Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005858.1 Corchorus capsularis cultivar CVL-1 contig05876, 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, 964
Length: 1608
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:1185 original size:332 final size:333
Alignment explanation
Indices: 1--1359 Score: 1901
Period size: 332 Copynumber: 4.1 Consensus size: 333
*
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGCTTTAATCAGAAATTAATTTGATAAAAAA
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
* * * *
66 TAGGAAAAA-AATATTTCAAGCCTGAAAGGCCCACAAATCTTTTTGAAGTTGAATTATACATTTT
66 TAGGAAAAACAATATTTCAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTGAATTATATATTTT
* *
130 TTATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAGTTTTAGCT
131 TTATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGCC
* * * *
195 GAAATCATGTACTAATCATCACGGTTTCTCGCTGAAAACGCGGTACGGGGCCCCGACTTAGTTTT
196 GAAATCGTGAACTAATCATCACGGTTTCTGGCTGAAAACGCGGTACGGGGCCCCGACTCAGTTTT
* * * *
260 GCATGATTTTTGGCATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTCAGCCACAT
261 GCATGATTTTTGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTAAGCCATAT
* *
325 TGGATTTA
326 TCGATGTA
* * * *
333 AGGATTTGTTTTTATGAACATCTCAATCTTGTTTCGATTTAATCAGAAATTAATTTGCAAAAAAA
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTG-ATAAAAA
* * *
398 ATAGGATTAAACCATATTTAAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTG-ATTATATATT
65 ATAGGA-AAAACAATATTTCAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTGAATTATATATT
* * *
462 TTTGATGAGTATTGTGGCTAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAAATTTAG
129 TTTTATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAG
* * ** * * * * *
527 CCGAAATCGCGTACTAATCATCACGGTTTCTGGCTGAAAACAAGTTTCGGGACACTG-CTCAGTT
194 CCGAAATCGTGAACTAATCATCACGGTTTCTGGCTGAAAACGCGGTACGGGGCCCCGACTCAGTT
* * * * * * *
591 TTGCATGAGTTTTGGCGTAGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCAGCAAT
259 TTGCATGATTTTTGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTAAGCCAT
656 ATTCGATGTA
324 ATTCGATGTA
*
666 AGGATTTG-TTTTCCGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
* * *
730 TAGGAAAAAAAATATTTCAAGCATGAAAAGCCCATAAATATTTTTGATGTTGAATTAT-TCATTT
66 TAGGAAAAACAATATTTCAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTGAATTATAT-ATTT
* *
794 TTTATAAGTATTGTGGCCAAAAATTGAGGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGC
130 TTTATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGC
* * *
859 CGAAATCGTGAACTAATCATCACGGTTTCTGGCAGAAAACGCGGTACGGGGCCCCGGCACAGTTT
195 CGAAATCGTGAACTAATCATCACGGTTTCTGGCTGAAAACGCGGTACGGGGCCCCGACTCAGTTT
* * * *
924 TGCATGATTTTTGGTATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTAAGTCATA
260 TGCATGATTTTTGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTAAGCCATA
989 TTCGATGTA
325 TTCGATGTA
998 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGA-AAAAAA
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
* * * * * * *
1062 TAGGAAAAACCATATTTGAAGCATGAAAAGCCTATAAATCTTTATGATG-TGACTTATATATTTG
66 TAGGAAAAACAATATTTCAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTGAATTATATATTTT
* * * * * * * *
