Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015713.1 Corchorus capsularis cultivar CVL-1 contig15734, 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: 26848
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:565 original size:33 final size:32
Alignment explanation
Indices: 465--569 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 32
455 TTGCAAAGAG
465 TGTTTTAGATGTTGTTTGTGATGATACTAAATC
1 TGTTTTAG-TGTTGTTTGTGATGATACTAAATC
* * * *
498 TAATTTGAGTGTTGTTT-TCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGT-GATGATACTAAATC
531 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGTGATGATACTAAATC
564 TGTTTT
1 TGTTTT
570 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
32 4 0.07
33 50 0.83
34 6 0.10
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.49
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGTGATGATACTAAATC
Found at i:2766 original size:30 final size:30
Alignment explanation
Indices: 2726--2784 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2716 CAAGGGGGAG
2726 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
2756 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
2785 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:5269 original size:70 final size:70
Alignment explanation
Indices: 5195--5338 Score: 261
Period size: 70 Copynumber: 2.1 Consensus size: 70
5185 ACTTGATCTT
*
5195 GAATTAACAATAATTTGATTCAAGGGTATTGGTGACTTGTTGAGTTTGATAAGCAGCAACAATTC
1 GAATTAACAATAATTTGATTCAAGGGTATTGGTGACTTGTTGAATTTGATAAGCAGCAACAATTC
5260 TTCAA
66 TTCAA
* *
5265 GAATTGACAATAATTTGATTCAAGGGTCTTGGTGACTTGTTGAATTTGATAAGCAGCAACAATTC
1 GAATTAACAATAATTTGATTCAAGGGTATTGGTGACTTGTTGAATTTGATAAGCAGCAACAATTC
5330 TTCAA
66 TTCAA
5335 GAAT
1 GAAT
5339 AAGCAGCAGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (70 bp):
GAATTAACAATAATTTGATTCAAGGGTATTGGTGACTTGTTGAATTTGATAAGCAGCAACAATTC
TTCAA
Found at i:8734 original size:2 final size:2
Alignment explanation
Indices: 8727--8774 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
8717 ATAAACAGAA
8727 AT AT AT AT A- AT AT AT AT CA- AT A- AT A- AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
8765 AT AT AT AT AT
1 AT AT AT AT AT
8775 TAAAAGGGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
1 5 0.12
2 34 0.85
3 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:8738 original size:21 final size:21
Alignment explanation
Indices: 8714--8763 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
8704 AATTTAATTG
8714 AATATA-AACAGA-AATATATAT
1 AATATATAACA-ATAATA-ATAT
*
8735 AATATATATCAATAATAATAT
1 AATATATAACAATAATAATAT
8756 AATATATA
1 AATATATA
8764 TATATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
AATATATAACAATAATAATAT
Found at i:24151 original size:41 final size:41
Alignment explanation
Indices: 24104--24276 Score: 202
Period size: 41 Copynumber: 4.2 Consensus size: 41
24094 ATGTGCTTAG
* * * * *
24104 GGACTTTGACATAGATGCCTCTGTGTTATAAATGAGCTTGA
1 GGACTTTGAGAGAGATGCCCCTGTGTTATAAATGTGTTTGA
* * *
24145 GGACTTTAGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGG
1 GGACTTT-GAGAGAGATGCCCCTGTGTTATAAATGTGTTTGA
** * *
24187 GGACTTTGTTATAGATGCCTCTGTGTTATAAATGTGTTTGA
1 GGACTTTGAGAGAGATGCCCCTGTGTTATAAATGTGTTTGA
* * *
24228 GGACTTTGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGG
1 GGACTTTGAGAGAGATGCCCCTGTGTTATAAATGTGTTTGA
24269 GGACTTTG
1 GGACTTTG
24277 GGGAGAGAGA
Statistics
Matches: 109, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 76 0.70
42 33 0.30
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (41 bp):
GGACTTTGAGAGAGATGCCCCTGTGTTATAAATGTGTTTGA
Found at i:24201 original size:83 final size:82
Alignment explanation
Indices: 24069--24276 Score: 314
Period size: 83 Copynumber: 2.6 Consensus size: 82
24059 GTTTTATCAC
* * * *
24069 CTTTGAGAGA-TTGCCCTTGTGTTA-CA-TGTGCTTAGGGACTTTGACATAGATGCCTCTGTGTT
1 CTTTGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGACATAGATGCCTCTGTGTT
24131 ATAAATGAGCTTGAGGA
66 ATAAATGAGCTTGAGGA
**
24148 CTTTAGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGTTATAGATGCCTCTGTGT
1 CTTT-GAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGACATAGATGCCTCTGTGT
* *
24213 TATAAATGTGTTTGAGGA
65 TATAAATGAGCTTGAGGA
24231 CTTTGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTG
1 CTTTGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTG
24277 GGGAGAGAGA
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
79 4 0.03
80 6 0.05
81 13 0.11
82 43 0.37
83 51 0.44
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (82 bp):
CTTTGAGAGAGTTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGACATAGATGCCTCTGTGTT
ATAAATGAGCTTGAGGA
Found at i:24786 original size:35 final size:35
Alignment explanation
Indices: 24715--24833 Score: 134
Period size: 35 Copynumber: 3.4 Consensus size: 35
24705 TTGTTGTAGC
*
24715 CCCCAAGTATTGAATGATGAATGA-G-TGCTGCAGT
1 CCCCAAGTGTTGAATGATGAA-GAGGTTGCTGCAGT
* * *
24749 CCCCAAGCGTTGAATGGTGAAGAGGTTGCTGGAGT
1 CCCCAAGTGTTGAATGATGAAGAGGTTGCTGCAGT
* * **
24784 CCCCAAATGTTGAATGATGAAGGGGTTGCTGCAAC
1 CCCCAAGTGTTGAATGATGAAGAGGTTGCTGCAGT
*
24819 CCCCAAGTGCTGAAT
1 CCCCAAGTGTTGAAT
24834 CTGATGAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
33 2 0.03
34 19 0.27
35 49 0.70
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (35 bp):
CCCCAAGTGTTGAATGATGAAGAGGTTGCTGCAGT
Done.