Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012459.1 Corchorus capsularis cultivar CVL-1 contig12480, 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: 95791
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:613 original size:334 final size:333
Alignment explanation
Indices: 1--1093 Score: 1595
Period size: 333 Copynumber: 3.3 Consensus size: 333
* * * * *
1 ATTAATCGAAACAAGATTTAAATGCTCGTAAAAACAACTCCTTAAATGCCCTATGGGTAAAATTT
1 ATTAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTAAATGCACTATGGCTAAAATTT
* * *
66 TACTAGATCAATATAAATATTTCAAGGAGTCTCGGTGTCAAAAATCATGCAAAACTGAGTCGGGA
66 TACTAGATCAATATAGATATTTCAAGGAGTCTCTGTGTCAAAAATCATGCAAAA-TGAGTCGGGG
* * * *
131 CCCCAAAACGCCTTTTTAGCG-AAAATTGTGATGGTTTGTACACGGTTTTGGCTAAAATTTTGCA
130 CCCCGAAACGCGTTTTTAGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGC-
** ** *
195 AAAAAAC-GACCGGAAAAAAATCTTCCTCAATTTTTAGATAAAATACCCAAAAAATATGTACAAT
194 AAAAAACTGACCGGATTAATTTCTTCCTCAATTTTTAGATAAAATACCCAAAAAATATATACAAT
259 TTAACGCCAAGAAGATTGAAGGCCTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAA
259 TTAACGCCAAGAAGATTGAAGGCCTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAA
*
324 TAAATTT-ATA
324 TTAATTTCA-A
* * * ** * *
334 ATTAATCGACACAATATTCATATTCTTATAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTT
1 ATTAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTAAATGCACTATGGCTAAAATTT
* * *
399 TAGTAGAT-AGATATAGATATTTCAAGGAGTCTTTGTGTTAAAAATCATGCAAAATAGAGTCGGG
66 TACTAGATCA-ATATAGATATTTCAAGGAGTCTCTGTGTCAAAAATCATGCAAAAT-GAGTCGGG
*
463 GCCCCGAAACGCGTTTTTAGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAAGTTTGC
129 GCCCCGAAACGCGTTTTTAGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGC
*
528 AAAAAACTGACCGGATTAATTTCTTCCTCAATTTTTAGATAAAATACCCAAAAAATGTATACAAT
194 AAAAAACTGACCGGATTAATTTCTTCCTCAATTTTTAGATAAAATACCCAAAAAATATATACAAT
* * * *
593 TTAACGCCAAGAATATTGAAGGCCTTTTCACGCTTTTAATGTCGTTTTTCATAA-TTTTTCTTAA
259 TTAACGCCAAGAAGATTGAAGGCCTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAA
657 TTAATTTCAA
324 TTAATTTCAA
* * *
667 ATTAATCGAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATGCACTATGGGTAAAATTT
1 ATTAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTAAATGCACTATGGCTAAAATTT
* *
732 TACTAAATCAATATAGATATTTCAAGGAGTCTCTGT-TCCAAAAATCATGCAAAATTGAGTCGAG
66 TACTAGATCAATATAGATATTTCAAGGAGTCTCTGTGT-CAAAAATCATGCAAAA-TGAGTCGGG
* *
796 GCCCCGAAACGTGTTTTTAGCGAAAAATTGTGATGGTTAGTACACGGCTTTGACTAAAATTTTGC
129 GCCCCGAAACGCGTTTTTAGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGC
861 AAAAAACTGACCGGATTAATTTCTTCCTCAATTTTTAGATAAAATACCCAAAAAAATATATACAA
194 AAAAAACTGACCGGATTAATTTCTTCCTCAATTTTTAGATAAAATACCC-AAAAAATATATACAA
* * * * *
926 TTTAACACCATGAAGATTGAAGGCCTTTTCACGATTTTGATATCGGTTTTCATAATTTTTTATGA
258 TTTAACGCCAAGAAGATTGAAGGCCTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGA
991 ATTAATTTCAA
323 ATTAATTTCAA
* * * * *
1002 ATTAATGGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGCCTAAAATTT
1 ATTAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTAAATGCACTATGGCTAAAATTT
* *
1067 TATTAGATAAATATAGATATTTCAAGG
66 TACTAGATCAATATAGATATTTCAAGG
1094 TGTAATACCG
Statistics
Matches: 677, Mismatches: 73, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
332 3 0.00
333 369 0.55
334 206 0.30
335 99 0.15
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (333 bp):
ATTAATCGAAACAAGATTCAAATTCTCGTAAAAACAAATCCTTAAATGCACTATGGCTAAAATTT
TACTAGATCAATATAGATATTTCAAGGAGTCTCTGTGTCAAAAATCATGCAAAATGAGTCGGGGC
CCCGAAACGCGTTTTTAGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAA
AAAACTGACCGGATTAATTTCTTCCTCAATTTTTAGATAAAATACCCAAAAAATATATACAATTT
AACGCCAAGAAGATTGAAGGCCTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAATT
AATTTCAA
Found at i:4366 original size:335 final size:333
Alignment explanation
Indices: 3755--4555 Score: 1311
Period size: 335 Copynumber: 2.4 Consensus size: 333
3745 GGGCGTGACA
* * *
3755 CAAGGAGTCTCTCTGCCAAAAATCATGTAAAACTGAGTCGGGGCCTTGAAACGCGTTTTTAGCGA
1 CAAGGAGTCTCTGTGCCAAAAATCATGCAAAACTGAGTCGGGGCC-CGAAACGCGTTTTTAGCGA
3820 AAAATTGTGATGGTTAGTACACGGTTTTG-CTAAAATTTTGCAAAAAACTGACCGGATTAATTTC
65 AAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTGACCGGATTAATTTC
*
3884 TTCCTCAATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTTAAGGC
130 TTCCTCAATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGC
* *
3949 CTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAATTAATTTTTAATTAATCGAAACA
195 CTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTTAAATTAATCGAAACA
* * * *
4014 AGATTCAGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTATTAGAT-AGAT
260 AGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACTAGATCA-AT
*
4078 ATAGATATTT
324 ATAAATATTT
*
4088 CAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGTCCCGAAACGCGTTTTTAGCGA
1 CAAGGAGTCTCTGTGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCGAAACGCGTTTTTAGCGA
4153 AAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTGACCGGATTAATTTC
65 AAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTGACCGGATTAATTTC
4218 TTCCTCAATTTTTAGATAAAATACCCAAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGG
130 TTCCTCAATTTTTAGATAAAATACCC-AAAAAATATATACAATTTAACGCCAAGAAGATTGAAGG
* *
4283 TCTTTTCACGCTTTTAATATCGTTTTTCATAA-TTTTTCTTAATTAATTTTGAAATTAATCGAAA
194 CCTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTT-AAATTAATCGAAA
* * *
4347 CAAGATTTAAATGCTCGTAAAAACAAATCGTTAAATGCACTGTGGGTAAAATTTTACTAGATCAA
258 CAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACTAGATCAA
4412 TATAAATATTT
323 TATAAATATTT
* * * * *
4423 CAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGTGGCCCCAAAACGCGTTCTTAGCGA
1 CAAGGAGTCTCTGTGCCAAAAATCATGCAAAACTGAGTCG-GGGCCCGAAACGCGTTTTTAGCGA
* *
4488 AAAATTGTGATGGTTAGTACACAGTTTTGACTAAAATTTTGCTAAAAACTGACCGGATTAATTTC
65 AAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTGACCGGATTAATTTC
4553 TTC
130 TTC
4556 GAGGGTCTGA
Statistics
Matches: 437, Mismatches: 25, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
333 87 0.20
334 80 0.18
