Inconsistent Blat Results

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James Kozubek

unread,
Apr 24, 2015, 12:20:38 PM4/24/15
to gen...@soe.ucsc.edu
Hi, 

This is probably a common problem. I am blatting a virus against HG38 and if I use a small section of my sequence I get an interesting hit, but if I blat the entire virus I no longer get the hit. Am I doing something wrong?



If I submit a short sequence from my HCV virus...

GGCGCACAGGTAGAGGAAGAC

I get this hit...

BLAT Search Results

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq           21     1    21    21 100.0%     2   +   24872687  24872707     21


...But if I submit my entire HCV virus I no longer get that hit


 ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq           25  9545  9578  9678  85.2%     1   -   99120181  99120212     32
browser details YourSeq           21  7654  7674  9678 100.0%     4   -   51867001  51867021     21
browser details YourSeq           21   979   999  9678 100.0%    16   -   17970801  17970821     21
browser details YourSeq           21  1800  1826  9678  88.9%    12   +  117124846 117124872     27
browser details YourSeq           20  3261  3298  9678  76.4%     7   -    3875585   3875622     38

ACCCGCCCCTAATAGGGGCGACACTCCGCCATGAATCACTCCCCTGTGAGGAACTACTGTCTTCACGCAGAAAGCGTCTA
GCCATGGCGTTAGTATGAGTGTCGTACAGCCTCCAGGCCCCCCCCTCCCGGGAGAGCCATAGTGGTCTGCGGAACCGGTG
AGTACACCGGAATTGCCGGGAAGACTGGGTCCTTTCTTGGATAAACCCACTCTATGCCCGGCCATTTGGGCGTGCCCCCG
CAAGACTGCTAGCCGAGTAGCGTTGGGTTGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGGGA
GGTCTCGTAGACCGTGCACCATGAGCACAAATCCTAAACCTCAAAGAAAAACCAAAAGAAACACCAACCGTCGCCCACAA
GACGTTAAGTTTCCGGGCGGCGGCCAGATCGTTGGCGGAGTATACTTGTTGCCGCGCAGGGGCCCCAGGTTGGGTGTGCG
CGCGACAAGGAAGACTTCGGAGCGGTCCCAGCCACGTGGAAGGCGCCAGCCCATCCCTAAAGATCGGCGCTCCACTGGCA
AATCCTGGGGAAAACCAGGATACCCCTGGCCCCTATACGGGAATGAGGGACTCGGCTGGGCAGGATGGCTCCTGTCCCCC
