Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011159.1 Corchorus capsularis cultivar CVL-1 contig11180, 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: 8453
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Found at i:1535 original size:10 final size:11
Alignment explanation
Indices: 1515--1539 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1505 GAGCGAAAAG
1515 TTTCTTTTTTT
1 TTTCTTTTTTT
1526 TTTCTTTTTTT
1 TTTCTTTTTTT
1537 TTT
1 TTT
1540 ATCAGAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:1611 original size:12 final size:12
Alignment explanation
Indices: 1594--1648 Score: 101
Period size: 12 Copynumber: 4.5 Consensus size: 12
1584 TTAATACAGG
1594 TATCGACGGATA
1 TATCGACGGATA
1606 TATCGAACGGATA
1 TATCG-ACGGATA
1619 TATCGACGGATA
1 TATCGACGGATA
1631 TATCGACGGATA
1 TATCGACGGATA
1643 TATCGA
1 TATCGA
1649 GGTATCGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 30 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:1628 original size:25 final size:24
Alignment explanation
Indices: 1594--1648 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
1584 TTAATACAGG
1594 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
1619 TATCGACGGATATATCGACGGATA
1 TATCGACGGATATATCGACGGATA
1643 TATCGA
1 TATCGA
1649 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:3027 original size:10 final size:10
Alignment explanation
Indices: 3012--3037 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3002 AATTTAATAT
3012 GGATATTTAC
1 GGATATTTAC
3022 GGATATTTAC
1 GGATATTTAC
3032 GGATAT
1 GGATAT
3038 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:3074 original size:40 final size:39
Alignment explanation
Indices: 3030--3117 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 39
3020 ACGGATATTT
*
3030 ACGGATATATCGAGATTTATCGA-GATATCGAT-AA-ATATCG
1 ACGGATATA-CG-GATATATCGACGATAT--ATCAAGATATCG
*
3070 ACGGATACACGGATATATCGACGGATATATCAAGATATCG
1 ACGGATATACGGATATATCGAC-GATATATCAAGATATCG
3110 ACGGATAT
1 ACGGATAT
3118 TTAATTCCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 11 0.27
39 4 0.10
40 26 0.63
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (39 bp):
ACGGATATACGGATATATCGACGATATATCAAGATATCG
Found at i:3076 original size:20 final size:20
Alignment explanation
Indices: 3053--3117 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
3043 GATTTATCGA
3053 GATATCGATAAATATCGACG
1 GATATCGATAAATATCGACG
*
3073 GATACACGGAT--ATATCGACG
1 GATA-TC-GATAAATATCGACG
3093 GATAT--ATCAAGATATCGACG
1 GATATCGAT-AA-ATATCGACG
3113 GATAT
1 GATAT
3118 TTAATTCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
16 2 0.05
20 31 0.84
21 1 0.03
22 3 0.08
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (20 bp):
GATATCGATAAATATCGACG
Found at i:5525 original size:10 final size:10
Alignment explanation
Indices: 5510--5539 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5500 TTCAAAAATC
5510 ATAGATATAT
1 ATAGATATAT
*
5520 ATAGATAGAT
1 ATAGATATAT
5530 ATAGATATAT
1 ATAGATATAT
5540 TTCTAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (10 bp):
ATAGATATAT
Found at i:6647 original size:2 final size:2
Alignment explanation
Indices: 6642--6672 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6632 ACACACACAC
6642 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6673 TAAAAAGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:7706 original size:2 final size:2
Alignment explanation
Indices: 7699--7725 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7689 ATGATAACTA
7699 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7726 CTTGATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.