Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023497.1 Corchorus olitorius cultivar O-4 contig23530, 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: 28951
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:631 original size:85 final size:87
Alignment explanation
Indices: 471--642 Score: 303
Period size: 85 Copynumber: 2.0 Consensus size: 87
461 AAATTAAAAT
*
471 GGTAAAAATAAAATAGTTATAATAATATTGAATTTTAATTAAATAAAAAATATATTTTTTAGTAG
1 GGTAAAAATAAAATAGTTATAATAATATTGAATTTTAATTAAATAAAAAATAGATTTTTTAGTAG
*
536 AATAATTGTAAAAGTTTATTTC
66 AATAACTGTAAAAGTTTATTTC
*
558 GGTAAAAATAAAATATTTATAATAATATTGAA-TTTAATTAAAT-AAAAATAGATTTTTTAGTAG
1 GGTAAAAATAAAATAGTTATAATAATATTGAATTTTAATTAAATAAAAAATAGATTTTTTAGTAG
621 AATAACTGTAAAAGTTTATTTC
66 AATAACTGTAAAAGTTTATTTC
643 TAAAAAAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
85 40 0.49
86 11 0.13
87 31 0.38
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (87 bp):
GGTAAAAATAAAATAGTTATAATAATATTGAATTTTAATTAAATAAAAAATAGATTTTTTAGTAG
AATAACTGTAAAAGTTTATTTC
Found at i:678 original size:14 final size:13
Alignment explanation
Indices: 659--697 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
649 AAATTGTAAA
659 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
672 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
686 ATTTAAAAAATT
1 ATTTAAAAAATT
698 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:821 original size:133 final size:123
Alignment explanation
Indices: 684--938 Score: 384
Period size: 133 Copynumber: 2.0 Consensus size: 123
674 TTTAAGAAAT
684 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAAT
1 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAAT----T
* *
749 AGGTATAAGGTTATTAGATTTAATTAAATAAAAAATAGAGTTTTTTAGTTGAGTAAAACTGTAAA
62 A--TA-AA-GATATTAGATTTAATTAAAT-AAAAATAGAG-TTTTTAGTTGAGTAAAACTATAAA
814 AGC
121 AGC
*
817 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATAA
1 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATTATAA
*
882 AGATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
939 TTTAAACAAT
Statistics
Matches: 118, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
123 25 0.21
124 9 0.08
125 19 0.16
126 2 0.02
127 2 0.02
129 2 0.02
133 59 0.50
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (123 bp):
ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATTATAA
AGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGC
Found at i:1288 original size:1 final size:1
Alignment explanation
Indices: 1282--1309 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1272 AGAAGAGAAG
1282 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1310 CTACTGACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5524 original size:35 final size:34
Alignment explanation
Indices: 5484--5588 Score: 147
Period size: 35 Copynumber: 3.0 Consensus size: 34
5474 CAGATAAAAC
* * *
5484 AATACTAGCTCTTCCGGAGCATTCAATAAAATTTG
1 AATACT-GCTCTTCTGGAGCCTTCAATCAAATTTG
5519 AATACTGGCTCTTCTGGAGCCTTCAATCAAATTTG
1 AATACT-GCTCTTCTGGAGCCTTCAATCAAATTTG
*
5554 AATACTGACTTTTCTGGAGCCTTCAATCAAATTTG
1 AATACTG-CTCTTCTGGAGCCTTCAATCAAATTTG
5589 CATTACCTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 1 0.02
35 63 0.98
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (34 bp):
AATACTGCTCTTCTGGAGCCTTCAATCAAATTTG
Found at i:8764 original size:29 final size:29
Alignment explanation
Indices: 8722--8782 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
8712 TCATCCTTAA
8722 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
*
8751 TATGACAACTTCGGGTGTCAAAGTGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
8780 TAT
1 TAT
8783 ATTTTTGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAATGATAC
Found at i:8915 original size:32 final size:33
Alignment explanation
Indices: 8850--8922 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
8840 ATAATTTTTA
* * *
8850 ATGATAATGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
8883 ATGATAAAGAAAGGTAGAA-GAAGAGATCATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
*
8915 ATGTTAAA
1 ATGATAAA
8923 TAAACTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 18 0.50
33 18 0.50
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.21
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
Found at i:10295 original size:22 final size:22
Alignment explanation
Indices: 10270--10312 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10260 AGAAATTTAG
* *
10270 AACAAGACCTGAGCAGGAGTTT
1 AACAACACCTGACCAGGAGTTT
*
10292 AACAACACCTGCCCAGGAGTT
1 AACAACACCTGACCAGGAGTT
10313 GTTGCGGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (22 bp):
AACAACACCTGACCAGGAGTTT
Found at i:15454 original size:2 final size:2
Alignment explanation
Indices: 15447--15549 Score: 165
Period size: 2 Copynumber: 52.5 Consensus size: 2
15437 AGTTCTTCAC
15447 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
15488 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
15530 -G GG AG GG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
15550 ATGGAACACT
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
1 2 0.02
2 92 0.98
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18575 original size:17 final size:16
Alignment explanation
Indices: 18530--18571 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
18520 CGGATCACTT
18530 GTGATCTAAGATCACCA
1 GTGATC-AAGATCACCA
*
18547 GTGATGCAAGATCACCG
1 GTGAT-CAAGATCACCA
18564 GTGATCAA
1 GTGATCAA
18572 AGATTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (16 bp):
GTGATCAAGATCACCA
Found at i:28591 original size:23 final size:23
Alignment explanation
Indices: 28548--28591 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
28538 TAATATTTTT
*
28548 AATTAAAATAGTAAAATGATAAA
1 AATTAAAATAGTAAAAGGATAAA
*
28571 AATT-AAATAGTTATAAGGATA
1 AATTAAAATAG-TAAAAGGATA
28592 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (23 bp):
AATTAAAATAGTAAAAGGATAAA
Done.