pairagon CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGAC------TG CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGTGgtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from Exonerate_protein2genome CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGAC------TG CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGTGgtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from Exonerate_coding2genome CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGAC------TG CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTGTGgtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc Alignment from GeneWise CAGTGACG GGTGAGCCTGCAACTTGGATGACCTTTGTCATCTCCTACTGGGGTGAGCAGATCGGACAGAAGATCCGAAAGATCACAGACTGC-- CAGTGGCAgtgaggttaggggcaggacagaattaatctgagcatttgcagGGTGAACCTGCAACCTGGATGACCTTTATCATTTCCTACTGGGGTGAGCAGATTGGTCAGAAGATCCGAAAGATCACAGATCTCCTgtggtcagtaggtatccccattccccaatataagggagcagtcaggttgctgc #### Tcirg1_ID182_5 --> 1 - 0 Original Alignment tTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGACG--------- GGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagcTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTGGCAAGTCTGTGCgtatttttaggggcaggacatgtcccgcttgtgctgtttcagGGTGAACC Alignment from CESAR tTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGACG GGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagcTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTG---gcaagtctgtgcgtatttttaggggcaggacagaattaatctgagcatttgcagGGTGAACC Alignment from Spaln_aa2Genome TTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTG ACGGGTGA gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagCTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTGgcaagtctgtgcgtatttttaggggcaggacatgtcccgcttgtgctgtttcag---GGTGA Alignment from Spaln_nt2Genome TTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGACG- GGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagCTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTGGCAAgtctgtgcgtatttttaggggcaggacatgtcccgcttgtgctgtttcagGGTGAACC Alignment from Pairagon TTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGAC---------------------------------------------------GGGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagCTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTGGCAAGTCTGTGCGTATTTTTAGGGGCAGGACATGTCCCGCTTGTGCTGTTTCAGGGTGAACC Alignment from Exonerate_protein2genome TTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGACG GGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagCTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTG---gcaagtctgtgcgtatttttaggggcaggacatgtcccgcttgtgctgtttcagGGTGAACC Alignment from Exonerate_coding2genome TTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGACG GGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagCTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTG---gcaagtctgtgcgtatttttaggggcaggacatgtcccgcttgtgctgtttcagGGTGAACC Alignment from GeneWise TTTTGTGGCAGGTGCTGTGGAGCCCTACAAGGCTGCGGCCCTGGAGCGCCTGCTGTGGAGAGCTTGCCGCGGCTTCCTCATTGCCAGCTTTCGGGAGACTGAGGGGCAGCTGGAGGACCCAGTGACG---------------------------------------------------GGTGAGCC gaaaagggggagttgagaggagtctgcaatggatatctttcttccctcagCTTTGTGGCAGGTGCAGTGGAACCCTACAAGGCTGCAGCCTTAGAGCGCCTGCTGTGGAGAGCATGCCGTGGCTTTCTCATTGCTAGTTTTCGTGAGACCGAAGGGCAGTTGAAGGATCCAGTGGCAAGTCTGTGCGTATTTTTAGGGGCAGGACATGTCCCGCTTGTGCTGTTTCAGGGTGAACC #### Tctn3_ID7990_11 --> 0 - 2 Original Alignment ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTA------ag gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCaggtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from CESAR ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTA------ag gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCaggtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from Spaln_aa2Genome ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTAAGA----- gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCAGgtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from Spaln_nt2Genome ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTA------AG gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCAGgtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from Pairagon ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTAAGACCCAG gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCAGgtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from Exonerate_protein2genome ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTA------AG gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCAGgtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from Exonerate_coding2genome ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTA------AG gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCAGgtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat Alignment from GeneWise ATGACCCTGTTGCAGAGCGAGGGTAATGGGCTTTGCTCTGCTAAGAGACACGCAGTACAGTTTGGAGTGAACGCAGTATCTGGGTGCCAGTTA------AG gtaacaacctcactgatcccttatcacttatttttgttttgtgcatatagATGACCCTACTGCAGAGTGAGGCTAATGGAGTTTGCTCTGCTAAGAGACATGCAGTGCAATTTGGTGTGAATGCATTCTCTGGGTGCCAATTGGGAGCCAGgtatgtggcttgtatgaaatgactctgtgatgagactttactagttggat #### Tctn3_ID7996_5 --> 0 - 1 Original Alignment GCTGGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAg gtTTCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacag---GGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCAggtacgatctgacacttcttttctcttcaggaTTTCTAGAGACTAAGAGCA Alignment from CESAR GCTGGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAg gtTTCCTAGAGAGTAAAAGCA accatttaaagataccattttttcacaaaactccacctcccttggcacag---GGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCAggtactgtagaaaccaccatttcttcccaggaTTTCTAGAGACTAAGAGCA Alignment from Spaln_aa2Genome GCTGGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCA-----------------------------GGTTTCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacag---GGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCAGGTACGATCTGACACTTCTTTTCTCTTcaGGATTTCTAGAGACTAAGAGCA Alignment from Spaln_nt2Genome GCTGGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAGGT-----------------------------TTCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacag---GGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCAGGTACGATCTGACACTTCTTTTCTCTTCAGGATTTCTAGAGACTAAGAGCA Alignment from Pairagon GCTGGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAGGT-----------------------------TTCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacag---GGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCAGGTACGATCTGACACTTCTTTTCTCTTCAGGATTTCTAGAGACTAAGAGCA Alignment from Exonerate_protein2genome GGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAGGTT TCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacagGGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCA---GgtacgatctgacacttcttttctcttcaggatTTCTAGAGACTAAGAGCA Alignment from Exonerate_coding2genome GGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAGGTT TCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacagGGGGATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCA---GgtacgatctgacacttcttttctcttcaggatTTCTAGAGACTAAGAGCA Alignment from GeneWise GCTGGGGATCCCATCCTGACCTACTACCCGAGCTGGTCTGTGGTGAGCTTACTGAGGCAGCCTGCAGCGGTGGGAGCTGGGGGACTTTGTGCCGAGAGCAACCCTGCAG GTTTCCTAGAGAGTAAAAGCA atttaaagataccattttttcagttcaaaactccacctcccttggcacagGGG---GATCCCATCCTGACATACTACCCAAGCTGGTCCGTGGTAAGCTTACTAAGACAACCTGCAGCTGTAGGAGCTGGCGGACTTTGTGCAGAGAGCAACCCAGCAGgtacgatctgacacttcttttctcttcagGATTTCTAGAGACTAAGAGCA #### Tdrd1_ID12205_6 --> 0 - 0 Original Alignment GTTGACTGTCCCCCGGGAGTTACTAAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG gcctcagcccaatatctatgagcacttgtcctgagtctttctttccctag---------------GAAGTT---AGACAAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct Alignment from CESAR GTTGACTGTCCCCCGGGAGTTACTAAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG caggcaagatgggtggcctcagcccttgtcctgagtctttctttccctag---------------GAAGTT---AGACAAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct Alignment from Spaln_aa2Genome GTTACTAAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG gcctcagcccaatatctatgagcacttgtcctgagtctttctttccctagGAAGTTAGACAAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct Alignment from Spaln_nt2Genome GGAGTTACTAAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG gcctcagcccaatatctatgagcacttgtcctgagtctttctttccctagGAAGT---TAGACAAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct Alignment from Pairagon ACTGTCCCCCGGGAGTTACTAAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG gcctcagcccaatatctatgagcacttgtcctgagtctttctttccctaggaagttagAC----------------------AAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct