Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006896.1 Corchorus capsularis cultivar CVL-1 contig06917, 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: 20419
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:938 original size:18 final size:18
Alignment explanation
Indices: 901--936 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
891 TTGAATTAAT
*
901 TCTTCAATAGTCTTCAAA
1 TCTTCAAAAGTCTTCAAA
919 TCTTCAAAATGTCTTCAA
1 TCTTCAAAA-GTCTTCAA
937 TCACGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAGTCTTCAAA
Found at i:16285 original size:65 final size:65
Alignment explanation
Indices: 16207--16524 Score: 340
Period size: 66 Copynumber: 4.9 Consensus size: 65
16197 AAATTGAACG
* *
16207 TAAACTT-AGATGCACAAGACAAAAATGATCCTTCGACCGGAAGGGTATTTTGGAAATGAAAATA
1 TAAACTTGA-ATGCAAAAGACAAAAATGACCCTTCGACCGGAAGGGTATTTTGGAAATGAAAATA
16271 C
65 C
* * * * *
16272 TAAACTTGGATGCACAAGACAAAGATGATCCTTCGACCGGAAGGGTATTCTTGGAAATGAGAATA
1 TAAACTTGAATGCAAAAGACAAAAATGACCCTTCGACCGGAAGGGTATT-TTGGAAATGAAAATA
16337 C
65 C
* * * * * * * *
16338 TAAACTTGAATGCAAGAGACAATACTGACCCTTTGACCGAAATGGTATTCTTGGGAATGAGAATA
1 TAAACTTGAATGCAAAAGACAAAAATGACCCTTCGACCGGAAGGGTATT-TTGGAAATGAAAATA
16403 C
65 C
* * *
16404 TAAACTTGAATGCAAAAGACAATACTGACCCTTTC-ACC-GAA--GTATTTTGGAGAAAGAAAAT
1 TAAACTTGAATGCAAAAGACAAAAATGACCC-TTCGACCGGAAGGGTATTTTGGA-AATGAAAAT
16465 AC
64 AC
* * * *
16467 TAAACTTAAATACGAAAAGACAAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAA
1 TAAACTTGAATGC-AAAAGACAAAAATGACCCTTCGACCGGAAGGGTA-TTTTGGAAA
16525 AACAAAATAA
Statistics
Matches: 217, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
62 4 0.02
63 28 0.13
64 18 0.08
65 50 0.23
66 103 0.47
67 7 0.03
68 7 0.03
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (65 bp):
TAAACTTGAATGCAAAAGACAAAAATGACCCTTCGACCGGAAGGGTATTTTGGAAATGAAAATAC
Found at i:17609 original size:19 final size:20
Alignment explanation
Indices: 17585--17623 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17575 CCCAAGACTA
17585 TTCTATT-TTCCTCCTTTTC
1 TTCTATTCTTCCTCCTTTTC
*
17604 TTCTATTCTTCTTCCTTTTC
1 TTCTATTCTTCCTCCTTTTC
17624 CTTTACTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTATTCTTCCTCCTTTTC
Found at i:17756 original size:13 final size:13
Alignment explanation
Indices: 17738--17764 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17728 TTCCCCTCCG
17738 TCCTTTCTCTCTC
1 TCCTTTCTCTCTC
17751 TCCTTTCTCTCTC
1 TCCTTTCTCTCTC
17764 T
1 T
17765 TACCAACCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (13 bp):
TCCTTTCTCTCTC
Found at i:19403 original size:7 final size:7
Alignment explanation
Indices: 19383--19427 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
19373 AAATGAAAAC
*
19383 TCTTTCT
1 TCTTTTT
19390 TCTTTTTT
1 TC-TTTTT
19398 TCTTTTT
1 TCTTTTT
19405 TCTTTTT
1 TCTTTTT
19412 TCTCGTTTT
1 TCT--TTTT
19421 TCTTTTT
1 TCTTTTT
19428 GGTACTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 21 0.62
8 6 0.18
9 7 0.21
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:19407 original size:15 final size:16
Alignment explanation
Indices: 19382--19427 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
19372 TAAATGAAAA
*
19382 CTCTTTCTTCTTTTTT
1 CTCTTTTTTCTTTTTT
19398 -TCTTTTTTCTTTTTT
1 CTCTTTTTTCTTTTTT
*
19413 CTCGTTTTTCTTTTT
1 CTCTTTTTTCTTTTT
19428 GGTACTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (16 bp):
CTCTTTTTTCTTTTTT
Found at i:19420 original size:16 final size:15
Alignment explanation
Indices: 19389--19427 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
19379 AAACTCTTTC
*
19389 TTCTTTTTTTCTTTT
1 TTCTTTTTTTCGTTT
19404 TTCTTTTTTCTCGTTT
1 TTCTTTTTT-TCGTTT
19420 TTCTTTTT
1 TTCTTTTT
19428 GGTACTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (15 bp):
TTCTTTTTTTCGTTT
Found at i:20228 original size:21 final size:21
Alignment explanation
Indices: 20195--20243 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
20185 AAGAATTGTA
**
20195 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
20215 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
20236 GCATTCCT
1 GC-TTCCT
20244 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Done.