Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010373.1 Corchorus capsularis cultivar CVL-1 contig10394, 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: 2114
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:277 original size:127 final size:133
Alignment explanation
Indices: 7--280 Score: 289
Period size: 127 Copynumber: 2.1 Consensus size: 133
1 TATATA
* ** *
7 CTGCCAAAAATACACGCAGAAAGTGAGTTGGGCCCCGTAAACGCCATTTTTAGCCCAATGACAGT
1 CTGCAAAAAATACACGCAGAAAGTGAGCGGGGCCCCGTAAACGCCATTTTTAGCCCAATAACAGT
* * * ***
72 GATGGTTTAGTACGCGATTTCCGTTAAGAATTGACCCGAAAATTGTTGTTTGAAATTTTGCCAAA
66 GATGG-TTA-TACACGATTTCCGCTAAGAATTGACCCAAAAAAAATTGTTTGAAATTTTGCCAAA
*
137 AAATT
129 AAACT
*
142 CTGCAAAAAAT-CACGCAGAAA-TGAGCCGGGGCCCCG-AAACG-CATTTTTAGCTCAATAACAG
1 CTGCAAAAAATACACGCAGAAAGTGAG-CGGGGCCCCGTAAACGCCATTTTTAGCCCAATAACAG
*
203 TGAT-G-T-TACACGATTTCGGCTAAGAATTGACCCAAAAAAAAATT-TTCTGAAAATTTTGCCA
65 TGATGGTTATACACGATTTCCGCTAAGAATTGACCC-AAAAAAAATTGTT-TG-AAATTTTGCCA
* *
264 CAATACT
127 AAAAACT
271 C-G-AAAAAATA
1 CTGCAAAAAATA
281 AAATAAATGA
Statistics
Matches: 119, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
127 33 0.28
128 9 0.08
129 17 0.14
131 1 0.01
132 22 0.18
133 9 0.08
134 18 0.15
135 10 0.08
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (133 bp):
CTGCAAAAAATACACGCAGAAAGTGAGCGGGGCCCCGTAAACGCCATTTTTAGCCCAATAACAGT
GATGGTTATACACGATTTCCGCTAAGAATTGACCCAAAAAAAATTGTTTGAAATTTTGCCAAAAA
ACT
Found at i:1494 original size:326 final size:324
Alignment explanation
Indices: 141--2113 Score: 2474
Period size: 326 Copynumber: 6.1 Consensus size: 324
131 GCCAAAAAAT
* * *
141 TCTGCAAAAAATCACGCAGAAATGAGCCGGGGCCCCGAAACGCATTTTTAGCTCAATAACAGTGA
1 TCTGCCAAAAATCACGCAGAAATGAGCCGGGG-TCCGAAACGCATTTTTAGCCCAATAACAGTGA
** *
206 T-G-T--TACACGATTTCGGCTAAGAATTGACCCAAAAAAAAATTTTCTGAAAATTTTGCCACAA
65 TGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACAA
* * *
267 TACTCGAAAAAATAAAATAAATGAATGTATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCG
130 TACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCG
* * * * * * *
332 TTTGTTCAATTTTTTTGTCCGAATTT-ATTTTAATTAAATCGAAAGAAAATTTAAATGCTCGTAA
195 TTT-TTCCATTTTTTTTTCCGAATTTAATTCTAA-TAAATCGAAACAAAATTCAGATACTCGTAA
* * * * * *
396 AAACGAATCCTTAAATCTAATGTGGCTGAGATTTAGTTCGATGAATAAAGATAATTCAAGGAGGC
258 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGGC
461 TA
323 TA
* * * ** *
463 TCTGCCAATAATAACGCCA-AACTGAGCCGGTGGTCCGAAACGCGGTTTTAGACCAATAACAGTG
1 TCTGCCAAAAATCACG-CAGAAATGAGCCGG-GGTCCGAAACGCATTTTTAGCCCAATAACAGTG
** * ** ** * ** *
527 ATGGTTAGTACACGATTTCAACTATGAATTGACCCGTAATTTTTTTTTCAAAAATTTTTTCCACA
64 ATGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACA
*
592 ATACTCGTAAAAATCAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATC
129 ATACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATC
* * *
657 GTTTTTTCA--TATTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATACTCGTAAA
194 GTTTTTCCATTTTTTTTTCCGAATTTAATTCTAATAAATCGAAACAAAATTCAGATACTCGTAAA
* *
720 AACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCATTGAATAGAGATATTTCAAGGAGGCT
259 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGGCT
785 A
324 A
* * *
786 TCTGCCAAAAATCACGCAGAAATGAGTC-TGGTCCCCGAAACGCATTTTTAGCCCATTAACAGTG