1126 TAATGATTATTTTAGTCAAAAATTG-AGAAAAATTATATTGGGTCAATTTTTTACAAAATTTTAG
131 TTATGAGTATTGTGGCCAAAAATTGAAGAAAAA-TATTTTGGTTCAA-TTTTTGCAAAATTTTAG
* * *
1190 CCGAAATCGTGAA-TAAACTATCACGGTTTCTGGCTGAAAGCGC-GTTCTGGGGCCCCGACTCAG
194 CCGAAATCGTGAACTAATC-ATCACGGTTTCTGGCTGAAAACGCGGTAC-GGGGCCCCGACTCAG
* *
1253 TTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCC
257 TTTTGCATGATTTTTGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTAAGCC
1318 ATATTCGATGTA
322 ATATTCGATGTA
1330 AGGATTTGTTTTTACGAGCATCTAAATCTT
1 AGGATTTGTTTTTACGAGCATCTAAATCTT
1360 TCCTTGAAAT
Statistics
Matches: 907, Mismatches: 108, Indels: 24
0.87 0.10 0.02
Matches are distributed among these distances:
330 48 0.05
331 175 0.19
332 390 0.43
333 138 0.15
334 119 0.13
335 37 0.04
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (333 bp):
AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
TAGGAAAAACAATATTTCAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTGAATTATATATTTT
TTATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGCC
GAAATCGTGAACTAATCATCACGGTTTCTGGCTGAAAACGCGGTACGGGGCCCCGACTCAGTTTT
GCATGATTTTTGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTAAGCCATAT
TCGATGTA
Found at i:1350 original size:665 final size:664
Alignment explanation
Indices: 1--1359 Score: 2077
Period size: 665 Copynumber: 2.0 Consensus size: 664
*
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGCTTTAATCAGAAATTAATTTGATAAAAAA
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
* * *
66 TAGGAAAAAAATATTTCAAGCCTGAAAGGCCCACAAATCTTTTTGAAGTTGAATTATACATTTTT
66 TAGGAAAAAAATATTTCAAGCATGAAAAGCCCACAAATATTTTTGAAGTTGAATTATACATTTTT
* * *
131 TATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAGTTTTAGCTG
131 TATAAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGCCG
* * **
196 AAATCATGTACTAATCATCACGGTTTCTCGCTGAAAACGCGGTACGGGGCCCCGACTTAGTTTTG
196 AAATCATGAACTAATCATCACGGTTTCTCGCAGAAAACGCGGTACGGGGCCCCGACACAGTTTTG
*
261 CATGATTTTTGGCATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTCAGCCACATT
261 CATGATTTTTGGCATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTAAGCCACATT
* * * *
326 GGATTTAAGGATTTGTTTTTATGAACATCTCAATCTTGTTTCGATTTAATCAGAAATTAATTTGC
326 CGATGTAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTG-
* *
391 AAAAAAAATAGGATTAAACCATATTTAAAGCATGAAAAGCCCATAAATCTTTTTGAAGTTGATTA
390 AAAAAAAATAGGATAAAACCATATTTAAAGCATGAAAAGCCCATAAATCTTTATGAAGTTGATTA
* * * * *
456 TATATTTTTGATGAGTATTGTGGCTAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAA
455 TATATTTGTAATGAGTATTGTGGCTAAAAATTGAAGAAAAATATATTGGGTCAATTTTTACAAAA
* * *
521 ATTTAGCCGAAATCGCGTACTAATCATCACGGTTTCTGGCTGAAAACAAGTTTCGGGACACTGCT
520 ATTTAGCCGAAATCGCGTAATAAACATCACGGTTTCTGGCTGAAAACAAGTTTCGGGACACCGCT
*
586 CAGTTTTGCATGAGTTTTGGCGTAGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCA
585 CAGTTTTGCATGAGTTTTGGCGTAGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTAA
651 GCAATATTCGATGTA
650 GCAATATTCGATGTA
*
666 AGGATTTG-TTTTCCGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
1 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
* * *
730 TAGGAAAAAAAATATTTCAAGCATGAAAAGCCCATAAATATTTTTGATGTTGAATTATTCATTTT
