Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014553.1 Corchorus capsularis cultivar CVL-1 contig14574, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8564
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1589 original size:331 final size:330
Alignment explanation
Indices: 412--3218 Score: 3818
Period size: 331 Copynumber: 8.6 Consensus size: 330
402 GATTGGATTT
*
412 TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAACGATATT-GAAAGCGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTCAT-AAAAATAGAAAAAACGATATTAG-AAGCGTGAAAA
* * * *
476 CCCTTTCAATCTTTTTGACATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGA
64 TCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGA
** * *
541 GAACTTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACAATTTTT
129 -AAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTT
* * * * *
606 GGCTAAAACCGCGTTCCGGGGCCTCGGCTCAGTTTTTCTTGATTTTTTACGCCAAGACTTTTTGA
193 GGCTAAAACAGCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGA
* *
671 AATATCTATATTTATGTAACCAAATTTCAGCCAGATTGGATTGAAGGATTTGTTTTTACGAGCAT
258 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
736 CTGAATCA
323 CTGAATCA
*** * *
744 TATTTCGATTTAAATAGAAATTAATTCAATAAAAATAGGAAAAACGATATT-GAAAGCGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTC-ATAAAAATAGAAAAAACGATATTAG-AAGCGTGAAAA
* * * * *
808 ACCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGTCCAAAAATTAAGGA
64 TCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATG-
* *
873 AAAAATTTTCGGGTCAA----T------TTTT-GCCGAAATCATGTACTATCCATCACTATTTTT
128 AAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTT
* * * * *
927 GGCTAAAACCGCGTTTCTGGGCCCCGACTCAGTTTTTCATGATTATTTACGCCAAGA-TTCCTTG
193 GGCTAAAACAGCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTT-CTTG
* * * * *
991 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGAA
257 AAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCA
*
1056 TCTAAATCA
322 TCTGAATCA
*** * * * * **
1065 TATTTCGATTTAAATGGAAATTAATTCAGTAAAAATAGGAAAGACGATATT-GAAATTGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTCA-TAAAAATAGAAAAAACGATATTAG-AAGCGTGAAAA
* * * *
1129 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGCCCAAAAATTGAGGA
64 TCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATG-
* * *
1194 AAAAATTTTCGGGTCAATATTTGCAAAATTTTAGCCGAAATCATGTACTATCTATCACGATTTTT
128 AAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTT
* *
1259 GGCTAAAACAGCGTTCCGGGGCCCCGGCTCAGTTTTTCATAATTTTTTACGCCAAGACTTCTTGA
193 GGCTAAAACAGCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGA
*
1324 AATGTCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
258 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
1389 CTGAATCA
323 CTGAATCA
* *
1397 TATTTCGATTTTCTTAGAATTTCATTCGTAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATC
1 TATTTCGATTTTCTTAGAATTTAATTCATAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATC
1462 ATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGAAA
66 ATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGAAA
* * *
1527 AACTTTTCGAGTCAACTTTTGCAAAATTTTAACCGAAATCATATACTATCCATCACGATTTTTGG
131 AA-TTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGG
* * *
1592 CTAAAA-ACGCGCTACAGGGCCCCGGCTTAG-TTTTCAATGATTTTTTACGCCAAGACTTCTTGA
195 CTAAAACA-GCGTTACGGGGCCCCGGCTCAGTTTTTC-ATGATTTTTTACGCCAAGACTTCTTGA
* * *
1655 AATATCTATATTTATCTAACCAAATTTCAGTCAGATTCGATTTAAGGATTTGTTCTTACGAGCAT
258 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
1720 CTGAATCA
323 CTGAATCA
1728 TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAAT
1 TATTTCGATTTTCTTAGAATTTAATTCAT-AAAAATAGAAAAAACGATATTAGAAGCGTGAAAAT
* * *
1793 CATTTCAATATTTTTGGCATTGGATTATATATTTTTTACGAGTATTGTGTGCAAAAATTGATG-A
65 CATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGAA
* *
1857 AAA---TCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCAATCACGATTTTTGA
130 AAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGG
* * * * * *
1919 CTAAAACCGCGCTACGGGGCCCCGACTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTGGAAA
195 CTAAAACAGCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGAAA
* * * *
1984 TATCTATATTTATCTAACCAAATTTCAACCAGATTCGATTTAAGGATTTGTTCTTACGAGTATCT
260 TATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATCT
*
2049 TAATCA
325 GAATCA
*
2055 -ATTTTCGAATTTCTTAGAATTTAATTCATAAAAAATAGAAAAAAACGATATTAGAAGCGTGAAA
1 TA-TTTCGATTTTCTTAGAATTTAATTCAT-AAAAATAG-AAAAAACGATATTAGAAGCGTGAAA
*
2119 ATCATTTCCATCTTTTTGGCATTGGAA-TATATATTTTTTTACGAGTATTGTGTCC-AAAATTGA
63 ATCATTTCAATCTTTTTGGCATT-GAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAATTGA
* *
2182 TG-AAAATTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATGATGTACTATCCATCACGATTT
126 TGAAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTT
** * * *
2246 TTGAATAAAA-ACGCGTTACGGGGCCCCAGCTCTGTTTTTCATGATTTTTTACGCCAAGACTCCT
191 TTGGCTAAAACA-GCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCT
* * * * *
2310 TGAAATATCTATATTTATTTAACCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAG
255 TGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAG
*
2375 CATCTGAATTA
320 CATCTGAATCA
*** *
2386 TATTTCGATTTAAATAGAATTTAATTCAATAAAAATAGGAAAAACGATATT-GAAAGCGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTC-ATAAAAATAGAAAAAACGATATTAG-AAGCGTGAAAA
* * * *
2450 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGTGTATTGTGTCCAAAAATTG-CGA
64 TCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGA
* *
2514 AACAAATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTT
129 AA-AATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTT
* * * * * *
2579 GGCTAAAACCGCGTTCCGGGGCCCCGGCTTA-CTTTTCATGATTTTTTGCGCCAAGACTTCTTAA
193 GGCTAAAACAGCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGA
*
2643 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAAGATTTGTTTTTACGAGCAT
258 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
*
2708 CTGAATTA
323 CTGAATCA
*
2716 TATTTCGATTTTCTAAGAATTTAATTCATAAAAACTAGAAAAAACGATATTAGAAGCGTGAAAAT
1 TATTTCGATTTTCTTAGAATTTAATTCATAAAAA-TAGAAAAAACGATATTAGAAGCGTGAAAAT
*
2781 CATTTCAATCTTTTTGGCATTGGATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGAA
65 CATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGAA
2846 AAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTG
130 AAAT-TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTG
* * * *
2911 ACTAAAA-ACGCGCTACGGGGCCCCGGCTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGA
194 GCTAAAACA-GCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGA
* * * *
2975 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTCGATTTAAGGATTTGGTCTTACGAGTAT
258 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
*
3040 CTTAATCA
323 CTGAATCA
*
3048 -ATTTTCGAATTTCTTAGAATTTAATTC------AT-------A--ATATTAGAAGCGTGAAAAT
1 TA-TTTCGATTTTCTTAGAATTTAATTCATAAAAATAGAAAAAACGATATTAGAAGCGTGAAAAT
3097 CATTTCAATCTTTTTGGCATTGGAA-TATATATTTTTTTACGAGTATTGTGTCCAAAAATTGATG
65 CATTTCAATCTTTTTGGCATT-GAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAATTGATG
* * *
3161 AAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATGATGTACTATCGATCA
128 AAAAA-TTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCA
3219 TATTGAAATC
Statistics
Matches: 2239, Mismatches: 187, Indels: 113
0.88 0.07 0.04
Matches are distributed among these distances:
316 46 0.02
317 87 0.04
318 2 0.00
320 3 0.00
321 287 0.13
322 4 0.00
325 2 0.00
326 2 0.00
327 209 0.09
328 72 0.03
329 54 0.02
330 272 0.12
331 673 0.30
332 521 0.23
333 5 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
TATTTCGATTTTCTTAGAATTTAATTCATAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATC
ATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGATGAAA
AATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGC
TAAAACAGCGTTACGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGAAAT
ATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
AATCA
Found at i:2239 original size:658 final size:659
Alignment explanation
Indices: 412--3218 Score: 3893
Period size: 658 Copynumber: 4.3 Consensus size: 659
402 GATTGGATTT
*
412 TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAC
1 TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAG
*
477 CCTTTCAATCTTTTTGACATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAG
66 CCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGA-
* *
542 AACTTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACAATTTTTG
130 AA---ATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTG
* * *
607 GCTAAAACCGCGTTCCGGGGCCTCGGCTCAGTTTTTCTTGATTTTTTACGCCAAGACTTTTTGAA
192 GCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGAA
* *
672 ATATCTATATTTATGTAACCAAATTTCAGCCAGATTGGATTGAAGGATTTGTTTTTACGAGCATC
257 ATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATC
** * *
737 TGAATCATATTTCG-ATTTAAATAGAAATTAATTCA-ATAAAAATAGGAAAAACGATATT-GAAA
322 TGAATCATATTTCGAATTT-CTTAGAATTTAATTCATA-AAAAATAGAAAAAACGATATTAG-AA
* * *
799 GCGTGAAAAACCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGTCCAAA
384 GCGTGAAAATCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAA
* * *
864 AATTAAGGAAAAAATTTTCGGGTCAA----T------TTTT-GCCGAAATCATGTACTATCCATC
449 AATTGATG-AAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATC
* * * * * * * * *
918 ACTATTTTTGGCTAAAACCGCGTTTCTGGGCCCCGACTCAGTTTTTCATGATTATTTACGCCAAG
513 ACGATTTTTGACTAAAAACGCGCTACGGGGCCCCGGCTTAGTTTTTCATGATTTTTTACGCCAAG
* * * *
983 ATTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTT
578 ACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTCGATTTAAGAATTTGTTCT
* *
1048 TACGAGAATCTAAATCA
643 TACGAGCATCTGAATCA
*** * * * **
1065 TATTTCGATTTAAATGGAAATTAATTCAGT-AAAAATAGGAAAGACGATATTGAAATTGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTCA-TAAAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
*
1129 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGCCCAAAAATTGAGGA
65 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGG-
* *
1194 AAAAATTTTCGGGTCAATATTTGCAAAATTTTAGCCGAAATCATGTACTATCTATCACGATTTTT
129 -AAAA--TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTT
* *
1259 GGCTAAAACAGCGTTCCGGGGCCCCGGCTCAGTTTTTCATAATTTTTTACGCCAAGACTTCTTGA
191 GGCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGA
*
1324 AATGTCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
256 AATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * *
1389 CTGAATCATATTTCGATTTTCTTAGAATTTCATTCGT-AAAAATAGAAAAAACGATATTAGAAGC
321 CTGAATCATATTTCGAATTTCTTAGAATTTAATTCATAAAAAATAGAAAAAACGATATTAGAAGC
1453 GTGAAAATCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAA
386 GTGAAAATCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAA
* * *
1518 TTGATGAAAAACTTTTCGAGTCAACTTTTGCAAAATTTTAACCGAAATCATATACTATCCATCAC