CGAGGTTCCCGTCCCTCTTGGGGCCCCAATGACCCCCGGCATAGGTCGCGCAACGTGGGTAAGGTCATCGATACCCTAAC
GTGCGGCTTTGCCGACCTCATGGGGTACATCCCTGTCGTGGGCGCCCCGCTCGGCGGCGTCGCCAGAGCTCTCGCGCATG
GCGTGAGAGTCCTGGAGGACGGGGTTAATTTTGCAACAGGGAACTTACCCGGTTGCTCCTTTTCTATCTTCTTGCTGGCC
CTGCTGTCCTGCATCACCACCCCGGTCTCCGCTGCCGAAGTGAAGAACATCAGTACCGGCTACATGGTGACTAACGACTG
CACCAATGACAGCATTACCTGGCAGCTCCAGGCTGCTGTCCTCCACGTCCCCGGGTGCGTCCCGTGCGAGAAAGTGGGGA
ATGCATCTCAGTGCTGGATACCGGTCTCACCGAATGTGGCCGTGCAGCGGCCCGGCGCCCTCACGCAGGGCTTGCGGACG
CACATCGACATGGTTGTGATGTCCGCCACGCTCTGCTCTGCCCTCTACGTGGGGGACCTCTGCGGTGGGGTGATGCTCGC
AGCCCAAATGTTCATTGTCTCGCCGCAGCACCACTGGTTTGTCCAAGACTGCAATTGCTCCATCTACCCTGGTACCATCA
CTGGACACCGCATGGCATGGGACATGATGATGAACTGGTCGCCCACGGCTACCATGATCTTGGCGTACGCGATGCGTGTC
CCCGAGGTCATTATAGACATCATTAGCGGGGCTCATTGGGGCGTCATGTTCGGCTTGGCCTACTTCTCTATGCAGGGAGC
GTGGGCGAAAGTCGTTGTCATCCTTCTGTTGGCCGCCGGGGTGGACGCGCGCACCCATACTGTTGGGGGTTCTGCCGCGC
AGACCACCGGGCGCCTCACCAGCTTATTTGACATGGGCCCCAGGCAGAAAATCCAGCTCGTTAACACCAATGGCAGCTGG
CACATCAACCGCACCGCCCTGAACTGCAATGACTCCTTGCACACCGGCTTTATCGCGTCTCTGTTCTACACCCACAGCTT
CAACTCGTCAGGATGTCCCGAACGCATGTCCGCCTGCCGCAGTATCGAGGCCTTCCGGGTGGGATGGGGCGCCTTGCAAT
ATGAGGATAATGTCACCAATCCAGAGGATATGAGACCCTATTGCTGGCACTACCCACCAAGGCAGTGTGGCGTGGTCTCC
GCGAAGACTGTGTGTGGCCCAGTGTACTGTTTCACCCCCAGCCCAGTGGTAGTGGGCACGACCGACAGGCTTGGAGCGCC
CACTTACACGTGGGGGGAGAATGAGACAGATGTCTTCCTATTGAACAGCACTCGACCACCGCTGGGGTCATGGTTCGGCT
GCACGTGGATGAACTCTTCTGGCTACACCAAGACTTGCGGCGCACCACCCTGCCGTACTAGAGCTGACTTCAACGCCAGC
ACGGACCTGTTGTGCCCCACGGACTGTTTTAGGAAGCATCCTGATACCACTTACCTCAAATGCGGCTCTGGGCCCTGGCT
CACGCCAAGGTGCCTGATCGACTACCCCTACAGGCTCTGGCATTACCCCTGCACAGTTAACTATACCATCTTCAAAATAA
GGATGTATGTGGGAGGGGTTGAGCACAGGCTCACGGCTGCATGCAATTTCACTCGTGGGGATCGTTGCAACTTGGAGGAC
AGAGACAGAAGTCAACTGTCTCCTTTGTTGCACTCCACCACGGAATGGGCCATTTTACCTTGCTCTTACTCGGACCTGCC
CGCCTTGTCGACTGGTCTTCTCCACCTCCACCAAAACATCGTGGACGTACAATTCATGTATGGCCTATCACCTGCCCTCA