Alignment from Exonerate_protein2genome TTACTAAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG gcctcagcccaatatctatgagcacttgtcctgagtctttctttccctaggAAGTTAGACAAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --AAAGAAATAACAGCGGGTGCTGAGAGAGTAATGTTCTCTGATTTGAGAAGTCTCCAACTCAAGAAAACCATGGAGATAAAG gcctcagcccaatatctatgagcacttgtcctgagtctttctttccctaggaagTTAGACAAATAACAGTAGGTGCTGAGAGAGTTATGTTCTCTGATTTAAGAACTCTTCAGCTGATGAAAACAATGGAGATAAAAgtaggtggaattgtctgctcctttcctcaatatctcacatgtgatcctct #### Tectb_ID11563_6 --> 1 - 2 Original Alignment gTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGgg ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagg---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGgggtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from CESAR gTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGgg aaattcaattttgtaatggtattgtctgtttaaaatgtccccttccctagg---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGgggtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from Spaln_aa2Genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGGG ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagG---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGGGgtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from Spaln_nt2Genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGGG ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagG---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGGGgtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from Pairagon GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGGG ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagG---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGGGgtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from Exonerate_protein2genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGGG ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagG---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGGGgtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from Exonerate_coding2genome GTTCAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGGG ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagG---AAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGGGgtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca Alignment from GeneWise CAAAGTGGTCTTGAATAGCTGCTGGGCCACCCCCTCGGCTGACTTCATGTACCCCTTACAGTGGCAGCTCATCAATAAGGG ttcaattttgtaatggtattgttttctgtttaaaatgtccccttccctagGAAAGTGGTCTTGAATAGCTGCTGGGCAACCCCCTTGGCTGACTTCATGTACCCTTTACAGTGGCAGCTTATCAATAAGGGgtcagtaccaataacaactacatgatgctggtatgtttcttggaccccca #### Tjp2_ID5278_9 --> 1 - 1 Original Alignment cTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAg ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagcACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCA---AATCAACAA---------ggtatgttgtcatgtaacgtatgctattcttttatctatctaaaacataga Alignment from CESAR cTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAg ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagcACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAATCAACAA------------ggtatgttgtcatgtaacgtatgctattcttttatctatctaaaacataga Alignment from Spaln_aa2Genome CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAG ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagCACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAATCAACAAGGTATGTTGTCATgtaacgtatgctattcttttatctatctaaaacataga Alignment from Spaln_nt2Genome CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGG ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagCACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTA---TGGCCAGTAAGGAGCCAAATCAACAAGgtatgttgtcatgtaacgtatgctattcttttatctatctaaaacataga Alignment from Pairagon CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCA ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagCACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTAT---GGCCAgtaaggagccaaatcaacaaggtatgttgtcatgtaacgtatgctattcttttatctatctaaaacataga Alignment from Exonerate_protein2genome CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAG ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagCACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAATCAACAAGGTATGTTGTCATgtaacgtatgctattcttttatctatctaaaacataga Alignment from Exonerate_coding2genome ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagcactaaagaagaaacatccggcaaactgtcaagaatgggagccatgcccacatcattcaaggacacaggtagccccacagctgcaggagttatggccagtaaggagccaaatcaacaaggtatgttgtcatgtaacgtatgctattcttttatctatctaaaacataga Alignment from GeneWise CTCAAGAGAGGAGACCTCAGGCAGACTATCCAGGATGGGTGCCACTCCCACGCCGTTCAAGTCCACGGGGGACATCACAGCTGCGGGGGTCACAGAGGCCAGCAGGGAGCCCAGGTACCAGGAAGAAGGCCCAG ttgttattcaataaagcattgaccatagtctctctctcttatcttttaagCACTAAAGAAGAAACATCCGGCAAACTGTCAAGAATGGGAGCCATGCCCACATCATTCAAGGACACAGGTAGCCCCACAGCTGCAGGAGTTATG---GCCAGTAAGGAGCCAAATCAACAAGGTATGTTGTCATgtaacgtatgctattcttttatctatctaaaacataga #### Tle4_ID3625_13 --> 2 - 0 Original Alignment ca---TCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagctTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from CESAR ca---TCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagctTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from Spaln_aa2Genome CA---TCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagCTTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from Spaln_nt2Genome CAT---CAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagCTTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from Pairagon CATCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagctttctccag-------CCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from Exonerate_protein2genome CA---TCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagCTTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from Exonerate_coding2genome CA---TCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagCTTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt Alignment from GeneWise --GCATCAAGCCTGAGGACCCCGATGGCTGTACCTTGTCCATATCCAACCCCCTTTGGGATCGTGCCCCATGCTGGGATGAACGGAGAGCTGACCAGCCCCGGAGCCGCCTATGCTGGGCTACACAACATCTCCCCCCAGATGAGTGCAGCTGCTGCTGCAGCTGCGGCAGCAGCAGCCTATGGAAGATCACCTGTG ttatcttaagctaaggcaagatgacttttctgtttgcctctgctttacagCTTTCTCCAGCCTAAGGACACCAGTAGCAGTGCCTTGTCCATATCCAACACCACTTGGAATTGTGCCACATGCAGGAACGAATGGAGAGCTGACCAGCCCTGGGGCTGCTTATGGTGGGCTCCACAATGTGTCCCCCCAGATGAGTGCTTCCACTGCTGCTGCCACAGCAGCAGCGGCTTATGGAAGATCACCTGTGgtaactcctgcatatatgtaggtctgttaaagtgcaaagctggtacattt #### Tm7sf2_ID1412_8 --> 2 - 1 Original Alignment ttATTGGTTACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTg tgttttcaccttccttctccagctgtgcctgctcttacctgtctctccagtt---------TATATC------TGGGCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAggtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac Alignment from CESAR ttATTGGTTACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTg taggctttgtgttttcaccttcctttgcctgctcttacctgtctctccagtt---------TATATC------TGGGCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAggtgagctgggttggctaagtttttgagggccaaatttcttttgtgccttc Alignment from Spaln_aa2Genome TTATTGGTTACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTG tgttttcaccttccttctccagctgtgcctgctcttacctgtctctccagTT---------TATATCTGG------GCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAGgtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac Alignment from Spaln_nt2Genome CATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTG tgttttcaccttccttctccagctgtgcctgctcttacctgtctctccagTTTATATC--TGGGCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAGgtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac Alignment from Pairagon TTATTGGTTACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTG tgttttcaccttccttctccagctgtgcctgctcttacctgtctctccagTT---------TATATCT------GGGCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAGgtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac Alignment from Exonerate_protein2genome TTATTGGTTACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTG tgttttcaccttccttctccagctgtgcctgctcttacctgTCTCTCCAGTTTATATCTGG------GCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAGgtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac Alignment from Exonerate_coding2genome TTATTGGTTACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTG tgttttcaccttccttctccagctgtgcctgctcttacctgTCTCTCCAGTTTATATCTGG------GCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAGgtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac Alignment from GeneWise ACTACATCTTCCGAGGGGCCAACTCCCAGAAAAACACATTCAGGAAGAATCCTTCTGACCCCAGCGTGGCTG