Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013554.1 Corchorus capsularis cultivar CVL-1 contig13575, 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: 48188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:769 original size:16 final size:16
Alignment explanation
Indices: 746--778 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
736 GTGAGTTTAA
746 TTTGTTATTT-GTTTG
1 TTTGTTATTTGGTTTG
761 TTTGTTTATTTGGTTTG
1 TTTG-TTATTTGGTTTG
778 T
1 T
779 AGGTAGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.06, C:0.00, G:0.21, T:0.73
Consensus pattern (16 bp):
TTTGTTATTTGGTTTG
Found at i:1307 original size:45 final size:45
Alignment explanation
Indices: 1257--1344 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
1247 ATAGAGTAGT
1257 GGAATTACTAAAAGATCCCTA-CCTCGAATTAATGATAAGCTGGGG
1 GGAATTACTAAAAGATCCCTACCCT-GAATTAATGATAAGCTGGGG
* *
1302 GGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
1 GGAATTACTAAAAGATCCCTACCCTGAATTAATGATAAGCTGG
1345 AGAAGTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
GGAATTACTAAAAGATCCCTACCCTGAATTAATGATAAGCTGGGG
Found at i:3717 original size:31 final size:31
Alignment explanation
Indices: 3676--3741 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
3666 AACTTTATAT
* *
3676 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCATT-TTCTTTAAAACATA
3707 TTTCCAATTGTACCATTTTCTTTAAAACATA
1 TTTCCAATTGTACCATTTTCTTTAAAACATA
3738 TTTC
1 TTTC
3742 GAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTTAAAACATA
Found at i:4009 original size:19 final size:20
Alignment explanation
Indices: 3982--4020 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3972 TACTATTCTT
3982 TTTTGAATTT-AATATTTTAA
1 TTTTGAATTTCAAT-TTTTAA
4002 TTTT-AATTTCAATTTTTAA
1 TTTTGAATTTCAATTTTTAA
4021 ATGTCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAA
Found at i:4301 original size:22 final size:22
Alignment explanation
Indices: 4192--4301 Score: 100
Period size: 22 Copynumber: 4.9 Consensus size: 22
4182 TGTCTCTATG
4192 TGGTTATCAAAATTTCATAAG-A
1 TGGTTATCAAAATTTCAT-AGTA
* * *
4214 TGGTTATTATAATTTC-TGAGGA
1 TGGTTATCAAAATTTCAT-AGTA
*
4236 -GGTTATCAAAATTCCATAGTGTA
1 TGGTTATCAAAATTTCATA--GTA
*
4259 GTGGTTACCAAAATTTCATAGTA
1 -TGGTTATCAAAATTTCATAGTA
*
4282 TGGTTACCAAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
4302 GATCAAGTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
21 16 0.22
22 36 0.49
23 5 0.07
25 16 0.22
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGTA
Found at i:4514 original size:22 final size:21
Alignment explanation
Indices: 4466--4772 Score: 108
Period size: 22 Copynumber: 13.8 Consensus size: 21
4456 TTTCATGGGG
* *
4466 AGGTTATCAAAATTTTATAGCG
1 AGGTTATCAAAATTTCATAG-A
*
4488 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
4510 AGGTTAT-AAAAGTCTTAATTTCATA
1 AGGTTATCAAAA-T-TTCA--T-AGA
* *
4535 AGGAGTA-CGAAAATTTGATAGA
1 AGG-TTATC-AAAATTTCATAGA
*
4557 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
4576 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
*
4599 GATCGAATTATCAAAATTT-ATAGAA
1 -A--G-GTTATCAAAATTTCATAG-A
* *
4624 AGATTATTAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
4644 TGTTGTTATCAAAATTTCAAAGTG
1 AG--GTTATCAAAATTTCATAG-A
* *
4668 AGGTTATCATAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
*
4688 TGGGATTAT-AAGAATTTCATAGA
1 -AGG-TTATCAA-AATTTCATAGA
* * * * *
4711 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
4733 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
4755 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
4773 AAATGTGATT
Statistics
Matches: 218, Mismatches: 39, Indels: 56
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.01
20 11 0.05
21 26 0.12
22 132 0.61
23 11 0.05
24 7 0.03
25 20 0.09
26 5 0.02
27 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:4906 original size:20 final size:20
Alignment explanation
