'UCE_alignments_fasta.tar.gz' contains multiple sequence alignments of ultraconserved elements in FASTA format, one file per UCE. Coordinates of UCEs are given in 'hg38_UCE_coordinates.bed'.

UCE coordinates were obtained from UCbase2.0 (http://ucbase.unimore.it/downloads/; Wed Apr  3 15:08:09 CEST 2019) and lifted to hg38. Alignments between 116 placental mammals were obtained from the 120way alignment. Sequences with insertions or deletions and N's were removed.


REFERENCES 
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Lomonaco, V., Martoglia, R., Mandreoli, F., Anderlucci, L., Emmett, W., Bicciato, S., & Taccioli, C. (2014). UCbase 2.0: ultraconserved sequences database (2014 update). Database, 2014.

Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004). Ultraconserved elements in the human genome. Science, 304(5675), 1321-1325.