335 267 0.61
336 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (333 bp):
CAAGGAGTCTCTGTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCGAAACGCGTTTTTAGCGAA
AAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTGACCGGATTAATTTCT
TCCTCAATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCC
TTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTTAAATTAATCGAAACAA
GATTCAAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACTAGATCAATAT
AAATATTT
Found at i:5294 original size:332 final size:331
Alignment explanation
Indices: 4689--6841 Score: 2848
Period size: 332 Copynumber: 6.5 Consensus size: 331
4679 ATTACAGAAT
* * *
4689 AATTTTTAGATAAAATACCCAAAAAAATGTATACAATTTAACGCTAAGAAAATTGAAGGCCTTTT
1 AATTTTTAGATAAAATACCC-AAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTT
* * * * *
4754 CACGGTTTTAATGTCGTTTTTCATAA-TTTTCCTTAATTAATTTCAAATTAATCGAAACAAGATT
65 CACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATT
* * * * * ** *
4818 TAAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGGTAAAATTTTACCAGACCA-ATATAGA
130 CAGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGA-TAGATATAGA
*
4882 TATTTCAAGGAGTCTCTGTGCCAAAAATCAAGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTT
194 TATTTCAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTT
* * * * * *
4947 AGCGAAAAATTGTGATG-CGTACACGGTTTTGACTAAAATTTTGTAAAAAACTAACCGGATTAAT
259 AGCGAAAAATTGTGATGTAGTACACGGTTTTGGCTAAAATTTTGCAAAAAAATAACCAGA-AAAT
5011 TTCTTCCTC
323 TTCTTCCTC
*
5020 AATTTTTAGATAAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTTAAGGCCTTTT
1 AATTTTTAGAT-AAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTT
* *
5085 CACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAACCAAGATT
65 CACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATT
*
5150 CAGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCAAAAATTTTAGTAGATAGATATAGAT
130 CAGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGATAGATATAGAT
*
5215 ATTTCAAGGAATCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTA
195 ATTTCAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTA
* *
5280 GCGAAATATTGTGATG--GTACACGGTTTTGGCTAAAATTTTGCAAAAAAAATGACCAGAAAAAT
260 GCGAAAAATTGTGATGTAGTACACGGTTTTGGCTAAAATTTTGC-AAAAAAATAACCAG-AAAAT
5343 TTCTTCCTC
323 TTCTTCCTC
* * *
5352 AATTTTTCGATAAAATACCCAAATAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTTA
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTTC
* * *
5417 ACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAATAAATTTATAATTAATCGAAACAAGATTC
66 ACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATTC
* *
5482 TA-ATTCTCATAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAAATAGATATAGAT
131 -AGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGATAGATATAGAT
* * * * *
5546 ATTTCAAGGAGTTTTTGCGCCAAAAATACATACAAAATTGAGTCGGGGCCCCGAATCGCGTTTTT
195 ATTTCAAGGAGTCTCTGTGCCAAAAAT-CATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTT
* * *
5611 AGCGAAAAATTGTGATTGTTAGTACACGGTTTCTGGCTAAAATTTAGCAAAAAAATGACCGGAAA