CAAAATACATCGTCCGATGGGAGTGGGTAATACTCTTATTCCTGCTCTTAGCGGACGCCAGGGTTTGCGCCTGCTTATGG
ATGCTCATCTTGTTGGGCCAGGCCGAAGCAGCACTAGAGAAGCTGGTCATCTTGCACGCTGCGAGCGCAGCTAGCTGCAA
TGGCTTCCTATATTTTGTCATCTTTTTCGTGGCTGCTTGGTACATCAAGGGTCGGGTAGTCCCCTTAGCTACCTATTCCC
TCACTGGCCTGTGGTCCTTTAGCCTACTGCTCCTAGCATTGCCCCAACAGGCTTATGCTTATGACGCATCTGTGCATGGC
CAGATAGGAGCGGCTCTGCTGGTAATGATCACTCTCTTTACTCTCACCCCCGGGTATAAGACCCTTCTCAGCCGGTTTTT
GTGGTGGTTGTGCTATCTCCTGACCCTGGGGGAAGCCATGATTCAGGAGTGGGTACCACCCATGCAGGTGCGCGGCGGCC
GCGATGGCATCGCGTGGGCCGTCACTATATTCTGCCCGGGTGTGGTGTTTGACATTACCAAATGGCTTTTGGCGTTGCTT
GGGCCTGCTTACCTCTTAAGGGCCGCTTTGACACATGTGCCGTACTTCGTCAGAGCTCACGCTCTGATAAGGGTATGCGC
TTTGGTGAAGCAGCTCGCGGGGGGTAGGTATGTTCAGGTGGCGCTATTGGCCCTTGGCAGGTGGACTGGCACCTACATCT
ATGACCACCTCACACCTATGTCGGACTGGGCCGCTAGCGGCCTGCGCGACTTAGCGGTCGCCGTGGAACCCATCATCTTC
AGTCCGATGGAGAAGAAGGTCATCGTCTGGGGAGCGGAGACGGCTGCATGTGGGGACATTCTACATGGACTTCCCGTGTC
CGCCCGACTCGGCCAGGAGATCCTCCTCGGCCCAGCTGATGGCTACACCTCCAAGGGGTGGAAGCTCCTTGCTCCCATCA
CTGCTTATGCCCAGCAAACACGAGGCCTCCTGGGCGCCATAGTGGTGAGTATGACGGGGCGTGACAGGACAGAACAGGCC
GGGGAAGTCCAAATCCTGTCCACAGTCTCTCAGTCCTTCCTCGGAACAACCATCTCGGGGGTTTTGTGGACTGTTTACCA
CGGAGCTGGCAACAAGACTCTAGCCGGCTTACGGGGTCCGGTCACGCAGATGTACTCGAGTGCTGAGGGGGACTTGGTAG
GCTGGCCCAGCCCCCCTGGGACCAAGTCTTTGGAGCCGTGCAAGTGTGGAGCCGTCGACCTATATCTGGTCACGCGGAAC
GCTGATGTCATCCCGGCTCGGAGACGCGGGGACAAGCGGGGAGCATTGCTCTCCCCGAGACCCATTTCGACCTTGAAGGG
GTCCTCGGGGGGGCCGGTGCTCTGCCCTAGGGGCCACGTCGTTGGGCTCTTCCGAGCAGCTGTGTGCTCTCGGGGCGTGG
CCAAATCCATCGATTTCATCCCCGTTGAGACACTCGACGTTGTTACAAGGTCTCCCACTTTCAGTGACAACAGCACGCCA
CCGGCTGTGCCCCAGACCTATCAGGTCGGGTACTTGCATGCTCCAACTGGCAGTGGAAAGAGCACCAAGGTCCCTGTCGC
GTATGCCGCCCAGGGGTACAAAGTACTAGTGCTTAACCCCTCGGTAGCTGCCACCCTGGGGTTTGGGGCGTACCTATCCA
AGGCACATGGCATCAATCCCAACATTAGGACTGGAGTCAGGACCGTGATGACCGGGGAGGCCATCACGTACTCCACATAT
GGCAAATTTCTCGCCGATGGGGGCTGCGCTAGCGGCGCCTATGACATCATCATATGCGATGAATGCCACGCTGTGGATGC