1 TCTGCCAAAAATCACGCAGAAATGAGCCGGGGT--CCGAAACGCATTTTTAGCCCAATAACAGTG
*
850 ATGGTTGTTAGTACACGATTTCGGCTAAGATTTGACCCAAAAAA--ATTTTCTGAAATTTTTGCC
64 AT-G--GTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCC
*
913 ACAATACTCGGAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAAT
126 ACAATACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAAT
* *
978 ATCGTTTGTT-CAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTC
191 ATCGTTT-TTCCATTTTTTTTTCCGAATTTAATTCTAA-TAAATCGAAACAAAATTCAGATACTC
* * * * * * * * *
1042 GTAAAATCGAATCGTTAAATCCAATGTAGCTGATATTTGGTTCGATGAATAGAAATATTTCATGT
254 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGG
*
1107 AGGGTA
319 AGGCTA
* **
1113 TCTGTCAAAAATCACGCA-AAACTGAGCCGGGAGTCCGAAACGCGGTTTTAGCCCAATAACAGTG
1 TCTGCCAAAAATCACGCAGAAA-TGAGCCGGG-GTCCGAAACGCATTTTTAGCCCAATAACAGTG
* * * *
1177 ATGATTAGTATACGATTTCGGCTAAGAATTGATCCAAAAAATTCTTTTCTGAAATTTTTGCCACA
64 ATGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACA
* * * *
1242 ATACTCAG-AAAAATAATATAATTGAATACATAAAAAATTGAAGGGTTTTTTACACATCCAATAT
129 ATACTC-GTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATAT
* *
1306 CGTTTTTCCATTTGTTTTTTACGAATTTAATTCCAATAAAATCGAAACAAAATTCAGATACTCGT
193 CGTTTTTCCATTT-TTTTTTCCGAATTTAATTCTAAT-AAATCGAAACAAAATTCAGATACTCGT
*
1371 AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAG
256 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAG
1436 GCTA
321 GCTA
** * * * * * * *
1440 TCTGCCAAAAATCACGCAGAACCGAGACGAGGTCCGAAACGCGTATGTAGCCCAATAATAGTAAT
1 TCTGCCAAAAATCACGCAGAAATGAGCCGGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGAT
* ** * * ** * ** *
1505 GGTTAGCACACGATTTCAACTACGAATTGACCC-GAATTTTTTTTTCAAAAATTTTTTCCACAAT
66 GGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACAAT
* * *
1569 ACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGCTTTT-ACACATTCAATATCGT
131 ACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCGT
* *
1633 TTTTCCATTTGTTTTTTACGAATTTAATTCCAATAAAATCGAAACAAAATTCAGATACTCGTAAA
196 TTTTCCATTT-TTTTTTCCGAATTTAATTCTAAT-AAATCGAAACAAAATTCAGATACTCGTAAA
* * *
1698 AACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCATTGAATAGAGATCTTTCAAGGAGGCT
259 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGGCT
1763 A
324 A
* * * *
1764 TTTGCCAAAAATCACGAAGAAATGAGCCGGGGACCCGAAACGCATTTTTAGCCCATTAACAGTGA
1 TCTGCCAAAAATCACGCAGAAATGAGCCGGGG-TCCGAAACGCATTTTTAGCCCAATAACAGTGA
* *
1829 TGGTTAGTACACGATTTCGGCTAAGATTTGACCCAAAAAAAT-TTTTCTGAAATTTTTGCCACAA
65 TGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACAA
* * *
1893 TACTCGGAAAAATAATATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCA
130 TACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCG
* * * *
1958 TTTTTTCA--TTTTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATGCTTGTAAAA
195 TTTTTCCATTTTTTTTTCCGAATTTAATTCTAATAAATCGAAACAAAATTCAGATACTCGTAAAA
** * ** * * ** *
2021 ATGAATTCTTATTTCCAATGTGGATGAGATTTAGTTTGATGAATAGAGATATTTCAAGGAGGTTA
260 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGGCTA
2086 TCTGCCAAAAATCACGCA-AAACTGAGCC
1 TCTGCCAAAAATCACGCAGAAA-TGAGCC
2114 T
Statistics
Matches: 1426, Mismatches: 193, Indels: 64
0.85 0.11 0.04
Matches are distributed among these distances:
321 6 0.00
322 156 0.11
323 172 0.12
324 300 0.21
325 193 0.14
326 330 0.23