259 AGCGAAAAATTGTGA-TG-TAGTACACGGTTT-TGGCTAAAATTTTGCAAAAAAATAACCAG-AA
5676 AATTTCTTCCTC
320 AATTTCTTCCTC
* *
5688 AATTTTTAGATAAAATACCCAAAAAATATATACAATTCAACGCCAAGAAGATTGAAGGCCTTTTA
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTTC
* * * *
5753 ACACTTTTGATATCGTTTTTCATAATTTTTTCTGAATAAATTTATAATTAATCGAAACAAGATTC
66 ACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATTC
5818 AGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGATAGATATAGATA
131 AGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGATAGATATAGATA
* * * * * * *
5883 TTTCAAGGAGTCTTTGTGCCAAAAATCACGCAAAACTGAGCCGGGGCTCCAAAACGTGTTTTTAG
196 TTTCAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAG
* * * * *
5948 CTAAAATTTGTGATGGTTAGTACACGGTTTTGCCTAAAATTTTGCAAAAAATTACCCAGAAAATT
261 CGAAAAATTGTGAT-G-TAGTACACGGTTTTGGCTAAAATTTTGCAAAAAAATAACCAGAAAATT
*
6013 TTTTCCTC
324 TCTTCCTC
* * **
6021 AATTTTAAGATAAAATACCCATAAAATATATACAATTTAACGCCAAGAAGATTGAAGGGTTTTTC
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTTC
* *
6086 ACGGTTTTAATATCGTTTTTCATAA-TTTTTCTGAATTAATTTCAAATTAATCGAAACAAGATTC
66 ACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATTC
*
6150 AG-TTGCTCGCAAAAACAAATCCTTAAATGCAGTGTGGC-ACAAATTTTAGTAGATAGATATAGA
131 AGATT-CTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTA-AAATTTTAGTAGATAGATATAGA
* * *
6213 TATTTCAAGGAGTCTCTGTGCC-AAAATCAAGCAAAATTGAGTCGGGACCCCGAAACGCGGTTTT
194 TATTTCAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTT
* *** *
6277 AGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGCAAAAAACCGA-CAGGATT
259 AGCGAAAAATTGTGAT-G-TAGTACACGGTTTTGGCTAAAATTTTGCAAAAAAATAACCA-GA-A
*
6341 AATTCCTTCCTC
320 AATTTCTTCCTC
* * * * *
6353 AATTTTTTGATAAAATACCCATAAAATATATACAATTTAACGCCAAAAAGATTGAATGTCTTTTC
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTTC
* * * * *
6418 ACGCTTTTAATGTTGTTTTTCATAA-TTTTTCTTAATTAATTTCAAATTAATCGAAACAAGATTT
66 ACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATTC
* * * * *
6482 AAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACTAGATCA-ATATAAAT
131 AGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGAT-AGATATAGAT
* * * *
6546 ATTTCAAGGAGTCTCCGTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCAAAACGCGTTTTTA
195 ATTTCAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTA
* * * *
6611 GCGAAAAATTGTGGTGGTTACTACACGGTTTTGGCTAAAATTTTGCAAAAAGATTACCCAGAAAA
260 GCGAAAAATTGTGAT-G-TAGTACACGGTTTTGGCTAAAATTTTGCAAAAA-AATAACCAGAAAA
*
6676 TTTTTTCCTC
322 TTTCTTCCTC
* * * *
6686 AATTTTAAGATAAAATACCCATAAAATATAT--AATTGAACGCC-AGAAAGATTGAAGGACTTTT
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAG-AAGATTGAAGGCCTTTT
** * * * * * *
6748 CACGCTTTTAATATTATATTTC-TTATTTTTTATAAATTAATTTTTAATGAAATCGAAACAAGAT
65 CACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAAT-TAATCGAAACAAGAT
* * * *
6812 TTAGATGT-TCGGAAAAATAAATTCTTAAAT
129 TCAGAT-TCTCGTAAAAACAAATCCTTAAAT
6842 CTAATGTCGC
Statistics
Matches: 1635, Mismatches: 159, Indels: 55
0.88 0.09 0.03
Matches are distributed among these distances:
