Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010459.1 Corchorus capsularis cultivar CVL-1 contig10480, 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: 13468
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:382 original size:70 final size:70
Alignment explanation
Indices: 306--512 Score: 270
Period size: 78 Copynumber: 2.8 Consensus size: 70
296 TAACTAAAAT
*
306 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
371 AGTTG
66 AGTTG
*
376 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGAGATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
441 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * *
454 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGA
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
513 TTTGAGTAAA
Statistics
Matches: 120, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
70 47 0.39
71 3 0.03
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 62 0.52
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:384 original size:78 final size:78
Alignment explanation
Indices: 300--469 Score: 313
Period size: 78 Copynumber: 2.2 Consensus size: 78
290 TTTTTTTAAC
* * *
300 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGAGATTAGATTTAATTATATAAAAATAGA
365 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
378 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGAGATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGAGATTAGATTTAATTATATAAAAATAGA
443 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
456 TAAAATAGTAAAAT
1 TAAAATAGTAAAAT
470 AAAATAATTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGAGATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:2287 original size:27 final size:29
Alignment explanation
Indices: 2257--2322 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
2247 GAAACTTGGA
2257 TGCT-CTT-ATCCAAATACTCATCTGTTT
1 TGCTGCTTAATCCAAATACTCATCTGTTT
2284 TGCTGCTTACATCCAAATACTCATCTGTTT
1 TGCTGCTTA-ATCCAAATACTCATCTGTTT
*
2314 TGATGCTTA
1 TGCTGCTTA
2323 CATCTGCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 4 0.11
28 3 0.09
30 28 0.80
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (29 bp):
TGCTGCTTAATCCAAATACTCATCTGTTT
Found at i:2298 original size:30 final size:30
Alignment explanation
Indices: 2264--2326 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
2254 GGATGCTCTT
*
2264 ATCCAAATACTCATCTGTTTTGCTGCTTAC
1 ATCCAAATACTCATCTGTTTTGATGCTTAC
2294 ATCCAAATACTCATCTGTTTTGATGCTTAC
1 ATCCAAATACTCATCTGTTTTGATGCTTAC
2324 ATC
1 ATC
2327 TGCTATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (30 bp):
ATCCAAATACTCATCTGTTTTGATGCTTAC
Found at i:2519 original size:30 final size:30
Alignment explanation
Indices: 2485--2543 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2475 TGCTCTTATC
2485 CAAATATTCAGCTGTCATACTGCTTACATT
1 CAAATATTCAGCTGTCATACTGCTTACATT
* ** *
2515 CAAATATTCATCTGTTTTGCTGCTTACAT
1 CAAATATTCAGCTGTCATACTGCTTACAT
2544 ATGCTATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (30 bp):
CAAATATTCAGCTGTCATACTGCTTACATT
Found at i:2709 original size:217 final size:218
Alignment explanation
Indices: 2183--2711 Score: 604
Period size: 218 Copynumber: 2.4 Consensus size: 218
2173 GAAGAAAGTT
* * ** * * * *
2183 TTGACAGAATTATAGAGAAAGAATTCCACCTATGACTAGTTTCAGCCTACTTTCAACCAAATTAG
1 TTGACAGAATTATAGAGAAAGAATTCTACCTGTGACCGGTTTCAACCCATTTTCAACCAAATCAG
* * ** *
2248 AAACTTG-GATGCTCTTATCCAAATACTCATCTGTTTTGCTGCTTACATCCAAATACTCATCTGT
66 AAACTTGAG-TGCTCTTATCCAAATATTCAGCTGTCATACTGCTTACATCCAAATACTCATCTGT
* * * * *
2312 TTTGATGCTTACATCTGCTATTTTCAATTAAAAGTTATATAAGTAGCAGTGTGAAATGGAAATAA
130 TTTGATGCTTACATATGCTATTTCCAATAAAAAGTTATATAAGTAGCAATGTGAAATAGAAATAA
* * * *
2377 CAATTTATGTGGTCATAAAAATTT
195 CAATTAAAGTGCTCATAAAAATTA
* * *
2401 TTGACGGAATTATAGAGAAAGAATTCTACCTGTGACTGGTTTCAGCCCATTTTCAACCAAATCAG
1 TTGACAGAATTATAGAGAAAGAATTCTACCTGTGACCGGTTTCAACCCATTTTCAACCAAATCAG
* *
2466 AAACTTGAGTGCTCTTATCCAAATATTCAGCTGTCATACTGCTTACATTCAAATATTCATCTGTT
66 AAACTTGAGTGCTCTTATCCAAATATTCAGCTGTCATACTGCTTACATCCAAATACTCATCTGTT
* * * *
2531 TTGCTGCTTACATATGCTATTTCCAAATAAAAAAGTTGTATAAGTAGCAATTTGAAATAGAAATC
131 TTGATGCTTACATATGCTATTTCC-AAT-AAAAAGTTATATAAGTAGCAATGTGAAATAGAAATA
**
2596 GTAA-TAAAG-GCT-ATATAAAATTA
194 ACAATTAAAGTGCTCATA-AAAATTA
* * *
2619 TT-ACAGAATTCA-AGATACAA-CATTCTACCTGTGACCGGTTTCAACCCATTTTTAACCAAATC
1 TTGACAGAATT-ATAGAGA-AAGAATTCTACCTGTGACCGGTTTCAACCCATTTTCAACCAAATC
* * *
2681 AGAAACTCGAGTGCTCCTATCTAAATATTCA
64 AGAAACTTGAGTGCTCTTATCCAAATATTCA