327 264 0.19
328 3 0.00
329 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (324 bp):
TCTGCCAAAAATCACGCAGAAATGAGCCGGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGAT
GGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACAAT
ACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCGT
TTTTCCATTTTTTTTTCCGAATTTAATTCTAATAAATCGAAACAAAATTCAGATACTCGTAAAAA
CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGGCTA
Found at i:1518 original size:650 final size:646
Alignment explanation
Indices: 141--2107 Score: 2575
Period size: 650 Copynumber: 3.0 Consensus size: 646
131 GCCAAAAAAT
* * * * * * * *
141 TCTGCAAAAAATCACGCAGAAATGAGCCGGGGCCCCGAAACGCATTTTTAGCTCAATAACAG---
1 TCTGCCAAAAATCACGCAGAAACGAGAC-AGGTCCCGAAACGCATATGTAGCCCAATAACAGTAA
* *
203 TGATGTT---ACACGATTTCGGCTAAGAATTGACCCAAAAAAAAATTTTCTGAAAATTTTGCCAC
65 TGGTGTTAGCACACGATTTCGGCTAAGAATTGACCC-AAAAAAAATTTTCTGAAATTTTTGCCAC
* *
265 AATACTCGAAAAAATAAAATAAATGAATGTATAAAAAATTGAAGGGTTTTTCACGCATCCAATAT
129 AATACTCGAAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATAT
* * * *
330 CGTTTGTTCAATTTTTTTGTCCGAATTTATTT-TAATTAAATCGAAAGAAAATTTAAATGCTCGT
194 CGTTTGTTCAATTTTTTT-TCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGT
* * *
394 AAAAACGAATCCTTAAATCTAATGTGGCTGAGATTTAGTTCGATGAATA-AAGATAATTCAAGGA
258 AAAAACGAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAA-ATATTTCAAGGA
* * * *
458 GGCTATCTGCCAATAATAACGCCAAACTGAGCCGGTGGTCCGAAACGCGGTTTTAGACCAATAAC
322 GGCTATCTGCCAAAAATCACGCAAAACTGAGCCGG-GGTCCGAAACGCGGTTTTAGCCCAATAAC
** * * *** ** *
523 AGTGATGGTTAGTACACGATTTCAACTATGAATTGACCCGTAATTTTTTTTTCAAAAATTTTTTC
386 AGTGATGGTTAGTACACGATTTCGGCTAAGAATTGACCC-AAAAAATTTTTTCTGAAATTTTTGC
588 CACAATACTCGTAAAAATCAA-ATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCA
450 CACAATACTCG-AAAAAT-AATATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCA
*
652 ATATCGTTTTTTCATATTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATACTCGT
513 ATATCGTTTTTTCATTTTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATACTCGT
*
717 AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCATTGAATAGAGATATTTCAAGGAG
578 AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAG
782 GCTA
643 GCTA
* * * * * * *
786 TCTGCCAAAAATCACGCAGAAATGAGTCTGGTCCCCGAAACGCATTTTTAGCCCATTAACAGTGA
1 TCTGCCAAAAATCACGCAGAAACGAGACAGGT-CCCGAAACGCATATGTAGCCCAATAACAGTAA
* *
851 TGGTTGTTAGTACACGATTTCGGCTAAGATTTGACCC-AAAAAAATTTTCTGAAATTTTTGCCAC
65 TGG-TGTTAGCACACGATTTCGGCTAAGAATTGACCCAAAAAAAATTTTCTGAAATTTTTGCCAC
*
915 AATACTCGGAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATAT
129 AATACTCGAAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATAT
980 CGTTTGTTCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTA
194 CGTTTGTTCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTA
* * * * * *
1045 AAATCGAATCGTTAAATCCAATGTAGCTGATATTTGGTTCGATGAATAGAAATATTTCATGTAGG
259 AAAACGAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAAATATTTCAAGGAGG
* *
1110 GTATCTGTCAAAAATCACGCAAAACTGAGCCGGGAGTCCGAAACGCGGTTTTAGCCCAATAACAG
324 CTATCTGCCAAAAATCACGCAAAACTGAGCCGGG-GTCCGAAACGCGGTTTTAGCCCAATAACAG
* * *
1175 TGATGATTAGTATACGATTTCGGCTAAGAATTGATCCAAAAAATTCTTTTCTGAAATTTTTGCCA
388 TGATGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATT-TTTTCTGAAATTTTTGCCA