66 TAGG-AAAAAAATATTTCAAGCATGAAAAGCCCACAAATATTTTTGAAGTTGAATTATACATTTT
*
795 TTATAAGTATTGTGGCCAAAAATTGAGGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGCC
130 TTATAAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGCC
* * *
860 GAAATCGTGAACTAATCATCACGGTTTCTGGCAGAAAACGCGGTACGGGGCCCCGGCACAGTTTT
195 GAAATCATGAACTAATCATCACGGTTTCTCGCAGAAAACGCGGTACGGGGCCCCGACACAGTTTT
* * *
925 GCATGATTTTTGGTATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTAAGTCATAT
260 GCATGATTTTTGGCATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTAAGCCACAT
*
990 TCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTG
325 TCGATGTAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTG
* * *
1055 -AAAAAAATAGGA-AAAACCATATTTGAAGCATGAAAAGCCTATAAATCTTTATGATG-TGACTT
390 AAAAAAAATAGGATAAAACCATATTTAAAGCATGAAAAGCCCATAAATCTTTATGAAGTTGA-TT
* * *
1117 ATATATTTGTAATGATTATTTTAG-TCAAAAATTG-AGAAAAATTATATTGGGTCAATTTTTTAC
454 ATATATTTGTAATGAGTATTGTGGCT-AAAAATTGAAGAAAAA-TATATTGGGTCAA-TTTTTAC
* * * ** *
1180 AAAATTTTAGCCGAAATCGTG-AATAAACTATCACGGTTTCTGGCTGAAAGCGCG-TTCTGGGGC
516 AAAAATTTAGCCGAAATCGCGTAATAAAC-ATCACGGTTTCTGGCTGAAAACAAGTTTC-GGGAC
* * * *
1243 CCCGACTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCA
579 ACCG-CTCAGTTTTGCATGAGTTTTGGCGTAGAGACTCCTTGAAATATATATATTCATCTAATCA
*
1308 AATCTAAGCCATATTCGATGTA
643 AATCTAAGCAATATTCGATGTA
1330 AGGATTTGTTTTTACGAGCATCTAAATCTT
1 AGGATTTGTTTTTACGAGCATCTAAATCTT
1360 TCCTTGAAAT
Statistics
Matches: 628, Mismatches: 57, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
661 11 0.02
662 87 0.14
663 65 0.10
664 143 0.23
665 322 0.51
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (664 bp):
AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGATAAAAAA
TAGGAAAAAAATATTTCAAGCATGAAAAGCCCACAAATATTTTTGAAGTTGAATTATACATTTTT
TATAAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTTTGCAAAATTTTAGCCG
AAATCATGAACTAATCATCACGGTTTCTCGCAGAAAACGCGGTACGGGGCCCCGACACAGTTTTG
CATGATTTTTGGCATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTAAGCCACATT
CGATGTAAGGATTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGA
AAAAAAATAGGATAAAACCATATTTAAAGCATGAAAAGCCCATAAATCTTTATGAAGTTGATTAT
ATATTTGTAATGAGTATTGTGGCTAAAAATTGAAGAAAAATATATTGGGTCAATTTTTACAAAAA
TTTAGCCGAAATCGCGTAATAAACATCACGGTTTCTGGCTGAAAACAAGTTTCGGGACACCGCTC
AGTTTTGCATGAGTTTTGGCGTAGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTAAG
CAATATTCGATGTA
Found at i:1414 original size:81 final size:81
Alignment explanation
Indices: 1279--1440 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
1269 GCGTCGAGAC
1279 TCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCATATTCGATGTAAGGATTTGTTTTTA
1 TCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCATATTCGATGTAAGGATTTGTTTTTA
1344 CGAGCATCTAAATCTT
66 CGAGCATCTAAATCTT
1360 TCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCATATTCGATGTAAGGATTTGTTTTTA
1 TCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCATATTCGATGTAAGGATTTGTTTTTA
1425 CGAGCATCTAAATCTT
66 CGAGCATCTAAATCTT
1441 GTTTCGATTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (81 bp):
TCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCATATTCGATGTAAGGATTTGTTTTTA
CGAGCATCTAAATCTT
Done.