2712 TCTGCTATAT
Statistics
Matches: 267, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
217 80 0.30
218 148 0.55
219 7 0.03
220 32 0.12
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (218 bp):
TTGACAGAATTATAGAGAAAGAATTCTACCTGTGACCGGTTTCAACCCATTTTCAACCAAATCAG
AAACTTGAGTGCTCTTATCCAAATATTCAGCTGTCATACTGCTTACATCCAAATACTCATCTGTT
TTGATGCTTACATATGCTATTTCCAATAAAAAGTTATATAAGTAGCAATGTGAAATAGAAATAAC
AATTAAAGTGCTCATAAAAATTA
Found at i:3286 original size:239 final size:239
Alignment explanation
Indices: 2862--3819 Score: 1619
Period size: 239 Copynumber: 4.0 Consensus size: 239
2852 CTTCTTCGAC
* *
2862 TGATTCGAAAACTTGACTGCCCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTACAATTT
1 TGATCCGAAAACTTGACTGCCCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTGCAATTT
* * *
2927 CCAAATGAAAGTTGTATAAGTAGCAGGAAATAATGAAATTACCAACATATATGGCCATAAAACAT
66 CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCATAAAACAT
* *
2992 TTTGACATGAATATAAAGAAAGAAATCTACATGTGACCGGTTTCAGCCCATTTTCAACAATACCA
131 TTTGACATGAATATAAAGAAAGAATTCTACATGTGACCGGTTTCAGCCCATTTTCAACTATACCA
* *
3057 GAAACTTGAGTGCTCCTATCCAAATATTCATCTATTATGTCGCT
196 GAAACTTGAGCGCTCCTATCCAAATATTCATCTGTTATGTCGCT
* * *
3101 TGATCCGAAAACCTGACTACTCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTGCAATTT
1 TGATCCGAAAACTTGACTGCCCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTGCAATTT
*
3166 CGAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCATAAAACAT
66 CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCATAAAACAT
* *
3231 TATGACATGAATATAAAGAAAGAATTCTACATGTGACCGGTTTCAGCCCATTTTCAACCATACCA
131 TTTGACATGAATATAAAGAAAGAATTCTACATGTGACCGGTTTCAGCCCATTTTCAACTATACCA
* *
3296 GAAACTTGAGCGCTCTTATCCAAATATTCATCTTTTATGTCGCT
196 GAAACTTGAGCGCTCCTATCCAAATATTCATCTGTTATGTCGCT
* * * * **
3340 TGATTCGAAAGCTTTACTGCCCCTATCCAAATACTCATCTATTATCCCACTTACATCTGCAATTT
1 TGATCCGAAAACTTGACTGCCCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTGCAATTT
*
3405 CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGACCATAAAACAT
66 CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCATAAAACAT
** *
3470 TTTGACATGAATATAAAGAAAGAATTCTACCCGTGACCGGTTTTAGCCCATTTTCAACTATACCA
131 TTTGACATGAATATAAAGAAAGAATTCTACATGTGACCGGTTTCAGCCCATTTTCAACTATACCA
3535 GAAACTTGAGCGCTCCTATCCAAATATTCATCTGTTATGTCGCT
196 GAAACTTGAGCGCTCCTATCCAAATATTCATCTGTTATGTCGCT
* * *
3579 TGATCCGAAAACTTGAATGCCCCTATCCAAATACTCATCTGTTATCCCGTGTATATCTGCAATTT
1 TGATCCGAAAACTTGACTGCCCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTGCAATTT
*
3644 CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCACAAAACAT
66 CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCATAAAACAT
*
3709 TTTGACATGAATATAAAGAAAGAATTCTACCTGTGACCGGTTTCAGCCCATTTTCAACTATACCA
131 TTTGACATGAATATAAAGAAAGAATTCTACATGTGACCGGTTTCAGCCCATTTTCAACTATACCA
*
3774 GAAACTTGAGCGCTCCTATCCAAATATTCATCGGTTATGTCGCT
196 GAAACTTGAGCGCTCCTATCCAAATATTCATCTGTTATGTCGCT
3818 TG
1 TG
3820 TATCTGTTAT
Statistics
Matches: 672, Mismatches: 47, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
239 672 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (239 bp):
TGATCCGAAAACTTGACTGCCCCTATCCAAATACTCATCTGTTATCCCGTTTACATCTGCAATTT
CCAAATGAAAGTTGTATAAGTAGCGGGAAACAATGAAATTAGCAACATATATGGCCATAAAACAT
TTTGACATGAATATAAAGAAAGAATTCTACATGTGACCGGTTTCAGCCCATTTTCAACTATACCA
GAAACTTGAGCGCTCCTATCCAAATATTCATCTGTTATGTCGCT
Found at i:7640 original size:6 final size:6
Alignment explanation
Indices: 7629--7659 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
7619 CCATCAGATA
7629 ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
7660 ATAAAGTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCTAT
Found at i:11773 original size:22 final size:25
Alignment explanation
Indices: 11748--11799 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
11738 AATTATTAAA
11748 TTATTAATTTT-A-TA-TATGTATT
1 TTATTAATTTTAATTATTATGTATT
* *
11770 TTATTAGTTTTAATTATTATTTATT
1 TTATTAATTTTAATTATTATGTATT
11795 TTATT
1 TTATT
11800 TAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 1 0.04
24 2 0.08
25 12 0.48
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTATTAATTTTAATTATTATGTATT
Found at i:12750 original size:11 final size:11
Alignment explanation
Indices: 12734--12765 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12724 ACAACGTAAT
12734 AAAAACAAAAC
1 AAAAACAAAAC
*
12745 AAAAACGAAAC
1 AAAAACAAAAC
12756 AAAAACAAAA
1 AAAAACAAAA
12766 AACAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Done.