Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005036.1 Corchorus capsularis cultivar CVL-1 contig05054, 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: 2411
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Found at i:1067 original size:333 final size:331
Alignment explanation
Indices: 1--1583 Score: 2073
Period size: 332 Copynumber: 4.8 Consensus size: 331
* * * * * * * *
1 TTTTTTTTACTAGCATCCCAAACTGGTTTCAATTTAATTAGAAATTAATTAGGAACAAATAGGAA
1 TTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAA
* * * *
66 AAATGATATTAAAAGCGTGAGAACTCCTTCAATCTTTTTTGTGTTGAATTATATATTTTTTATTA
66 AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
* * * * ** *
131 GTATTGTGGCCAAAGATTGAGCATATATGTATCAAGTCAACTTTTTGCAAAATTTTAGCCGAAAT
131 GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAAT
* * * * **
196 CTTGTACTAACCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCACAGCTCAGTTTTGTATG
196 CGT-TACTAACCATCACGATTTTTGACTAAAAATGCGTTCCGAGGCCCCAGCTCAGTTTTACATG
** * * * * * *
261 ATTTTTGGTGCTAAGACTCATTGAAATGTCTATATTTATTGAACGAAATCTCACCCATATTGGAA
260 ATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCAGCCACATTGGAA
*
326 TAAAGGA
325 TTAAGGA
* * * *
333 TTTTTTTTTACTAGCATCTCAATTCGGTTTCGATTTCATTAAAAATTAATTCGGAAAAAAATAGG
1 -TTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATAGG
* * * * *
398 AAAAATGATATTAGAAGCGTGAAAACTCCTACAAT-ATTTTTTGTGTTGAGTTATATGTTTTTTA
64 AAAAATGATATTAGAAGCATGAGAACTCCTTCAATCA-TTTTTGTGTTGAATTATATATTTTTTA
* ** ** * *
462 AGAGTATTGTGGTAAAAAATTGAATAGAAATGTTTTGGGTCAATTTTTTACAAAATTTTAGCCGA
128 TGAGTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGA
* * *
527 AATCGTGTACTAACCATCACGATTTTTGACTAAAAA-GCCGTTCTG-GG-GCCAGACTCGGTTTT
193 AATCGT-TACTAACCATCACGATTTTTGACTAAAAATG-CGTTCCGAGGCCCCAG-CTCAGTTTT
* * * * *
589 ACATGATTTTTGGCACCAAGACTCATTGAAATTTCTATATTTATGGAAAGAAAACTCAGCGAAAT
255 ACATGATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCAGCCACAT
654 TGGAATTAAGGA
320 TGGAATTAAGGA
* * * * * *
666 TTTTTTGTACCAGCATCTCAATCCGGTTTCGATTTAACTAGAAATTAATTCGGAAAAAATACGAA
1 TTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAA
* *
731 AAATGGTATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTCTTGAATTATATATTTTTTATGA
66 AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
* *
796 GTATTGTAGCCAAAAATTGAGCAGAAATGTTTCGAGTCAATTTTTTTGCAAAATTTTAGCCGAAA
131 GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAA-TTTTTTGCAAAATTTTAGCCGAAA
* * * *
861 TCGTTCACTAACCATCACGATTTTTGACTAAATATGCGTTCCTAGGCCCCTGCTCAGTATTACAT
195 TCGTT-ACTAACCATCACGATTTTTGACTAAAAATGCGTTCCGAGGCCCCAGCTCAGTTTTACAT
** ** *
926 GATTTTTTACTTCAGGACTCATTGAAATATCTATATTTATCGAAAGAAATCTC-GACCACATTGG
259 GATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCAG-CCACATTGG
990 AATTAAGGA
323 AATTAAGGA
* *
999 TTTTTTTTACTAGCAACT-AATCCTGTTTCGATTTAATTAGAAATTAATTCGTAAAAAAATATGA
1 TTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAGAAATTAATTCG-AAAAAAATAGGA
* * * *
