Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014482.1 Corchorus capsularis cultivar CVL-1 contig14503, 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: 40360
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:25 original size:2 final size:2
Alignment explanation
Indices: 18--46 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8 CGAAGACTAG
18 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47 TAAGTAATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4360 original size:19 final size:20
Alignment explanation
Indices: 4310--4373 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
4300 GCTGCTCTAA
4310 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTA-C
* * *
4331 TAATATAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAC
4350 TAATCTCATCTGTACAGTTAC
1 TAATCTCATCTGTACAG-TAC
4371 TAA
1 TAA
4374 ACAATGTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.43
20 1 0.03
21 19 0.54
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:7123 original size:83 final size:83
Alignment explanation
Indices: 7015--7181 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
7005 TTTCACAGAA
*
7015 TTCTTTCAACCCTTCTTTTTCAGAATA-CTTAAAACTACACAACCTAAAATCGATTTACCCCTTT
1 TTCTTTCAACCCTTCTTTTTCAGAATACCCT-AAACTACACAACCTAAAATCGATTTACCCCTTT
7079 ATGTTCTAAGTTTCTGGGT
65 ATGTTCTAAGTTTCTGGGT
* *
7098 TTCTTTCAACCCTTCTTTTTTAGAATACCCTAAACTACACAACCTAAAATCGATTTCCCCCTTTA
1 TTCTTTCAACCCTTCTTTTTCAGAATACCCTAAACTACACAACCTAAAATCGATTTACCCCTTTA
7163 TGTTCTAAGTTTCTGGGT
66 TGTTCTAAGTTTCTGGGT
7181 T
1 T
7182 CAATTTAATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 78 0.98
84 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.40
Consensus pattern (83 bp):
TTCTTTCAACCCTTCTTTTTCAGAATACCCTAAACTACACAACCTAAAATCGATTTACCCCTTTA
TGTTCTAAGTTTCTGGGT
Found at i:12104 original size:14 final size:16
Alignment explanation
Indices: 12078--12109 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12068 AGAGATCGAA
12078 TTCTTCTACCAAT-TT
1 TTCTTCTACCAATGTT
12093 TTCTTC-ACCAATGTT
1 TTCTTCTACCAATGTT
12108 TT
1 TT
12110 GAATTACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.53
Consensus pattern (16 bp):
TTCTTCTACCAATGTT
Found at i:15540 original size:13 final size:13
Alignment explanation
Indices: 15522--15546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15512 GTTTAAATTC
15522 AATTTGTAATTAG
1 AATTTGTAATTAG
15535 AATTTGTAATTA
1 AATTTGTAATTA
15547 TCTAAGTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
AATTTGTAATTAG
Found at i:15877 original size:31 final size:30
Alignment explanation
Indices: 15816--15879 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
15806 CCGATTTCAA
* **
15816 TCACCACCTCCAATAATCTTCCTGTCAAGC
1 TCACCACCTCCAATAATCCTCCTGGAAAGC
15846 TCACCACCTCCAATTACA-CCTCCTGGAAAGC
1 TCACCACCTCCAA-TA-ATCCTCCTGGAAAGC
15877 TCA
1 TCA
15880 AATGGATGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 13 0.45
31 15 0.52
32 1 0.03
ACGTcount: A:0.28, C:0.41, G:0.08, T:0.23
Consensus pattern (30 bp):
TCACCACCTCCAATAATCCTCCTGGAAAGC
Found at i:20676 original size:29 final size:29
Alignment explanation
Indices: 20650--20707 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
20640 TATGTAATTT
*
20650 TATTTATCAATTAAATTAAAATATAATAA
1 TATTTATAAATTAAATTAAAATATAATAA
20679 TATTTATAAATTAAATTAAAATATTAATA
1 TATTTATAAATTAAATTAAAATA-TAATA
20708 TAAAATCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TATTTATAAATTAAATTAAAATATAATAA
Found at i:20822 original size:62 final size:63
Alignment explanation
Indices: 20729--20854 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 63
20719 TTCTTTACAG
*
20729 CATGAAGTCTTCCACTAAATGTGAATTACTTATTTTTAATTGCTTCATCCGTATAAAAATTTC
1 CATGAAGTCTTCCACTAAATGTGAATTACTTAGTTTTAATTGCTTCATCCGTATAAAAATTTC
* *
20792 CATGACGTCTTCTACTAAA-GTGAATTACTTAGTTTTAATTGCTTCATCCGTATAAAAATTTC