TACCTCCATTCTCGGCATCGGAACGGTCCTTGATCAAGCAGAGACAGCCGGGGTCAGACTAACTGTGCTGGCTACGGCCA
CACCCCCCGGGTCAGTGACAACCCCCCATCCCGATATAGAAGAGGTAGGCCTCGGGCGGGAGGGTGAGATCCCCTTCTAT
GGGAGGGCGATTCCCCTATCCTGCATCAAGGGAGGGAGACACCTGATTTTCTGCCACTCAAAGAAAAAGTGTGACGAGCT
CGCGGCGGCCCTTCGGGGCATGGGCTTGAATGCCGTGGCATACTATAGAGGGTTGGACGTCTCCATAATACCAGCTCAGG
GAGATGTGGTGGTCGTCGCCACCGACGCCCTCATGACGGGGTACACTGGAGACTTTGACTCCGTGATCGACTGCAATGTA
GCGGTCACCCAAGCTGTCGACTTCAGCCTGGACCCCACCTTCACTATAACCACACAGACTGTCCCACAAGACGCTGTCTC
ACGCAGTCAGCGCCGCGGGCGCACAGGTAGAGGAAGACAGGGCACTTATAGGTATGTTTCCACTGGTGAACGAGCCTCAG
GAATGTTTGACAGTGTAGTGCTTTGTGAGTGCTACGACGCAGGGGCTGCGTGGTACGATCTCACACCAGCGGAGACCACC
GTCAGGCTTAGAGCGTATTTCAACACGCCCGGCCTACCCGTGTGTCAAGACCATCTTGAATTTTGGGAGGCAGTTTTCAC
CGGCCTCACACACATAGACGCCCACTTCCTCTCCCAAACAAAGCAAGCGGGGGAGAACTTCGCGTACCTAGTAGCCTACC
AAGCTACGGTGTGCGCCAGAGCCAAGGCCCCTCCCCCGTCCTGGGACGCCATGTGGAAGTGCCTGGCCCGACTCAAGCCT
ACGCTTGCGGGCCCCACACCTCTCCTGTACCGTTTGGGCCCTATTACCAATGAGGTCACCCTCACACACCCTGGGACGAA
GTACATCGCCACATGCATGCAAGCTGACCTTGAGGTCATGACCAGCACGTGGGTCCTAGCTGGAGGAGTCCTGGCAGCCG
TCGCCGCATATTGCCTGGCGACTGGATGCGTTTCCATCATCGGCCGCTTGCACGTCAACCAGCGAGTCGTCGTTGCGCCG
GATAAGGAGGTCCTGTATGAGGCTTTTGATGAGATGGAGGAATGCGCCTCTAGGGCGGCTCTCATCGAAGAGGGGCAGCG
GATAGCCGAGATGTTGAAGTCCAAGATCCAAGGCTTGCTGCAGCAGGCCTCTAAGCAGGCCCAGGACATACAACCCGCTA
TGCAGGCTTCATGGCCCAAAGTGGAACAATTTTGGGCCAGACACATGTGGAACTTCATTAGCGGCATCCAATACCTCGCA
GGATTGTCAACACTGCCAGGGAACCCCGCGGTGGCTTCCATGATGGCATTCAGTGCCGCCCTCACCAGTCCGTTGTCGAC
CAGTACCACCATCCTTCTCAACATCATGGGAGGCTGGTTAGCGTCCCAGATCGCACCACCCGCGGGGGCCACCGGCTTTG
TCGTCAGTGGCCTGGTGGGGGCTGCCGTGGGCAGCATAGGCCTGGGTAAGGTGCTGGTGGACATCCTGGCAGGATATGGT
GCGGGCATTTCGGGGGCCCTCGTCGCATTCAAGATCATGTCTGGCGAGAAGCCCTCTATGGAAGATGTCATCAATCTACT
GCCTGGGATCCTGTCTCCGGGAGCCCTGGTGGTGGGGGTCATCTGCGCGGCCATTCTGCGCCGCCACGTGGGACCGGGGG
AGGGCGCGGTCCAATGGATGAACAGGCTTATTGCCTTTGCTTCCAGAGGAAACCACGTCGCCCCTACTCACTACGTGACG
