Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013290.1 Corchorus capsularis cultivar CVL-1 contig13311, 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: 21944
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1234 original size:12 final size:12
Alignment explanation
Indices: 1217--1241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1207 GGCAGACACG
1217 TGCAAATGTATT
1 TGCAAATGTATT
1229 TGCAAATGTATT
1 TGCAAATGTATT
1241 T
1 T
1242 CAGTAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGCAAATGTATT
Found at i:1510 original size:23 final size:22
Alignment explanation
Indices: 1459--1510 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1449 CCAAAAACCG
*
1459 GGGTCCCGGTTGGGGGTCAACT
1 GGGTCCCGGTTGGGGATCAACT
*
1481 GGGTCCCGGGTT-GGGATCAAGT
1 GGGTCCC-GGTTGGGGATCAACT
1503 GGGATCCC
1 GGG-TCCC
1511 AATTGAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.12, C:0.23, G:0.44, T:0.21
Consensus pattern (22 bp):
GGGTCCCGGTTGGGGATCAACT
Found at i:4092 original size:27 final size:27
Alignment explanation
Indices: 4029--4098 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
4019 GCCTGAGCTG
* *
4029 CCCCATCATAATAACCGAACCCAGCAC
1 CCCCAACATAATAACCGAACCCAACAC
* ** *
4056 CCCCATCATAATAACCGGGCTCAACAC
1 CCCCAACATAATAACCGAACCCAACAC
* *
4083 CCTCAACATAGTAACC
1 CCCCAACATAATAACC
4099 CGGTTGACCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.36, C:0.41, G:0.09, T:0.14
Consensus pattern (27 bp):
CCCCAACATAATAACCGAACCCAACAC
Found at i:4359 original size:13 final size:14
Alignment explanation
Indices: 4297--4372 Score: 59
Period size: 16 Copynumber: 5.2 Consensus size: 14
4287 ACATATTAAC
*
4297 ATTATAATTAATTA
1 ATTAAAATTAATTA
*
4311 AATAGAAATATAATTA
1 ATTA-AAAT-TAATTA
4327 ATCGT-AAA-TAACTCTA
1 AT--TAAAATTAA-T-TA
4343 ATTAAAATTAA-TA
1 ATTAAAATTAATTA
4356 ATTAAAATTAATTA
1 ATTAAAATTAATTA
4370 ATT
1 ATT
4373 TCAATATTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
13 13 0.26
14 12 0.24
15 7 0.14
16 17 0.34
18 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (14 bp):
ATTAAAATTAATTA
Found at i:4447 original size:15 final size:13
Alignment explanation
Indices: 4420--4474 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4410 TATTAAAACT
4420 AATAATTTTAAAA
1 AATAATTTTAAAA
4433 AATAATTTTAAAAAA
1 AATAATTTT--AAAA
**
4448 AATAACCTTAAAA
1 AATAATTTTAAAA
*
4461 TATAA-TTTAAAA
1 AATAATTTTAAAA
4473 AA
1 AA
4475 AAAAAATAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.20
13 17 0.49
15 11 0.31
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATTTTAAAA
Found at i:4553 original size:32 final size:31
Alignment explanation
Indices: 4517--4596 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
4507 CAGCCATGGA
*
4517 AAGGCCGCACCCTAGGGGCAGCCTGCCGTGGC
1 AAGGCCG-ACCCCAGGGGCAGCCTGCCGTGGC
* * *
4549 AAGGCTGACCCCATGGTGCGGCCTGCCGTGGC
1 AAGGCCGACCCCA-GGGGCAGCCTGCCGTGGC
*
4581 AAGACCGACCCCAGGG
1 AAGGCCGACCCCAGGG
4597 TGCGACCTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 7 0.17
32 33 0.82
ACGTcount: A:0.17, C:0.36, G:0.36, T:0.10
Consensus pattern (31 bp):
AAGGCCGACCCCAGGGGCAGCCTGCCGTGGC
Found at i:4599 original size:32 final size:32
Alignment explanation
Indices: 4537--4612 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
4527 CCTAGGGGCA
* * *
4537 GCCTGCCGTGGCAAGGCTGACCCCATGGTGCG
1 GCCTGCCGTGGCAAGACCGACCCCAGGGTGCG
4569 GCCTGCCGTGGCAAGACCGACCCCAGGGTGCG
1 GCCTGCCGTGGCAAGACCGACCCCAGGGTGCG
* *
4601 ACCTACCGTGGC
1 GCCTGCCGTGGC
4613 GCGGCCGCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.14, C:0.37, G:0.36, T:0.13
Consensus pattern (32 bp):
GCCTGCCGTGGCAAGACCGACCCCAGGGTGCG
Found at i:4729 original size:20 final size:20
Alignment explanation
Indices: 4706--4745 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4696 CGACTCAGCC
*
4706 CCTAGATCTATTTTTTTACA
1 CCTAGATCTAATTTTTTACA
4726 CCTAGATCTAATTTTTTACA
1 CCTAGATCTAATTTTTTACA
4746 TCCATTCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (20 bp):
CCTAGATCTAATTTTTTACA
Found at i:4936 original size:13 final size:13
Alignment explanation
Indices: 4905--4929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4895 TAGGGTTTTG
4905 ATGAAGAAGTTGA
1 ATGAAGAAGTTGA
4918 ATGAAGAAGTTG
1 ATGAAGAAGTTG
4930 TTTGAAGTAA
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:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (13 bp):
ATGAAGAAGTTGA
Found at i:5195 original size:16 final size:16
Alignment explanation
Indices: 5144--5197 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5134 GGTTAATGTC
*
5144 TCGGGTTATTCGGATT
1 TCGGGTCATTCGGATT
