Hi We have identified a sequence on human chr22 that web-based BLAT struggles to identify when presented as a query. When you BLAT a large sequence around this region (3000 bp), BLAT identifies the correct region on chr22. However, when you BLAT the first 50 bp of the same sequence, chr22 does not even come up in the BLAT results even though it has 100% identity to the queried sequence. The problem remains when you BLAT the first 60bp but is corrected when you BLAT the first 70bp.
Can you please explain why BLAT behaves this way? The query sequence is below. GAGGTTGCAGTGAGCTGAGATTGTGCCACTGCACTCTAGCCTGGGGAACAGAGCGAGATTTGGTCTCCAAAAACAAAACACAACAACAACAAAAAAATGGAGACAAGGGCAGCAAAAGGGAGGTCACCCACAAAGCGTGCATGTGTCTCGTGATTTTTTTTTCTTTTTTTTTCTTTGTGAGACAGAGTCTTGCTCTGTTGCCCAGGCTGGAGTACAGTGGCGCAATCTGGGTTCACTGCAAGCTCTGCCTCCCGGGTTCATGCCATTCTTCGTTACATCTAGAGAATGTCTAACGCCTCTTCTGGATAGATATTCAGGCGCCCGCCACCACCACGCTTGGCTAATTTTTTGTATTTTTTAGTAGACACAGGGTTTCACCATCTTAGCCATGATGTTCTCAATCTCCTGACCTCGTAATCTGCCCACCTCCGCCTTCCAAAGTGCTGGGATTACAGGCATGAGCCACCGTGCCTGGACCTTGTATTCTAATTGAGACAGGGTCTCACTTTGTCACCCAGACTGGAGTGCAGTGGCATGATCATGGCTGTCTGCAGCCTCGACCTCCTGGGGCTAAGCACTCCTCCCAACTAAGGCTGCTGAGTAGCTGGGACCACAGGCGTGTGCCACCACGACCAGCTAATTTTTTTTTTTTTTTTTTTTTTTTTTTAAATACAGGGTCTCGCTATCTCGCTCAGGCTGGTCTCTAACTCCTGGGCTCAAGCTATCTTCCCACCTCAGCTTCCCAATGTGCTGGGATTACAGGTGTGAGCCACTGCGCCTGGCCTGTGTCCCGTGTTTCGATTGCATGTTTACAGCGGCAGGGTGTGTGTGTGTGGGTGTGTGTGCGCGTGCGTGTGGTGGGGCAGTGGGGGGCTTCTCCTCCTTCAGACAACAAATATGTGTGGAGCTCTGACCTACCAGGCCCACTGCCAGATGCAGGAGGCACAAAGATGACCAAATCAGCCATAGTGGGGGTTGCGGAGTTCACA! TGCCTCGGGAAACAGAGGAATCAATAGGCTCTTATTGGACAGTGTGGTTACCTGCAGGGCAGGGACAGCTTGCCTGGGGGTGTCAGGGCAGGGTTCCCAGCTGAGGCCCCAAGGAGTGGGGAAGCCAGTGAGCAAGCACAGGGGAGAATTCCAGGTAAGGGAGCCCAGGCTGGAGTCCCAGAGGGGAGAGAAGGCGTGGAAGCAGCATGTGCTTGGGAGAGAGGCGGGTGCGTGAGAGGTGTGGGGAGGGTATTGGAAGTAAGGGGCATGGCTGGAGCAGGGGCAGAGGGAAAGAGAGAACGTCCCTGAAGACCCTGGGAAGCCTGGTGCTCAGCGTGACCCCAGGGAGAAACAGGCTTGTTGGGTGAGAGGGAGAAAGAAGCTTCTCCACGTCTCACGGGATGTCCTCCCCTGGACCCCACCAGCTCCCCGTCCACACCGGGCACCCACCTCTGCAGCAGCTGCTTCAGGCTGAACACGTGCGAGGGCTCCTGGGAGGCCTCTACCTGCAGCACGTGCTCTATGGCTCTCCGCTTGTAGGTCAGCAAGTTCTCCATTTCCTAAGGAGGCACAGTTGGCTGGTGGGCAGGGATCCAGGCTGCAGACGAGGTCTCTGCCCCTCCTAGCCCTGCCCTCTGCTCTCAGCTGAGCCCCTCTCGGCAAAGGGGCACACAGCCCCAGCCCTGGCTAGTCAGCCCCACGATTCTGAACGAGTCTTTGCTTCGCCTCAGTCACAGCCAGCCTGGTCTTGCCTGCGGCCAGGGACAGTTGAAGAGATCAGGTGGGATGATGGAGAGGAAGGGGAATCTCTGTCAACTGCCAAGTGCTTTGCAAAGGCATGAAATTAGGGTCCGGAGGCCACGAACCATCTGGGGTTGGCAGTTTCATCTGGTTCAACGAATGCCATCATTCTCAGTGGCAGAAAGGGACTGGCAGAAAGGGCGCATTTCTGGGGCTTCCAAGCTCCCCCATGATGTGTGGCTCACTC! TGTGAGGACAGCCTCAGGCCCACTGCCTGGGGCTGCAGAGGGGGGCATCTCCCATCTACCCATGCCTGAG AATGCAGGACAAGAGGACCAAATGCCCCTCTTGACTCGCCCAGGAGGAAGCCCCTGGGGGCACTGCACTTGTCAATTCAGTGGGTGAAATGCAGAAAGAAGGGAGTGTCTGCTGTCTGCCATCTGTAAATTGGATCCTTATAATAGCCCCTGAGCTAGCTGAGCTCATGCAAGGAACATTTACTGAGCCCTTACTAGGTGCCAGGATTGGGGATGTGGTGACAGAGATGGACATGATCCTTATCCTTATGGGATCTGCCGTCATTCTTTTTTTTTTTTTTTTTTTTTTTTTTGGGAGACGGAGTTTCCCTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCAATCTCGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCGGCCTCCCAAGTAGCTGGGATGACAGGCATGTGCCACCACGCCCAGCTAATTTTGTACTTTCAGTAGAGACGGGATTTCTCCATGTTGGTCAGGCTGGTCTCGAAATCCTGACCTCAGGTGATCCGCCAGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCATCTGGCCGATCTGTGGTCATTCTATGGACAAGAAAACTGAAACTGATGAGACTTGTGTCACAACTGATAGGCTGAGACCTTGGCAAGAAAATGACAGGATGTCAGAGCTGGCCAGGTCATTGAGCCCAACCTCATTTTACACGTGCGGGAACTAAGGCCCAGAGAGGCAAAGTAACTTGCCAGGGGTCACCCAGCAGGTAAACCAGGCCAGGACTCAGACGCAGAGACAGTACTGGTTATGGGTAGTGGTGGTCAGAGGGGTCAGTCCTTGTTCCTTCAGTTCACATTTAGGGCTGTCATGTGTGGTGGTGCAATGTGGACACAGTGCAAAGGCATTCGACTGGGTGTGAGTGCAGTGTGCCGGCCCAGCTGTGTGCCCTAGAA thanks! Shaun Shaun Cordes, PhD | Customer Support Scientist | Complete Genomics, Inc. Toll-free: (855) 267-5358 | Direct: (650) 943-2651 [email protected] Complete Genomics User Community community.completegenomics.com --- ________________________________ The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
