Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001056.1 Corchorus capsularis cultivar CVL-1 contig01056, 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: 15444
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:662 original size:56 final size:57
Alignment explanation
Indices: 486--688 Score: 347
Period size: 57 Copynumber: 3.6 Consensus size: 57
476 ATAACCTGAC
486 CGAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAACTCGATAACCCAGT
1 CGAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAACTCGATAACCCAGT
*
543 CGAACCCCATTTGACCAGAGAAAGTAAAACAACCTGATACAAACTCGATAACCCAGT
1 CGAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAACTCGATAACCCAGT
* * **
600 CGAACCCCATTTGACCAGAGAAAGT-AAACGATCTGATACAAATTCGATAACCTGGT
1 CGAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAACTCGATAACCCAGT
656 CGAACCCCATTTGACCAGAGAAAGT-AAACGACC
1 CGAACCCCATTTGACCAGAGAAAGTAAAACGACC
689 CGAACCTGTC
Statistics
Matches: 139, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
56 58 0.42
57 81 0.58
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.17
Consensus pattern (57 bp):
CGAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAACTCGATAACCCAGT
Found at i:719 original size:113 final size:113
Alignment explanation
Indices: 465--683 Score: 325
Period size: 113 Copynumber: 1.9 Consensus size: 113
455 GTCAAATCTA
* *
465 ATACAAACTCAATAA-CCTGACCGAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAA
1 ATACAAACTC-ATAACCCAGA-CAAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAA
529 CTCGATAACCCAGTCGAACCCCATTTGACCAGAGAAAGTAAAACAACCTG
64 CTCGATAACCCAGTCGAACCCCATTTGACCAGAGAAAGTAAAACAACCTG
* * * *
579 ATACAAACTCGATAACCCAGTCGAACCCCATTTGACCAGAGAAAGT-AAACGATCTGATACAAAT
1 ATACAAACTC-ATAACCCAGACAAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAAC
**
643 TCGATAACCTGGTCGAACCCCATTTGACCAGAGAAAGTAAA
65 TCGATAACCCAGTCGAACCCCATTTGACCAGAGAAAGTAAA
684 CGACCCGAAC
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
113 55 0.57
114 39 0.40
115 3 0.03
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.17
Consensus pattern (113 bp):
ATACAAACTCATAACCCAGACAAACCCCATTTGACCAGAGAAAGTAAAACGACCTGATACAAACT
CGATAACCCAGTCGAACCCCATTTGACCAGAGAAAGTAAAACAACCTG
Found at i:1219 original size:11 final size:12
Alignment explanation
Indices: 1177--1217 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1167 CCCCTTTCTA
*
1177 TATAAAATAAAT
1 TATAAAATTAAT
*
1189 TATCAAA-TAAT
1 TATAAAATTAAT
1200 TATAAAATTAAT
1 TATAAAATTAAT
1212 TATAAA
1 TATAAA
1218 TTTGTTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAAATTAAT
Found at i:3340 original size:41 final size:41
Alignment explanation
Indices: 3291--3390 Score: 182
Period size: 41 Copynumber: 2.4 Consensus size: 41
3281 CAATTCAATC
*
3291 TCGTCTCAGGACGTTAAAACAGTTTTTCTTCACTTTCAGCA
1 TCGTCTCAGGACGTTAAAACAATTTTTCTTCACTTTCAGCA
*
3332 TCGTCTCAGGACGTTAAAACAATTTTTCTTTACTTTCAGCA
1 TCGTCTCAGGACGTTAAAACAATTTTTCTTCACTTTCAGCA
3373 TCGTCTCAGGACGTTAAA
1 TCGTCTCAGGACGTTAAA
3391 TATTTGTTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (41 bp):
TCGTCTCAGGACGTTAAAACAATTTTTCTTCACTTTCAGCA
Found at i:4585 original size:131 final size:129
Alignment explanation
Indices: 4416--4666 Score: 378
Period size: 131 Copynumber: 1.9 Consensus size: 129
4406 AATATTTTTT
* * *
4416 AAAATTCTAATATAGCTAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAA
1 AAAATTCTAATATAGATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAAGTATAA
*