tgttttcaccttccttctccagctgtgcctgctcttacctgtctctccagTTTATATCTGG------GCAAACTCTGAGAAAAACACTTTCAGGCAGAATCCTTGTGAGCGGAGTGCAGCAGgtgagctgggttggctaagtttttgagggcgtttgtgggtcttccttgac #### Tm7sf2_ID1416_4 --> 2 - 1 Original Alignment gcTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCA---g ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcaggtTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGATggtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from CESAR gcTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCA---g ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcaggtTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGATggtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from Spaln_aa2Genome GCTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCA---G ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcagGTTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGATGgtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from Spaln_nt2Genome GCTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCAG--- ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcagGTTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGATGgtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from Pairagon GCTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCAG--- ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcagGTTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGATGgtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from Exonerate_protein2genome GCTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCAG ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcagGTTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGatggtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from Exonerate_coding2genome GCTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCAG ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcagGTTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGatggtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg Alignment from GeneWise GCTTCCAGGCTCTGGTGCTAACAGCCCTGTTGATGGGGCTGGGGGTGTCAGTGGGGCTGCCCCTGGGGGCACTCCCTGGAATGCTCCTGCCCTTGGCCTTTGCGACCACTCTCACCAGCTTTATCTTCAGCCTCCTCCTCTATGCGAAGGCTTTGGTAGCTCCTGCCTCAGCCCTGGCTCCTGGGGGAAACTCAGGA- ctttcctagtatgtgtactgtccctgagtcaggttctggctctcttgcagGTTACCAGGCTGTTGTTTTGTCAGCACTGTTAATGGGGCTGGGTGTATCTGTGGGGTTCCCCCTTGCAGGATTACCTGGAATGCTCCTGCCACTGGCCTTGGCAACCACTCTCACCAGGTTTGTCTTCAGCCTACTACTCTACACAAAGGCTTTGGTAACACCTGCCTTAGCTTTGAACTCCGGGGGAAACTCAGATGgtgcgtagggtgcccagcagatctcagaaggtgcgggactagtgaaggtg #### Tm7sf2_ID1417_3 --> 0 - 1 Original Alignment GTGGCCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATg ttgatatgacctatgttgtgtgaaccacctcctttttcattcccatgcag------GAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATggtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from CESAR GTGGCCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATg tcccccttgatatgacctatgttgtcacctcctttttcattcccatgcag------GAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATggtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from Spaln_aa2Genome GTGGCCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATG ttgatatgacctatgttgtgtgaaccacctcctttttcattcccatgcag------GAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATGgtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from Spaln_nt2Genome CCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATG ttgatatgacctatgttgtgtgaaccacctcctttttcattcccatgcag--GAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATGgtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from Pairagon GTGGCCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATG ttgatatgacctatgttgtgtgaaccacctcctttttcattcccatgcag------GAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATGgtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from Exonerate_protein2genome GTGGCCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATG ttgatatgacctatgttgtgtgaaccacctcctttttcattcccATGCAGGAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATGgtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from Exonerate_coding2genome GTGGCCGAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATG ttgatatgacctatgttgtgtgaaccacctcctttttcattcccATGCAGGAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATGgtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac Alignment from GeneWise GAAGGCCTGGAACTGAAGGACAAGAGTCGCCTGCGCTACCCTATTAATG ttgatatgacctatgttgtgtgaaccacctcctttttcattcccatgcagGAAGGTGTAGAACTGAAGGATAAGAGTCGCTTGCAATACCCTATTAATGgtgagtcagttgtactcaacctaaatcagctttttggcactgaaatttac #### Tm7sf2_ID1418_2 --> 2 - 0 Original Alignment gcGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG ttatactcatgctccaatccaaagtgaatctgctcttttccttcttccaggt------GCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt Alignment from CESAR gcGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG agggcattatactcatgctccaatcgaatctgctcttttccttcttccaggt------GCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgaaccacatgctg Alignment from Spaln_aa2Genome GCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG ttatactcatgctccaatccaaagtgaatctgctcttttccttcttccagGT------GCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt Alignment from Spaln_nt2Genome GCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG ttatactcatgctccaatccaaagtgaatctgctcttttccttcttccagG------TGCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt Alignment from Pairagon GCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG ttatactcatgctccaatccaaagtgaatctgctcttttccttcttccagGT------GCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt Alignment from Exonerate_protein2genome GCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG ttatactcatgctccaatccaaagtgaatctgctcttttccttcttccagGT------GCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt Alignment from Exonerate_coding2genome GCGTCGCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG ttatactcatgctccaatccaaagtgaatctgctcttttccttcttccagGT------GCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt Alignment from GeneWise GGCCTCCCAGGCCCCACTGGAATTCGGGGGGCCGTTGGGCGTC------GCGGCTTTACTGATCCTGCTGCCTGCCACCATGTTCCACCTGCTCCTGGCGGCTCGCTCGGGCCCGGCGCGCCTCCTGGCCCTACCGGCCTATCTGCCTGGGCTGGAGGAGCTGTGGAGCCCATGGGCTCTGCTGCTATTGTTCATCTGGCTCGGCCTGCAGGTGGCGCTCTATTTGCTGCCTGCACGCAAG TTATACTCATGCTCCAATCCAAAGTGAATCTGCTCTTTTCCTTCTTCCAGGTGCTTTATTGATACTGCTGCCAGCTACCATGTCTCACTACCTCCTTGCTGCTCACTCAGGGCCAGCACGACTACTGGCCCTACCGGCATACCTACCTGGTCTGGAAGAACTATGGAGCCCATGGGCCCTGCTTCTCCTGTTCATCTGGCTTGGTCTGCAGGTGGCACTCTATCTGCTGCCTGCATGCAGGgtgagcgatctcccccttgatatgacctatgttgtgtgttaaaagaattt #### Tmem179b_ID2369_4 --> 1 - 0 Original Alignment cTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCTGAA ctatctttatcattcttattacacttattgtgccttggtcccctcctcagcTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCC---gtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc Alignment from CESAR cTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCTGAA ctatctttatcattcttattacacttattgtgccttggtcccctcctcagcTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCC---gtgagtagttgcaagcatcgataaggagacatcaatatgcttggctc Alignment from Spaln_aa2Genome CTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCT ctatctttatcattcttattacacttattgtgccttggtcccctcctcagCTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCCgtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc Alignment from Spaln_nt2Genome CTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCT ctatctttatcattcttattacacttattgtgccttggtcccctcctcagCTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCCgtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc Alignment from Pairagon CTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCT ctatctttatcattcttattacacttattgtgccttggtcccctcctcagCTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCCgtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc Alignment from Exonerate_protein2genome CTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCT ctatctttatcattcttattacacttattgtgccttggtcccctcctcagCTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCCgtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc Alignment from Exonerate_coding2genome CTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCT ctatctttatcattcttattacacttattgtgccttggtcccctcctcagCTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACCGCCgtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc Alignment from GeneWise CTGCTCTGAAGCCCAGAAAACCTCATGGACACCTTCAGGAACTGCTGTGCAGTTTTACTCCAACCTACATACTGCTGAA ctatctttatcattcttattacacttattgtgccttggtcccctcctcagCTGCTCCGAAGCACAGAAGACTGCTTGGACACCTTTGGGAACTGCTGTGCAGCTTTACTCCAACCTACACACC---GCCgtgagtagttgcaagcatcgataaggagacatcaatatgcttggctctgc #### Tmem179b_ID2370_3 --> 1 - 2 Original Alignment aGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTCCTTGAACCTTACAATTag tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagaGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATC------------------aggtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from CESAR aGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTCCTTGAACCTTACAATTag tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagaGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATC------------------aggtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from Spaln_aa2Genome AGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTC tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagAGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATCAGgtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from Spaln_nt2Genome AGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTC tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagAGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATCAGgtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from Pairagon AGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTCCTTGAACCTTACAATTAG tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagAGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATC------------------AGgtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from Exonerate_protein2genome AGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTC tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagAGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATCAGgtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from Exonerate_coding2genome AGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTC tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagAGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATCAGgtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc Alignment from GeneWise AGGTTCTATAGGGCTCCGAATTGCTTTGGCCATCTCAGCTACAGCCATCTTCCTGATCTTAGTGTCTGCCTGTATACTTCGATTTGGCACCAATTCTTTCTGCAATTCCATCATCTC tcggtttactttgtggtaggttgttaatccccctttttctctgttaatagAGGCTCTATAGGGCTCCGGATTGCTCTGGCCATCTCAGCTACAGCTATCTTCCTGATTTTAGTATCCGCTTGCATAGTCCGATTTGGCACAAATTCTTTCTGTAACTCCATTATCAGgtacgttgaagaataggtgttgaggttgtatatcatctactgagagttgc #### Trmt112_ID1861_2 --> 0 - 0 Original Alignment GCCACTGAGGTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC gtctaacctggacaactctcaaattctcactcaaacttttctttttgtag---------GTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from CESAR GCCACTGAGGTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC cagatggaagtctaacctggacaacctcactcaaacttttctttttgtag---------GTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from Spaln_aa2Genome GCCACTGAGGTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC gtctaacctggacaactctcaaattctcactcaaacttttctttttgtag---------GTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from Spaln_nt2Genome GCCACTGAGGTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC gtctaacctggacaactctcaaattctcactcaaacttttctttttgtag---------GTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from Pairagon GCCACTGAGGTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC gtctaacctggacaactctcaaattctcactcaaacttttctttttgtag---------GTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from Exonerate_protein2genome GTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC gtctaacctggacaactctcaaattctcactcaaacttttctttttgtagGTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from Exonerate_coding2genome gtctaacctggacaactctcaaattctcactcaaacttttctttttgtaggtctgtattaaccctgtggaatttaaccctgagttagtggcacgtatgatccctaaagtagagtgggcagcacttgttcgggctgcagatactgtgagagccctattcttcctaggatatcttagtttctggacccctttcta Alignment from GeneWise GTCCGCATCAACCCCGTGGAGTTCAACCCGGAGTTCGTGGCGCGGATGATCCCCAAAGTGGAGTGGGCGGCGCTTGTGCAGGCAGCGGACACC gtctaacctggacaactctcaaattctcactcaaacttttctttttgtagGTCTGTATTAACCCTGTGGAATTTAACCCTGAGTTAGTGGCACGTATGATCCCTAAAGTAGAGTGGGCAGCACTTGTTCGGGCTGCAGATACTgtgagagccctattcttcctaggatatcttagtttctggacccctttcta #### Trmt112_ID1862_3 --> 0 - 0 Original Alignment ---------TTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcagGAAGGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from CESAR ---------TTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcagGAAGGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from Spaln_aa2Genome GCGGACACCTTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcagGAAGGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from Spaln_nt2Genome --------CTTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcagGAAGGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from Pairagon TTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcaggaagggtccttgaatttagctgcag----------------TGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from Exonerate_protein2genome ACACCTTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcaggaagGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from Exonerate_coding2genome GCGGCGCTTGTGCAGGCAGCGGACACCTTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAG gacccctttctagtaattatagtgtctagcagGCCCTGTGTGTATTTCAGGAAGGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAgtgagcaacctggaccacaatgcccagatgtctatagttgttacaagcct Alignment from GeneWise ---------TTAAACTTGGCCGAGGTACCCAAAGAGCCGACTGAAGGCTATGAGCACGACGAGACATTTTTGAGGAAGATGCACCACGTGTTGCTTGAGGTT----------------------------------------------- gacccctttctagtaattatagtgtctagcaggccctgtgtgtatttcagGAAGGGTCCTTGAATTTAGCTGCAGTGCCCCGAGAGCCGACTGAGGGCTATGAGCATGATGAAACATTTTTGAGGGAGATGCGTCATGTACTTCTTGAAGTGAGCAACCTGGACCACAATGCCCAGATGTCTATAGTTGTTACAAGCCT #### Ubxn1_ID2444_8 --> 0 - 1 Original Alignment ---------------GTTAGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGg ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcagGATCGATACAAACAAGTTAGGCTGCCTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGggtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta Alignment from CESAR ---------------GTTAGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGg ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcagGATCGATACAAACAAGTTAGGCTGCCTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGggtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta Alignment from Spaln_aa2Genome TTAGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGG ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcaggatcgatacaaacaagTTAGGCTGCCTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGGgtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta Alignment from Spaln_nt2Genome GTTAGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGG ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcaggatcgatacaaacaagTTAGGCTGC-CTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGGgtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta Alignment from Pairagon ---------------GTTAGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGG ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcagGATCGATACAAACAAGTTAGGCTGCCTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGGgtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta Alignment from Exonerate_protein2genome GTTAGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGG ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcaggatcgatacaaacaaGTTAGGCTGCCTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGGgtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta Alignment from Exonerate_coding2genome No alignment No alignment Alignment from GeneWise --AGGCTGCCTGATGGGACTTCACTGACCCAGACTTTCCGGGCCCGGGAACAGCTGGCAGCTGTGAGGCTCTACGTGGAGCTTCACCGTGGGGAGGAGCCTGGACAGGACCAGGACCCTGTGCAGTTGCTCAGTGGCTTCCCCAGACGGGCTTTCTCAGAGGCTGATATGGAACGGCCTCTGCAGGAACTGG ggcaactacagaaaatgccgctcattggttgtctcatttgtttccatcaggatcgatacaaacaagTTAGGCTGCCTGATGTCACTTCACTGACCCAGACTTTCCGGATCCAGGAAGAGTTGGCAGCTGTGAGGCTTTATGTAGAGCTCCATCACGGTGAGGAACCCGGACAGGATCAGGACCCTGTACAATTGCTCAGTGGATTCCCCAGACGGGCTTTCTCTGAAGCTGACATGGAGCGGCCTTTACAGAGACTGGgtaggctttgtattcctacatttatgcacattgtcttgaggcacatgcta #### Unc93b1_ID214_5 --> 1 - 0 Original Alignment g------ATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCAC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggTGTAGAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATgtaggcgtgcttcaggaagcccttgtagtgggtgggcataacagactggg Alignment from CESAR gATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCAC tgacacaaggaaaaaactgtcatagtgtgcacagtgtttgctccacacaggtgtagaATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATgtaggcgtgcttcaggaagcccttgtagtgggtgggcataacagactggg