* * *
1240 CAATACTCAGAAAAATAATATAATTGAATACATAAAAAATTGAAGGGTTTTTTACACATCCAATA
452 CAATACTC-GAAAAATAATATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATA
* * * *
1305 TCGTTTTTCCATTTGTTTTTTACGAATTTAATTCCAATAAAATCGAAACAAAATTCAGATACTCG
516 TCGTTTTTTCA--T-TTTTTTCCGAATTTATTTCTAAT-AAATCGAAACAAAATTCAGATACTCG
1370 TAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGA
577 TAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGA
1435 GGCTA
642 GGCTA
* * *
1440 TCTGCCAAAAATCACGCAGAACCGAGACGAGGT-CCGAAACGCGTATGTAGCCCAATAATAGTAA
1 TCTGCCAAAAATCACGCAGAAACGAGAC-AGGTCCCGAAACGCATATGTAGCCCAATAACAGTAA
** * * ***** ** *
1504 T-G-GTTAGCACACGATTTCAACTACGAATTGACCCGAATTTTTTTTTCAAAAATTTTTTCCACA
65 TGGTGTTAGCACACGATTTCGGCTAAGAATTGACCCAAAAAAAATTTTCTGAAATTTTTGCCACA
* * * *
1567 ATACTCGTAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGCTTTT-ACACATTCAATATC
130 ATACTCGAAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATC
* * * * *
1631 GTTT-TTCCATTTGTTTTTTACGAATTTAATTCCAATAAAATCGAAACAAAATTCAGATACTCGT
195 GTTTGTT-CAATT-TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGT
* * * *
1695 AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTC-ATTGAATAGAGATCTTTCAAGGA
258 AAAAACGAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGA-TGAATAGAAATATTTCAAGGA
* * * ** *
1759 GGCTATTTGCCAAAAATCACG-AAGAAATGAGCCGGGGACCCGAAACGCATTTTTAGCCCATTAA
322 GGCTATCTGCCAAAAATCACGCAA-AACTGAGCCGGGG-TCCGAAACGCGGTTTTAGCCCAATAA
* *
1823 CAGTGATGGTTAGTACACGATTTCGGCTAAGATTTGACCCAAAAAAATTTTTCTGAAATTTTTGC
385 CAGTGATGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTTTTTCTGAAATTTTTGC
1888 CACAATACTCGGAAAAATAATATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAA
450 CACAATACTC-GAAAAATAATATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAA
* * *
1953 TATCATTTTTTCATTTTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATGCTTGTA
514 TATCGTTTTTTCATTTTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATACTCGTA
** * ** * * * **
2018 AAAATGAATTCTTATTTCCAATGTGGATGAGATTTAGTTTGATGAATAGAGATATTTCAAGGAGG
579 AAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGG
*
2083 TTA
644 CTA
2086 TCTGCCAAAAATCACGCA-AAAC
1 TCTGCCAAAAATCACGCAGAAAC
2108 TGAGCCT
Statistics
Matches: 1166, Mismatches: 131, Indels: 50
0.87 0.10 0.04
Matches are distributed among these distances:
644 2 0.00
645 56 0.05
646 101 0.09
647 20 0.02
648 3 0.00
649 26 0.02
650 499 0.43
651 264 0.23
652 27 0.02
653 45 0.04
654 120 0.10
655 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (646 bp):
TCTGCCAAAAATCACGCAGAAACGAGACAGGTCCCGAAACGCATATGTAGCCCAATAACAGTAAT
GGTGTTAGCACACGATTTCGGCTAAGAATTGACCCAAAAAAAATTTTCTGAAATTTTTGCCACAA
TACTCGAAAAAATAAAATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCG
TTTGTTCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATACTCGTAAA
AACGAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAAATATTTCAAGGAGGCT
ATCTGCCAAAAATCACGCAAAACTGAGCCGGGGTCCGAAACGCGGTTTTAGCCCAATAACAGTGA
TGGTTAGTACACGATTTCGGCTAAGAATTGACCCAAAAAATTTTTTCTGAAATTTTTGCCACAAT
ACTCGAAAAATAATATAATTGAATGCATAAAAAATTGAAGGGTTTTTCACGCATCCAATATCGTT
TTTTCATTTTTTTCCGAATTTATTTCTAATAAATCGAAACAAAATTCAGATACTCGTAAAAACAA
ATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATAGAGATATTTCAAGGAGGCTA
Done.