Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008031.1 Corchorus capsularis cultivar CVL-1 contig08052, 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: 23011
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:4854 original size:15 final size:15
Alignment explanation
Indices: 4836--4868 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4826 TAAATTTCAA
4836 TAAAATAA-AATATAT
1 TAAAATAATAATAT-T
4851 TAAAATAATAATATT
1 TAAAATAATAATATT
4866 TAA
1 TAA
4869 TTTTTATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATAATAATATT
Found at i:5172 original size:14 final size:14
Alignment explanation
Indices: 5126--5173 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5116 ACGTCCACCG
5126 TTATTCCATTGACA
1 TTATTCCATTGACA
* *
5140 TTATT-TATGGGACCA
1 TTATTCCAT-TGA-CA
5155 TTATTCCATTGACA
1 TTATTCCATTGACA
5169 TTATT
1 TTATT
5174 TATGGGATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 2 0.07
14 14 0.52
15 9 0.33
16 2 0.07
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (14 bp):
TTATTCCATTGACA
Found at i:6169 original size:35 final size:35
Alignment explanation
Indices: 6130--6200 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
6120 TCTCTGGTGC
6130 TCGTGCGTCCTTCTCGGAAGAGGAAAAGCGAGAGA
1 TCGTGCGTCCTTCTCGGAAGAGGAAAAGCGAGAGA
6165 TCGTGCGTCCTTCTCGGAAGAGGAAAAGCGAGAGA
1 TCGTGCGTCCTTCTCGGAAGAGGAAAAGCGAGAGA
6200 T
1 T
6201 GCGCAAGCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (35 bp):
TCGTGCGTCCTTCTCGGAAGAGGAAAAGCGAGAGA
Found at i:10306 original size:13 final size:14
Alignment explanation
Indices: 10282--10331 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
10272 AAAAAAGATC
10282 TTCAAGAAAATG-CT
1 TTCAA-AAAATGACT
10296 TTCAAAAAATGACT
1 TTCAAAAAATGACT
*
10310 TTC-AAAAATGAGTT
1 TTCAAAAAATGA-CT
10324 TTCAAAAA
1 TTCAAAAA
10332 GGTTTTGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 14 0.44
14 14 0.44
15 4 0.12
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (14 bp):
TTCAAAAAATGACT
Found at i:11322 original size:87 final size:87
Alignment explanation
Indices: 11176--11343 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
11166 GTTTGAAAGT
* * * *
11176 TTCTTAAGATGAGAAACTAATCCAGAAATATCAATTGAGTTGGGAATATCAATGTATGATCAAAT
1 TTCTTAAGATGAGAAACTAATCCAGAAACATAAATTAAGTTGGGAATATCAATGCATGATCAAAT
*
11241 TGGAGGAAGATTTGGGAAATAA
66 TGGAAGAAGATTTGGGAAATAA
* * * * * *
11263 TTCTTGAGGTGAGAAGCTAATTCAGAACCATAAATTAAGTTGGGAATATCGATGCATGATCAAAT
1 TTCTTAAGATGAGAAACTAATCCAGAAACATAAATTAAGTTGGGAATATCAATGCATGATCAAAT
*
11328 TGGAAGAAGGTTTGGG
66 TGGAAGAAGATTTGGG
11344 GCATCAACTA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (87 bp):
TTCTTAAGATGAGAAACTAATCCAGAAACATAAATTAAGTTGGGAATATCAATGCATGATCAAAT
TGGAAGAAGATTTGGGAAATAA
Found at i:11690 original size:47 final size:47
Alignment explanation
Indices: 11630--11733 Score: 199
Period size: 47 Copynumber: 2.2 Consensus size: 47
11620 AACTTGATTC
11630 GATCATGGGGGCATATAGAAAGATGACTGAGGTCTCCGACTTGAACT
1 GATCATGGGGGCATATAGAAAGATGACTGAGGTCTCCGACTTGAACT
*
11677 GATCATGGGGGCATATAGAAAGATGATTGAGGTCTCCGACTTGAACT
1 GATCATGGGGGCATATAGAAAGATGACTGAGGTCTCCGACTTGAACT
11724 GATCATGGGG
1 GATCATGGGG
11734 CATGAAGTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (47 bp):
GATCATGGGGGCATATAGAAAGATGACTGAGGTCTCCGACTTGAACT
Found at i:12230 original size:35 final size:34
Alignment explanation
Indices: 12147--12312 Score: 143
