Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015004.1 Corchorus capsularis cultivar CVL-1 contig15025, 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: 45496
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:574 original size:4 final size:4
Alignment explanation
Indices: 567--613 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
557 GTGTGTGTAT
567 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
614 TAAAAAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:713 original size:2 final size:2
Alignment explanation
Indices: 706--733 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
696 TAAAAGATTA
706 AT 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 AT
734 TATGTGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6624 original size:7 final size:7
Alignment explanation
Indices: 6612--6636 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6602 CAATATTAAA
6612 AAAAAAG
1 AAAAAAG
6619 AAAAAAG
1 AAAAAAG
6626 AAAAAAG
1 AAAAAAG
6633 AAAA
1 AAAA
6637 GTGAAGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:16341 original size:29 final size:31
Alignment explanation
Indices: 16272--16341 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
16262 ATCAGGGGAT
*
16272 AAAATGTCCTGGATTTGGAAGTTTAGGGGGC
1 AAAATGTCCTGGATTTGGAAGTTTAGGAGGC
*
16303 AAAATATCCT-GATTT-GAAGTTTAGGAGGC
1 AAAATGTCCTGGATTTGGAAGTTTAGGAGGC
*
16332 AAAACGTCCT
1 AAAATGTCCT
16342 TGAAGCAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 21 0.60
30 5 0.14
31 9 0.26
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAATGTCCTGGATTTGGAAGTTTAGGAGGC
Found at i:27404 original size:21 final size:21
Alignment explanation
Indices: 27375--27415 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27365 CTTTACCTAT
27375 TTCCCTTAATTCTATTATTTA
1 TTCCCTTAATTCTATTATTTA
* *
27396 TTCCTTTAATTTTATTATTT
1 TTCCCTTAATTCTATTATTT
27416 TCTATGGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCCCTTAATTCTATTATTTA
Found at i:37600 original size:18 final size:17
Alignment explanation
Indices: 37554--37589 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
37544 ATGTTTGAGC
37554 ATGTAGAGAAATATCTG
1 ATGTAGAGAAATATCTG
37571 ATGTAGAGAAATATCTG
1 ATGTAGAGAAATATCTG
37588 AT
1 AT
37590 TGTAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (17 bp):
ATGTAGAGAAATATCTG
Found at i:38024 original size:5 final size:5
Alignment explanation
Indices: 38014--38049 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
38004 TGGGCTACTA
*
38014 GGGTT GGGTT GAGTT GGGTT GGGTT GGGTT GGGTT G
1 GGGTT GGGTT GGGTT GGGTT GGGTT GGGTT GGGTT G
38050 AATTCAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.58, T:0.39
Consensus pattern (5 bp):
GGGTT
Found at i:40079 original size:20 final size:20
Alignment explanation
Indices: 40054--40093 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40044 TCATAATATA
40054 AATTCAAAATTTTTTTTATT
1 AATTCAAAATTTTTTTTATT
40074 AATTCAAAATTTTTTTTATT
1 AATTCAAAATTTTTTTTATT
40094 CATGAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTCAAAATTTTTTTTATT
Found at i:43223 original size:24 final size:25
Alignment explanation
Indices: 43190--43237 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
43180 TCCCCTCCTT
** *
43190 AATTATTAGTTTATATATATAAGTC
1 AATTATTAGTACATACATATAAGTC
43215 AATT-TTAGTACATACATATAAGT
1 AATTATTAGTACATACATATAAGT
43238 ATTATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (25 bp):
AATTATTAGTACATACATATAAGTC
Found at i:44380 original size:29 final size:30
Alignment explanation
Indices: 44301--44380 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
44291 GCTAAATACC
* *
44301 CAAAAAAATCTCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCTCTTATGTTTT-CTTTCGGGA
* *
44332 CAAAATAATCCCTCATGTTTT-TTTCGGGA
1 CAAAATAATCTCTTATGTTTTCTTTCGGGA
* *
44361 CAAATTAATCTCTTACGTTT
1 CAAAATAATCTCTTATGTTT
44381 AAAAAATGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 23 0.56
31 18 0.44
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCTCTTATGTTTTCTTTCGGGA
Found at i:44540 original size:31 final size:31
Alignment explanation
Indices: 44502--44583 Score: 157
Period size: 31 Copynumber: 2.7 Consensus size: 31
44492 TTTGTCCAAA
44502 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
44533 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
1 AAAAACATAAGGGATTTTTTTGTCCCAAAAG
44564 AAAAA-ATAAGGGATTTTTTT
1 AAAAACATAAGGGATTTTTTT
44584 AGTATTTAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 15 0.29
31 36 0.71
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.32
Consensus pattern (31 bp):
AAAAACATAAGGGATTTTTTTGTCCCAAAAG
Found at i:44573 original size:30 final size:30
Alignment explanation
Indices: 44492--44583 Score: 152
Period size: 31 Copynumber: 3.1 Consensus size: 30
44482 AAGGGACTAA
*
44492 TTTGT-CCAAAA-AAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAAATAAGGGATTTT
44520 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAA-ATAAGGGATTTT
44551 TTTGTCCCAAAAGAAAAAATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAAATAAGGGATTTT
44581 TTT
1 TTT
44584 AGTATTTAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
28 5 0.08
29 6 0.10
30 19 0.32
31 30 0.50
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAAATAAGGGATTTT
Found at i:45270 original size:134 final size:133
Alignment explanation
Indices: 45024--45289 Score: 365
Period size: 134 Copynumber: 2.0 Consensus size: 133
45014 TTATTAAATA
* * * * ** *
45024 TCATTGTTTAAATTTTTATAGTTTTACACAACTAAAAACTCTATTTTTTATTTAATTTAATTTAA
1 TCATTGTTTAAACTTTTACAATTTTACACAACTAAAAAATCTATTTTTTATTTAATCAAATTAAA
* *
45089 TATTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAATTTAGATATATTAGAAT
66 TATTTATAAATATTCTATTTTTACCACTTTACTATTTTAATTAAAAAA-TTAGATATATTAGAAT
45154 TTTG
130 TTTG
** *
45158 TCATTGTTTAAACTTTTACAATTTTACTTAATTAAAAAATCTA-TTTTTATTTAATCAAATCTAA
1 TCATTGTTTAAACTTTTACAATTTTACACAACTAAAAAATCTATTTTTTATTTAATCAAAT-TAA
* *
45222 TATATTTATAACTATTCTGTTTTTACCACTTTACTATTTTAATT-AAAAATTAGATATATTAGAA
65 -ATATTTATAAATATTCTATTTTTACCACTTTACTATTTTAATTAAAAAATTAGATATATTAGAA
45286 TTTT
129 TTTT
45290 TAAATATATA
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 34 0.29
134 43 0.37
135 39 0.34
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (133 bp):
TCATTGTTTAAACTTTTACAATTTTACACAACTAAAAAATCTATTTTTTATTTAATCAAATTAAA
TATTTATAAATATTCTATTTTTACCACTTTACTATTTTAATTAAAAAATTAGATATATTAGAATT
TTG
Found at i:45386 original size:30 final size:30
Alignment explanation
Indices: 45350--45412 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
45340 ACTAAATACT
45350 AAAAAAATCCCTTATG-TTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTT-GGAC
45380 AAAAAAATCCCTTATGTTTTTCTTTTGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGAC
45410 AAA
1 AAA
45413 TTAGTCACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (30 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGAC
Done.