Alignment from Spaln_aa2Genome GATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCACTTGAGCTTCGCGTGTGCCCAGCTGCCC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggtgtagAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATGTAGGCGTGCTTCAGGAAGCCCTTGTAgtgggtgggcataacagactggg Alignment from Spaln_nt2Genome GATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCAC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggtgtagAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATgtaggcgtgcttcaggaagcccttgtagtgggtgggcataacagactggg Alignment from Pairagon GATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCAC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggtgtagAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATgtaggcgtgcttcaggaagcccttgtagtgggtgggcataacagactggg Alignment from Exonerate_protein2genome GATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCACTTGAGCTTCGCGTGTGCCCAGCTGCCC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggtgtagAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATGTAGGCGTGCTTCAGGAAGCCCTTGTAgtgggtgggcataacagactggg Alignment from Exonerate_coding2genome GATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCACTTGAGCTTCGCGTGTGCCCAGCTGCCC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggtgtagAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATGTAGGCGTGCTTCAGGAAGCCCTTGTAgtgggtgggcataacagactggg Alignment from GeneWise GATGTCCCAGAAGTACTATGAATACTCCCACTACAAGGAGCAAGATGAGCAGGGACCTCAGCAGCGCCCACCACGAGGTTCCCACGCACCCTATCTCCTGGTTTTCCAGGCCATCTTCTATAGCTTCTTCCAC aaggaaaaaactgtcatagtgtgcagttattcagtgtttgctccacacaggtgtagAATGTCTCAGAAATACTACGAATATTCACATTACAAGGAGCAGGATGACCAGGGACCTCAACAACACCCACCACATGGACTACACACACCTTTTCTGCTGGTCTTCCATACTAACTTTTACAGTTTCTTGCATgtaggcgtgcttcaggaagcccttgtagtgggtgggcataacagactggg #### Unc93b1_ID215_6 --> 0 - 1 Original Alignment ---------TTGAGCTTCGCGTGTGCCCAGCTGCCCATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCg cctactgcaatgacagacttctctcatacacctttcccttctgatgttagTACTTTTCCTTGAGCTTC---TTTGCTCAG------ATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTggtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from CESAR ---------TTGAGCTTCGCGTGTGCCCAGCTGCCCATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCg cctactgcaatgacagacttctctcatacacctttcccttctgatgttagTACTTTTCCTTGAGCTTC---TTTGCTCAG------ATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTggtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from Spaln_aa2Genome ATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCG cctactgcaatgacagacttctctcatacacctttcccttctgatgttagtacttttccttgagcttctttgctcagATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTGgtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from Spaln_nt2Genome ATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCG cctactgcaatgacagacttctctcatacacctttcccttctgatgttagtacttttccttgagcttctttgctcagATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTGgtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from Pairagon CCACTTGAGCTTCGCGTGTGCCCAGCTGCCCATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCG cctactgcaatgacagacttctctcatacacctttcccttctgatgttagtacttttccttgagcttctttgctcag-------------------------------ATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTGgtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from Exonerate_protein2genome ATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCG cctactgcaatgacagacttctctcatacacctttcccttctgatgttagtacttttccttgagcttctttgctcagATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTGgtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from Exonerate_coding2genome ATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCG cctactgcaatgacagacttctctcatacacctttcccttctgatgttagtacttttccttgagcttctttgctcagATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTGgtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca Alignment from GeneWise ATGATTTACTTCCTCAACAACTACCTGTATGACCTGAACCACACACTGATCAACGTGCAGAGCTGCG cctactgcaatgacagacttctctcatacacctttcccttctgatgttagtacttttccttgagcttctttgctcagATGATTTACTTCCTCAACAACTATCTGTATGACCTAAACCATACACTTATCAATGTACAGATATGTGgtgagcttgtgatatcctagtaagttagtctttgttccatattcagtcca #### Vegfb_ID1956_4 --> 0 - 2 Original Alignment ------ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCag aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagTGTATCATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCaggtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from CESAR ------ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCag aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagTGTATCATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCaggtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from Spaln_aa2Genome ATCCTCATGATCCAG------TACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAG aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagTGTATCATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGgtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from Spaln_nt2Genome ------ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAG aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagTGTATCATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGgtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from Pairagon ------ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAG aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagTGTATCATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGgtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from Exonerate_protein2genome ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAG aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagtgtatcATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGgtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from Exonerate_coding2genome ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAG aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagtgtatcATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGgtctgagacaattccaggacccatggtctggcatgtgttagggccgcatg Alignment from GeneWise ------ATCCTCATGATCCAGTACCCGAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGACCAAAAAAAAAGGAGAGTGCTGTGAAGCCAGACAG aagtttacctcttagcttcttgggaacacaaagcattgtgtctcctttagTGTATCATCCTCATGATCCAGTACCCAAGCAGTCAGCTGGGGGAGATGTCCCTGGAAGAACACAGCCAATGTGAATGCAGGTCTGAGACAATTCCAGGACCCATGGTCTGGCATGTgttagggccgcatg #### Vegfb_ID1957_3 --> 2 - 0 Original Alignment tgGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGT---GTGACTGTGCAGCGCTGTGGTGGCTGC---TGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagtgGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGC------------------------------------------gtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca Alignment from CESAR tgGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGCTGC---TGCCCTGACGATGGCCTGGAATGTGTGCCCACTGGGCAACACCAAGTCCGAATGCAG agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagtgGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGC------------------------------------------gtgagtga Alignment from Spaln_aa2Genome TGGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGC agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagTGGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCgtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca Alignment from Spaln_nt2Genome TGGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGC agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagTGGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCgtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca Alignment from Pairagon TGGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGT---GACTGTGCAGCGCTGTGGTG---GCTGCTGCCCTGACGATGGC agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagTGGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCgtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca Alignment from Exonerate_protein2genome TGGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGC agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagTGGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCgtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca Alignment from Exonerate_coding2genome TGGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGC---TGCTGCCCTGACGATGGC agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagTGGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCgtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca Alignment from GeneWise TGGTGCCATGGATAGACGTTTATGCACGTGCCACATGCCAGCCCAGGGAGGTGGTGGTGCCTCTGAGCATGGAACTCATGGGCAATGTGGTCAAACAACTAGTGCCCAGCTGTGTG---ACTGTGCAGCGCTGTGGTGGCTGCTGC---CCTGACGATGGC