Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012704.1 Corchorus capsularis cultivar CVL-1 contig12725, 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: 18122
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5222 original size:33 final size:32
Alignment explanation
Indices: 5144--5248 Score: 79
Period size: 33 Copynumber: 3.2 Consensus size: 32
5134 TTGCAAAGAG
* * **
5144 TGTTTTAGATGTTGTTTGCGATGATACTAACCC
1 TGTTTTAGGTGTTGTTTGCGATGA-AATAAATC
**
5177 TAATTT-GAGTGTTGTTTGCGATGACAATAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGA-AATAAATC
* *
5210 TGTTTTAGGTGTTTTTTTTC-ATGAAACTAAATC
1 TGTTTTAGGTG-TTGTTTGCGATGAAA-TAAATC
5243 TGTTTT
1 TGTTTT
5249 GGATGCTAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
32 3 0.05
33 47 0.82
34 7 0.12
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (32 bp):
TGTTTTAGGTGTTGTTTGCGATGAAATAAATC
Found at i:5950 original size:52 final size:52
Alignment explanation
Indices: 5885--5985 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
5875 GTTTTTCCTA
*
5885 CAATAACTTCTGTCCCGAAGTTGTACAAGTTCTGGACCGAAATTGTCCTGCG
1 CAATAACTTCTGTCCCGAAGTTGAACAAGTTCTGGACCGAAATTGTCCTGCG
* *
5937 CAATAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCT
1 CAATAACTTCTGTCCCGAAGTTGAACAAGTTCTGGACCGAAATTGTCCT
5986 AAAATTCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (52 bp):
CAATAACTTCTGTCCCGAAGTTGAACAAGTTCTGGACCGAAATTGTCCTGCG
Found at i:10337 original size:20 final size:20
Alignment explanation
Indices: 10301--10339 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10291 AAATACAAGG
*
10301 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
10321 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
10340 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:11067 original size:19 final size:19
Alignment explanation
Indices: 11043--11081 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11033 AACTGCCAAT
*
11043 ACAATGA-AGTTCAAAGGTA
1 ACAATGACAG-TCAAACGTA
11062 ACAATGACAGTCAAACGTA
1 ACAATGACAGTCAAACGTA
11081 A
1 A
11082 AGAATGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (19 bp):
ACAATGACAGTCAAACGTA
Found at i:13521 original size:17 final size:17
Alignment explanation
Indices: 13487--13521 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13477 AAGAAGAAGG
*
13487 AAAAGAAAAATGGAAAA
1 AAAAGAAAAATAGAAAA
13504 AAAAGAAAAATCAGAAAA
1 AAAAGAAAAAT-AGAAAA
13522 TTAAAAGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAATAGAAAA
Found at i:17631 original size:32 final size:32
Alignment explanation
Indices: 17565--17636 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
17555 TGCAGCAAAA
* *
17565 TAGCGGCGTCTAATGAAGCAAACGCCACTATT
1 TAGCGGCGCCTAATGAAGCAAACACCACTATT
* *
17597 TAGCGGCGCCTAATGAAGCAAACACCGCTCTT
1 TAGCGGCGCCTAATGAAGCAAACACCACTATT
*
17629 TAGTGGCG
1 TAGCGGCG
17637 TCTATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (32 bp):
TAGCGGCGCCTAATGAAGCAAACACCACTATT
Found at i:18001 original size:213 final size:213
Alignment explanation
Indices: 17652--18114 Score: 836
Period size: 213 Copynumber: 2.2 Consensus size: 213
17642 TAAAACAAAA
* *
17652 GCCGCTATTTAGTGGAGTCCAACTGGGAGTCCGGTTGAAACGTTCAATTTGGGCGAAGTCACTGT
1 GCCGCTATTTAGTGGAGTCCAAATGGGAGCCCGGTTGAAACGTTCAATTTGGGCGAAGTCACTGT
* *
17717 CCTGACTGGGTGCCCACTTGACCCACAACCCGGCCCCCAGTTGAGCCTTTCTAATTTCTAAATAT
66 CCTGACCGGGTGCCCACTTGACCCACAACCCGGCCCCCAATTGAGCCTTTCTAATTTCTAAATAT
*
17782 TAATATTTTCTAATTTTAATTTCTAAAATAGCGGTGTCTGTTGTCTAAAACGCCACTATTTAGCA
131 TAATATTTTCTAATTTTAATTTCTAAAATAGCGGCGTCTGTTGTCTAAAACGCCACTATTTAGCA
17847 GCGTCTATTGAAGTAGAC
196 GCGTCTATTGAAGTAGAC
*
17865 GCCGCTATTTAGTGGAGTCCAAATGGGAGGCCGGTTGAAACGTTCAATTTGGGCGAAGTCACTGT
1 GCCGCTATTTAGTGGAGTCCAAATGGGAGCCCGGTTGAAACGTTCAATTTGGGCGAAGTCACTGT
* *
17930 CCTGACCGGGTGCCCACTTGACCCCCAACCGGGCCCCCAATTGAGCCTTTCTAATTTCTAAATAT
66 CCTGACCGGGTGCCCACTTGACCCACAACCCGGCCCCCAATTGAGCCTTTCTAATTTCTAAATAT
*
17995 TAATATTTTCTAATTTTAATTTCTAAAATAGTGGCGTCTGTTGTCTAAAACGCCACTATTTAGCA
131 TAATATTTTCTAATTTTAATTTCTAAAATAGCGGCGTCTGTTGTCTAAAACGCCACTATTTAGCA
18060 GCGTCTATTGAAGTAGAC
196 GCGTCTATTGAAGTAGAC
*
18078 GCCGCTATTTAGTGGAGTCCAAATGGAAGCCCGGTTG
1 GCCGCTATTTAGTGGAGTCCAAATGGGAGCCCGGTTG
18115 CCCCTCAA
Statistics
Matches: 240, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
213 240 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (213 bp):
GCCGCTATTTAGTGGAGTCCAAATGGGAGCCCGGTTGAAACGTTCAATTTGGGCGAAGTCACTGT
CCTGACCGGGTGCCCACTTGACCCACAACCCGGCCCCCAATTGAGCCTTTCTAATTTCTAAATAT
TAATATTTTCTAATTTTAATTTCTAAAATAGCGGCGTCTGTTGTCTAAAACGCCACTATTTAGCA
GCGTCTATTGAAGTAGAC
Done.