Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006227.1 Corchorus capsularis cultivar CVL-1 contig06246, 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, 889
Length: 1482
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:866 original size:333 final size:332
Alignment explanation
Indices: 1--1482 Score: 2266
Period size: 334 Copynumber: 4.5 Consensus size: 332
*
1 TAAGAGATATATAATTCA-ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCATTTTT
1 TAAGAGATATATAATT-AGACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTT
*
65 -CTTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAAT
65 CCTTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
* *
129 CCTTTAATCCATTGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTCATTCTACC
130 CCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTCTACC
*
194 AAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACGGTGATGGTTAG
195 AAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * * *
259 TAGGCGTTTTCGTG-TAAAATTTTGC-AAAAACTGACCTGAAAAGTTTTTCCTCAATTTTTTGCC
260 TA-CCGATTTCG-GCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTGCC
*
322 ACAATACTCA
323 ACAATACTAA
*
332 TAAGAGATATATAATTCA-ACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTTTAATATCATTTT
1 TAAGAGATATATAATT-AGACGCCAAAAAAATTGAAGGG-TTTTTCACGCTTCTAATATCATTTT
* * * * *
396 CCCTTTTTTTTTCCTAATTAAATTATAATTAAATCGAAACAAGATTCAGATGCTCATAAAAAAAA
64 TCC-TTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAA
** *
461 ATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGAGGAATATAGATATTTCAAAGAGTCATTCCA
128 ATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTCTA
* * *
526 TCAAAAATCATGCAAAACTGAGGCGACGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
193 CCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
591 AGTACCTGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAA-TTCTTTG
258 AGTACC-GATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAACTT-TTTG
655 CCACAATACTAA
321 CCACAATACTAA
* * *
667 TAAGAGATATATAATTAGACGCCAAACAATTTGAAGGGTTTTTCACGCTTCTAATATTATTTTTC
1 TAAGAGATATATAATTAGACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTC
* *
732 CTTTTTTTAT-CTAATTTATTTCTAATTAAATCGAAATAAGATTGAGATGCTCATAAAAACAAAT
66 CTTTTTTT-TCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
*
796 CCTTTAATCCATTGTGGCTGAGATTTGGTTTGATAAATATAGATATTTCAAAGAGTCATTCTACC
130 CCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTCTACC
* *
861 AAAAATCATGCAAAACTGAGTCGATGCCCCCAAAATGCGTTTTAAGCCAAAAACCGTGATGGTTA
195 AAAAATCATGCAAAACTGAGTCGATG-CCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* *
926 GTACACGATTTCGGCTAGAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTCCC
259 GTAC-CGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTGCC
*
991 ACAGTACTAA
323 ACAATACTAA
* *
1001 TAAGAGATATATAATT-GAACGCCAAAAAAATTGAAGTGTTTTTCACGCTTCTAATATCATTTGT
1 TAAGAGATATATAATTAG-ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTT
* * * *
1065 -CTTTTTTTTCCTAATTTATTTCTAAATAAATCGAAAGAAGATTCAAATGATCATAAAAACAAAT
65 CCTTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
* * * *
1129 TCTTTAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAAGGGTCATTCTACC
130 CCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTCTACC
* *
1194 AAAAATCATGCAAAACTGAGTCGATGCCCCAAAATGCGTTTTTCGCCAAAAACCGTGATGGTTAG
195 AAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
1259 TACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAGAA-TTTTTCCTCAACTTTTTGCC
260 TA-CCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAA-AAGTTTTTCCTCAACTTTTTGCC
1323 ACAATACTAA
323 ACAATACTAA
* * * * * *
1333 TTAGAGATATATAATTAGAAGCCAACAAATTTGAAGGGTTTTCCACGCTTCTAATATTATTTTTC
1 TAAGAGATATATAATTAGACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTC
* * * *
1398 CTTTTCTAT-CTAATTTATTTCTAATTAAATCGAAACATGATTGAGATGCTCATAAAAACAAATC
66 CTTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATC
1462 CTTTAATCCATTGTGGCTGAG
131 CTTTAATCCATTGTGGCTGAG
Statistics
Matches: 1050, Mismatches: 83, Indels: 35
0.90 0.07 0.03
Matches are distributed among these distances:
331 38 0.04
332 248 0.24
333 297 0.28
334 387 0.37
335 80 0.08
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (332 bp):
TAAGAGATATATAATTAGACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTC
CTTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATC
CTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTCTACCA
AAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
ACCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTGCCACA
ATACTAA
Found at i:1272 original size:666 final size:666
Alignment explanation
Indices: 1--1482 Score: 2347
Period size: 666 Copynumber: 2.2 Consensus size: 666