agaaatgaaaaagtggaaaggtttttgggtattgtgttgtttctttgtagTGGTACCATGGATCGATGTCTATGCACGGTCTGTATGCCAACCGAGGGAGGTGGCAGCTCCACTGAGTATGAAACTTATGGGTAATATCGTCAAACAGCTGGTGCCAAGCTGTGTTGGAACTGTGCAGCGCTGTAGTGGGTGCTGCTGCCCTGATGATGGCgtgagtgactaatttgtatgtaagtacttggtagtatcagtctgtctaca #### Vldlr_ID5807_6 --> 2 - 1 Original Alignment ct---------TCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACg cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagcaGTTCTGACGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACagtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from CESAR ct------TCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACg gcacttcacttctgatgtctctagcagtcttcctgttctttgtgttttagcagttCTGACGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACagtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from Spaln_aa2Genome CT---------TCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACG cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagCAGTTCTGACGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACAgtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from Spaln_nt2Genome CT------TCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACG cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagcagTTCTGACGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACAgtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from Pairagon ---------CTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACG cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagCAGTTCTGACGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACAgtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from Exonerate_protein2genome CTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACG cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagcagttctgaCGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACAgtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from Exonerate_coding2genome CTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACG cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagcagttctgaCGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACAgtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga Alignment from GeneWise -----CCTTCTCGAACCTGCCGACCTGACCAGTTTGAATGTGAAGATGGTAGCTGTATCCACGGCAGCAGGCAATGCAATGGCATCCGAGACTGTGTTGATGGCTCTGATGAAGTCAACTGCAAAAACG cttcacttctgatgtctctagcagtctccttcctgttctttgtgttttagcagTTCTGACGTCTCAAACTTGCCGACCTGACCACTTTGAATGTGAGGATGGTACTTGCATCCATGGTAGCAGACAATGCAATGGGATCCAGGCTTGTGTTGATGGGTCTGATGAACTAAACTGTAGAAACAgtgagcgtctctttgagattgacaggtctgttcctttgccagaagagtga #### Vldlr_ID5811_10 --> 2 - 2 Original Alignment gc------------AAAGAGCCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCag atggcacttttcaagtaaataaatttttattttcttgttcttctgtccaggcTCTGGCTGTGACAAAGAGCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCaggtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from CESAR gc------------AAAGAGCCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCag atggcacttttcaagtaaataaatttttattttcttgttcttctgtccaggcTCTGGCTGTGACAAAGAGCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCaggtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from Spaln_aa2Genome CCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCAG atggcacttttcaagtaaataaatttttattttcttgttcttctgtccaggctctggctgtgacaaagagCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCAGgtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from Spaln_nt2Genome GCAAAGAGCC------------GAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCAG atggcacttttcaagtaaataaatttttattttcttgttcttctgtccagGCTCTGGCTGTGACAAAGAGCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCAGgtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from Pairagon G------------CAAAGAGCCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCAG atggcacttttcaagtaaataaatttttattttcttgttcttctgtccagGCTCTGGCTGTGACAAAGAGCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCAGgtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from Exonerate_protein2genome GCAAAGAGCCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCAG atggcacttttcaagtaaataaatttttattttcttgttcttctgtccaggctctggctgtgACAAAGAGCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCAGgtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from Exonerate_coding2genome GCAAAGAGCCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCAG atggcacttttcaagtaaataaatttttattttcttgttcttctgtccaggctctggctgtgACAAAGAGCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCAGgtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca Alignment from GeneWise CCGAGTCTGATCTTCACTAATCGAAGAGACATCAGGAAGATTGGCCTAGAGAGAAAGGAATACATCCAACTTGTAGAGCAACTAAGGAACACGGTGGCTCTCGATGCGGACATTGCAGCTCAGAAGCTGTTTTGGGCTGATCTCAGCCAGAAGGCCATCTTCAG atggcacttttcaagtaaataaatttttattttcttgttcttctgtccaggctctggctgtgacaaagagCCAAGTCTGATATTCACTAATCGAAGAGACATCAGAAAGATCGGCTTAGAAAGAAAAGAGTATATCCAACTTGTAGATCAATTGAGAAACACAGTGGCTCTTGATGCAGAAATTGCAGCTCAAAAGCTATTTTGGGCTGATTTTAGCCAGCAGGCTATTTTCAGgtaaggtaaatcagcctttcacagatgtctgggaagcatgcttagtggca #### Vldlr_ID5814_13 --> 2 - 0 Original Alignment acCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gaagtcaatgtacttgctctctgatgtggtggcttctattctggtctcagac------AAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from CESAR acCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gtctatgaagtcaatgtacttgctcgtggtggcttctattctggtctcagac------AAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from Spaln_aa2Genome CTCGACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gtacttgctctctgatgtggtggcttctattctggtctca gACAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from Spaln_nt2Genome TCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gaagtcaatgtacttgctctctgatgtggtggcttctattctggtctcagACAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from Pairagon TCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gaagtcaatgtacttgctctctgatgtggtggcttctattctggtctcagACAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from Exonerate_protein2genome TCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gaagtcaatgtacttgctctctgatgtggtggcttctattctggtctcagACAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from Exonerate_coding2genome TCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gaagtcaatgtacttgctctctgatgtggtggcttctattctggtctcagACAAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg Alignment from GeneWise TCGACCTTGTCAAAAGCCGCCTCTACTGGCTGGATTCCAAGTTGCACATGCTCTCTAGTGTGGACCTGAATGGTCAAGATCGTAGGATAGTGCTCAAGTCTCTGGAGTTCCTAGCTCATCCTCTTGCACTCACCATATTTGAG gaagtcaatgtacttgctctctgatgtggtggcttctattctggtctcagAC---------AAAAGCCGTCTCTACTGGTTAGATGCCAAGTTACACATGCTCTCTAGTGTTGACCTTAATGGTCAATATCGTAGGATTGTACTCAAGTCACTAAAGTTTCTAGCTCATCCTCTTGCCCTCTCTATATTTGAGgtgagttataccatatgaccttgtatcaatgaacttcgtaaaaaaagagg #### Vps13a_ID4057_66 --> 0 - 1 Original Alignment GGTTTTGTAAGTGGCATTACAGGGATTGTTACAAAGCCAATTAAAg aaggtgggctgttacaattctattaatctttggcctctcgttcctttcag------GTAAGTGGTATTACTGGCATTGTTTCAGAACCAATAAAAggtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from CESAR GGTTTTGTAAGTGGCATTACAGGGATTGTTACAAAGCCAATTAAAg caacaaaaggtgggctgttacaattatctttggcctctcgttcctttcag------GTAAGTGGTATTACTGGCATTGTTTCAGAACCAATAAAAggtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from Spaln_aa2Genome GGTTTTGTAAGTGGCATTACAGGGATTGTTACAAAGCCAATTAAAG aaggtgggctgttacaattctattaatctttggcctctcgttcctttcag------GTAAGTGGTATTACTGGCATTGTTTCAGAACCAATAAAAGgtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from Spaln_nt2Genome GTAAGTGGCATTACAGGGATTGTTACAAAGCCAATTAAAG aaggtgggctgttacaattctattaatctttggcctctcgttcctttcagGTAAGTGGTATTACTGGCATTGTTTCAGAACCAATAAAAGgtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from Pairagon GGTTTTGTAAGTGGCATTACAGGGATTGTTACAAAGCCAATTAAAG aaggtgggctgttacaattctattaatctttggcctctcgttcctttcag------GTAAGTGGTATTACTGGCATTGTTTCAGAACCAATAAAAGgtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from Exonerate_protein2genome GGTTTTGTAAGTGGCATTACAGGGATTGTTACAAAGCCAATTAAAG aaggtgggctgttacaattctattaatctttggcctctcgttcctttcag------GTAAGTGGTATTACTGGCATTGTTTCAGAACCAATAAAAGgtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from Exonerate_coding2genome aaggtgggctgttacaattctattaatctttggcctctcgttcctttcaggtaagtggtattactggcattgtttcagaaccaataaaaggtaggacctgatatatctcttgcttatatcattcctatttgggcatagtt Alignment from GeneWise GG aaggtgggctgttacaattctattaatctttggcctctcgttcctttcaggtaagtggtattactggcattgtttcagaaccaataaaaggtaggacctgatatatctcttgcttatatcattcctatttgggcatagTT #### Vps13a_ID4058_65 --> 2 - 0 Original Alignment gtGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT