Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011735.1 Corchorus capsularis cultivar CVL-1 contig11756, 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: 54817
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:15594 original size:58 final size:58
Alignment explanation
Indices: 15504--15614 Score: 222
Period size: 58 Copynumber: 1.9 Consensus size: 58
15494 TTGGATATTA
15504 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCGCTG
1 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCGCTG
15562 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTT
1 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTT
15615 TACTTTCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (58 bp):
TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCGCTG
Found at i:15624 original size:58 final size:58
Alignment explanation
Indices: 15504--15627 Score: 221
Period size: 58 Copynumber: 2.1 Consensus size: 58
15494 TTGGATATTA
*
15504 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCGCTG
1 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCACTG
* *
15562 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTTACTT
1 TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCACTG
15620 TCATTTTA
1 TCATTTTA
15628 ACATCTCTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (58 bp):
TCATTTTAGGTTCTACAAACCTAGATCTTAGTTTCATTACCCAACATCAATTTCACTG
Found at i:20587 original size:9 final size:9
Alignment explanation
Indices: 20575--20602 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20565 AAATCCTAAT
20575 TAACCTATA
1 TAACCTATA
20584 TAACCTATA
1 TAACCTATA
20593 TAACCTATA
1 TAACCTATA
20602 T
1 T
20603 GAATCACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (9 bp):
TAACCTATA
Found at i:24333 original size:26 final size:27
Alignment explanation
Indices: 24298--24348 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
24288 TTTTTAAAGC
24298 AATTTCTTTTTTTAAAAAAAAATCGCA
1 AATTTCTTTTTTTAAAAAAAAATCGCA
* *
24325 AATTT-TTTTTTTATAGAAAAATCG
1 AATTTCTTTTTTTAAAAAAAAATCG
24349 AAAAAGGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (27 bp):
AATTTCTTTTTTTAAAAAAAAATCGCA
Found at i:24395 original size:34 final size:33
Alignment explanation
Indices: 24329--24396 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
24319 ATCGCAAATT
* * ***
24329 TTTTTTTTATAGAAAAATCGAAAAAGGGAAAAC
1 TTTTTTTTAAAGAAAAAACGAAAAAACAAAAAC
24362 TTTTTTTTAAAGAAAAAACGGAAAAAACAAAAAC
1 TTTTTTTTAAAGAAAAAAC-GAAAAAACAAAAAC
24396 T
1 T
24397 AATTCTTGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (33 bp):
TTTTTTTTAAAGAAAAAACGAAAAAACAAAAAC
Found at i:37950 original size:6 final size:6
Alignment explanation
Indices: 37939--37974 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
37929 TTATTTCCTA
* *
37939 CAAGAG CAAGAG CAAGAG CAAGAG TATGAG CAAGAG
1 CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG
37975 TATGAGCCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.33, T:0.06
Consensus pattern (6 bp):
CAAGAG
Found at i:37975 original size:12 final size:12
Alignment explanation
Indices: 37942--37981 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
37932 TTTCCTACAA
* *
37942 GAGCAAGAGCAA
1 GAGCAAGAGTAT
37954 GAGCAAGAGTAT
1 GAGCAAGAGTAT
37966 GAGCAAGAGTAT
1 GAGCAAGAGTAT
37978 GAGC
1 GAGC
37982 CAGAAACAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.10
Consensus pattern (12 bp):
GAGCAAGAGTAT
Found at i:49331 original size:31 final size:31
Alignment explanation
Indices: 49283--49359 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
49273 GATGTCGTTG
* * *
49283 ACGTGGCAATGCTACGCAACACAAAAATGCC
1 ACGTTGCAATGCCACGCAACACAAAAATACC
*
49314 ATGTTGCAATGCCACGCAACACAAAAATACC
1 ACGTTGCAATGCCACGCAACACAAAAATACC
49345 ACGTTGCAATGCCAC
1 ACGTTGCAATGCCAC
49360 ATCATCGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.16
Consensus pattern (31 bp):
ACGTTGCAATGCCACGCAACACAAAAATACC
Found at i:49506 original size:29 final size:30
Alignment explanation
Indices: 49445--49509 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
49435 GGCAAAATGC
*
49445 CCAAAATTGAGAATGTAGGGGGTAAAATAT
1 CCAAAATTGAGAATGTAGGGGGTAAAACAT
* * * *
49475 CCAAAATTGA-AGTTTAGTGGGTAAAACGT
1 CCAAAATTGAGAATGTAGGGGGTAAAACAT
49504 CCAAAA
1 CCAAAA
49510 GCTACAAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (30 bp):
CCAAAATTGAGAATGTAGGGGGTAAAACAT
Done.