330 5 0.00
331 445 0.27
332 610 0.37
333 224 0.14
334 27 0.02
335 60 0.04
336 250 0.15
337 14 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (331 bp):
AATTTTTAGATAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGGCCTTTTC
ACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAAACAAGATTC
AGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGATAGATATAGATA
TTTCAAGGAGTCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAG
CGAAAAATTGTGATGTAGTACACGGTTTTGGCTAAAATTTTGCAAAAAAATAACCAGAAAATTTC
TTCCTC
Found at i:6638 original size:999 final size:998
Alignment explanation
Indices: 4689--6841 Score: 3000
Period size: 999 Copynumber: 2.2 Consensus size: 998
4679 ATTACAGAAT
* * * *
4689 AATTTTTAGATAAAATACCCAAAAAAATGTATACAATTTAACGCTAAGAAAATTGAAGGCCTTTT
1 AATTTTTAGATAAAATACCC-AAAAAATATATACAATTCAACGCCAAGAAGATTGAAGGCCTTTT
* * * *
4754 CACGGTTTTAATGTCGTTTTTCATAA-TTTTCCTTAATTAATTTCA-AATTAATCGAAACAAGAT
65 CACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAATTT-ATAATTAATCGAAACAAGAT
* * *
4817 TTAAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGGTAAAATTTTACCAGACCAATATAGA
129 TTAGATTCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACCAGACCAATATAGA
* * *
4882 TATTTCAAGGAGTCTCTGTGCCAAAAATCAAGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTT
194 TATTTCAAGGAGTCTCTGTGCCAAAAATCAAGCAAAACTGAGCCGGGGCCCCAAAACGCGTTTTT
* * * *
4947 AGCGAAAAATTGTGATGCGTACACGGTTTTGACTAAAATTTTGTAAAAAACTAACCGGATTAATT
259 AGCGAAAAATTGTGATGAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTAACCAGATAAATT
* *
5012 TCTTCCTCAATTTTTAGATAAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTTAA
324 TCTTCCTCAATTTTAAGATAAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAA
* *
5077 GGCCTTTTCACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAATTAATTTCTAATTAATCGAA
389 GGCCTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCAAATTAATCGAA
* *
5142 CCAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCAAAAATTTTAGTAGATAG
454 ACAAGATTCAGATTCTCGCAAAAACAAATCCTTAAATGCAGTGTGGCAAAAATTTTAGTAGATAG
* *
5207 ATATAGATATTTCAAGGAATCTCTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACG
519 ATATAGATATTTCAAGGAATCTCTGTGCCAAAAATCAAGCAAAATTGAGTCGGGACCCCGAAACG
* * * *
5272 CGTTTTTAGCGAAATATTGTGATGGTACACGGTTTTGGCTAAAATTTTGCAAAAAAAATGACCAG
584 CGGTTTTAGCGAAAAATTGTGATGGTACACGGTTTTGACTAAAATTTTGCAAAAAAAACGACCAG
* *
5337 AAAAATTTCTTCCTCAATTTTTCGATAAAATACCCAAATAATATATACAATTTAACGCCAAGAAG
649 AAAAATTCCTTCCTCAATTTTTCGATAAAATACCCAAATAATATATACAATTTAACGCCAAAAAG
*
5402 ATTGAAGGCCTTTTAACGCTTTTGATATCGTTTTTCATAATTTTTTCTGAATAAATTTATAATTA
714 ATTGAAGGCCTTTTAACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATAAATTTATAATTA
* * *
5467 ATCGAAACAAGATTCTAATTCTCATAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGT
779 ATCGAAACAAGATTCTAATGCTCATAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACT
* * ** * *
5532 AAATAGATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATACATACAAAATTGAGTCGGGGCCC
