Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005721.1 Corchorus capsularis cultivar CVL-1 contig05739, 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: 3098
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:672 original size:333 final size:331
Alignment explanation
Indices: 1--3098 Score: 4086
Period size: 333 Copynumber: 9.3 Consensus size: 331
* * *
1 ACAATACTCGTAAAAAAATATATAA-TAAATGCCAAAAAGATTGAAAAGCTTTTCACGCTCTCAA
1 ACAATACTCGT--AAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAA
65 TATCGTTTTTCCTA-TTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGT
64 TATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGT
* * * *
129 AAAAACAAATTCTTCAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATAATTCAATGAG
129 AAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * * * * * * *
194 GCTTGGCGTCAAAAATCATGCAAAATTAAGTCGGGGCACCGGAACACGTTTTTAGCCAAAAATCG
194 TCTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCG
* * ** * *
259 TGATGGATAGTACACGATTTCGGCTAAAATTTTGCAGAAATTGACATGAAAAGTTTTTTCTCAAT
259 TGATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAAT
*
324 TTTTGGAT
324 TTTTGGAC
** *
332 ACAATACTCGTATAAAATATATAATTCAATGCCAAAATTATTGAAAGGATTTTCACGC-TTCTAA
1 ACAATACTCGTA-AAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTC-AA
* * * * *
396 TATCGTTTTTTCTATTTTTTA-TGATTTAAATTCTAAGAAAATCGAAATATGATTCAGATGCCCG
64 TATCGTTTTTCCTA-TTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCG
* * * * * * *
460 TAAGAACAAATCCTTAAATCCAATCTAGCTGAAATTTGGTTAGATAAATATGGATATTTCAAGGA
128 TAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* * * * * * *
525 GCCTTCGTGTAAACAATCATCAAAAACTGAGCAGGGGCCCCGGAACGTGTTTTTTTA-CCAAAAA
193 GTCTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCG--TTTTTAGCCAAAAA
* *
589 TCGTGATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTGTCCTC
256 TCGTGATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTC
*
654 AATTTTTGGGC
321 AATTTTTGGAC
* * * * * *
665 TCAATACTCGTAGATAATATATAATTCAATGTCAAAAATATTGAAATGCTATTCACGCTTTCAAT
1 ACAATACTCGTA-AAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAAT
* * * *
730 ATCGTTTTTCCTATTTTTACTTAATTAATTTCTTATAAAATAGAAATATAATTCAGATGCTCGTA
65 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTA
*
795 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATATAGATATTTC-A--A-T
130 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
** * * * * *
856 CTTAACGTCAAAAATCATGCAAAACAGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAATTGT
195 CTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGT
* * * * *
921 GATAGATAGTACACGATTTCGGATATAA-TTTGCAAAAATTGACCCGAAAAATTTTTGCTCAATT
260 GATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATT
985 TTTGGAC
325 TTTGGAC
* * *
992 ACAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTATTCTCGCTTTCAAT
1 ACAATACTCGT-AAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAAT
* * *
1057 ATCGTTTTTCCTATTTTTACTGAATTAATTTATAATAAAATAGAAATATAATTCAGATGCTCGTA
65 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTA
*
1122 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGT
130 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
** *
1187 CTTGGCGTAAAAAATCATGAAACAA-TGAGCCGGGGCCCTAGAACGCGTATTTAGCCAAAAATCG
195 CTTGGCGTAAAAAATCATGAAA-AACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCG
* * * *
1251 TGATGGATAGTGCATGATTTCGGCTAAAAGTTTGCAAAAATTTAGCCGAAAAATTTTTCCTCAAT
259 TGATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAAT
1316 TTTTGGAC
324 TTTTGGAC
*
1324 ACAATACTCGTAAAAATATATAATTCAATGCCAAAAAGATTGAAACGC-TTTCACGCTTTCAATA
1 ACAATACTCGTAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAATA
* * * ** * * *
1388 TCGTTTTTCCTACTTTTACAGAATTAATTTTTTTTAAAATCAAAATATGATTCAAATGCTTGTAA
66 TCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTAA
* *
1453 AAACAAATTCTTAAATCCAATGTAGCTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTC
131 AAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * *
1518 TTGGCGTAGAAAATCATGAAAAACTGAGCCGAGGCCCTGGAACGAGTTTTTAGCCAAAAATCGTA
196 TTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGTG
* *
1583 ATGGATAGTACATGATTTTGGCTAAAATTTTGCAAAAATTGACCCGAGAAATTTTTCCTCAATTT
261 ATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTT
1648 TTGGAC
326 TTGGAC
**
1654 ACAATACTCAAAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAATA
1 ACAATACTCGTAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAATA
* * * *
1719 TCATTTTTCTTATTTTTACTGAATTAATTTCTATTAAAATCGAAATATGATTCAAATGCTCGTAA
66 TCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTAA
* * *
1784 AAA-AAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGGTATTTCAATGAGGC
131 AAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* *** ** * * * *
1848 TTGGCGTAAAAAAATCATGACAAACTGAGCCGGGGCCCTAAAACAAGTATTTATCCAGAAATTGT
196 TTGGCGT-AAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGT
* * * ** *
1913 GATGAATAGTATATGATTTCGGCTAAAATGTTGCAAAAATT-ATCCCGAAATTTTTTTTTCTCAA
260 GATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCCGAAA-AATTTTTCCTCAA
*
1977 TTTTTGGGC
323 TTTTTGGAC
* * * *
1986 ACAATACTCGTAAATAATATTTAATTAAATGCCAAAAAGATTGAAAGTCTATTCACGCTTTCAAT
1 ACAATACTCGTAAA-AATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAAT
*
2051 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATAGAAATATGATTCAGATGCTCGTA
65 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTA
* *
2116 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATATATATATTTCAATGA
130 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG-A-ATATAGATATTTCAAGGA
* * * * ** * *
2181 GGCTTGGCGTAAAAAATCATGACAAACTGAGCCGGGGCCCTGAAACAAGTATTTAGCCAAAAATT
193 GTCTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATC
* * * * *
2246 GTGATGAATAGTATATGATTTCGGCTAAAATGTTGCAAAAATTTGACCCGAAAATTTTTTTCTCA
258 GTGATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGAAAAATTTTTCCTCA
2311 ATTTTTGGAC
322 ATTTTTGGAC
* * * * *
2321 ACAGTTCTCGTTAAAAATATATAATTCAATGCCTAAAAGATTGAATGGCTTTTCACGCTTTTAAT
1 ACAATACTCG-TAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAAT
* * * * * * *
2386 ATCGTTTTTTCTATTTTTACAGAATTAATTTCTATTTAAATCGAAATCTAATTCAGATGCTAGTA
65 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTA
* * *
2451 AAAACAAATTATTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGAAGT
130 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * * * * * *
2516 CTTGGCGTAAATAATCAAGAAAAACTGAGCCGGGGCCCCGTAGCGTGTTTTTAGCCAAAGATTGT
195 CTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGT
* * *
2581 GATGGATTGTATATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTTCCTCAAT
260 GATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAA-ATTTTTCCTCAAT
2646 TTTTGGAC
324 TTTTGGAC
*
2654 ACAATACTCGTAAAAAGTATATAATTCAATGCCAAAAAGATTGAAAGGCTATTCACGCTTTCAAT
1 ACAATACTCGTAAAAA-TATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAAT
* * * * * *
2719 ATCGTTTTTCCTATTTTTACTAAATTAATTTCTATTTAAATCAAAATATGATTTAGATGCTGGT-
65 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTA
*** * * *
2783 -AAACTTTTTTTTAAATCCAATGTGGTTGAGATTTGGTTAGAGGAATATAGATATTTCAAGGAGT
130 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * *
2847 CTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGTAGCACGTTTTTAGCCAAAAATCGT
195 CTTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGT
* * * *
2912 GATGGATAGTAAATGATTTCGGCTAAAATTTTGCAAAAATTGAACCGAAATATTTTTCATCAATT
260 GATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATT
2977 TTTGGAC
325 TTTGGAC
* * * * *
2984 CCAATACTCGTCAAAAATATATAATCCAATGCCAAAAATATTGAAGGGCTTTTCACGCTTTGAAT
1 ACAATACTCGT-AAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAAT
* *
3049 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTATTTAAATCAGAAATAT
65 ATCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATC-GAAATAT
Statistics
Matches: 2451, Mismatches: 283, Indels: 66
0.88 0.10 0.02
Matches are distributed among these distances:
327 220 0.09
328 36 0.01
329 39 0.02
330 489 0.20
331 504 0.21
332 235 0.10
333 575 0.23
334 49 0.02
335 264 0.11
336 39 0.02
337 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (331 bp):
ACAATACTCGTAAAAATATATAATTCAATGCCAAAAAGATTGAAAGGCTTTTCACGCTTTCAATA
TCGTTTTTCCTATTTTTACTGAATTAATTTCTAATAAAATCGAAATATGATTCAGATGCTCGTAA
AAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
TTGGCGTAAAAAATCATGAAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGTG
ATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTT
TTGGAC
Done.