Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010359.1 Corchorus capsularis cultivar CVL-1 contig10380, 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: 17257
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:10173 original size:2 final size:2
Alignment explanation
Indices: 10166--10192 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10156 TCACCACAAT
10166 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 T
10193 TCTTTCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16627 original size:333 final size:332
Alignment explanation
Indices: 15728--17134 Score: 1429
Period size: 334 Copynumber: 4.2 Consensus size: 332
15718 TCCCGTTATT
*
15728 GATTTCGGCTAAAATTTTG-CAAAATTGACCCGGAAATTTTTCTCCTCAATTTTTGAACACAATA
1 GATTTCGGCTAAAATTTTGAAAAAATTGACCC-GAAA-TTTTCTCCTCAATTTTTGAACACAATA
* * * ** *
15792 CTCATAAAAAATATACAACTCAAAGTAA-GAA-AGATTGAAGGGCT-TCTCACGCTTCTAATATC
64 CTCATAAAAAATATACAA-TCAAA-CAACAAACACATTGAAACGCTAT-GCACGCTTCTAATATC
* * * * *
15854 -ATATTCCAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAAGC-GGATTGAGATGTTTGT
126 GATATTCC-ATTTTTTTT-CCGAATAAATTTCTAACTAAATCGAAA-CAGGATTCAGATGCTCGT
* * * *
15917 AAAAAGAAATCCTTAAATCCAATGTAGCTGGGATTTCATTAGATGAATAAAGATATTTCAATTG-
188 AAAAACAAATCCTTAAATCCAAAGTAGCTGAGATTTCGTTAGATGAATAAAGATATTTCAA-TGA
* * * * * *
15981 GTCTTGGTGCCAAAAATCATGCAAAACTGAGTCGGGACACTGGAACGCGATTTTAGCCAAAATCC
252 GTCTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGGCACCGGAACGCGTTTTTAGCAAAAATCC
16046 GTGATGGTTTAGTACAC
317 GTGATGG-TTAGTACAC
* * ** *
16063 GATTTCGGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCAATTTTTGGTCACGATAC
1 GATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAT-TTTCTCCTCAATTTTTGAACACAATAC
** * * * *
16128 TCATAAAAATATATTTAATTAAACACCAAACACATTGAAACGCTATGGACGCTTCTAATATCGGT
65 TCATAAAAA-ATATACAATCAAACAACAAACACATTGAAACGCTATGCACGCTTCTAATATCGAT
* ** *
16193 -TTTCATAATTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
129 ATTCCATTTTTTTTCCGAATAAATTTCTAACTAAATCGAAACAGGATTCAGATGCTCGTAAAAAC
* * * * * * * * *
16257 AAATCCTTAATTCCAATGTGGGTGAGATTTGGTTAGATGGATATAA-ATATTTGAAAGAGACTTG
194 AAATCCTTAAATCCAAAGTAGCTGAGATTTCGTTAGATGAATA-AAGATATTTCAATGAGTCTTG
* * * * *
16321 GTGCCAAAAATCATGAAAAACAGAGCCGGGGCCCCGAAACGCGTTTTTA-TAAAAATTCGTGATG
258 GTGCCAAAAATCATGCAAAACAGAGCCGGGGCACCGGAACGCGTTTTTAGCAAAAATCCGTGATG
*
16385 GTTAGTACAT
323 GTTAGTACAC
* *
16395 GATTTCGGCTAAAAATTTG-AAAAATTGACCCGAAAGCTTTTCTCCTAAATTTTTGAACACAATA
1 GATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAA--TTTTCTCCTCAATTTTTGAACACAATA
* * ** *
16459 CTCATAAAAAATATACAACTCAAAGTAAGAAA-A-ATTGAAGGGCT-TCTCACGCTTCTAATATC
64 CTCATAAAAAATATACAA-TCAAA-CAACAAACACATTGAAACGCTAT-GCACGCTTCTAATATC
** * * * *
16521 -ATATTCCAATTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAAGC-GGATTGAGATGTTTGT
126 GATATTCC-ATTTTTTTT-CCGAATAAATTTCTAACTAAATCGAAA-CAGGATTCAGATGCTCGT
* * * *
16584 AAAAAGAAATCTTTAAATACAAAGTAGCTGAGATTTCGTTAGATGAATAAAGATATTTCAATGGG
188 AAAAACAAATCCTTAAATCCAAAGTAGCTGAGATTTCGTTAGATGAATAAAGATATTTCAATGAG
* * * * ** * *
16649 TCTTGGTGACAACAATCATGCAAAACTGAGCTGGGGCAATGGAACACGTTTTTAGCTAAAAAACC
253 TCTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGGCACCGGAACGCGTTTTTAGC-AAAAATCC