Indices: 4881--4928 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
4871 TGAAGTAATC
*
4881 AAAATTTGAAGGAGGATATA
1 AAAATTTCAAGGAGGATATA
* *
4901 AAAA-TTCAGGGAGGATATC
1 AAAATTTCAAGGAGGATATA
4920 AAAATTTCA
1 AAAATTTCA
4929 TATGAAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (20 bp):
AAAATTTCAAGGAGGATATA
Found at i:4943 original size:22 final size:22
Alignment explanation
Indices: 4916--5477 Score: 148
Period size: 22 Copynumber: 25.7 Consensus size: 22
4906 TCAGGGAGGA
4916 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
4938 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4960 TTTCAAAATTTCACAAG-AGAGT
1 TATCAAAATTTCATATGAAG-GT
* *
4982 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
5003 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
5026 TAACAAACA-TTCATAATG-AGGT
1 TATCAAA-ATTTCAT-ATGAAGGT
** * *
5048 TATCAAAAAATCATAGGGAA-AT
1 TATCAAAATTTCATA-TGAAGGT
* *
5070 TATTAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
5086 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * * *
5108 TAGCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
5131 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
5154 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
5176 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
5198 TATCAAAATTTCAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
5220 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * *
5242 TTTTAAATTTTCATA--ACGTGAT
1 TATCAAAATTTCATATGAAG-G-T
* * *
5264 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * ***
5286 TATCAACATCTCATAGTTTTGGT
1 TATCAAAATTTCATA-TGAAGGT
5309 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
5331 TATCAAAATTTCATGTTG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
5353 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
5375 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
5397 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * * **
5419 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
5441 TATTAAAATTTCATACGAAGGT
1 TATCAAAATTTCATATGAAGGT
5463 TATCAAAATTTCATA
1 TATCAAAATTTCATA
5478 ATGGGATCAT
Statistics
Matches: 397, Mismatches: 99, Indels: 88
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.02
18 2 0.01
20 4 0.01
21 21 0.05
22 284 0.72
23 74 0.19
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:5136 original size:45 final size:44
Alignment explanation
Indices: 5084--5190 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 44
5074 AAAATTTGTA
* *
5084 GTTATCAAGATTTCATAAGAA-AGTTAGCAAAATTTTATAGGGAG
1 GTTATCAA-ATTTCATAAGAAGAGTTAGCAAAATTTCATAGCGAG
* * * *
5128 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATC-AAATTTCATAAGAAGAGTTAGCAAAATTTCATAGCGAG
5174 GTTATCACAATTTCATA
1 GTTATCA-AATTTCATA
5191 GTGTGATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
44 2 0.04
45 28 0.54
46 22 0.42
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
GTTATCAAATTTCATAAGAAGAGTTAGCAAAATTTCATAGCGAG
Found at i:5520 original size:22 final size:22
Alignment explanation
Indices: 5492--5535 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5482 GATCATAAAC
5492 AATAGAG-TAATTATCATAATTT
1 AATAGAGAT-ATTATCATAATTT
*
5514 AATAGAGATGTTATCATAATTT
1 AATAGAGATATTATCATAATTT
5536 CATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (22 bp):
AATAGAGATATTATCATAATTT
Found at i:8665 original size:20 final size:19
Alignment explanation
Indices: 8627--8670 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
8617 TTGTAATCTC
*
8627 TGATTATTGATTAATAAAAG
1 TGATTATTGATTAA-AAAAA
8647 TGATTATTTGA-TAAAAAAA
1 TGATTA-TTGATTAAAAAAA
8666 TGATT
1 TGATT
8671 TGAGCCCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 9 0.41
21 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
TGATTATTGATTAAAAAAA
Found at i:9077 original size:18 final size:18
Alignment explanation
Indices: 9054--9094 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