* * *
5160 TCGAGTCATACGGATC
1 TCGGGTCATTCGGATT
*
5176 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGATT
5192 TCGGGT
1 TCGGGT
5198 TATTTGTGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.35
Consensus pattern (16 bp):
TCGGGTCATTCGGATT
Found at i:8030 original size:33 final size:33
Alignment explanation
Indices: 7992--8088 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
7982 CGGCCTCAAG
7992 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
8025 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
** *
8058 ACCGGCCACGCGACAAGGACATGCCCGGCCA
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCA
8089 CAACCAGCCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.21, C:0.40, G:0.30, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
Found at i:8099 original size:33 final size:33
Alignment explanation
Indices: 7992--8132 Score: 160
Period size: 33 Copynumber: 4.3 Consensus size: 33
7982 CGGCCTCAAG
*
7992 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGACATGCCCGGCCATC
*
8025 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGACATGCCCGGCCATC
**
8058 ACCGGCCACGCGACAAGGACATGCCCGGCCA-C
1 ACCGGCCACGCGACTTGGACATGCCCGGCCATC
* ** * * *
8090 AACCAGCCACATGACTCGGCCATGCCTGGCCA-C
1 -ACCGGCCACGCGACTTGGACATGCCCGGCCATC
8123 AACCGGCCAC
1 -ACCGGCCAC
8133 ATGATCTCTT
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 1 0.01
33 95 0.99
ACGTcount: A:0.22, C:0.42, G:0.27, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGACATGCCCGGCCATC
Found at i:9004 original size:23 final size:23
Alignment explanation
Indices: 8971--9014 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
8961 AATTAGTACC
8971 TTTAATAAAATCCAAAGTCTTTT
1 TTTAATAAAATCCAAAGTCTTTT
*
8994 TTTAATCAAATCCAAAGTCTT
1 TTTAATAAAATCCAAAGTCTT
9015 GTAAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (23 bp):
TTTAATAAAATCCAAAGTCTTTT
Found at i:9030 original size:26 final size:23
Alignment explanation
Indices: 8971--9035 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
8961 AATTAGTACC
* *
8971 TTTAATAAAATCCAAAGTCTTTT
1 TTTAATCAAATCCAAAGTCTTTG
8994 TTTAATCAAATCCAAAGTCTTGTAAG
1 TTTAATCAAATCCAAAGTCTT-T--G
*
9020 TTTAATCAAATTCAAA
1 TTTAATCAAATCCAAA
9036 TTCCAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.56
24 1 0.03
26 15 0.42
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (23 bp):
TTTAATCAAATCCAAAGTCTTTG
Found at i:9278 original size:22 final size:22
Alignment explanation
Indices: 9245--9303 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
9235 AAAATAAAGC
9245 AAAGAAAACAATTAAAGAAAATT
1 AAAG-AAACAATTAAAGAAAATT
9268 -AAGAAAGCAATT-AAGAAAATT
1 AAAGAAA-CAATTAAAGAAAATT
9289 AAAGGAAACAATTAA
1 AAA-GAAACAATTAA
9304 TCAGAGAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 12 0.38
22 15 0.47
23 5 0.16
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (22 bp):
AAAGAAACAATTAAAGAAAATT
Found at i:10895 original size:12 final size:12
Alignment explanation
Indices: 10880--10904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10870 TCCAGCAAAA
10880 TCTTCCAAACTT
1 TCTTCCAAACTT
10892 TCTTCCAAACTT
1 TCTTCCAAACTT
10904 T
1 T
10905 TTTTTTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTTCCAAACTT
Found at i:11786 original size:19 final size:21
Alignment explanation
Indices: 11757--11801 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
11747 AGAAAGAAGA
*
11757 AGAAGAGAAAAAGAA-AAAAG
1 AGAAAAGAAAAAGAAGAAAAG
11777 -GAAAAGAAAAAGAAGAAAAG
1 AGAAAAGAAAAAGAAGAAAAG
11797 AGAAA
1 AGAAA
11802 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 13 0.59
20 5 0.23
21 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
AGAAAAGAAAAAGAAGAAAAG
Found at i:11810 original size:36 final size:36
Alignment explanation
Indices: 11749--11817 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
11739 ACGGGTTGAG
*
11749 AAAGAAGAAGAAGAGAAAAAGAAAAAAGGAAAAGAA
1 AAAGAAGAAGAAGAGAAAAAGAAAAAAAGAAAAGAA
11785 AAAGAAGAA-AAGAGAAATTAA-AAAAAAAGAAAA
1 AAAGAAGAAGAAGAGAAA--AAGAAAAAAAGAAAA
11818 AAGCCACGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 8 0.27
36 20 0.67
37 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (36 bp):
AAAGAAGAAGAAGAGAAAAAGAAAAAAAGAAAAGAA
Found at i:13406 original size:13 final size:13
Alignment explanation
Indices: 13373--13406 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13363 TCAAAATTTG
13373 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
*
13386 AAGCAAAAGAAAA
1 AAGAAAAAGAAAA
13399 AAGAAAAA
1 AAGAAAAA
13407 AATGGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Done.