* * * *
1 TAAGAGATATATAATTCA-ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCATTTTT
1 TAAGAGATATATAATT-AGACGCCAAACAATTTGAAGGGTTTTTCACGCTTCTAATATTATTTTT
*
65 -CTTTTTTT-TCCTAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAA
65 CCTTTTTTTAT-CTAATTTATTTCTAATTAAATCGAAACAAGATTGAGATGCTCATAAAAACAAA
*
128 TCCTTTAATCCATTGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTCATTCTAC
129 TCCTTTAATCCATTGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAAGAGTCATTCTAC
* *
193 CAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACGGTGATGGTTA
194 CAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTAAGCCAAAAACCGTGATGGTTA
** * * * *
258 GTAGGCGTTTTCGTGTAAAATTTTGCAAAAACTGACCTGAAAAGTTTTTCCTCAATTTTTTGCCA
259 GTACACGATTTCGTGTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTCCCA
* *
323 CAATACTCATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTTTAAT
324 CAATACTAATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAAT
* * *
388 ATCATTTTCCCTTTTTTTTTCCTAATTAAATTATAATTAAATCGAAACAAGATTCAGATGCTCAT
389 ATCATTTT-CCTTTTTTTTTCCTAATTAAATTATAAATAAATCGAAACAAGATTCAAATGATCAT
* * *
453 AAAAAAAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGAGGAATATAGATATTTCAAAGAG
453 AAAAAAAAATCCTTTAATCCAATGTGGCTAAGATTTGGTTAGAGAAATATAGATATTTCAAAGAG
*
518 TCATTCCATCAAAAATCATGCAAAACTGAGGCGACGCCCCAAAACGCGTTTTTAGCCAAAAACCG
518 TCATTCCACCAAAAATCATGCAAAACTGAGGCGACGCCCCAAAACGCGTTTTTAGCCAAAAACCG
*
583 TGATGGTTAGTACCTGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAA-AAGTTTTTCCTCA
583 TGATGGTTAGTACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAGAA-TTTTTCCTCA
647 A-TTCTTTGCCACAATACTAA
647 ACTT-TTTGCCACAATACTAA
667 TAAGAGATATATAATTAGACGCCAAACAATTTGAAGGGTTTTTCACGCTTCTAATATTATTTTTC
1 TAAGAGATATATAATTAGACGCCAAACAATTTGAAGGGTTTTTCACGCTTCTAATATTATTTTTC
*
732 CTTTTTTTATCTAATTTATTTCTAATTAAATCGAAATAAGATTGAGATGCTCATAAAAACAAATC
66 CTTTTTTTATCTAATTTATTTCTAATTAAATCGAAACAAGATTGAGATGCTCATAAAAACAAATC
* *
797 CTTTAATCCATTGTGGCTGAGATTTGGTTTGATAAATATAGATATTTCAAAGAGTCATTCTACCA
131 CTTTAATCCATTGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAAGAGTCATTCTACCA
*
862 AAAATCATGCAAAACTGAGTCGATGCCCCCAAAATGCGTTTTAAGCCAAAAACCGTGATGGTTAG
196 AAAATCATGCAAAACTGAGTCGATG-CCCCAAAACGCGTTTTAAGCCAAAAACCGTGATGGTTAG
*
927 TACACGATTTCG-GCTAGAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTCCC
260 TACACGATTTCGTG-TAAAATTTTGC-AAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTCCC
* * *
991 ACAGTACTAATAAGAGATATATAATTGAACGCCAAAAAAATTGAAGTG-TTTTTCACGCTTCTAA
323 ACAATACTAATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAA
* * * *
1055 TATCATTTGT-C-TTTTTTTTCCTAATTTATTTCTAAATAAATCGAAAGAAGATTCAAATGATCA
388 TATCATTT-TCCTTTTTTTTTCCTAATTAAATTATAAATAAATCGAAACAAGATTCAAATGATCA
* * * *
1118 TAAAAACAAATTCTTTAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAAGG
452 TAAAAAAAAATCCTTTAATCCAATGTGGCTAAGATTTGGTTAGAGAAATATAGATATTTCAAAGA
* * * * *
1183 GTCATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAATGCGTTTTTCGCCAAAAACC
517 GTCATTCCACCAAAAATCATGCAAAACTGAGGCGACGCCCCAAAACGCGTTTTTAGCCAAAAACC
1248 GTGATGGTTAGTACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAGAATTTTTCCTCA
582 GTGATGGTTAGTACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAGAATTTTTCCTCA
1313 ACTTTTTGCCACAATACTAA
647 ACTTTTTGCCACAATACTAA
* * *
1333 TTAGAGATATATAATTAGAAGCC-AACAAATTTGAAGGGTTTTCCACGCTTCTAATATTATTTTT
1 TAAGAGATATATAATTAGACGCCAAAC-AATTTGAAGGGTTTTTCACGCTTCTAATATTATTTTT
* *
1397 CC-TTTTCTATCTAATTTATTTCTAATTAAATCGAAACATGATTGAGATGCTCATAAAAACAAAT
65 CCTTTTTTTATCTAATTTATTTCTAATTAAATCGAAACAAGATTGAGATGCTCATAAAAACAAAT
1461 CCTTTAATCCATTGTGGCTGAG
130 CCTTTAATCCATTGTGGCTGAG
Statistics
Matches: 755, Mismatches: 51, Indels: 21
0.91 0.06 0.03
Matches are distributed among these distances:
665 85 0.11
666 357 0.47
667 154 0.20
668 79 0.10
669 80 0.11
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (666 bp):
TAAGAGATATATAATTAGACGCCAAACAATTTGAAGGGTTTTTCACGCTTCTAATATTATTTTTC
CTTTTTTTATCTAATTTATTTCTAATTAAATCGAAACAAGATTGAGATGCTCATAAAAACAAATC
CTTTAATCCATTGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAAGAGTCATTCTACCA
AAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGT
ACACGATTTCGTGTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAACTTTTTCCCACA
ATACTAATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAATAT
CATTTTCCTTTTTTTTTCCTAATTAAATTATAAATAAATCGAAACAAGATTCAAATGATCATAAA
AAAAAATCCTTTAATCCAATGTGGCTAAGATTTGGTTAGAGAAATATAGATATTTCAAAGAGTCA
TTCCACCAAAAATCATGCAAAACTGAGGCGACGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGA
TGGTTAGTACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAGAATTTTTCCTCAACTT
TTTGCCACAATACTAA
Done.