4481 GGATATTAGATTTAATTAAATAAGAGATAGACTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
66 GGATATTACATTTAATTAAATAA-A-ATAGACTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
4546 A
129 A
* * *
4547 AAAATTTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAATTATA
1 AAAA-TTCTAATATAGATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAAGTATA
* * *
4611 AGGATATTACATTTAATTAAATAAAATATAGTTTTTAGTTGAGTAAAATTATAAAA
65 AGGATATTACATTTAATTAAATAAAATAGACTTTTTAGTTGAGTAAAACTATAAAA
4667 AGTTTAAACA
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
129 28 0.26
130 1 0.01
131 66 0.61
132 14 0.13
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (129 bp):
AAAATTCTAATATAGATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAAGTATAA
GGATATTACATTTAATTAAATAAAATAGACTTTTTAGTTGAGTAAAACTATAAAAGTATATTTA
Found at i:4927 original size:16 final size:16
Alignment explanation
Indices: 4902--5047 Score: 136
Period size: 16 Copynumber: 9.2 Consensus size: 16
4892 AGTCAGTTTT
*
4902 TTTCGTGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
4918 TTTCGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
*
4934 -TTCGGGTCAATCGGG
1 TTTCGGGTCATTCGGG
*
4949 TTTCGGGTCAATCGGG
1 TTTCGGGTCATTCGGG
* * *
4965 TCTCGGGTTATTCGCG
1 TTTCGGGTCATTCGGG
* *
4981 TCTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* *
4997 TCTCGGGTTAATT-GGG
1 TTTCGGG-TCATTCGGG
*
5013 TTTCGGGTCATTC-GC
1 TTTCGGGTCATTCGGG
*
5028 TTCTCGGGTTATTCGGG
1 TT-TCGGGTCATTCGGG
5045 TTT
1 TTT
5048 GTGTTTAGAC
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
15 20 0.18
16 83 0.75
17 7 0.06
ACGTcount: A:0.08, C:0.18, G:0.34, T:0.39
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:4987 original size:32 final size:32
Alignment explanation
Indices: 4911--5047 Score: 170
Period size: 32 Copynumber: 4.3 Consensus size: 32
4901 TTTTCGTGTC
* *
4911 ATTCGGGTTTCGGGTCATTTGGGT-TCGGGTC
1 ATTCGGGTTTCGGGTCATTCGGGTCTCGGGTT
* *
4942 AATCGGGTTTCGGGTCAATCGGGTCTCGGGTT
1 ATTCGGGTTTCGGGTCATTCGGGTCTCGGGTT
* * *
4974 ATTCGCGTCTCGGGTTATTCGGGTCTCGGGTT
1 ATTCGGGTTTCGGGTCATTCGGGTCTCGGGTT
**
5006 AATT-GGGTTTCGGGTCATTCGCTTCTCGGGTT
1 -ATTCGGGTTTCGGGTCATTCGGGTCTCGGGTT
5038 ATTCGGGTTT
1 ATTCGGGTTT
5048 GTGTTTAGAC
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
31 24 0.27
32 62 0.70
33 3 0.03
ACGTcount: A:0.09, C:0.18, G:0.35, T:0.38
Consensus pattern (32 bp):
ATTCGGGTTTCGGGTCATTCGGGTCTCGGGTT
Found at i:5003 original size:48 final size:48
Alignment explanation
Indices: 4908--5045 Score: 170
Period size: 48 Copynumber: 2.9 Consensus size: 48
4898 TTTTTTTCGT
* * * * * *
4908 GTCATTCGGGTTTCGGGTCATTTGGGT-TCGGGTCAATCGGGTTTCGG
1 GTCAATCGGGTTTCGGGTCATTCGCGTCTCGGGTTATTCGGGTCTCGG
* *
4955 GTCAATCGGGTCTCGGGTTATTCGCGTCTCGGGTTATTCGGGTCTCGG
1 GTCAATCGGGTTTCGGGTCATTCGCGTCTCGGGTTATTCGGGTCTCGG
* * *
5003 GTTAATTGGGTTTCGGGTCATTCGCTTCTCGGGTTATTCGGGT
1 GTCAATCGGGTTTCGGGTCATTCGCGTCTCGGGTTATTCGGGT
5046 TTGTGTTTAG
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 22 0.29
48 55 0.71
ACGTcount: A:0.09, C:0.19, G:0.36, T:0.37
Consensus pattern (48 bp):
GTCAATCGGGTTTCGGGTCATTCGCGTCTCGGGTTATTCGGGTCTCGG
Found at i:5465 original size:14 final size:13
Alignment explanation
Indices: 5446--5480 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
5436 AAAAAGAGTT
5446 TATTCTATTTTCTA
1 TATTCTATTTT-TA
*
5460 TATTCTATTTTTT
1 TATTCTATTTTTA
5473 TATTCTAT
1 TATTCTAT
5481 AAAGTAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTCTATTTTTA
Found at i:5618 original size:16 final size:16
Alignment explanation