9044 TTGTAATATC
**
9054 TGATTATTTATTTGAAAA
1 TGATTATTTATAAGAAAA
9072 TGATTATTTATAAGAAAA
1 TGATTATTTATAAGAAAA
9090 TGATT
1 TGATT
9095 TGGGCCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TGATTATTTATAAGAAAA
Found at i:9881 original size:19 final size:19
Alignment explanation
Indices: 9841--9877 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9831 AATTTTTAAG
9841 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
9860 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
9878 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:14309 original size:20 final size:23
Alignment explanation
Indices: 14279--14331 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
14269 GATTTAACTT
14279 TTTATTAAA-ATTTTTAATTTTA-
1 TTTATTAAATA-TTTTAATTTTAC
*
14301 TTT-TTAAATATTTTATTTTTAC
1 TTTATTAAATATTTTAATTTTAC
14323 TTTATTAAA
1 TTTATTAAA
14332 AAAATAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 15 0.56
22 7 0.26
23 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATTAAATATTTTAATTTTAC
Found at i:18171 original size:15 final size:15
Alignment explanation
Indices: 18089--18177 Score: 53
Period size: 15 Copynumber: 5.9 Consensus size: 15
18079 TTAGGTTAGG
18089 TATT-TATATTACATA
1 TATTATATATTA-ATA
18104 TATTACTATA-TAATA
1 TATTA-TATATTAATA
* *
18119 TA-TATTTATTTTATCA
1 TATTATATA-TTAAT-A
*
18135 TATAATAT-TTCAA-A
1 TATTATATATT-AATA
*
18149 TGAATATATATTAATA
1 T-ATTATATATTAATA
18165 TATTATATATTAA
1 TATTATATATTAA
18178 AAATAATTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
13 3 0.05
14 4 0.07
15 32 0.57
16 10 0.18
17 7 0.12
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATATATTAATA
Found at i:23342 original size:43 final size:42
Alignment explanation
Indices: 23244--23354 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 42
23234 CTTGTGTTAC
* * * * *
23244 ATGTGGTTAGGGACTTTGATATAGA-TGCCTCTGTGTTATGA
1 ATGTGCTTGGGGACTTTGAGAGAGAGTGCCCCTGTGTTATGA
*
23285 ATGTGCTTGAGGACTTTGAGAGAGAGTTGCCCCTGTGTTAT-A
1 ATGTGCTTGGGGACTTTGAGAGAGAG-TGCCCCTGTGTTATGA
* *
23327 ATTGTGTTTGGGGACTTTGGGGAGAGAG
1 A-TGTGCTTGGGGACTTT-GAGAGAGAG
23355 AAATGCCCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 20 0.35
42 2 0.04
43 27 0.47
44 8 0.14
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35
Consensus pattern (42 bp):
ATGTGCTTGGGGACTTTGAGAGAGAGTGCCCCTGTGTTATGA
Found at i:32072 original size:17 final size:18
Alignment explanation
Indices: 32050--32085 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32040 CCATGTGTCC
32050 TTTTT-GTACACGTGGCA
1 TTTTTGGTACACGTGGCA
*
32067 TTTTTGGTACATGTGGCA
1 TTTTTGGTACACGTGGCA
32085 T
1 T
32086 GCCATGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.44
Consensus pattern (18 bp):
TTTTTGGTACACGTGGCA
Found at i:36066 original size:2 final size:2
Alignment explanation
Indices: 36059--36087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36049 TATTAATTAG
36059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36088 CTAGTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38415 original size:11 final size:11
Alignment explanation
Indices: 38399--38424 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38389 TAACAAAAAC
38399 CTTATAGTACT
1 CTTATAGTACT
38410 CTTATAGTACT
1 CTTATAGTACT
38421 CTTA
1 CTTA
38425 GTAATTGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (11 bp):
CTTATAGTACT
Found at i:46436 original size:30 final size:28
Alignment explanation
Indices: 46402--46466 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
46392 TAGTATTTTT
*
46402 GGCAAAT-TACTTGGATTTGGAAGTTCATGG
1 GGCAAATGTAC-T-GATTT-GAAGTTCATGA
46432 GGCAAAATGTACTGATTTGAAGTTCATGA
1 GGC-AAATGTACTGATTTGAAGTTCATGA
46461 GGCAAA
1 GGCAAA
46467 AAGGGTAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 8 0.25
31 5 0.16
32 3 0.09
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (28 bp):
GGCAAATGTACTGATTTGAAGTTCATGA
Done.