aggttttatctgataagtttaggatactgatgcactttggttttgtacaggt---------------GCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from CESAR gtGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT acaccagtgaggaaaaggttttatcactgatgcactttggttttgtacaggt---------------GCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from Spaln_aa2Genome GGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT ttttatctgataagtttaggatactgatgcactttggttttgtaca gGTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from Spaln_nt2Genome GTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT aggttttatctgataagtttaggatactgatgcactttggttttgtacagG---TGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from Pairagon GTGGGCTAGCTGGTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT aggttttatctgataagtttaggatactgatgcactttggttttgtacagG---------------TGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from Exonerate_protein2genome CTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT aggttttatctgataagtttaggatactgatgcactttggttttgtacagGTGCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from Exonerate_coding2genome aggttttatctgataagtttaggatactgatgcactttggttttgtacaggtgcctctaaactgactagcgctatgtcgaaaggagtagcagccatgaccatggatgaagactaccagcagaaaagaaaagaagcaatgaataagcggccagctggactaagagagggcatcacccgaggagggaaaggtttagtctctgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata Alignment from GeneWise GTGCTGCCTCCAAAATCACCAGTGCTATGGCTAAAGGAGTAGCGGCCATGACCATGGATGAAGACTACCAGCAGAAGAGGAGAGAAGCAATGAATAAGCAGCCTGCTGGCCTTCGAGAGGGCATCACTCGAGGAGGAAAAGGCCTTGTCTCT aggttttatctgataagtttaggatactgatgcactttggttttgtacagGT---GCCTCTAAACTGACTAGCGCTATGTCGAAAGGAGTAGCAGCCATGACCATGGATGAAGACTACCAGCAGAAAAGAAAAGAAGCAATGAATAAGCGGCCAGCTGGACTAAGAGAGGGCATCACCCGAGGAGGGAAAGGTTTAGTCTCTgtaaggcctcaccgtgtcttggattacatagaaggactgtttcattcata #### Vps13a_ID4093_30 --> 2 - 1 Original Alignment ctTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA------g aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagcaCTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACggtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from CESAR ctTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA------g aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagcaCTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACggtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from Spaln_aa2Genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA------G aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACGgtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from Spaln_nt2Genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAG------ aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACGgtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from Pairagon CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAAG------ aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACGgtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from Exonerate_protein2genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA------G aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACGgtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from Exonerate_coding2genome CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA------G aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACGgtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc Alignment from GeneWise CTTTAAAGCTACCCACGAATGAAGATATTATTACCTTGCAGCTTTTGGCAGAATTATCTTGTCTACAGATTTTTATTCAGGATCAGAAACAAAACATTTCTGAAATTAAAATTGAA------G aggtcatttgtaaatgatctctggtacctaggatatttccctccctatagCACTAAAGGTACCTATAAATGAAGACATTATTACATTGCAGCTTGTGGCAGAATTATCATGTTTAAAAATTCTCATCCAGGATCAGAAACAGAATGTATCAGAAATTAAAATCGAAGACTACGgtaagtataaatatttcctgtttaaggataaacaaaattcaaaaggcagc #### Vps13a_ID4109_14 --> 0 - 0 Original Alignment ------GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from CESAR ------GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from Spaln_aa2Genome GAGTTGGAGAAA------ACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from Spaln_nt2Genome GAGTTGGAGA------AAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from Pairagon ------GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from Exonerate_protein2genome ------GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from Exonerate_coding2genome ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagcctaccgagttggagaaaactttggatgttttgaacatgcctataagtagacagcaagcagaggttgaagtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc Alignment from GeneWise ------GAGTTGGAGAAAACTTTGGATGTTTTTAATATAACCATAGCTAGACAACAGGCAGAAGTTGAG ctaatattaggagggttttatctatagacacttccctgtgcttttcgcagCCTACCGAGTTGGAGAAAACTTTGGATGTTTTGAACATGCCTATAAGTAGACAGCAAGCAGAGGTTGAAgtgagtccactctgtcatttaaatgatcatgagccattttatttcttctc #### Vps37c_ID2983_3 --> 2 - 0 Original Alignment agAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAG--- tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagagAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGAgtacgtcaagcattgctccttgatttggcttattccaaactgtactgtct Alignment from CESAR agAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAG--- tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagagAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGAgtacgtcaagcattgctccttgatttggcttattccaaactgtactgtct Alignment from Spaln_aa2Genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAGGCC tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGAgtacgtcaagcattgctccttgatttggcttattccaaactgtactgtct Alignment from Spaln_nt2Genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAGG-- tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGAgtacgtcaagcattgctccttgatttggcttattccaaactgtactgtct Alignment from Pairagon AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAGGCCATGGCTGAGAAATTCCTGGAA tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGA---------------------GGGAgtacgtcaagcattgctccttgatttggcttattccaaactgtactgtct Alignment from Exonerate_protein2genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAGGCCATG tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGA---gtacgtcaagcattgctccttgatttggcttattccaaactgtactg Alignment from Exonerate_coding2genome AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAGGCCATG tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGA---gtacgtcaagcattgctccttgatttggcttattccaaactgtactg Alignment from GeneWise AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAGGCC tttgttatcagatttaattaaggcaatgcactctgttctctgtcccccagAGAAATTTTCCTCAGCCCTGCAGCCTGGGACCTTATTGGACCTCCTGCAGATTGAAGGTATGAAGATTGAGGAGGACTCAGAGGGAgtacgtcaagcattgctccttgatttggcttattccaaactgtactgtct #### Vwce_ID2964_18 --> 2 - 0 Original Alignment acTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATCTGCCAG actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagacTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATC------gtaagattccgtgggagagggaacccggagctaacagtttgccctcatgg Alignment from CESAR acTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATCTGCCAG actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagacTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATC------gtaagattccgtgggagagggaacccggagctaacagtttgccc Alignment from Spaln_aa2Genome ACTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATC actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagACTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATCgtaagattccgtgggagagggaacccggagctaacagtttgccctcatgg Alignment from Spaln_nt2Genome ACTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATC actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagACTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATCgtaagattccgtgggagagggaacccggagctaacagtttgccctcatgg Alignment from Pairagon ACTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATC actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagACTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATCgtaagattccgtgggagagggaacccggagctaacagtttgccctcatgg Alignment from Exonerate_protein2genome ACTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATC actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagACTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATCgtaagattccgtgggagagggaacccggagctaacagtttgccctcatgg Alignment from Exonerate_coding2genome actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagactgtaattttgaagggagaaaggtagtcaatggtcaggttttcaccttagatgatgagccctgtacccggtgcatcgtaagattccgtgggagagggaacccggagctaacagtttgccctcatgg Alignment from GeneWise ACTGTAACTTCGAAGGGAGAAAGGTAGTGAATGGTCAGGTGTTCACCTTGGATGATGAGCCCTGTACCCGGTGCATCTGCCAGCTGG actgcctcgcagactcccctgcccttgctcttttgcttcactctggacagACTGTAATTTTGAAGGGAGAAAGGTAGTCAATGGTCAGGTTTTCACCTTAGATGATGAGCCCTGTACCCGGTGCATCGTAAGATTCCgtgggagagggaacccggagctaacagtttgccctcatgg #### Wdr74_ID2312_2 --> 2 - 0 Original Alignment ggGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA------ aagttcatgtattcagccacctcattatgttctttgttttcatcccttaggaGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACAA---CGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAGATGATgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from CESAR ggGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA------ aagttcatgtattcagccacctcattatgttctttgttttcatcccttaggaGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACAA---CGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAGATGATgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from Spaln_aa2Genome GGGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA------ aagttcatgtattcagccacctcattatgttctttgttttcatcccttagGAGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACAA---CGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAGATGATgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from Spaln_nt2Genome GGGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA-ATCTT aagttcatgtattcagccacctcattatgttctttgttttcatcccttagGAGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACA---ACGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAGATGATgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from Pairagon GGGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA------ aagttcatgtattcagccacctcattatgttctttgttttcatcccttagGAGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACA---ACGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAGATGATgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from Exonerate_protein2genome GGGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA aagttcatgtattcagccacctcattatgttctttgttttcatcccttagGAGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACAA---CGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAgatgatgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from Exonerate_coding2genome GGGTGAACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA aagttcatgtattcagccacctcattatgttctttgttttcatcccttagGAGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACAA---CGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAgatgatgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa Alignment from GeneWise -------------------------------------------------------AACCTTCAGCGGAAACATGCGGCAAATTTCACACCGTCCGGACAGCCGCGGCGGGAGGAGGCAGTGAATGCTCTGTGCTGGGGCACTGGCGGCGAGACCCAA------ AAGTTCATGTATTCAGCCACCTCATTATGTTCTTTGTTTTCATCCCTTAGGAGTGAACCTTCAGTGTAAACACACAGCCAATTTTGCTCCATTGGGACAA---CGGAGGGAGCAGGCTGTGAATGCTCTGTGCTGGGGTACTGGCAGTGAGACCCAAGATGATgtaataaggccatatctctgtaaaaggcacaagagttgtagaattttcaa #### Wdr74_ID2318_8 --> 1 - 1 Original Alignment t---------------------------------TCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAg taaggcacttcaggagccacataaatcctttcttttccttccattaatagtGCTCTGTATGAAGCTGGAGAATCGTTAAAGATATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAggtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct Alignment from CESAR aatggtctgccattcgtttgtatcagcttgtatttcattgagcagtagttt Alignment from Spaln_aa2Genome GGCAATTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG taaggcacttcaggagccacataaatcctttcttttccttccattaatagtgctctgtatgaagctggagaatcgttaaag---ATATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAGgtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct Alignment from Spaln_nt2Genome TT--CCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG taaggcacttcaggagccacataaatcctttcttttccttccattaatagtgctctgtatgaagctggagaatcgttaaagATATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAGgtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct Alignment from Pairagon --TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG taaggcacttcaggagccacataaatcctttcttttccttccattaatagtgctctgtatgaagctggagaatcgttaaagATATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAGgtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct Alignment from Exonerate_protein2genome TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG taaggcacttcaggagccacataaatcctttcttttccttccattaatagtgctctgtatgaagctggagaatcgttaaagatATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAGgtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct Alignment from Exonerate_coding2genome TTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG taaggcacttcaggagccacataaatcctttcttttccttccattaatagtgctctgtatgaagctggagaatcgttaaagatATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAGgtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct Alignment from GeneWise -------------------------------AATTCCGTCATCGTAGGGAACACTCATGGGCAGCTGGCAGAAATTGATTTTCGGCAAG taaggcacttcaggagccacataaatcctttcttttccttccattaatagTGCTCTGTATGAAGCTGGAGAATCGTTAAAGATATCTGTCATTGTGGGGAATACTCATGGTCAGCTGGCAGAGATTGACTTTCGACAAGgtgagagtgccattgtgttcttgagaatgaatgtattctgccaaagctct #### Wnt8b_ID9022_5 --> 2 - 0 Original Alignment ggGGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaattttttataggg------------------GGTGGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from CESAR ggGGCCAAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG ccataccaggatttccatgccttatatataatctttttaattttttatagggGGT------------------GGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Spaln_aa2Genome AAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaattttttatagGG------------GGTGGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Spaln_nt2Genome GGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaattttttatagGGGGTGGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Pairagon AAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaattttttatag------------GGGGTGGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Exonerate_protein2genome GGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaaTTTTTTATAGGGGGTGGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from Exonerate_coding2genome GGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaaTTTTTTATAGGGGGTGGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag Alignment from GeneWise AAGGTTGGCTCTGGGGAGGCTGCAGTGACAACGTGGGCTTCGGAGAGGCAATTTCCAAGCAGTTTGTGGATGCCCTCGAGACAGGACAAGATGCCCGGGCAGCCATGAATCTGCACAACAATGAGGCTGGCCGCAAG gccttatagatccgctcgaacatttatataatctttttaattttttatagGGGGT------------GGATGCAGTGACAATGCAGGCTTTGGAGAGGCAATTTCCAAGCAATTTGTTGATGTTCTCAAGTCAGGGCAGGATGCCCGAGCAGCCATAAACTTGCACAACAATGAAGCTGGCCACAAGgtaggtccaatagtggttgatggcatgcatcatgagacctgtcattgtag #### Zfand5_ID4879_2 --> 2 - 2 Original Alignment ggACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAag gttttataatggagataaatcagcaatttcttgttacacttgttttttagga---GCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAaggtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from CESAR ggACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAag tgtgttttataatggagataaatcaatttcttgttacacttgttttttagga---GCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAaggtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from Spaln_aa2Genome GGACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAAG gttttataatggagataaatcagcaatttcttgttacacttgttttttagGA---GCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAAGgtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from Spaln_nt2Genome GACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAAG gttttataatggagataaatcagcaatttcttgttacacttgttttttagG--AGCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAAGgtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from Pairagon GGACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAAG gttttataatggagataaatcagcaatttcttgttacacttgttttttagG---AGCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAAGgtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from Exonerate_protein2genome GGACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAAG gttttataatggagataaatcagcaatttcttgttacacttgttttttagGA---GCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAAGgtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from Exonerate_coding2genome GGACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAAG gttttataatggagataaatcagcaatttcttgttacacttgttttttagGA---GCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAAGgtatgtagtgccatttcattttctagtctctacttctaagcctttaacct Alignment from GeneWise GGACAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGATGCTGGTTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATCAAG gttttataatggagataaatcagcaatttcttgttacacttgttttttagGA---GCCAGTGGCTCTAATAGTCCCACATCAGATGCTGCATCAGCTCAGGAACCAGATGCTGGGTTGAATAACTGTGAGGGTGCTGCTGGTAGTACTTCTGACAAATCAAGgtatgtagtgccatttcattttctagtctctacttctaagcctttaacct ####