1063 AAAATGATATTTGAAGCATCAGAACTCCTTCAATCCTTTTTGTGTTCAATTATATATTTTTTATG
65 AAAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATG
* *
1128 ATTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAATTTTAGCTGAAA
130 AGTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAA
* * * *
1193 TCGTGCACTAACCATCATGATTTTTTACTAAAAATGCGTTCCGAGGCCCCTGCTCAGTTTTACAT
195 TCGT-TACTAACCATCACGATTTTTGACTAAAAATGCGTTCCGAGGCCCCAGCTCAGTTTTACAT
*
1258 GATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAACGAAATCTCAGCCACATTGGA
259 GATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCAGCCACATTGGA
1323 ATTAAGGA
324 ATTAAGGA
* * **
1331 TTTTTTTTACTAGCAACTCAATCCGGTTTCAATTTAATTAGAAATTAATTCGTAAAAAATATAAA
1 TTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAA
* * *
1396 AAATGATATTAGAAGCATGAGAACTCATTCAATCCTTTTTGTGTTCAATTATATATTTTTTATGA
66 AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
* * * *
1461 TTATTGTGGCCAAAAATTGATCAGAAATGTTTCGGGTCAATATTTTGCAAAATTTTAGTCGAAAT
131 GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAAT
* *
1526 CGTGTACTAACCATCACGATTTTTGACTAAAAA-GCGTTTCGGGGCCCCAGCTCAGTTT
196 CGT-TACTAACCATCACGATTTTTGACTAAAAATGCGTTCCGAGGCCCCAGCTCAGTTT
1584 CGGGGCCCCA
Statistics
Matches: 1099, Mismatches: 136, Indels: 32
0.87 0.11 0.03
Matches are distributed among these distances:
331 123 0.11
332 468 0.43
333 347 0.32
334 161 0.15
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (331 bp):
TTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGGAA
AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAAT
CGTTACTAACCATCACGATTTTTGACTAAAAATGCGTTCCGAGGCCCCAGCTCAGTTTTACATGA
TTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCAGCCACATTGGAAT
TAAGGA
Found at i:1334 original size:665 final size:663
Alignment explanation
Indices: 1--1581 Score: 2168
Period size: 665 Copynumber: 2.4 Consensus size: 663
* * * * * *
1 TTTTTTTTACTAGCATCCCAAACTGGTTTCAATTTAATTAGAAATTAATTAGGAACAAATAGGAA
1 TTTTTTTTACTAGCATCTCAATCCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATACGAA
* * * *
66 AAATGATATTAAAAGCGTGAGAACTCCTTCAATCTTTTTTGTGTTGAATTATATATTTTTTATTA
66 AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
* * * * * *
131 GTATTGTGGCCAAAGATTGAGCATATATGTATCAAGTCAACTTTTTGCAAAATTTTAGCCGAAAT
131 GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGAGTCAATTTTTTGCAAAATTTTAGCCGAAAT
* * * **
196 CTTGTACTAACCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCACAGCTCAGTTTTGTATG
196 CGT-TACTAACCATCACGATTTTTGACTAAAAACGCGTTCCGAGGCCACAGCTCAGTATTACATG
* * * * *
261 ATTTTTGGTGCTAAGACTCATTGAAATGTCTATATTTATTGAACGAAATCTCACCCATATTGGAA
260 ATTTTT-GTACTAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCACCCACATTGGAA
* * *
326 TAAAGGATTTTTTTTTACTAGCATCTCAATTCGGTTTCGATTTCATTAAAAATTAATTCGGAAAA
324 TAAAGGATTTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAAAAATTAATTCGGAAAA
* * * * * *
391 AAATAGGAAAAATGATATTAGAAGCGTGAAAACTCCTACAATATTTTTTGTGTTGAGTTATATGT