16714 GTGATGGTTAGTACAC
317 GTGATGGTTAGTACAC
* * * * ** *
16730 GATTTCAGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCTATTTTTGCCCACGATAC
1 GATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAT-TTTCTCCTCAATTTTTGAACACAATAC
* * * * * * *
16795 TCATAAAAATATATATAATTAAACACCAAACACATTGAAACGCTATGGAGGCTTCCAATATCGGT
65 TCATAAAAA-ATATACAATCAAACAACAAACACATTGAAACGCTATGCACGCTTCTAATATCGAT
* *
16860 TTTCC-TTTTTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
129 ATTCCATTTTTTTTCCGAATAAATTTCTAACTAAATCGAAACAGGATTCAGATGCTCGTAAAAAC
* * * ** *
16924 AAATCCGTAAATCCAAAGTGGCTGAGATTTGGTTAGATGAATACTGATATTTCAATGAGTCTTGA
194 AAATCCTTAAATCCAAAGTAGCTGAGATTTCGTTAGATGAATAAAGATATTTCAATGAGTCTTGG
** * * *
16989 CACCAAAAATCATGCAAAACTA-AGCCGGGGC-CCGGAACGCATTTTTAGCCAAAAT-TGTGATG
259 TGCCAAAAATCATGCAAAAC-AGAGCCGGGGCACCGGAACGCGTTTTTAGCAAAAATCCGTGATG
17051 GTTAGTACAC
323 GTTAGTACAC
* * *
17061 GATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTCT--GCAATTTTTTG-ACACAAT
1 GATTTCGGCTAAAATTTTGAAAAAATTGACCCG--AAATTTTCTCCTCAA-TTTTTGAACACAAT
*
17123 ACTCGTAAAAAA
63 ACTCATAAAAAA
17135 AGTGATTCAA
Statistics
Matches: 871, Mismatches: 167, Indels: 74
0.78 0.15 0.07
Matches are distributed among these distances:
329 1 0.00
330 19 0.02
331 99 0.11
332 79 0.09
333 167 0.19
334 261 0.30
335 150 0.17
336 87 0.10
337 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (332 bp):
GATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAATTTTCTCCTCAATTTTTGAACACAATACT
CATAAAAAATATACAATCAAACAACAAACACATTGAAACGCTATGCACGCTTCTAATATCGATAT
TCCATTTTTTTTCCGAATAAATTTCTAACTAAATCGAAACAGGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAAAGTAGCTGAGATTTCGTTAGATGAATAAAGATATTTCAATGAGTCTTGGTG
CCAAAAATCATGCAAAACAGAGCCGGGGCACCGGAACGCGTTTTTAGCAAAAATCCGTGATGGTT
AGTACAC
Found at i:17000 original size:667 final size:665
Alignment explanation
Indices: 15727--17134 Score: 2200
Period size: 667 Copynumber: 2.1 Consensus size: 665
15717 ATCCCGTTAT
* * *
15727 TGATTTCGGCTAAAATTTTGCAAAATTGACCCGGAAATTTTTCTCCTCAATTTTTGAACACAATA
1 TGATTTCGGCTAAAATTTTGAAAAATTGACCC-GAAAATTTTCTCCTAAATTTTTGAACACAATA
*
15792 CTCATAAAAAATATACAACTCAAAGTAAGAAAGATTGAAGGGCTTCTCACGCTTCTAATATCATA
65 CTCATAAAAAATATACAACTCAAAGTAAGAAAAATTGAAGGGCTTCTCACGCTTCTAATATCATA
15857 TTCCAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAAGCGGATTGAGATGTTTGTAAAAA
130 TTCCAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAAGCGGATTGAGATGTTTGTAAAAA
* * * *
15922 GAAATCCTTAAATCCAATGTAGCTGGGATTTCATTAGATGAATAAAGATATTTCAATTGGTCTTG
195 GAAATCCTTAAATACAAAGTAGCTGAGATTTCATTAGATGAATAAAGATATTTCAATGGGTCTTG
* * * * *
15987 GTGCCAAAAATCATGCAAAACTGAGTCGGGACACTGGAACGCGATTTTAGCCAAAATCCGTGATG
260 GTGACAAAAATCATGCAAAACTGAGTCGGGACAATGGAACACGATTTTAGCAAAAAACCGTGATG
*
16052 GTTTAGTACACGATTTCGGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCAATTTTT
325 GTTTAGTACACGATTTCAGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCAATTTTT
** *
16117 GGTCACGATACTCATAAAAATATATTTAATTAAACACCAAACACATTGAAACGCTATGGACGCTT
390 GCCCACGATACTCATAAAAATATATATAATTAAACACCAAACACATTGAAACGCTATGGACGCTT
*
16182 CTAATATCGGTTTTCATAATTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGATGC
455 CCAATATCGGTTTTCATAATTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGATGC
* * * * * *
16247 TCGTAAAAACAAATCCTTAATTCCAATGTGGGTGAGATTTGGTTAGATGGATATAAATATTTGAA
520 TCGTAAAAACAAATCCGTAAATCCAAAGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAA
*** * *
16312 AGAGACTTGGTGCCAAAAATCATGAAAAAC-AGAGCCGGGGCCCCGAAACGCGTTTTTA-TAAAA
585 AGAGACTTGACACCAAAAATCATGAAAAACTA-AGCCGGGG-CCCGAAACGCATTTTTAGCAAAA
16375 ATTCGTGATGGTTAGTACA
648 ATT-GTGATGGTTAGTACA
* *
16394 TGATTTCGGCTAAAAATTTGAAAAATTGACCCGAAAGCTTTTCTCCTAAATTTTTGAACACAATA
1 TGATTTCGGCTAAAATTTTGAAAAATTGACCCGAAA-ATTTTCTCCTAAATTTTTGAACACAATA
16459 CTCATAAAAAATATACAACTCAAAGTAAGAAAAATTGAAGGGCTTCTCACGCTTCTAATATCATA
65 CTCATAAAAAATATACAACTCAAAGTAAGAAAAATTGAAGGGCTTCTCACGCTTCTAATATCATA
*
16524 TTCCAATTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAAGCGGATTGAGATGTTTGTAAAAA
130 TTCCAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAAGCGGATTGAGATGTTTGTAAAAA
* *
16589 GAAATCTTTAAATACAAAGTAGCTGAGATTTCGTTAGATGAATAAAGATATTTCAATGGGTCTTG
195 GAAATCCTTAAATACAAAGTAGCTGAGATTTCATTAGATGAATAAAGATATTTCAATGGGTCTTG
* * *
16654 GTGACAACAATCATGCAAAACTGAG-CTGGGGCAATGGAACACGTTTTTAGCTAAAAAACCGTGA
260 GTGACAAAAATCATGCAAAACTGAGTC-GGGACAATGGAACACGATTTTAGC-AAAAAACCGTGA
*
16718 TGG-TTAGTACACGATTTCAGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCTATTT
323 TGGTTTAGTACACGATTTCAGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCAATTT
*
16782 TTGCCCACGATACTCATAAAAATATATATAATTAAACACCAAACACATTGAAACGCTATGGAGGC
388 TTGCCCACGATACTCATAAAAATATATATAATTAAACACCAAACACATTGAAACGCTATGGACGC
* **
16847 TTCCAATATCGGTTTTCCTTTTTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGAT
453 TTCCAATATCGGTTTTCATAATTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGAT
*
16912 GCTCGTAAAAACAAATCCGTAAATCCAAAGTGGCTGAGATTTGGTTAGATGAATACT-GATATTT
518 GCTCGTAAAAACAAATCCGTAAATCCAAAGTGGCTGAGATTTGGTTAGATGAATA-TAAATATTT
* * * * *
16976 CAATGAGTCTTGACACCAAAAATCATGCAAAACTAAGCCGGGGCCCGGAACGCATTTTTAGCCAA
582 CAAAGAGACTTGACACCAAAAATCATGAAAAACTAAGCCGGGGCCCGAAACGCATTTTTAGCAAA
17041 AATTGTGATGGTTAGTACA
647 AATTGTGATGGTTAGTACA
* * * *
17060 CGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTCTGC-AATTTTTTG-ACACAAT
1 TGATTTCGGCTAAAATTTTG-AAAAATTGACCCG-AAAATTTTCTCCTAAATTTTTGAACACAAT
*
17123 ACTCGTAAAAAA
64 ACTCATAAAAAA
17135 AGTGATTCAA
Statistics
Matches: 679, Mismatches: 54, Indels: 18
0.90 0.07 0.02
Matches are distributed among these distances:
665 18 0.03
666 61 0.09
667 582 0.86
668 18 0.03
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (665 bp):
TGATTTCGGCTAAAATTTTGAAAAATTGACCCGAAAATTTTCTCCTAAATTTTTGAACACAATAC
TCATAAAAAATATACAACTCAAAGTAAGAAAAATTGAAGGGCTTCTCACGCTTCTAATATCATAT
TCCAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAAGCGGATTGAGATGTTTGTAAAAAG
AAATCCTTAAATACAAAGTAGCTGAGATTTCATTAGATGAATAAAGATATTTCAATGGGTCTTGG
TGACAAAAATCATGCAAAACTGAGTCGGGACAATGGAACACGATTTTAGCAAAAAACCGTGATGG
TTTAGTACACGATTTCAGCTAAAATTTTGAAAAAATTGACCCGATATAATTCTCCTCAATTTTTG
CCCACGATACTCATAAAAATATATATAATTAAACACCAAACACATTGAAACGCTATGGACGCTTC
CAATATCGGTTTTCATAATTTTTCCGAATAAATTTCTAACTAAATCGAAACATGATTCAGATGCT
CGTAAAAACAAATCCGTAAATCCAAAGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAA
GAGACTTGACACCAAAAATCATGAAAAACTAAGCCGGGGCCCGAAACGCATTTTTAGCAAAAATT
GTGATGGTTAGTACA
Done.