844 AAATAGATATAAATATTTCAAGGAGTCTCCGCGCCAAAAATACATACAAAACTGAGCCGGGGCCC
* * * *
5597 CGAATCGCGTTTTTAGCGAAAAATTGTGATTGTTAGTACACGGTTTCTGGCTAAAATTTAGCAAA
909 CAAAACGCGTTTTTAGCGAAAAATTGTGATGGTTACTACACGGTTT-TGGCTAAAATTTAGCAAA
*
5662 AAAATGA-CCGGAAAAATTTCTTCCTC
973 AAAATGACCCAG-AAAATTTCTTCCTC
*
5688 AATTTTTAGATAAAATACCCAAAAAATATATACAATTCAACGCCAAGAAGATTGAAGGCCTTTTA
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTCAACGCCAAGAAGATTGAAGGCCTTTTC
* * * * *
5753 ACACTTTTGATATCGTTTTTCATAATTTTTTCTGAATAAATTTATAATTAATCGAAACAAGATTC
66 ACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAATTTATAATTAATCGAAACAAGATTT
* ** *
5818 AGATTCTCGTAAAAACAAATCCTTAAATGCAGTGTGGCTAAAATTTTAGTAGA-TAGATATAGAT
131 AGATTCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACCAGACCA-ATATAGAT
* * * *
5882 ATTTCAAGGAGTCTTTGTGCCAAAAATCACGCAAAACTGAGCCGGGGCTCCAAAACGTGTTTTTA
195 ATTTCAAGGAGTCTCTGTGCCAAAAATCAAGCAAAACTGAGCCGGGGCCCCAAAACGCGTTTTTA
* * * * *
5947 GCTAAAATTTGTGATGGTTAGTACACGGTTTTGCCTAAAATTTTGCAAAAAATTACCCAGA-AAA
260 GCGAAAAATTGTGAT-G--AGTACACGGTTTTGACTAAAATTTTGCAAAAAACTAACCAGATAAA
* *
6011 TTTTTTCCTCAATTTTAAGAT-AAAATACCCATAAAATATATACAATTTAACGCCAAGAAGATTG
322 TTTCTTCCTCAATTTTAAGATAAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTG
** *
6075 AAGGGTTTTTCACGGTTTTAATATCGTTTTTCATAA-TTTTTCTGAATTAATTTCAAATTAATCG
387 AAGGCCTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCAAATTAATCG
*
6139 AAACAAGATTCAG-TTGCTCGCAAAAACAAATCCTTAAATGCAGTGTGGCACAAATTTTAGTAGA
452 AAACAAGATTCAGATT-CTCGCAAAAACAAATCCTTAAATGCAGTGTGGCAAAAATTTTAGTAGA
*
6203 TAGATATAGATATTTCAAGGAGTCTCTGTGCC-AAAATCAAGCAAAATTGAGTCGGGACCCCGAA
516 TAGATATAGATATTTCAAGGAATCTCTGTGCCAAAAATCAAGCAAAATTGAGTCGGGACCCCGAA
*
6267 ACGCGGTTTTAGCGAAAAATTGTGATGGTTAGTACACGGTTTTGACTAAAATTTTGC-AAAAAAC
581 ACGCGGTTTTAGCGAAAAATTGTGAT-G---GTACACGGTTTTGACTAAAATTTTGCAAAAAAAA
** *
6331 CGA-CAGGATTAATTCCTTCCTCAATTTTTTGATAAAATACCCATAA-AATATATACAATTTAAC
642 CGACCA-GAAAAATTCCTTCCTCAATTTTTCGATAAAATACCCA-AATAATATATACAATTTAAC
* * * * * * *
6394 GCCAAAAAGATTGAATGTCTTTTCACGCTTTTAATGTTGTTTTTCATAA-TTTTTCTTAATTAAT
705 GCCAAAAAGATTGAAGGCCTTTTAACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATAAAT
*
6458 TTCA-AATTAATCGAAACAAGATT-TAAATGCTCGTAAAAACAAATCCTTAAATGCACTGTGGCT
770 TT-ATAATTAATCGAAACAAGATTCT-AATGCTCATAAAAACAAATCCTTAAATGCACTGTGGCT
* * *
6521 AAAATTTTACTAGATCA-ATATAAATATTTCAAGGAGTCTCCGTGCCAAAAAT-CATGCAAAACT
833 AAAATTTTACTAAAT-AGATATAAATATTTCAAGGAGTCTCCGCGCCAAAAATACATACAAAACT
*
6584 GAGCCGGGGCCCCAAAACGCGTTTTTAGCGAAAAATTGTGGTGGTTACTACACGGTTTTGGCTAA
897 GAGCCGGGGCCCCAAAACGCGTTTTTAGCGAAAAATTGTGATGGTTACTACACGGTTTTGGCTAA
* * * *
6649 AATTTTGCAAAAAGATTACCCAGAAAATTTTTTCCTC
962 AATTTAGCAAAAAAATGACCCAGAAAATTTCTTCCTC
* * * *
6686 AATTTTAAGATAAAATACCCATAAAATATAT--AATTGAACGCC-AGAAAGATTGAAGGACTTTT
1 AATTTTTAGATAAAATACCCAAAAAATATATACAATTCAACGCCAAG-AAGATTGAAGGCCTTTT
** * * * * *
6748 CACGCTTTTAATATTATATTTC-TTATTTTTTATAAATTAATTTTTAATGAAATCGAAACAAGAT
65 CACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAATTTATAAT-TAATCGAAACAAGAT
* * *
