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
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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
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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