451 TTGATGAAAAA-TTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCAC
* *
1583 GATTTTTGGCTAAAAACGCGCTACAGGGCCCCGGCTTAG-TTTTCAATGATTTTTTACGCCAAGA
515 GATTTTTGACTAAAAACGCGCTACGGGGCCCCGGCTTAGTTTTTC-ATGATTTTTTACGCCAAGA
* * * * *
1647 CTTCTTGAAATATCTATATTTATCTAACCAAATTTCAGTCAGATTCGATTTAAGGATTTGTTCTT
579 CTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTCGATTTAAGAATTTGTTCTT
1712 ACGAGCATCTGAATCA
644 ACGAGCATCTGAATCA
*
1728 TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGAAAAAACGATATT-AGAAGCGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAACGATATTGA-AAGCGTGAAAA
* * * * * *
1792 TCATTTCAATATTTTTGGCATTGGATTATATATTTTTTACGAGTATTGTGTGCAAAAATTGATGA
65 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGA
* * *
1857 AAA-TCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCAATCACGATTTTTGACT
130 AAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCT
* * * * * *
1921 AAAACCGCGCTACGGGGCCCCGACTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTGGAAATA
195 AAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGAAATA
* * * * *
1986 TCTATATTTATCTAACCAAATTTCAACCAGATTCGATTTAAGGATTTGTTCTTACGAGTATCTTA
260 TCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
2051 ATCA-ATTTTCGAATTTCTTAGAATTTAATTCATAAAAAATAGAAAAAAACGATATTAGAAGCGT
325 ATCATA-TTTCGAATTTCTTAGAATTTAATTCATAAAAAATAG-AAAAAACGATATTAGAAGCGT
*
2115 GAAAATCATTTCCATCTTTTTGGCATTGGAA-TATATATTTTTTTACGAGTATTGTGTCC-AAAA
388 GAAAATCATTTCAATCTTTTTGGCATT-GAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAA
* *
2178 TTGATG-AAAATTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATGATGTACTATCCATCACG
451 TTGATGAAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACG
* * *
2242 ATTTTTGAATAAAAACGCGTTACGGGGCCCCAGCTCT-GTTTTTCATGATTTTTTACGCCAAGAC
516 ATTTTTGACTAAAAACGCGCTACGGGGCCCCGGCT-TAGTTTTTCATGATTTTTTACGCCAAGAC
* * * *
2306 TCCTTGAAATATCTATATTTATTTAACCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTA
580 TCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTCGATTTAAGAATTTGTTCTTA
*
2371 CGAGCATCTGAATTA
645 CGAGCATCTGAATCA
***
2386 TATTTCGATTTAAATAGAATTTAATTCA-ATAAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
1 TATTTCGATTTTCTTAGAATTTAATTCATA-AAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
* * *
2450 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGTGTATTGTGTCCAAAAATTGCGAA
65 GCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAG-G
2515 ACAAATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTG
129 A-AAA-TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTG
* * * *
2580 GCTAAAACCGCGTTCCGGGGCCCCGGCTTA-CTTTTCATGATTTTTTGCGCCAAGACTTCTTAAA
192 GCTAAAACCGCGTTCCGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGAA
*
2644 ATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAAGATTTGTTTTTACGAGCATC
257 ATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * *
2709 TGAATTATATTTCGATTTTCTAAGAATTTAATTCATAAAAACTAGAAAAAACGATATTAGAAGCG
322 TGAATCATATTTCGAATTTCTTAGAATTTAATTCATAAAAAATAGAAAAAACGATATTAGAAGCG
*
2774 TGAAAATCATTTCAATCTTTTTGGCATTGGATTATATATTTTTTACGAGTATTGTGTCCAAAAAT
387 TGAAAATCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAAT
2839 TGATGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACG
452 TGATGAAAAAT-TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACG
2904 ATTTTTGACTAAAAACGCGCTACGGGGCCCCGGCTTAGTTTTTCATGATTTTTTACGCCAAGACT
516 ATTTTTGACTAAAAACGCGCTACGGGGCCCCGGCTTAGTTTTTCATGATTTTTTACGCCAAGACT
* * * *
2969 CCTTGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTCGATTTAAGGATTTGGTCTTAC