6812 TTAGATGT-TCGGAAAAATAAATTCTTAAAT
129 TTAGAT-TCTCGTAAAAACAAATCCTTAAAT
6842 CTAATGTCGC
Statistics
Matches: 1022, Mismatches: 112, Indels: 43
0.87 0.10 0.04
Matches are distributed among these distances:
995 23 0.02
996 80 0.08
997 1 0.00
998 183 0.18
999 361 0.35
1000 188 0.18
1001 123 0.12
1002 63 0.06
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (998 bp):
AATTTTTAGATAAAATACCCAAAAAATATATACAATTCAACGCCAAGAAGATTGAAGGCCTTTTC
ACGCTTTTAATATCGTTTTTCATAATTTTTTCTAAATTAATTTATAATTAATCGAAACAAGATTT
AGATTCTCGTAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACCAGACCAATATAGATA
TTTCAAGGAGTCTCTGTGCCAAAAATCAAGCAAAACTGAGCCGGGGCCCCAAAACGCGTTTTTAG
CGAAAAATTGTGATGAGTACACGGTTTTGACTAAAATTTTGCAAAAAACTAACCAGATAAATTTC
TTCCTCAATTTTAAGATAAAAATACCCAAAAAATATATACAATTTAACGCCAAGAAGATTGAAGG
CCTTTTCACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATTAATTTCAAATTAATCGAAAC
AAGATTCAGATTCTCGCAAAAACAAATCCTTAAATGCAGTGTGGCAAAAATTTTAGTAGATAGAT
ATAGATATTTCAAGGAATCTCTGTGCCAAAAATCAAGCAAAATTGAGTCGGGACCCCGAAACGCG
GTTTTAGCGAAAAATTGTGATGGTACACGGTTTTGACTAAAATTTTGCAAAAAAAACGACCAGAA
AAATTCCTTCCTCAATTTTTCGATAAAATACCCAAATAATATATACAATTTAACGCCAAAAAGAT
TGAAGGCCTTTTAACGCTTTTAATATCGTTTTTCATAATTTTTTCTGAATAAATTTATAATTAAT
CGAAACAAGATTCTAATGCTCATAAAAACAAATCCTTAAATGCACTGTGGCTAAAATTTTACTAA
ATAGATATAAATATTTCAAGGAGTCTCCGCGCCAAAAATACATACAAAACTGAGCCGGGGCCCCA
AAACGCGTTTTTAGCGAAAAATTGTGATGGTTACTACACGGTTTTGGCTAAAATTTAGCAAAAAA
ATGACCCAGAAAATTTCTTCCTC
Found at i:30767 original size:24 final size:24
Alignment explanation
Indices: 30735--30784 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
30725 GTGTCATATC
30735 ATAGTTTTCTCGTTTTATGTTTTT
1 ATAGTTTTCTCGTTTTATGTTTTT
30759 ATAGTTTTCTCGTTTTATGTTTTT
1 ATAGTTTTCTCGTTTTATGTTTTT
30783 AT
1 AT
30785 TTTTTGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (24 bp):
ATAGTTTTCTCGTTTTATGTTTTT
Found at i:31944 original size:2 final size:2
Alignment explanation
Indices: 31932--31964 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31922 GTCCTCAAGG
*
31932 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31965 GGTTTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38872 original size:9 final size:9
Alignment explanation
Indices: 38858--38898 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
38848 AGGCAATTTA
38858 AGAACTTAC
1 AGAACTTAC
38867 AGAACTTAC
1 AGAACTTAC
* *
38876 AGAA--GAA
1 AGAACTTAC
38883 AGAACTTAC
1 AGAACTTAC
38892 AGAACTT
1 AGAACTT
38899 TCAAGTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
7 5 0.19
9 21 0.81
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (9 bp):
AGAACTTAC
Found at i:40759 original size:3 final size:3
Alignment explanation
Indices: 40751--40809 Score: 57
Period size: 3 Copynumber: 18.3 Consensus size: 3
40741 CGAAAACGAT
*
40751 AAG AAG AAG AAG AAG AGAG AA- AAG AAAG AAAG AAAG AAAG GAG AAG
1 AAG AAG AAG AAG AAG A-AG AAG AAG -AAG -AAG -AAG -AAG AAG AAG
40797 AAG AAG AAG AAG A
1 AAG AAG AAG AAG A
40810 GCAGAGTCGC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 31 0.61
