Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010135.1 Corchorus capsularis cultivar CVL-1 contig10156, 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: 57267
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6284 original size:21 final size:21
Alignment explanation
Indices: 6258--6300 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
6248 CTTTCGCCTT
6258 TATGAATGAAAAAAAAAGAAA
1 TATGAATGAAAAAAAAAGAAA
*
6279 TATGAATGAAAACAAAAGAAA
1 TATGAATGAAAAAAAAAGAAA
6300 T
1 T
6301 GAGTCTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.16
Consensus pattern (21 bp):
TATGAATGAAAAAAAAAGAAA
Found at i:6526 original size:11 final size:11
Alignment explanation
Indices: 6478--6526 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
6468 ATTTATTCAT
*
6478 TATTAATTAAC
1 TATTAATTAGC
6489 TATTAATTAG-
1 TATTAATTAGC
6499 -A-TAA-TA-C
1 TATTAATTAGC
6506 TATTAATTAGC
1 TATTAATTAGC
6517 TATTAATTAG
1 TATTAATTAG
6527 ATATAGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
9 4 0.12
10 2 0.06
11 20 0.62
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:7381 original size:29 final size:30
Alignment explanation
Indices: 7339--7411 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
7329 GAACCATGAG
* *
7339 GTTTAGTACGAAATTTAGCAACTT-T-AAAA
1 GTTTAGTACTAAATTGAGC-ACTTATGAAAA
*
7368 GTTTAGTACTAAATTGAGCATTTAGTGAAAA
1 GTTTAGTACTAAATTGAGCACTTA-TGAAAA
7399 GTTTAGTACTAAA
1 GTTTAGTACTAAA
7412 CTAATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 17 0.45
30 1 0.03
31 17 0.45
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (30 bp):
GTTTAGTACTAAATTGAGCACTTATGAAAA
Found at i:17867 original size:18 final size:18
Alignment explanation
Indices: 17844--17882 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
17834 TTGGTGTTGA
* *
17844 AGAAGAAGAAGGAGAAGG
1 AGAAGAAGAAAGAGAAAG
17862 AGAAGAAGAAAGAGAAAG
1 AGAAGAAGAAAGAGAAAG
17880 AGA
1 AGA
17883 GAGGGTGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAGAGAAAG
Found at i:18035 original size:2 final size:2
Alignment explanation
Indices: 18028--18069 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
18018 CTATAAAATA
18028 AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT -T AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT A
18070 CTAGGATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 32 0.86
3 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18047 original size:16 final size:16
Alignment explanation
Indices: 18028--18069 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
18018 CTATAAAATA
18028 ATATA-TATATATATAT
1 ATATACTATATATAT-T
18044 ATATACTATATATATT
1 ATATACTATATATATT
18060 ATATACTATA
1 ATATACTATA
18070 CTAGGATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATACTATATATATT
Found at i:18053 original size:21 final size:21
Alignment explanation
Indices: 18029--18072 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
18019 TATAAAATAA
18029 TATATATATATATATA-TATAC
1 TATATATAT-TATATACTATAC
18050 TATATATATTATATACTATAC
1 TATATATATTATATACTATAC
18071 TA
1 TA
18073 GGATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATATTATATACTATAC
Found at i:18432 original size:26 final size:26
Alignment explanation
Indices: 18403--18455 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
18393 ATACCTATAC
18403 TAATATATGATACATTCATTATAACA
1 TAATATATGATACATTCATTATAACA
18429 TAATATATGATACATTCATTATAACA
1 TAATATATGATACATTCATTATAACA
18455 T
1 T
18456 GACGTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (26 bp):
TAATATATGATACATTCATTATAACA
Found at i:32660 original size:2 final size:2
Alignment explanation
Indices: 32653--32678 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32643 AATATTTTGG
32653 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
32679 CCACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35676 original size:15 final size:14
Alignment explanation
Indices: 35656--35690 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
35646 TATAAATTAT
35656 TATAAAAACATTAAA
1 TATAAAAAC-TTAAA
*
35671 TATAAAAACTTATA
1 TATAAAAACTTAAA
35685 TATAAA
1 TATAAA
35691 TTATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TATAAAAACTTAAA
Found at i:45896 original size:20 final size:21
Alignment explanation
Indices: 45871--45923 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
45861 ACTAGCGCTG
*
45871 GGCG-CCCATGTGGTTTGCTT
1 GGCGACCCATGTGGTTTGCCT
* *
45891 GGCGCCCCATGTTGTTTGCCT
1 GGCGACCCATGTGGTTTGCCT
*
45912 CGCGACCCATGT
1 GGCGACCCATGT
45924 ACACCAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.08, C:0.32, G:0.30, T:0.30
Consensus pattern (21 bp):
GGCGACCCATGTGGTTTGCCT
Found at i:52999 original size:22 final size:22
Alignment explanation
Indices: 52974--53017 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52964 AAATGGCGAT
*
52974 GACAAGATCCAAGAAATTTTTC
1 GACAAGATCCAAGAAATGTTTC
52996 GACAAGATCCAAGAAATGTTTC
1 GACAAGATCCAAGAAATGTTTC
53018 ACTTGGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (22 bp):
GACAAGATCCAAGAAATGTTTC
Found at i:54342 original size:25 final size:26
Alignment explanation
Indices: 54288--54342 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
54278 GCCCGCCCAT
*
54288 ATTT-ATTTTTTAAAATAAATTAATA
1 ATTTAATTTTTTAAAATAAAATAATA
54313 A-TTAATTTTTTAATAA-AAAATAA-A
1 ATTTAATTTTTTAA-AATAAAATAATA
54337 ATTTAA
1 ATTTAA
54343 ACATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 20 0.77
26 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAATTTTTTAAAATAAAATAATA
Found at i:55206 original size:120 final size:120
Alignment explanation
Indices: 55055--55289 Score: 409
Period size: 120 Copynumber: 2.0 Consensus size: 120
55045 AAAATTCCAA
*
55055 TATATATAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTA
1 TATATATAAGTTTTCTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTA
55120 GATTTAACTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATT
66 GATTTAACTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATT
* *
55176 TATATATAAG-TTTCTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTA
1 TATATATAAGTTTTCTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTA
* *
55240 GATTTAATTAAATAAGAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
66 GATTTAACTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
55290 TTAAACAATG
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
119 36 0.33
120 63 0.58
121 10 0.09
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (120 bp):
TATATATAAGTTTTCTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTA
GATTTAACTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATT
Found at i:56896 original size:18 final size:19
Alignment explanation
Indices: 56873--56910 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
56863 TTATGTGATA
*
56873 GCTTAATTAA-TTGATTGG
1 GCTTAATGAATTTGATTGG
56891 GCTTAATGAATTTGATTGG
1 GCTTAATGAATTTGATTGG
56910 G
1 G
56911 TGAGTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
GCTTAATGAATTTGATTGG
Done.