GAGTCGGATGCGTCGCAGCGTGTGACCCAACTACTTGGCTCTCTTACTATAACCAGCCTACTCAGAAGACTCCACAATTG
GATAACTGAGGACTGCCCCATCCCATGCTCCGGATCCTGGCTCCGCGACGTGTGGGACTGGGTTTGCACCATCTTGACAG
ACTTCAAAAATTGGCTGACCTCTAAATTGTTCCCCAAGCTGCCCGGCCTCCCCTTCATCTCTTGTCAAAAGGGGTACAAG
GGTGTGTGGGCCGGCACTGGCATCATGACCACGCGCTGCCCTTGCGGCGCCAACATCTCTGGCAATGTCCGCCTGGGCTC
TATGAGGATCACAGGGCCTAAAACCTGCATGAACACCTGGCAGGGGACCTTTCCTATCAATTGCTACACGGAGGGCCAGT
GCGCGCCGAAACCCCCCACGAACTACAAGACCGCCATCTGGAGGGTGGCGGCCTCGGAGTACGCGGAGGTGACGCAGCAT
GGGTCGTACTCCTATGTAACAGGACTGACCACTGACAATCTGAAAATTCCTTGCCAACTACCTTCTCCAGAGTTTTTCTC
CTGGGTGGACGGTGTGCAGATCCATAGGTTTGCACCCACACCAAAGCCGTTTTTCCGGGATGAGGTCTCGTTCTGCGTTG
GGCTTAATTCCTATGCTGTCGGGTCCCAGCTTCCCTGTGAACCTGAGCCCGACGCAGACGTATTGAGGTCCATGCTAACA
GATCCGCCCCACATCACGGCGGAGACTGCGGCGCGGCGCTTGGCACGGGGATCACCTCCATCTGAGGCGAGCTCCTCAGT
GAGCCAGCTATCAGCACCGTCGCTGCGGGCCACCTGCACCACCCACAGCAACACCTATGACGTGGACATGGTCGATGCCA
ACCTGCTCATGGAGGGCGGTGTGGCTCAGACAGAGCCTGAGTCCAGGGTGCCCGTTCTGGACTTTCTCGAGCCAATGGCC
GAGGAAGAGAGCGACCTTGAGCCCTCAATACCATCGGAGTGCATGCTCCCCAGGAGCGGGTTTCCACGGGCCTTACCGGC
TTGGGCACGGCCTGACTACAACCCGCCGCTCGTGGAATCGTGGAGGAGGCCAGATTACCAACCGCCCACCGTTGCTGGTT
GTGCTCTCCCCCCCCCCAAGAAGGCCCCGACGCCTCCCCCAAGGAGACGCCGGACAGTGGGTCTGAGCGAGAGCACCATA
TCAGAAGCCCTCCAGCAACTGGCCATCAAGACCTTTGGCCAGCCCCCCTCGAGCGGTGATGCAGGCTCGTCCACGGGGGC
GGGCGCCGCCGAATCCGGCGGTCCGACGTCCCCTGGTGAGCCGGCCCCCTCAGAGACAGGTTCCGCCTCCTCTATGCCCC
CCCTCGAGGGGGAGCCTGGAGATCCGGACCTGGAGTCTGATCAGGTAGAGCTTCAACCTCCCCCCCAGGGGGGGGGGGTA
GCTCCCGGTTCGGGCTCGGGGTCTTGGTCTACTTGCTCCGAGGAGGACGATACCACCGTGTGCTGCTCCATGTCATACTC
CTGGACCGGGGCTCTAATAACTCCCTGTAGCCCCGAAGAGGAAAAGTTGCCAATCAACCCTTTGAGTAACTCGCTGTTGC
GATACCATAACAAGGTGTACTGTACAACATCAAAGAGCGCCTCACAGAGGGCTAAAAAGGTAACTTTTGACAGGACGCAA
GTGCTCGACGCCCATTATGACTCAGTCTTAAAGGACATCAAGCTAGCGGCTTCCAAGGTCAGCGCAAGGCTCCTCACCTT
GGAGGAGGCGTGCCAGTTGACTCCACCCCATTCTGCAAGATCCAAGTATGGATTCGGGGCCAAGGAGGTCCGCAGCTTGT
