Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010287.1 Corchorus capsularis cultivar CVL-1 contig10308, 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: 94811
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3011 original size:31 final size:31
Alignment explanation
Indices: 2973--3032 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2963 TCAGAGGCCT
*
2973 AATTGCTCAATTAA-TTCCACTTTAGGGACTC
1 AATTGCTCAATTAAGTT-CACTTCAGGGACTC
*
3004 AATTGCTCATTTAAGTTCACTTCAGGGAC
1 AATTGCTCAATTAAGTTCACTTCAGGGAC
3033 CTATTTGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (31 bp):
AATTGCTCAATTAAGTTCACTTCAGGGACTC
Found at i:3594 original size:21 final size:22
Alignment explanation
Indices: 3563--3604 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3553 TTTCTTTAAA
3563 AAAGAAAAAATGGATTTTTTTT
1 AAAGAAAAAATGGATTTTTTTT
*
3585 AAAG-AAAAATTGATTTTTTT
1 AAAGAAAAAATGGATTTTTTT
3605 ATTTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (22 bp):
AAAGAAAAAATGGATTTTTTTT
Found at i:4959 original size:11 final size:11
Alignment explanation
Indices: 4945--4969 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4935 CTGTAAAAAA
4945 AAATAATAAAT
1 AAATAATAAAT
4956 AAATAATAAAT
1 AAATAATAAAT
4967 AAA
1 AAA
4970 GAGCCAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:13079 original size:49 final size:49
Alignment explanation
Indices: 13021--13124 Score: 208
Period size: 49 Copynumber: 2.1 Consensus size: 49
13011 GAAACAGAGT
13021 TAACTATAGTGTTAGACTGACTAAACCTTAACAACTTACTAGAGTAAAC
1 TAACTATAGTGTTAGACTGACTAAACCTTAACAACTTACTAGAGTAAAC
13070 TAACTATAGTGTTAGACTGACTAAACCTTAACAACTTACTAGAGTAAAC
1 TAACTATAGTGTTAGACTGACTAAACCTTAACAACTTACTAGAGTAAAC
13119 TAACTA
1 TAACTA
13125 ACCCCTGGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (49 bp):
TAACTATAGTGTTAGACTGACTAAACCTTAACAACTTACTAGAGTAAAC
Found at i:13483 original size:20 final size:20
Alignment explanation
Indices: 13458--13495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13448 TGATTGTTTC
*
13458 ATTTTCCTTATTTCCTTAAG
1 ATTTTCCTCATTTCCTTAAG
*
13478 ATTTTCCTCGTTTCCTTA
1 ATTTTCCTCATTTCCTTA
13496 CTTATTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTTCCTCATTTCCTTAAG
Found at i:13765 original size:8 final size:8
Alignment explanation
Indices: 13752--13778 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
13742 TGTATATCAT
13752 TTTCCTTA
1 TTTCCTTA
13760 TTTCCTTA
1 TTTCCTTA
13768 TTTCCTTA
1 TTTCCTTA
13776 TTT
1 TTT
13779 TCTGGTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTCCTTA
Found at i:24969 original size:2 final size:2
Alignment explanation
Indices: 24962--25006 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
24952 TGCAGGTTTC
24962 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
25004 CT C
1 CT C
25007 ATGTAAATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:36019 original size:5 final size:6
Alignment explanation
Indices: 36004--36028 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35994 ATTTGGATGA
36004 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
36029 GGATTTGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:39211 original size:10 final size:9
Alignment explanation
Indices: 39176--39212 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
39166 TTTAAGAAGC
39176 TTTT-TTTT
1 TTTTCTTTT
39184 TTTTCTTTT
1 TTTTCTTTT
39193 TTTTCTTTT
1 TTTTCTTTT
39202 TTTTCATTTT
1 TTTTC-TTTT
39212 T
1 T
39213 GCAGTACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 4 0.15
9 18 0.67
10 5 0.19
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:63452 original size:42 final size:40
Alignment explanation
Indices: 63404--63482 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
63394 GTAATAACTC
*
63404 CTCCTAACTTGGATAGGAAAAGGAGTTCCAAGTAATTAAAAA
1 CTCCTAACTTGAATAGG-AAA-GAGTTCCAAGTAATTAAAAA