1 CATGAAGTCTTCCACTAAATGTGAATTACTTAGTTTTAATTGCTTCATCCGTATAAAAATTTC
20854 C
1 C
20855 TTATCCCAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 43 0.72
63 17 0.28
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (63 bp):
CATGAAGTCTTCCACTAAATGTGAATTACTTAGTTTTAATTGCTTCATCCGTATAAAAATTTC
Found at i:21683 original size:114 final size:114
Alignment explanation
Indices: 21483--21702 Score: 422
Period size: 114 Copynumber: 1.9 Consensus size: 114
21473 ATTAGGTACA
*
21483 AAAGAATATATTACAAAAGTTAGTACAATCGAAGAAAACTTTATATAGGAGGCTTCGTGTTTTGT
1 AAAGAATATATTACAAAAGTTAGTACAATCGAAGAAAACTTTATATAGGAGACTTCGTGTTTTGT
21548 GGTTTAGGTTTAATATATGTAAATGAGAGTTACAGCAATTGGGAGAAAG
66 GGTTTAGGTTTAATATATGTAAATGAGAGTTACAGCAATTGGGAGAAAG
21597 AAAGAATATATTACAAAAGTTAGTACAATCGAAGAAAACTTTATATAGGAGACTTCGTGTTTTGT
1 AAAGAATATATTACAAAAGTTAGTACAATCGAAGAAAACTTTATATAGGAGACTTCGTGTTTTGT
*
21662 GGTTTAGGTTTAATATATGTAAATGAGAGTTGCAGCAATTG
66 GGTTTAGGTTTAATATATGTAAATGAGAGTTACAGCAATTG
21703 CATGCGAGAA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (114 bp):
AAAGAATATATTACAAAAGTTAGTACAATCGAAGAAAACTTTATATAGGAGACTTCGTGTTTTGT
GGTTTAGGTTTAATATATGTAAATGAGAGTTACAGCAATTGGGAGAAAG
Found at i:24322 original size:21 final size:21
Alignment explanation
Indices: 24283--24324 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24273 CTTATAATAC
*
24283 TATAACATTTTTTATAACCTT
1 TATAACATTTTTTACAACCTT
24304 TATAAC-TTTTTTAGCAACCTT
1 TATAACATTTTTTA-CAACCTT
24325 AAAGAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (21 bp):
TATAACATTTTTTACAACCTT
Found at i:29238 original size:10 final size:10
Alignment explanation
Indices: 29223--29259 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
29213 TTTTGACCGG
*
29223 TGACATTACT
1 TGACATTAGT
29233 TGACATTAGT
1 TGACATTAGT
29243 TGAACATTAGT
1 TG-ACATTAGT
29254 TGACAT
1 TGACAT
29260 GAGATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (10 bp):
TGACATTAGT
Found at i:35610 original size:22 final size:22
Alignment explanation
Indices: 35584--35626 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
35574 GAAGCAAGAT
35584 AAACGCTCTCACAAAGAGTCCC
1 AAACGCTCTCACAAAGAGTCCC
*
35606 AAACGCTCTCACAAGGAGTCC
1 AAACGCTCTCACAAAGAGTCC
35627 TGCACGTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (22 bp):
AAACGCTCTCACAAAGAGTCCC
Found at i:36604 original size:20 final size:20
Alignment explanation
Indices: 36576--37115 Score: 470
Period size: 20 Copynumber: 26.6 Consensus size: 20
36566 CTTATGGAAG
*
36576 CTTTCAAGTGTCTAAGCGGA
1 CTTTCAAGTGTCTAAGTGGA
*
36596 CTTTTAAGTGTCTAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
36616 CTTTCAAG-GTGCATAAGTAGG-
1 CTTTCAAGTGT-C-TAAGT-GGA
* *
36637 CTTTCAAGTGTCTAACTAGA
1 CTTTCAAGTGTCTAAGTGGA
* *
36657 CTTTTAAGTGTCCAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
*
36677 CTTTCAAGGTGTCAAAGTAGG-
1 CTTTCAA-GTGTCTAAGT-GGA
* * *
36698 CTTTTAAGTGCCTAAGTGGG
1 CTTTCAAGTGTCTAAGTGGA
*
36718 CTTTCAAGTGTCCAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
36738 CTTTCAAG-GTGCATAAGTAGG-
1 CTTTCAAGTGT-C-TAAGT-GGA
*
36759 CTTTCAAGTGTCTAAGTAGA
1 CTTTCAAGTGTCTAAGTGGA
36779 CTTTCAAGTGT-TCAAGTGGA
1 CTTTCAAGTGTCT-AAGTGGA
* *
36799 CTTTCAAGGTGCCTAAGTAGA
1 CTTTCAA-GTGTCTAAGTGGA
* *
36820 CTTTTAAGTGCCTAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
* *
36840 CTTTCAAGTGTCCAAATGGA
1 CTTTCAAGTGTCTAAGTGGA
*
36860 CTTTCAAAGTGTCCAAGTGGA
1 CTTTC-AAGTGTCTAAGTGGA
*
36881 CTTTCAAGGTGCCTAAGTAGG-
1 CTTTCAA-GTGTCTAAGT-GGA
* *
36902 CTTTTAAGTGTCCAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
*
36922 CTTTCAAGTGCCTAAGTAGG-
1 CTTTCAAGTGTCTAAGT-GGA
* *
36942 CTTTCAAGTGCCTAAAGCAGG-
1 CTTTCAAGTGTCT-AAG-TGGA
* * * *
36963 CTTTTAAGTGCCTAAATGGG
1 CTTTCAAGTGTCTAAGTGGA
*
36983 CTTTCAAGTGTCCAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
*
37003 CTTTCAAAGTGTCTAAGTAGGT