Indices: 5597--5699 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 16
5587 GGTCAATTTT
5597 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
5613 TCGGGTC-TCACGGGTT
1 TCGGGTCAT-TCGGGTC
* * * *
5629 TTGGGTCATACAGGTT
1 TCGGGTCATTCGGGTC
* *
5645 TCGGGTTATTTGGGTC
1 TCGGGTCATTCGGGTC
* *
5661 ACGGGTCAGTCGGGTC
1 TCGGGTCATTCGGGTC
* * * *
5677 ACGGGTTAGTCGGGTT
1 TCGGGTCATTCGGGTC
5693 TCGGGTC
1 TCGGGTC
5700 TGGCGGGTTC
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
15 1 0.01
16 65 0.97
17 1 0.01
ACGTcount: A:0.10, C:0.19, G:0.39, T:0.32
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:5757 original size:16 final size:17
Alignment explanation
Indices: 5736--5767 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5726 GTAGTCAAAT
5736 CGGGTT-GGGCGGGTTA
1 CGGGTTCGGGCGGGTTA
5752 CGGGTTCGGGCGGGTT
1 CGGGTTCGGGCGGGTT
5768 GGGCGGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.03, C:0.16, G:0.56, T:0.25
Consensus pattern (17 bp):
CGGGTTCGGGCGGGTTA
Found at i:5772 original size:26 final size:27
Alignment explanation
Indices: 5736--5788 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
5726 GTAGTCAAAT
5736 CGGGTTGGGCGGGTT-A-CGGGTTCGGG
1 CGGGTTGGGC-GGTTAATCGGGTTCGGG
5762 CGGGTTGGGCGGTTAATCGGGTTCGGG
1 CGGGTTGGGCGGTTAATCGGGTTCGGG
5789 TCAGCTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.16
26 11 0.44
27 10 0.40
ACGTcount: A:0.06, C:0.15, G:0.55, T:0.25
Consensus pattern (27 bp):
CGGGTTGGGCGGTTAATCGGGTTCGGG
Found at i:9855 original size:16 final size:16
Alignment explanation
Indices: 9834--9865 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9824 AAGGAATATG
9834 CGGTTGATGGTAAGCT
1 CGGTTGATGGTAAGCT
9850 CGGTTGATGGTAAGCT
1 CGGTTGATGGTAAGCT
9866 TAATGGGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (16 bp):
CGGTTGATGGTAAGCT
Found at i:11402 original size:3 final size:3
Alignment explanation
Indices: 11394--11433 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
11384 CCACTGCAAT
* *
11394 TGA TGA TGA TGA TGA TGA TGA TGA TGA AGT TGA T-A TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
11434 GATCAGTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:14232 original size:27 final size:26
Alignment explanation
Indices: 14177--14239 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
14167 TGGCAATTAT
*
14177 ATATATTTTAATAATGGCATAATTAAA
1 ATATATTTTAATAATGACAT-ATTAAA
*
14204 ATATATTTTGATAATGACAGT-TTAGAA
1 ATATATTTTAATAATGACA-TATTA-AA
*
14231 ATATGTTTT
1 ATATATTTT
14240 TAAAAAAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 27 0.87
28 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (26 bp):
ATATATTTTAATAATGACATATTAAA
Found at i:14352 original size:75 final size:77
Alignment explanation
Indices: 14222--14384 Score: 217
Period size: 75 Copynumber: 2.2 Consensus size: 77
14212 TGATAATGAC
* * *
14222 AGTTTAGA-AATATGTTTTTAAAAAAGGGGTACAATCGGAAAACATGAAATTTCTCATTATTCGT
1 AGTTTAGATAATATATTTTTAAAAAAGGGGTACAATCCGAAAACATAAAATTTCTCATTATTCGT
*
14286 GCTTTTAGT-GTT
66 ACTTTTA-TAGTT
* * *
14298 AGTTTAGATAA-ATATTTTTAAAGAA-GGGTATAATCCGAAAACGTAAAATTTCTCATTATTCGT
1 AGTTTAGATAATATATTTTTAAAAAAGGGGTACAATCCGAAAACATAAAATTTCTCATTATTCGT
14361 ACTTTTATAGTT
66 ACTTTTATAGTT
*
14373 AGTATAGATAAT
1 AGTTTAGATAAT
14385 GGTGGTTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
74 1 0.01
75 53 0.70
76 20 0.26
77 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (77 bp):
AGTTTAGATAATATATTTTTAAAAAAGGGGTACAATCCGAAAACATAAAATTTCTCATTATTCGT
ACTTTTATAGTT
Done.