581 CCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTCGATTTAAGAATTTGTTCTTAC
* *
3034 GAGTATCTTAATCA
646 GAGCATCTGAATCA
* *
3048 -ATTTTCGAATTTCTTAGAATTTAATTCAT----AAT----------AT-TAG-AAGCGTGAAAA
1 TA-TTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
* *
3096 TCATTTCAATCTTTTTGGCATTGGAA-TATATATTTTTTTACGAGTATTGTGTCCAAAAATTGAT
65 GCCTTTCAATCTTTTTGGCATT-GAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAATTGA-
* * * * *
3160 GAAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATGATGTACTATCGATCA
127 GGAAAA---TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCA
3219 TATTGAAATC
Statistics
Matches: 1925, Mismatches: 180, Indels: 103
0.87 0.08 0.05
Matches are distributed among these distances:
646 40 0.02
647 35 0.02
648 50 0.03
651 5 0.00
652 101 0.05
653 319 0.17
654 6 0.00
655 1 0.00
656 1 0.00
657 2 0.00
658 485 0.25
659 43 0.02
660 129 0.07
661 162 0.08
662 295 0.15
663 251 0.13
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (659 bp):
TATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAG
CCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAA
AATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTA
AAACCGCGTTCCGGGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTTCTTGAAATAT
CTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
TCATATTTCGAATTTCTTAGAATTTAATTCATAAAAAATAGAAAAAACGATATTAGAAGCGTGAA
AATCATTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAT
GAAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTT
TGACTAAAAACGCGCTACGGGGCCCCGGCTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTTG
AAATATCTATATTTATCTAACCAAATCTCAGCCACATTCGATTTAAGAATTTGTTCTTACGAGCA
TCTGAATCA
Found at i:3294 original size:138 final size:140
Alignment explanation
Indices: 3088--3356 Score: 411
Period size: 138 Copynumber: 1.9 Consensus size: 140
3078 ATATTAGAAG
* *
3088 CGTGAAAATCATTTCAATCTTTTTGGCATTGGAATATATATTTTTTTACGAGTATTGTGTCCAAA
1 CGTGAAAAGCATTTCAATCTTTTTGGAATTGGAATATATATTTTTTTACGAGTATTGTGTCCAAA
3153 AATTGATG-AAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAAT-GATGTACTATCGA
66 AATTGA-GCAAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCG-TGTACTATCGA
3216 TCATATTGAAAT
129 TCATATTGAAAT
* * *
3228 CGTGAAAAGCTTTTCAATCTTTTTGGAATT-TATTATATA-TTTTTTACGAGTATTGTGTCCAAA
1 CGTGAAAAGCATTTCAATCTTTTTGGAATTGGAATATATATTTTTTTACGAGTATTGTGTCCAAA
* * * *
3291 AATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGTGTACTATCTATC
66 AATTGAGCAAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTATCGATC
3356 A
131 A
3357 CAATTGTTGG
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
137 1 0.01
138 82 0.69
139 8 0.07
140 27 0.23
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (140 bp):
CGTGAAAAGCATTTCAATCTTTTTGGAATTGGAATATATATTTTTTTACGAGTATTGTGTCCAAA
AATTGAGCAAAAATTTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTATCGATC
ATATTGAAAT
Found at i:3865 original size:332 final size:331
Alignment explanation
Indices: 3218--5092 Score: 1616
Period size: 332 Copynumber: 5.8 Consensus size: 331
3208 ACTATCGATC
* * * *
3218 ATATTGAAATCGTGAAAAGCTTTTCAATCTTTTTGGAATT-TATTATATATTTTTTACGAGTATT
1 ATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATT
3282 GTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGTGTA
66 GTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGTGTA
* * * *
3347 CTATCTATCACAATTGTTGGCTAAAAACGCGTTCAGGGACCCCCGCTCAGTTTTGCATGATTTTT
131 CTATCTATCACAATTTTTGGCTAAAAACGCGTTCCGGG-GCCCGGCTCAGTTTTGCATGATTTTT
* * *
3412 GACGCCAAGACTCGTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAA
195 GACGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTGGATTTAAGA
* * *
3477 ATTTGTTTTTACTAGCATTTGAATCATATTTCTATTTTATTAGAAATTAATTCAGTAAAAATAGG
260 GTTTGTTTTTACGAGCATTTGAATCATATTTCGATTTTATTAGAAATTAATTCAGTAAAAATAGG
* *
3542 AAACATG
325 AAAAACG
* *
3549 ATATTGAAAGCGTGAATAGCCTTTCAATCTTTTTGGCATTGAATTATATATTATTTACGAGTATT
1 ATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATT
* * * * * *
3614 GTGCCCAAAAATTGAGGACAAATTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTA
66 GTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGTGTA
* * *
3679 CTATCCATCACTATTTTTGGCTAAAAACGTGTTCCGGGGCACCGGCTCAGATTTT-CATGATTTT
131 CTATCTATCACAATTTTTGGCTAAAAACGCGTTCCGGGGC-CCGGCTCAG-TTTTGCATGATTTT
* * *
3743 TTACGCCAAGATTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTGGGTTTAAG
194 TGACGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTGGATTTAAG
* * *
3808 AGTTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAAATAGAAATTAATTCAGTAAAAATAG
259 AGTTTGTTTTTACGAGCATTTGAATCATATTTCGATTTTATTAGAAATTAATTCAGTAAAAATAG
3873 GAAAAACG
324 GAAAAACG
* * *
3881 ATATTGAAAGCGTTAAAAGCCTTTCAATCTTTTTGGCATTGGATTATATATTTTTTACAAGTATT
1 ATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATT
* *
3946 GTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTATATCCGAAATCGTATA
66 GTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGTGTA
* *
4011 CTATCTATCACAATTTTTGACTAAAAACGCGTTCCGGGGCCCTGACTCAGTTTTGCATGATTTTT
131 CTATCTATCACAATTTTTGGCTAAAAACGCGTTCCGGGGCCC-GGCTCAGTTTTGCATGATTTTT
* * * * * ** *
4076 GACGTCAAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGTCAGATTAAATTCAAG-
195 GACGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTGGATTTAAGA
* * * *
4140 GATTTGTTCTTACGAGCATTTGAATCATATTTCGGTTTTCTTAGAATTTAATTCA-TAAAAAATA
260 G-TTTGTTTTTACGAGCATTTGAATCATATTTCGATTTTATTAGAAATTAATTCAGT-AAAAATA
4204 GGAAAAACG
323 GGAAAAACG
* * ** *
4213 ATATT-AGAAGCGTGAAAATCATTTCAATAATTTTGGCATTGAATTATATATTTTATACGAGTA-
1 ATATTGA-AAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTAT
** * *
4276 T-TGT------A-T---C----------CGGGTCAATTTTTTTAAAATTATAACC-AGAATCGTG
65 TGTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGA-AATCGTG
* * * * * ** *
4319 TACTACACAATCATCATGATTTTTGGATAAAAATGCGTTTC-GGGCCACAACTCTGTTTTGCATG
129 TACTA-TCTATCA-CA--ATTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTGCATG
* * * * **
4383 ATTCTTGGCGCCAAGACTCCTT-AAATTATCTATATTCATCTAACCAAATCTCAGCCTCATCAGA
189 ATTTTTGACGCCAAGACTCCTTGAAA-TATCTATATTCATCTAACCAAATCTCAGACACATTGGA
* * * * * * * *
4447 TTTAAGTA-TTTGTTTTCACGAGCATCTGAATCTTGTTTTGATTTAAATAGAAATTAATT-A-AA
253 TTTAAG-AGTTTGTTTTTACGAGCATTTGAATCATATTTCGATTTTATTAGAAATTAATTCAGTA
* *
4509 AAAACAAGAAAAAACG
317 AAAA-TAGGAAAAACG
* * * * * * * * *
4525 ATATTGAAAACATGACAAGCCCTCCAAT-TGTTTTGACGTTAAATTATATATTTTTGT--GGGTA
1 ATATTGAAAGCGTGAAAAGCCTTTCAATCT-TTTTGGCATTGAATTATATATTTTT-TACGAGTA
* * ** * *
4587 TT-TTTGCCAAAAATTGAGGAAAAAAATTTCGAGTCAA----T------TTTTAGCCGAAATCGT
64 TTGTGT-CCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGT
* ** *
4641 GTACT-TACCATCACAATTTTTGGCT-AAAACGCGTTTTGGGGCCCCGACTCAGTTTTGCATGAA
128 GTACTAT-CTATCACAATTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCTCAGTTTTGCATG-A
* * * * *
4704 TTTTTG-CGCCAAGACTCC-TAAAAGTATCTATATTAATCTAACTAATTCTCA-ACCATATTGGA
190 TTTTTGACGCCAAGACTCCTTGAAA-TATCTATATTCATCTAACCAAATCTCAGA-CACATTGGA
* * * * * * * * * * * *
4766 TTGAAG-GATTTGTTTTTACAACCATCTGAATCTTGTTTCGA-TTAATTAGAAGTTAGCTCCGGA
253 TTTAAGAG-TTTGTTTTTACGAGCATTTGAATCATATTTCGATTTTATTAGAAATTA-ATTCAGT
* *
4829 AAAAACTAGAAAAAATG
316 AAAAA-TAGGAAAAACG
* * * * * * *