389 AAATAGGAAAAATGATATTAGAAGCATCAAAACTCCTACAATACTTTTTGTGTTCAATTATATAT
* * *
456 TTTTTAAGAGTATTGTGGTAAAAAATTGAATAGAAATGTTTTGGGTCAATTTTTTACAAAATTTT
454 TTTTTAAGAGTATTGTGGCAAAAAATTGAACAGAAATGTTTCGGGTCAATTTTTTACAAAATTTT
* * * *
521 AGCCGAAATCGTGTACTAACCATCACGATTTTTGACTAAAAAGCCGTTCTGGGGCCAGACTCGGT
519 AGCCGAAATCGTGCACTAACCATCACGATTTTTGACTAAAAAGCCGTTCCGGGCCCAGACTCAGT
* * *
586 TTTACATGATTTTTGGCACCAAGACTCATTGAAATTTCTATATTTATGGAAAGAAAACTCAGCGA
584 TTTACATGATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAAACTCAGCCA
651 AATTGGAATTAAGGA
649 AATTGGAATTAAGGA
* * * *
666 TTTTTTGTACCAGCATCTCAATCCGGTTTCGATTTAACTAGAAATTAATTCGGAAAAAATACGAA
1 TTTTTTTTACTAGCATCTCAATCCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATACGAA
* *
731 AAATGGTATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTCTTGAATTATATATTTTTTATGA
66 AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
*
796 GTATTGTAGCCAAAAATTGAGCAGAAATGTTTCGAGTCAATTTTTTTGCAAAATTTTAGCCGAAA
131 GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGAGTCAA-TTTTTTGCAAAATTTTAGCCGAAA
* * * * *
861 TCGTTCACTAACCATCACGATTTTTGACTAAATATGCGTTCCTAGGCCCCTGCTCAGTATTACAT
195 TCGTT-ACTAACCATCACGATTTTTGACTAAAAACGCGTTCCGAGGCCACAGCTCAGTATTACAT
*
926 GATTTTT-TACTTCAGGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCGA-CCACATTG
259 GATTTTTGTAC-T-AAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTC-ACCCACATTG
* * * *
989 GAATTAAGGA-TTTTTTTTACTAGCAACT-AATCCTGTTTCGATTTAATTAGAAATTAATTCGTA
321 GAATAAAGGATTTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAAAAATTAATTCGGA
* * * * *
1052 AAAAAATATGAAAAATGATATTTGAAGCATCAGAACTCCTTCAATCCTTTTTGTGTTCAATTATA
386 AAAAAATAGGAAAAATGATATTAGAAGCATCAAAACTCCTACAATACTTTTTGTGTTCAATTATA
* * * * *
1117 TATTTTTTATGATTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGGGTCAATTTTTTGCAAAAT
451 TATTTTTTAAGAGTATTGTGGCAAAAAATTGAACAGAAATGTTTCGGGTCAATTTTTTACAAAAT
* * * *
1182 TTTAGCTGAAATCGTGCACTAACCATCATGATTTTTTACTAAAAATG-CGTTCCGAGGCCCCTG-
516 TTTAGCCGAAATCGTGCACTAACCATCACGATTTTTGACTAAAAA-GCCGTTCCG-GG-CCCAGA
* *
1245 CTCAGTTTTACATGATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAACGAAATCT
578 CTCAGTTTTACATGATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAAACT
*
1310 CAGCCACATTGGAATTAAGGA
643 CAGCCAAATTGGAATTAAGGA
* * **
1331 TTTTTTTTACTAGCAACTCAATCCGGTTTCAATTTAATTAGAAATTAATTCGTAAAAAATATAAA
1 TTTTTTTTACTAGCATCTCAATCCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATACGAA
* * *
1396 AAATGATATTAGAAGCATGAGAACTCATTCAATCCTTTTTGTGTTCAATTATATATTTTTTATGA
66 AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
* * * * *
1461 TTATTGTGGCCAAAAATTGATCAGAAATGTTTCGGGTCAATATTTTGCAAAATTTTAGTCGAAAT
131 GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGAGTCAATTTTTTGCAAAATTTTAGCCGAAAT
* * *
1526 CGTGTACTAACCATCACGATTTTTGACTAAAAA-GCGTTTCGGGGCCCCAGCTCAGT
196 CGT-TACTAACCATCACGATTTTTGACTAAAAACGCGTTCCGAGGCCACAGCTCAGT
1582 TTCGGGGCCC
Statistics
Matches: 804, Mismatches: 103, Indels: 20