Period size: 35 Copynumber: 4.6 Consensus size: 34
12137 AAATTCAGCC
* * * *
12147 TCATCAAATCCTTATTTAAGGTCCCTTTTTAAGTG
1 TCATCAAAT-CTTGTTTAAGATCCCTGTTTAGGTG
12182 TCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTG
1 TCATC-AAATCTTGTTTAAGATCCCTGTTTAGGTG
* * * * *
12217 TCATCAAGATCTTGGTTCAAGATTCATCTTTAGGTT
1 TCATCAA-ATCTT-GTTTAAGATCCCTGTTTAGGTG
*
12253 TCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTG
1 TC--ATCAAAT-CTTGTTTAAGATCCCTGTTTAGGTG
*
12290 TCTTATCAAAATCATGTTTAAGA
1 TC--ATC-AAATCTTGTTTAAGA
12313 ATCGTGTTTA
Statistics
Matches: 107, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
34 2 0.02
35 36 0.34
36 23 0.21
37 34 0.32
38 12 0.11
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (34 bp):
TCATCAAATCTTGTTTAAGATCCCTGTTTAGGTG
Found at i:12287 original size:37 final size:36
Alignment explanation
Indices: 12149--12346 Score: 154
Period size: 37 Copynumber: 5.4 Consensus size: 36
12139 ATTCAGCCTC
* * * *
12149 ATCAAATCCTTATTTAAGGTCCCTTTTTAAGTGTC--
1 ATCAAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCTT
12184 ATCAAAATCTTGTTTAAGATCCCTGTTTAGGTGTC--
1 ATC-AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTT
* * * * *
12219 ATCAAGATCTTGGTTCAAGATTCATCTTTAGGTTTCTT
1 ATCAA-ATCTT-GTTTAAGATCCCTGTTTAGGTGTCTT
*
12257 ATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTT
1 ATCAAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCTT
* * * *
12294 ATCAAAATCATGTTTAAGAAT-CGTGTTTAGATTTCTT
1 ATC-AAATCTTGTTTAAG-ATCCCTGTTTAGGTGTCTT
*
12331 AACAAATCCTTGTTTA
1 ATCAAAT-CTTGTTTA
12347 GGTTTCAAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
34 2 0.02
35 34 0.26
36 27 0.20
37 56 0.42
38 13 0.10
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (36 bp):
ATCAAATCTTGTTTAAGATCCCTGTTTAGGTGTCTT
Found at i:12346 original size:74 final size:73
Alignment explanation
Indices: 12188--12346 Score: 205
Period size: 74 Copynumber: 2.2 Consensus size: 73
12178 AGTGTCATCA
* * * *
12188 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCATCAAGATCTTGGTTCAAGATTCATCTTTAGGT
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCATCAAAATCATGGTTCAAGAATCATCTTTAGAT
*
12252 TTCTTATC
66 TTCTTAAC
* * * *
12260 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCAT-GTTTAAGAATCGTGTTTAG
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTC--ATCAAAATCATGGTTCAAGAATCATCTTTAG
12324 ATTTCTTAAC
64 ATTTCTTAAC
12334 AAATCCTTGTTTA
1 AAATCCTTGTTTA
12347 GGTTTCAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
72 4 0.05
73 26 0.35
74 36 0.48
75 9 0.12
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (73 bp):
AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCATCAAAATCATGGTTCAAGAATCATCTTTAGAT
TTCTTAAC
Found at i:12515 original size:62 final size:59
Alignment explanation
Indices: 12441--12560 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 59
12431 TTCTTCAAAA
* * *
12441 ATCAAAACTCAAAATTAT-CATTTCAGCATTCCATTATTTGAAAATCAAAGTTCAATATTTGC
1 ATCAAAACTCAAAA-CATGCATTTCAGCATTCC---ATTCGAAAATCAAAGTTCAAAATTTGC
* *
12503 ATCAAAATTCAAAACATGCATTTCAGTATTCCATTCGAAAATCAAAGTTCAAAATTTG
1 ATCAAAACTCAAAACATGCATTTCAGCATTCCATTCGAAAATCAAAGTTCAAAATTTG
12561 TATTTCATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 24 0.46
61 2 0.04
62 26 0.50
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (59 bp):
ATCAAAACTCAAAACATGCATTTCAGCATTCCATTCGAAAATCAAAGTTCAAAATTTGC
Done.