4846 ATATTCG-AATCGTGACAAA-CCCTCCAATCTTTTTGGCGTTGAATTCTATA-TTTTTATGATTA
1 ATATT-GAAAGCGTGA-AAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTA
* * * * * * * *
4908 TTTTGGCAAAAAATTGAGGGAAAAAAATTTTCGAGTCAAATTTT-----A----AT-CGATATCG
64 TTGTGTCCAAAAATTGA--GCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCG
* * ** * * ** * *
4963 TGTATTAACTATCACGGTCTTTTGGCTAAAAACGCATTCTGGAATCCCGGCTCAGTTTTACGTGA
127 TGTACTATCTATCACAAT-TTTTGGCTAAAAACGCGTTCCGG-GGCCCGGCTCAGTTTTGCATGA
* * * *
5028 TTTTTGGCGCCAAGACTTCTTGAAGTATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
190 TTTTTGACGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTGGATT
5093 GAAAGTCTGA
Statistics
Matches: 1273, Mismatches: 196, Indels: 156
0.78 0.12 0.10
Matches are distributed among these distances:
309 1 0.00
310 35 0.03
311 14 0.01
312 58 0.05
313 116 0.09
314 20 0.02
318 23 0.02
319 108 0.08
320 14 0.01
321 70 0.05
322 10 0.01
323 55 0.04
324 18 0.01
325 73 0.06
326 3 0.00
327 1 0.00
329 1 0.00
330 3 0.00
331 47 0.04
332 592 0.47
333 11 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (331 bp):
ATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATT
GTGTCCAAAAATTGAGCAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTATCCGAAATCGTGTA
CTATCTATCACAATTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTG
ACGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATTGGATTTAAGAG
TTTGTTTTTACGAGCATTTGAATCATATTTCGATTTTATTAGAAATTAATTCAGTAAAAATAGGA
AAAACG
Found at i:6966 original size:52 final size:53
Alignment explanation
Indices: 6908--7316 Score: 449
Period size: 52 Copynumber: 8.1 Consensus size: 53
6898 AGACACGACA
* *
6908 CACACGAAGGTAG-ATGAGAAGACAGAGACCTCCGCAGGAGGCGAGGCCAGCAG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGC-G
* *
6961 -ACACGAAGGTA-CACGAGAAGAC--A-G----C-AAGTGAGGCGAGGCCAGAAG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAG-GAGGCGAGGCCAG-CG
* * *
7006 -ACACGAGGGTA-CACGAGAAGACACGAAG--T--G-A--A-GCGAGGCCAGAAG
1 CACACGAAGGTAGCACGAGAAGACA-GAGGCCTCCGCAGGAGGCGAGGCCAG-CG
*
7051 -ACACGAGGGTA-CACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
**
7102 CACACG-AGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
*
7154 CACACGAAGG-CGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
*
7206 CACACGAAGG-CGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
** *
7258 CACACG-AGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAGGCAAGGCCAGCG
1 CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
7310 CACACGA
1 CACACGA
7317 GAAGACACAC
Statistics
Matches: 323, Mismatches: 11, Indels: 44
0.85 0.03 0.12
Matches are distributed among these distances:
44 5 0.02
45 72 0.22
46 2 0.01
48 2 0.01
49 3 0.01
50 1 0.00
51 7 0.02
52 228 0.71
53 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.37, T:0.03
Consensus pattern (53 bp):
CACACGAAGGTAGCACGAGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCG
Found at i:7009 original size:45 final size:46
Alignment explanation
Indices: 6945--7074 Score: 219
Period size: 45 Copynumber: 2.9 Consensus size: 46
6935 ACCTCCGCAG
* *
6945 GAGGCGAGGCCAGCAGACACGAAGGTACACGAGAAGACAGC-AAGT
1 GAGGCGAGGCCAGAAGACACGAGGGTACACGAGAAGACAGCGAAGT
6990 GAGGCGAGGCCAGAAGACACGAGGGTACACGAGAAGACA-CGAAGT
1 GAGGCGAGGCCAGAAGACACGAGGGTACACGAGAAGACAGCGAAGT
*
7035 GAAGCGAGGCCAGAAGACACGAGGGTACACGAGAAGACAG
1 GAGGCGAGGCCAGAAGACACGAGGGTACACGAGAAGACAG
7075 AGGCCTCCGC
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
44 1 0.01
45 79 0.99
ACGTcount: A:0.38, C:0.21, G:0.37, T:0.04
Consensus pattern (46 bp):
GAGGCGAGGCCAGAAGACACGAGGGTACACGAGAAGACAGCGAAGT