0.87 0.11 0.02
Matches are distributed among these distances:
663 19 0.02
664 243 0.30
665 403 0.50
666 138 0.17
667 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (663 bp):
TTTTTTTTACTAGCATCTCAATCCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATACGAA
AAATGATATTAGAAGCATGAGAACTCCTTCAATCATTTTTGTGTTGAATTATATATTTTTTATGA
GTATTGTGGCCAAAAATTGAGCAGAAATGTTTCGAGTCAATTTTTTGCAAAATTTTAGCCGAAAT
CGTTACTAACCATCACGATTTTTGACTAAAAACGCGTTCCGAGGCCACAGCTCAGTATTACATGA
TTTTTGTACTAAGACTCATTGAAATATCTATATTTATCGAAAGAAATCTCACCCACATTGGAATA
AAGGATTTTTTTTTACTAGCAACTCAATCCGGTTTCGATTTAATTAAAAATTAATTCGGAAAAAA
ATAGGAAAAATGATATTAGAAGCATCAAAACTCCTACAATACTTTTTGTGTTCAATTATATATTT
TTTAAGAGTATTGTGGCAAAAAATTGAACAGAAATGTTTCGGGTCAATTTTTTACAAAATTTTAG
CCGAAATCGTGCACTAACCATCACGATTTTTGACTAAAAAGCCGTTCCGGGCCCAGACTCAGTTT
TACATGATTTTTGGCACCAAGACTCATTGAAATATCTATATTTATCGAAAGAAAACTCAGCCAAA
TTGGAATTAAGGA
Found at i:2259 original size:295 final size:293
Alignment explanation
Indices: 1857--2400 Score: 837
Period size: 295 Copynumber: 1.8 Consensus size: 293
1847 ATCTCAGCGA
1857 CATTGGAATTAAGGATTTTTTTTTACCAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAAT
1 CATTGGAATTAAGGATTTTTTTTTACCAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAAT
* *
1922 TCGGAAAAATACGAAAAATTGTATTAGAAGCATGAGAACTCCTGCAATCTTTTTTGTGTTGAATT
66 TCGAAAAAATACGAAAAATTGTATTAGAAGCATGAGAACTCCTGCAATATTTTTTGTGTTGAATT
* *
1987 ATACATTTTTTATGAGTATTGTAGCCA-AAATTTGAGC-AGAAATGTTTCGAG-TCAATTTTTTT
131 ATACAATTTTTATGAGTATTGTAGCCAGAAA-TTGA-CTAGAAATGTTACG-GCTCAA-TTTTTT
* * * *
2049 GCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGAATAAAAACGCGTTTCGCAGC
192 GAAAAATTTTAGCCGAAATCGTATACTAACCATCACGATTTTCGAATAAAAACGCGTTTCGCAGC
2114 CTCGGCTCAGTTTTGCATGATTTTTGGCGCCAACACT
257 CTCGGCTCAGTTTTGCATGATTTTTGGCGCCAACACT
*
2151 CATTGGAATTAAGGA-TTTTTTTTACTAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAAT
1 CATTGGAATTAAGGATTTTTTTTTACCAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAAT
* * *
2215 TCAGAAAAAAATAGGAAAAA-TGATATTAGAAGCGTGAGAACTCCTTCAATATTTTTTGTGTTGA
66 TC-G-AAAAAATACGAAAAATTG-TATTAGAAGCATGAGAACTCCTGCAATATTTTTTGTGTTGA
* * *
2279 GTTATATAATTTTTATGAGTATTGTGGCCAGAAATTGACTAGAAATGTTACGGCTCAATTTTTTG
128 ATTATACAATTTTTATGAGTATTGTAGCCAGAAATTGACTAGAAATGTTACGGCTCAATTTTTTG
* *
2344 AAAAATTTTAGCCGAAATCGTATACTAAGCATCACGATTTTCGACTAAAAACGCGTT
193 AAAAATTTTAGCCGAAATCGTATACTAACCATCACGATTTTCGAATAAAAACGCGTT
2401 CCGGGGCCCC
Statistics
Matches: 227, Mismatches: 17, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
293 50 0.22
294 78 0.34
295 96 0.42
296 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (293 bp):
CATTGGAATTAAGGATTTTTTTTTACCAGCATCTCAATCCGGTTTCGATTTAATTAGAAATTAAT
TCGAAAAAATACGAAAAATTGTATTAGAAGCATGAGAACTCCTGCAATATTTTTTGTGTTGAATT
ATACAATTTTTATGAGTATTGTAGCCAGAAATTGACTAGAAATGTTACGGCTCAATTTTTTGAAA
AATTTTAGCCGAAATCGTATACTAACCATCACGATTTTCGAATAAAAACGCGTTTCGCAGCCTCG
GCTCAGTTTTGCATGATTTTTGGCGCCAACACT
Done.