1 CTTTC-AAGTGTCTAAGT-GGA
* * *
37025 GTTT-AAGTGCCTAAGTGGG
1 CTTTCAAGTGTCTAAGTGGA
*
37044 CTTTCAAGTGTCCAAGTGGA
1 CTTTCAAGTGTCTAAGTGGA
* **
37064 CTTTCAAGTGCCTAAGTAAA
1 CTTTCAAGTGTCTAAGTGGA
* * *
37084 CTTTTATGTGTCTAAGTAGA
1 CTTTCAAGTGTCTAAGTGGA
*
37104 CTTTCAATTGTC
1 CTTTCAAGTGTC
37116 CAAATGGGCT
Statistics
Matches: 426, Mismatches: 67, Indels: 54
0.78 0.12 0.10
Matches are distributed among these distances:
19 18 0.04
20 270 0.63
21 120 0.28
22 18 0.04
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
CTTTCAAGTGTCTAAGTGGA
Found at i:36674 original size:61 final size:61
Alignment explanation
Indices: 36575--37110 Score: 563
Period size: 61 Copynumber: 8.8 Consensus size: 61
36565 CCTTATGGAA
* ** *
36575 GCTTTCAAGTGTCTAAGCGGACTTTTAAGTGTCTAAGTGGACTTTCAAGGTG-CATAAGTAG
1 GCTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTC-TAAGTAG
* * *
36636 GCTTTCAAGTGTCTAACTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTCAAAGTAG
1 GCTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTCTAAGTAG
* * * *
36697 GCTTTTAAGTGCCTAAGTGGGCTTTCAAGTGTCCAAGTGGACTTTCAAGGTG-CATAAGTAG
1 GCTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTC-TAAGTAG
* * * *
36758 GCTTTCAAGTGTCTAAGTAGACTTTCAAGTGTTCAAGTGGACTTTCAAGGTGCCTAAGTAG
1 GCTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTCTAAGTAG
* * * * * * *
36819 ACTTTTAAGTGCCTAAGTGGACTTTCAAGTGTCCAAATGGACTTTCAAAGTGTCCAAGT-G
1 GCTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTCTAAGTAG
* *
36879 GACTTTCAAGGTGCCTAAGTAGGCTTTTAAGTGTCCAAGTGGACTTTCAA-GTGCCTAAGTAG
1 G-CTTTCAA-GTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTCTAAGTAG
* * * * *
36941 GCTTTCAAGTGCCTAAAGCAGGCTTTTAAGTG-CCTAAATGGGCTTTCAA-GTGTCCAAGT-G
1 GCTTTCAAGTGCCT-AAGTAGACTTTTAAGTGTCC-AAGTGGACTTTCAAGGTGTCTAAGTAG
* * * *
37001 GACTTTCAAAGTGTCTAAGTAG-GTGTTTAAGTG-CCTAAGTGGGCTTTCAA-GTGTCCAAGT-G
1 G-CTTTC-AAGTGCCTAAGTAGACT-TTTAAGTGTCC-AAGTGGACTTTCAAGGTGTCTAAGTAG
* * * *
37062 GACTTTCAAGTGCCTAAGTAAACTTTTATGTGTCTAAGTAGACTTTCAA
1 G-CTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAA
37111 TTGTCCAAAT
Statistics
Matches: 412, Mismatches: 50, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
60 44 0.11
61 321 0.78
62 47 0.11
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (61 bp):
GCTTTCAAGTGCCTAAGTAGACTTTTAAGTGTCCAAGTGGACTTTCAAGGTGTCTAAGTAG
Found at i:37534 original size:26 final size:26
Alignment explanation
Indices: 37496--37547 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
37486 CACTTTTAGT
*
37496 TTAGGTTAACTAATTCATATTTAGGC
1 TTAGATTAACTAATTCATATTTAGGC
* *
37522 TTAGATTAGCTAATTCATCTTTAGGC
1 TTAGATTAACTAATTCATATTTAGGC
37548 ATCGCGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (26 bp):
TTAGATTAACTAATTCATATTTAGGC
Found at i:37674 original size:24 final size:25
Alignment explanation
Indices: 37646--37698 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
37636 AGTATTTTGC
*
37646 ATTTCGTTCATGTAGCTCAA-ACTA
1 ATTTCATTCATGTAGCTCAAGACTA
*
37670 ATTTCATTCATGTAGCTCAAGTCTA
1 ATTTCATTCATGTAGCTCAAGACTA
37695 ATTT
1 ATTT
37699 GGTCTTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (25 bp):
ATTTCATTCATGTAGCTCAAGACTA
Found at i:37946 original size:4 final size:4
Alignment explanation
Indices: 37937--37967 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
37927 TAGTTTTAGT
37937 TTTA TTTA TTTA TTTA TTATA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TT
37968 CTAGGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:37961 original size:13 final size:12
Alignment explanation
Indices: 37937--37967 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
37927 TAGTTTTAGT
37937 TTTATTTATTTA
1 TTTATTTATTTA
37949 TTTATTATATTTA
1 TTTATT-TATTTA
37962 TTTATT
1 TTTATT
37968 CTAGGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTATTTA
Done.