Found at i:7013 original size:20 final size:20
Alignment explanation
Indices: 6990--7058 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
6980 GACAGCAAGT
6990 GAGGCGAGGCCAGAAGACAC
1 GAGGCGAGGCCAGAAGACAC
** *
7010 GAGG-GTACACGAGAAGACAC
1 GAGGCG-AGGCCAGAAGACAC
7030 GAAGTGAAGCGAGGCCAGAAGACAC
1 G-A--G--GCGAGGCCAGAAGACAC
7055 GAGG
1 GAGG
7059 GTACACGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 1 0.03
20 17 0.47
21 1 0.03
22 1 0.03
23 1 0.03
24 1 0.03
25 13 0.36
26 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.39, T:0.03
Consensus pattern (20 bp):
GAGGCGAGGCCAGAAGACAC
Found at i:7049 original size:25 final size:25
Alignment explanation
Indices: 6976--7056 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
6966 AAGGTACACG
*
6976 AGAAGACA-GCAAGTGAGGCGAGGCC
1 AGAAGACACG-AAGTGAAGCGAGGCC
* * *
7001 AGAAGACACG-AGGGTA-C-A--CG
1 AGAAGACACGAAGTGAAGCGAGGCC
7021 AGAAGACACGAAGTGAAGCGAGGCC
1 AGAAGACACGAAGTGAAGCGAGGCC
7046 AGAAGACACGA
1 AGAAGACACGA
7057 GGGTACACGA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 11 0.26
21 4 0.09
22 2 0.05
23 2 0.05
24 3 0.07
25 20 0.47
26 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.36, T:0.04
Consensus pattern (25 bp):
AGAAGACACGAAGTGAAGCGAGGCC
Found at i:7071 original size:20 final size:20
Alignment explanation
Indices: 7001--7077 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
6991 AGGCGAGGCC
7001 AGAAGACACGAGGGTACACG
1 AGAAGACACGAGGGTACACG
* * *
7021 AGAAGACACGAAGTGAAGCGAGGCC
1 AGAAGACACG-AGGGTA-C-A--CG
7046 AGAAGACACGAGGGTACACG
1 AGAAGACACGAGGGTACACG
7066 AGAAGACA-GAGG
1 AGAAGACACGAGG
7078 CCTCCGCAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.09
20 19 0.41
21 4 0.09
22 2 0.04
23 2 0.04
24 4 0.09
25 11 0.24
ACGTcount: A:0.42, C:0.18, G:0.36, T:0.04
Consensus pattern (20 bp):
AGAAGACACGAGGGTACACG
Found at i:7317 original size:52 final size:52
Alignment explanation
Indices: 7038--7317 Score: 490
Period size: 52 Copynumber: 5.4 Consensus size: 52
7028 ACGAAGTGAA
* **
7038 GCGAGGCCAGAAG-ACACGAGGGTACACGAGAAGACAGAGGCCTCCGCAGGAG
1 GCGAGGCCAG-CGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
7090 GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
1 GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
*
7142 GCGAGGCCAGCGCACACGAAGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
1 GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
*
7194 GCGAGGCCAGCGCACACGAAGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
1 GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
7246 GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
1 GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
*
7298 GCAAGGCCAGCGCACACGAG
1 GCGAGGCCAGCGCACACGAG
7318 AAGACACACG
Statistics
Matches: 221, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
51 1 0.00
52 220 1.00
ACGTcount: A:0.29, C:0.30, G:0.39, T:0.02
Consensus pattern (52 bp):
GCGAGGCCAGCGCACACGAGGGCGCACGAGAAGACAGAGGCCTCCGCAGGAG
Found at i:8310 original size:45 final size:45
Alignment explanation
Indices: 8196--8320 Score: 196
Period size: 45 Copynumber: 2.8 Consensus size: 45
8186 GAAAACGTGC
* * *
8196 AGGAGATCAAGGAGAGCTTAGGATCCACGATTGCCAAATGCTTTA
1 AGGAGATCAAAGAGAGCTTAGGCTCCATGATTGCCAAATGCTTTA
*
8241 AGGAGATCAAAGAGAGCTTTGGCTCCATGATTGCCAAATGCTTTA
1 AGGAGATCAAAGAGAGCTTAGGCTCCATGATTGCCAAATGCTTTA
* *
8286 AGGAGATCAAAGAGAGCTTCGGCTCCATGACTGCC
1 AGGAGATCAAAGAGAGCTTAGGCTCCATGATTGCC
8321 GAGTGCACAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (45 bp):
AGGAGATCAAAGAGAGCTTAGGCTCCATGATTGCCAAATGCTTTA
Done.