Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007455.1 Corchorus capsularis cultivar CVL-1 contig07476, 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: 17240
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4408 original size:2 final size:2
Alignment explanation
Indices: 4401--4433 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4391 TCAAAAACAT
4401 TA TA 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 TA TA T
4434 CCCTTACGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6482 original size:10 final size:10
Alignment explanation
Indices: 6467--6502 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
6457 CAAACAACAA
6467 AAAAAAAACT
1 AAAAAAAACT
6477 AAAAAAAATCT
1 AAAAAAAA-CT
*
6488 AAAAAAAAAT
1 AAAAAAAACT
6498 AAAAA
1 AAAAA
6503 TTCACATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAAAACT
Found at i:6482 original size:11 final size:11
Alignment explanation
Indices: 6466--6502 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
6456 ACAAACAACA
6466 AAAAAAAAACT
1 AAAAAAAAACT
*
6477 AAAAAAAATCT
1 AAAAAAAAACT
6488 AAAAAAAAA-T
1 AAAAAAAAACT
6498 AAAAA
1 AAAAA
6503 TTCACATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAAAAAACT
Found at i:8124 original size:124 final size:124
Alignment explanation
Indices: 7899--8124 Score: 276
Period size: 124 Copynumber: 1.8 Consensus size: 124
7889 AACCACGCTA
* * * *
7899 CTGACGTCCTTTGTTGATGAAGAACAAGACTTCGGTTGAAGTGCCCAGCAGCACTTCTCGGTAAC
1 CTGACCTCCTTTGTGGATGAAGAACAAGACTTCGGTTGAAGTGCCCAGCAGCACTTCTCAGCAAC
* ** * * *
7964 GGAATCTCCTTCTCGGCAGATTGACACGTTAGCAAGGTTGCACCGGGTAAGCCATGTTG
66 GGAACCTCCTTCTCGAAAGAGTGACACGTCAACAAGGTTGCACCGGGTAAGCCATGTTG
* * * * *
8023 CTGACCTCTTTTGTGGATGAAGGATAAGACTTTGGTT-AGAGTGCCCAGTAGCACTT-TCTAGCA
1 CTGACCTCCTTTGTGGATGAAGAACAAGACTTCGGTTGA-AGTGCCCAGCAGCACTTCTC-AGCA
*
8086 GCGGAACCTCCTTCTCGAAAGAGTGACACGTCAACAAGG
64 ACGGAACCTCCTTCTCGAAAGAGTGACACGTCAACAAGG
8125 CAGTCCCACA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
123 3 0.04
124 81 0.96
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (124 bp):
CTGACCTCCTTTGTGGATGAAGAACAAGACTTCGGTTGAAGTGCCCAGCAGCACTTCTCAGCAAC
GGAACCTCCTTCTCGAAAGAGTGACACGTCAACAAGGTTGCACCGGGTAAGCCATGTTG
Found at i:8292 original size:11 final size:13
Alignment explanation
Indices: 8266--8293 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8256 AAATAGTAAT
8266 AGAGGTTTGGGAG
1 AGAGGTTTGGGAG
8279 AGAGGTTTGGGAG
1 AGAGGTTTGGGAG
8292 AG
1 AG
8294 TAGAGGTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.54, T:0.21
Consensus pattern (13 bp):
AGAGGTTTGGGAG
Found at i:10048 original size:14 final size:14
Alignment explanation
Indices: 10031--10059 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10021 ATACTTTTTT
10031 CTTCTATTTCAAGG
1 CTTCTATTTCAAGG
10045 CTTCTATTTCAAGG
1 CTTCTATTTCAAGG
10059 C
1 C
10060 CAAAACAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (14 bp):
CTTCTATTTCAAGG
Found at i:10893 original size:14 final size:16
Alignment explanation
Indices: 10864--10899 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
10854 AAAAATATTA
10864 TTTTCTGTTTCATTTT
1 TTTTCTGTTTCATTTT
10880 TTTTCT-TTTC-TTTT
1 TTTTCTGTTTCATTTT
10894 TTTTCT
1 TTTTCT
10900 CTCTCCCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 4 0.20
16 6 0.30
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTCTGTTTCATTTT
Found at i:12207 original size:24 final size:25
Alignment explanation
Indices: 12154--12215 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
12144 TTTTAATTAC
*
12154 AATAA-AGAAAATTTATTTGTTTTT
1 AATAATAGAAAATTTATTTGCTTTT
**
12178 TTTAATAGAAAATTTATTT-CTTTT
1 AATAATAGAAAATTTATTTGCTTTT
*
12202 AATAATATAAAATT
1 AATAATAGAAAATT
12216 ATTAAAGTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
AATAATAGAAAATTTATTTGCTTTT
Found at i:13723 original size:23 final size:23
Alignment explanation
Indices: 13692--13738 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
13682 TTTATGTTTT
*
13692 CAATTGATCATTTTAAT-TTTCAA
1 CAATGGATC-TTTTAATGTTTCAA
*
13715 CAATGGATCTTTTCATGTTTCAA
1 CAATGGATCTTTTAATGTTTCAA
13738 C
1 C
13739 GATTGGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (23 bp):
CAATGGATCTTTTAATGTTTCAA
Found at i:15047 original size:18 final size:17
Alignment explanation
Indices: 15021--15053 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
15011 AGGTACATAT
15021 TTTTCAAAAAATAATCA
1 TTTTCAAAAAATAATCA
15038 TTTTCAAAAAATAATC
1 TTTTCAAAAAATAATC
15054 GACGAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTTCAAAAAATAATCA
Found at i:15580 original size:165 final size:164
Alignment explanation
Indices: 15214--15655 Score: 618
Period size: 165 Copynumber: 2.7 Consensus size: 164
15204 TGAGTCATTT
* *
15214 GTCAATTGAGAAATGACCAAAAAGTTAAGTTATTTAATCCCTTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTT-AGTTATTTAATCCCCTAAAGAATCAAAAGTTAGGACAT
* * * * ** *
15279 TTAAGTAATTTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAA-AATAGTTCTCTAACTCAAAATCAAGCCTTG
* * *
15344 ATTGAGATCTTTTATTAATTCCACTACTCTATTCAA
129 ATAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
15380 GTCCATTGACAAATGACCAAAAAGATTACTTATTTAATCCCCTAAAGAATCCAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTAAAGAATCAAAAGTTAGGACAT
* *
15445 TTAAGTAATCTGCTAAGTAGGAAAAGAC-AAAAAAAAAGTTCTCTAACTCCAAAAGT-AAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAGTTCTCTAACT-CAAAA-TCAAGCCTT
* *
15508 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
128 GATAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
*
15545 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTAAAGAATCAAAAGTTAGGACAT
15610 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA-TAGTTCTCT
15656 CGCTCATTAA
Statistics
Matches: 243, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
164 13 0.05
165 131 0.54
166 89 0.37
167 10 0.04
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (164 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTAAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAGTTCTCTAACTCAAAATCAAGCCTTGAT
AGAGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:16984 original size:1 final size:1
Alignment explanation
Indices: 16978--17007 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16968 TTGAACATTT
16978 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17008 CCTCGAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.