CCGGGAGGGCCGTTAACCACATCAAGTCCGTGTGGAAGGACCTCCTGGAAGACCCACAAACACCAATTCCCACAACCATC
ATGGCCAAAAATGAGGTGTTCTGCGTGGACCCCGCCAAGGGGGGTAAGAAACCAGCTCGCCTCATCGTTTACCCTGACCT
CGGCGTCCGGGTCTGCGAGAAAATGGCCCTCTATGACATTACACAAAAGCTTCCTCAGGCGGTAATGGGAGCTTCCTATG
GCTTCCAGTACTCCCCTGCCCAACGGGTGGAGTATCTCTTGAAAGCATGGGCGGAAAAGAAGGACCCCATGGGTTTTTCG
TATGATACCCGATGCTTCGACTCAACCGTCACTGAGAGAGACATCAGGACCGAGGAGTCCATATACCAGGCCTGCTCCCT
GCCCGAGGAGGCCCGCACTGCCATACACTCGCTGACTGAGAGACTTTACGTAGGAGGGCCCATGTTCAACAGCAAGGGTC
AAACCTGCGGTTACAGACGTTGCCGCGCCAGCGGGGTGCTAACCACTAGCATGGGTAACACCATCACATGCTATGTGAAA
GCCCTAGCGGCCTGCAAGGCTGCGGGGATAGTTGCGCCCACAATGCTGGTATGCGGCGATGACCTAGTAGTCATCTCAGA
AAGCCAGGGGACTGAGGAGGACGAGCGGAACCTGAGAGCCTTCACGGAGGCCATGACCAGGTACTCTGCCCCTCCTGGTG
ATCCCCCCAGACCGGAATATGACCTGGAGCTAATAACATCCTGTTCCTCAAATGTGTCTGTGGCGTTGGGCCCGCGGGGC
CGCCGCAGATACTACCTGACCAGAGACCCAACCACTCCACTCGCCCGGGCTGCCTGGGAAACAGTTAGACACTCCCCTAT
CAATTCATGGCTGGGAAACATCATCCAGTATGCTCCAACCATATGGGTTCGCATGGTCCTAATGACACACTTCTTCTCCA
TTCTCATGGTCCAAGACACCCTGGACCAGAACCTCAACTTTGAGATGTATGGATCAGTATACTCCGTGAATCCTTTGGAC
CTTCCAGCCATAATTGAGAGGTTACACGGGCTTGACGCCTTTTCTATGCACACATACTCTCACCACGAACTGACGCGGGT
GGCTTCAGCCCTCAGAAAACTTGGGGCGCCACCCCTCAGGGTGTGGAAGAGTCGGGCTCGCGCAGTCAGGGCGTCCCTCA
TCTCCCGTGGAGGGAAAGCGGCCGTTTGCGGCCGATATCTCTTCAATTGGGCGGTGAAGACCAAGCTCAAACTCACTCCA
TTGCCGGAGGCGCGCCTACTGGACTTATCCAGTTGGTTCACCGTCGGCGCCGGCGGGGGCGACATTTTTCACAGCGTGTC
GCGCGCCCGACCCCGCTCATTACTCTTCGGCCTACTCCTACTTTTCGTAGGGGTAGGCCTCTTCCTACTCCCCGCTCGGT
AGAGCGGCACACACTAGGTACACTCCATAGCTAACTGTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTCTTTTTTTTTTTTTTCCCTCTTTCTTCCCTTCTCATCTTATTCTACTTTCTTTCTTGGTGGCTCCATCTTAGCCCT
AGTCACGGCTAGCTGTGAAAGGTCCGTGAGCCGCATGACTGCAGAGAGTGCCGTAACTGGTCTCTCTGCAGATCATGT

James Kozubek

unread,
Apr 24, 2015, 12:22:19 PM4/24/15
to gen...@soe.ucsc.edu
OK- I see. "it may miss sequences less than 25 bases"
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