* * *
63446 CTCCTAACTTGAATTGGACAGAGTTCCAATTAATTAA
1 CTCCTAACTTGAATAGGAAAGAGTTCCAAGTAATTAA
63483 TCAGTTGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.48
41 2 0.06
42 15 0.45
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (40 bp):
CTCCTAACTTGAATAGGAAAGAGTTCCAAGTAATTAAAAA
Found at i:64962 original size:14 final size:14
Alignment explanation
Indices: 64943--65054 Score: 70
Period size: 14 Copynumber: 8.1 Consensus size: 14
64933 TTTATTTTAT
64943 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
64957 AAATTCAGTTAAG-
1 AAATTCTTTTAAGA
* * *
64970 AAATTTTATTTTA-T
1 AAATTCT-TTTAAGA
64984 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
64998 AAATTCAGTTAAGA
1 AAATTCTTTTAAGA
* *
65012 AAATT-TATTTTA-T
1 AAATTCT-TTTAAGA
*
65025 AAATTCTTTTAAAA
1 AAATTCTTTTAAGA
**
65039 AAATTCAGTTAAGA
1 AAATTCTTTTAAGA
65053 AA
1 AA
65055 TTTTATTTTA
Statistics
Matches: 72, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
13 18 0.25
14 54 0.75
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (14 bp):
AAATTCTTTTAAGA
Found at i:64987 original size:27 final size:27
Alignment explanation
Indices: 64950--65071 Score: 84
Period size: 27 Copynumber: 4.4 Consensus size: 27
64940 TATAAATTCT
64950 TTTAAGAAAATTCAGTTAAGAAATTTTA
1 TTTAA-AAAATTCAGTTAAGAAATTTTA
* * ** * *
64978 TTTTATAAATTCTTTTAAGAAAATTCA
1 TTTAAAAAATTCAGTTAAGAAATTTTA
* * * * *
65005 GTTAAGAAAATTTATTTTATAAATTCTT-
1 TTTAA-AAAATTCAGTTAAGAAATT-TTA
*
65033 TTAAAAAAATTCAGTTAAGAAATTTTA
1 TTTAAAAAATTCAGTTAAGAAATTTTA
* *
65060 TTTTATAAATTC
1 TTTAAAAAATTC
65072 TTTAAAGAAA
Statistics
Matches: 67, Mismatches: 24, Indels: 7
0.68 0.24 0.07
Matches are distributed among these distances:
26 2 0.03
27 44 0.66
28 20 0.30
29 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (27 bp):
TTTAAAAAATTCAGTTAAGAAATTTTA
Found at i:64989 original size:41 final size:41
Alignment explanation
Indices: 64932--65097 Score: 296
Period size: 41 Copynumber: 4.0 Consensus size: 41
64922 TGTGCGGCTG
64932 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
64973 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
* *
65014 ATTTATTTTATAAATTCTTTTAAAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
*
65055 TTTTATTTTATAAATTCTTTAAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
65097 T
1 T
65098 GAAATTTTGT
Statistics
Matches: 119, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 101 0.85
42 18 0.15
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (41 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Found at i:65425 original size:11 final size:11
Alignment explanation
Indices: 65411--65448 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
65401 ATTCATAACA
65411 AATTTATAATT
1 AATTTATAATT
65422 AATTTATAATT
1 AATTTATAATT
65433 -ATTTGATAATT
1 AATTT-ATAATT
*
65444 TATTT
1 AATTT
65449 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:69392 original size:16 final size:15
Alignment explanation
Indices: 69351--69392 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
69341 AATATATATT
69351 TAAATAAAAATAAAA
1 TAAATAAAAATAAAA
69366 TAAATTAAAAAGT-AAA
1 TAAA-TAAAAA-TAAAA
69382 TAAATACAAAA
1 TAAATA-AAAA
69393 AATAGCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAATAAAAATAAAA
Found at i:74456 original size:2 final size:2
Alignment explanation
Indices: 74449--74474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74439 TCACGTATAC
74449 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
74475 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:74479 original size:2 final size:2
Alignment explanation
Indices: 74474--74498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74464 ACACACACAC
74474 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 A
