I have observed what appears to be an odd behaviour of BLAT, not reporting a large section of a good alignment. The two sequences below are identical for their first 939 bp. The longer one is the whole of an NCBI gene model in Xenopus. When I BLAT these against the Xenopus genome, the shorter one report bases 12-939 aligning in six exons, which I believe to be correct. The longer sequence however only reports an alignment in this region from base 770 to the end, over two exons. There is in addition a strong repeat sequence reported from about base 1800-1900 to the end. The failure to report the earlier exons from the longer sequence, would clearly have led me to draw an erroneous conclusion. Can you throw any light on this? Thanks for your help. mike
>XM_002942799.1-FIRST-939 ATGGCCCTTATGTTTATATTAGAGTATATATATATCATCTCTACTGTGGTTTTATTTTTAGATGCCATCTCCGTGTTACCGGCACCCAGAAATGTACGCATTGACTCATACAACCTGCAGCACAAATTGCTTTGGGATCCCATCGAATCGGAAAATGTAACTTACACAGTGCACTTACTCTATTCCAGGAACTATATAGGTGAGGATGAATATAATGACATTTGTGAGAACCTTACTGAGACCGTTTGTAATTTTACGGACGAGATCAACTTTGAGTTGAAGGTTATTTTGAGAGTACGAGCAGAACTGGGACCACTGCATTCCAGCTGGAGTGAAACATCTGAATTCCAAGCAATGAATCACACCAAAATAAGTCCTGTGAAATCTCTAACCGTGTCCTCCAGGGAGGCAGAACACAACAGTCTCTATGTCAGTTTTGAGTCTCCTCTACAACCAGAGATCATCCCACAAAAGGGCAAAATGAAGTATTTGTTACAATACTGGAAAAAAGGTTCTGCTGCAAAGACTAATCTATCGACAAACGGGACATTTCGTAAAATGACCGACCTGGAGGCCTCAGCTGAGTACTGTGTGTCGGTCACTGCTCTCCTGATGGGCCCTCATTACAGTCTGACTGGGGAGACAAGCCACATAGTGTGTGCCCAAACGCCAGCAACTCCAGGTTTAACTGCAGACAAAGTTATTTTTCTTTCGGTGGGACTCCTTCTTGGCTGTTGTATATTCCTGGGATTCAGCTATACTTTCTTCAGGCAGCGCAGACTGATCAAAATGTGGCTGTACCCCCCATACAGTATACCCCCCGACATAGAGCAGTACTTGCAAGATCCCCCCTTGAATGGATACCCGAACGAAAGCAAAGATATGGATTTGGCAGAAGTGCAGTACGATCACATTTCCATTGTGGAAAGTGAATCATGA >XM_002942799.1-ALL ATGGCCCTTATGTTTATATTAGAGTATATATATATCATCTCTACTGTGGTTTTATTTTTAGATGCCATCTCCGTGTTACCGGCACCCAGAAATGTACGCATTGACTCATACAACCTGCAGCACAAATTGCTTTGGGATCCCATCGAATCGGAAAATGTAACTTACACAGTGCACTTACTCTATTCCAGGAACTATATAGGTGAGGATGAATATAATGACATTTGTGAGAACCTTACTGAGACCGTTTGTAATTTTACGGACGAGATCAACTTTGAGTTGAAGGTTATTTTGAGAGTACGAGCAGAACTGGGACCACTGCATTCCAGCTGGAGTGAAACATCTGAATTCCAAGCAATGAATCACACCAAAATAAGTCCTGTGAAATCTCTAACCGTGTCCTCCAGGGAGGCAGAACACAACAGTCTCTATGTCAGTTTTGAGTCTCCTCTACAACCAGAGATCATCCCACAAAAGGGCAAAATGAAGTATTTGTTACAATACTGGAAAAAAGGTTCTGCTGCAAAGACTAATCTATCGACAAACGGGACATTTCGTAAAATGACCGACCTGGAGGCCTCAGCTGAGTACTGTGTGTCGGTCACTGCTCTCCTGATGGGCCCTCATTACAGTCTGACTGGGGAGACAAGCCACATAGTGTGTGCCCAAACGCCAGCAACTCCAGGTTTAACTGCAGACAAAGTTATTTTTCTTTCGGTGGGACTCCTTCTTGGCTGTTGTATATTCCTGGGATTCAGCTATACTTTCTTCAGGCAGCGCAGACTGATCAAAATGTGGCTGTACCCCCCATACAGTATACCCCCCGACATAGAGCAGTACTTGCAAGATCCCCCCTTGAATGGATACCCGAACGAAAGCAAAGATATGGATTTGGCAGAAGTGCAGTACGATCACATTTCCATTGTGGAAAGTGAATCATGACAGAAAAGCCATTATTGTAATGAAGGAACCCTTAAGAAGAGAATAGGTGA! GAAAGG C TGGAAAGGAGGAGGGGGCCCTCGGCAGCAATGTAGTAACACATACAGGGAGCCATGGGCATCGCTGGAAACCTATTTCAGGAATAATACTGTAAGCCAAGGTATCCAGCACTTTTATAACTCCCTGCGCTTACTTGCTGGAAATTGTATTTTAACAATAACTGAGGAACACAGCCTTGATATAAACTCACAGGCAAGAAACTCCCTTCCCAGGGCACAATGGTACCTTGGCAACGGAGCAGGCTACCTTAGTTACCTTTTGTGATGGAACGGAGTATCAGAGCTTGACAGAGAGGGCCCCGGCTGGCCTCAGACATTGCTACTTGCAACAAAATGGTATTTGCACTTATTTAGTGCCCATTAGAGGCATTTTTGTCAGTAGCCAATGAAACTGCTTGTTTTTGGACTAAGGGGAGAAACCAATGGAAACACAGAACATACAGACTCCTTGCAGATAGTGCCCAGGAAAGAACTGGAAATGCACACAAGCACACAGCCAGCCTGAGTGCACACTTACAGGCGGATAACATTGAAGTCAATGGCTGCACCGACGGTTCATAGCGGTATAGACACTCTCTCTGCCGGCAGAGAAGGCGCACAATGTGACATTGGCTGCTATGGGGGACGCCATGTGACTCCCGAATTTCACTCATTGCACTTGTGTGAAGGGGAGGAACACACAGTTCCATGAACGGATTCCCTTTTATTGCACTGCACTTTAACAGCAACATTAACAGAAGCTTGTTGTATTTTATTGCAATGCATTGTGAATGTTACTGTGCAACCACTTTCTAATAGACTTCTAACTTTTTTTCAAATGTTTTATGATTTTTATGACGTAAAAATGAATGAATCAAATCTCTGTGTACTTTAGTCTCTGTTCCAAATGTTCTCTGTTCATTTATGATCCCATGGGGAGTGGCCAGGTATCTATCAGACTTTCTAGGACTGGTCACCTTAAAGGAACAGTAACATCAAAAAATTAAAGTG! TTTTAA A GTAATTAATCTATAATGTGCTGTTGCTCTGCAAAAAACTGGTGTTTTTGCTTCAGAAAAGCTACTATATAAATATGTTGCTGTGTAGCCCCGGGGGCAGCCATTCAAGCTGGAAAAAAGGAGAAAAGGCACAGGTTACATAGCAGATAACTAGTAGATAAGCCCCATATAATGGGGGTTTATCTGTTATCTGATAAGTAACCTGTGCCTTTTCTCCTTTGAATGGCTGCCCCCATGGCTACACAGCAGCTTATTTATATAAACTATAGTAGCCTTTCTGAGGCAAACACACCAGTTGTAGCAATGCAGGGCAACAGTACATTATATTATAATTA Mike Gilchrist MRC National Institute for Medical Research The Ridgeway Mill Hill London NW7 1AA UK Tel: 0208 816 2451 Fax: 0208 906 4477 [email protected] http://www.nimr.mrc.ac.uk/research/mike-gilchrist/ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