4 18 0.35
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46853 original size:33 final size:33
Alignment explanation
Indices: 46808--46905 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 33
46798 TTTTGCCCTT
* *
46808 AGCCACGGTGGAGTCTCCCTACTAGGACGGCTC
1 AGCCACGATGGAGCCTCCCTACTAGGACGGCTC
* *
46841 AGCCACGATGGAGCCTCCCTACTAGGGCGGTTC
1 AGCCACGATGGAGCCTCCCTACTAGGACGGCTC
* * *
46874 AGCCACGACGGAGCCGCCCCACTAGGACGGCT
1 AGCCACGATGGAGCCTCCCTACTAGGACGGCT
46906 AGACTTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (33 bp):
AGCCACGATGGAGCCTCCCTACTAGGACGGCTC
Found at i:78365 original size:36 final size:36
Alignment explanation
Indices: 78322--78397 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
78312 TTTACTTTTA
78322 TTTTTCATATTCATTTTAAATGTTTATTATACTATT
1 TTTTTCATATTCATTTTAAATGTTTATTATACTATT
78358 TTTTTCATATTCATTTTAAATGTTTATTATACTATT
1 TTTTTCATATTCATTTTAAATGTTTATTATACTATT
78394 TTTT
1 TTTT
78398 GTTTGAATCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (36 bp):
TTTTTCATATTCATTTTAAATGTTTATTATACTATT
Found at i:80418 original size:41 final size:39
Alignment explanation
Indices: 80359--80462 Score: 145
Period size: 39 Copynumber: 2.6 Consensus size: 39
80349 ACACCGAAAG
*
80359 AGTGTAAATTACATGTGAATAGTAGACATACCAATAACTGA
1 AGTGTAAATTACATGTGAATAGTAGACAT--CAATAACCGA
* *
80400 AGTGTATATTACACGTGAATAGTAGACATCAATAACCGA
1 AGTGTAAATTACATGTGAATAGTAGACATCAATAACCGA
* *
80439 AATGTAAATTACATGTGAAGAGTA
1 AGTGTAAATTACATGTGAATAGTA
80463 ATCATAACGG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 29 0.52
41 27 0.48
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (39 bp):
AGTGTAAATTACATGTGAATAGTAGACATCAATAACCGA
Found at i:81722 original size:8 final size:8
Alignment explanation
Indices: 81711--81771 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
81701 TATTTATATT
81711 TATATACA
1 TATATACA
*
81719 TATAATATA
1 TAT-ATACA
81728 TATATACA
1 TATATACA
*
81736 TACATACA
1 TATATACA
*
81744 TACATACA
1 TATATACA
*
81752 TATATGCA
1 TATATACA
*
81760 TACATACA
1 TATATACA
81768 TATA
1 TATA
81772 ATAATTTTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
8 37 0.84
9 7 0.16
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (8 bp):
TATATACA
Found at i:81765 original size:4 final size:4
Alignment explanation
Indices: 81731--81769 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
81721 TAATATATAT
* *
81731 ATAC ATAC ATAC ATAC ATAC ATAT ATGC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
81770 TAATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:82226 original size:33 final size:33
Alignment explanation
Indices: 82162--82227 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
82152 TCACCCGGAG
** *
82162 CTTCTTCATTTGGTTTTTTTTTGGGCCAAAAAT
1 CTTCTTCATTTGGTTTTTTTTTAAGCAAAAAAT
* *
82195 CTTCTTCATTTGTTTTTTTTTTCAAGAAAAAAA
1 CTTCTTCATTTGGTTTTTTTTT-AAGCAAAAAA
82228 AGGGTTTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.52
Consensus pattern (33 bp):
CTTCTTCATTTGGTTTTTTTTTAAGCAAAAAAT
Done.