74499 GAAGATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77390 original size:18 final size:18
Alignment explanation
Indices: 77358--77405 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
77348 TTCTGTCACC
*
77358 CCCCATTTCCCTCTCTGAG
1 CCCC-TTTCCTTCTCTGAG
77377 CCCCTTTCCTTCTCTGAG
1 CCCCTTTCCTTCTCTGAG
*
77395 ACCCTTTCCTT
1 CCCCTTTCCTT
77406 TCCAGAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.08, C:0.46, G:0.08, T:0.38
Consensus pattern (18 bp):
CCCCTTTCCTTCTCTGAG
Found at i:79168 original size:29 final size:29
Alignment explanation
Indices: 79113--79187 Score: 132
Period size: 29 Copynumber: 2.5 Consensus size: 29
79103 AAGCAAATTT
79113 CCAAAACAATTAAATTTTTTTTTTGGCCAAA
1 CCAAAACAATT--ATTTTTTTTTTGGCCAAA
79144 CCAAAACAATTATTTTTTTTTTGGCCAAA
1 CCAAAACAATTATTTTTTTTTTGGCCAAA
79173 CCAAAACAATTATTT
1 CCAAAACAATTATTT
79188 ACTTCCATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 33 0.75
31 11 0.25
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (29 bp):
CCAAAACAATTATTTTTTTTTTGGCCAAA
Found at i:82825 original size:62 final size:65
Alignment explanation
Indices: 82747--82876 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 65
82737 AAATGCTCCA
*
82747 AATTTTGATTAGGATGAAGATGATTAG-AA-ATTATTAACTTTTAAGTAGT-ACTAGTAATTTGG
1 AATTTTGATTAGGATGAAGATGATTAGAAATATTATTAACTTTTAAGTACTAACTAGTAATTTGG
82809 AATTTTGATTAGGATGAAGATGATTAGAAATTATTATTAACTTTTAAGTACTAACTAGTAATTTG
1 AATTTTGATTAGGATGAAGATGATTAGAAA-TATTATTAACTTTTAAGTACTAACTAGTAATTTG
82874 G
65 G
82875 AA
1 AA
82877 GAATGGGCCA
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
62 27 0.43
63 2 0.03
65 19 0.30
66 15 0.24
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (65 bp):
AATTTTGATTAGGATGAAGATGATTAGAAATATTATTAACTTTTAAGTACTAACTAGTAATTTGG
Found at i:88631 original size:66 final size:65
Alignment explanation
Indices: 88523--88668 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 65
88513 GAGAGGGCAG
*
88523 TTCAGTAATTTTTT-CTTATTAGTAATTAACCAAAATTGAATTTCCTTTTTAA-AAGTTTTAGGG
1 TTCAGTAATTTTTTCCTTATTAGTAATCAACCAAAATTGAATTTCCTTTTTAAGAA-TTTTAGGG
*
88586 C
65 A
* * *
88587 TT-AGTAATTTTTTCCTTATTAGCGTAATCAACGAAGATTTAATTTCCTTTTTAAGAATTTTAGG
1 TTCAGTAATTTTTTCCTTATTA--GTAATCAACCAAAATTGAATTTCCTTTTTAAGAATTTTAGG
88651 GA
64 GA
88653 TTCAGTAAATTTTTTC
1 TTCAGT-AATTTTTTC
88669 TTCTTAATAT
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
63 11 0.15
64 9 0.13
66 37 0.52
67 5 0.07
68 9 0.13
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (65 bp):
TTCAGTAATTTTTTCCTTATTAGTAATCAACCAAAATTGAATTTCCTTTTTAAGAATTTTAGGGA
Found at i:88818 original size:114 final size:118
Alignment explanation
Indices: 88639--88848 Score: 347
Period size: 115 Copynumber: 1.8 Consensus size: 118
88629 TTTCCTTTTT
*
88639 AAGAATTTTAGGGATTCAGTAAATTTTTTCTTCTTAATATATAATTAAGAAAAATAAATTTCCTT
1 AAGAATTTTAGGGATTCAGTAAATTTTTTCTCCTTAATATATAATTAAGAAAAATAAATTTCCTT
88704 T-TAAAAAATTTAGGGTTGGGTAGAAAGAAACTGGTAGGGCTGGAAGAACTAG
66 TCTAAAAAATTTAGGGTTGGGTAGAAAGAAACTGGTAGGGCTGGAAGAACTAG
* * * *
88756 AAGAATTTTAGGGCTTTAGT-AATTTTTTC-CCTTATTA-ATGATTAAGAAAAATAAATTTCCTT
1 AAGAATTTTAGGGATTCAGTAAATTTTTTCTCCTTAATATATAATTAAGAAAAATAAATTTCCTT
88818 TCTAAAAAATTTAGGGTTGGGTAGAAAGAAA
66 TCTAAAAAATTTAGGGTTGGGTAGAAAGAAA
88849 GGGCTTGAAG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
114 25 0.29
115 35 0.40
116 9 0.10
117 18 0.21
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (118 bp):
AAGAATTTTAGGGATTCAGTAAATTTTTTCTCCTTAATATATAATTAAGAAAAATAAATTTCCTT
TCTAAAAAATTTAGGGTTGGGTAGAAAGAAACTGGTAGGGCTGGAAGAACTAG
Found at i:94785 original size:2 final size:2
Alignment explanation
Indices: 94778--94805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
94768 TATAACCTTA
94778 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
94806 GCTCTG
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
Done.