Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006400.1 Corchorus capsularis cultivar CVL-1 contig06421, 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: 24453
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Found at i:1589 original size:3 final size:3
Alignment explanation
Indices: 1581--1606 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1571 AAAAAATAGA
1581 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1607 CAAGTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2444 original size:3 final size:3
Alignment explanation
Indices: 2438--2467 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2428 TATAGTATAT
2438 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2468 TCACATGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2633 original size:25 final size:25
Alignment explanation
Indices: 2599--2715 Score: 209
Period size: 25 Copynumber: 4.7 Consensus size: 25
2589 TTAATACAGG
2599 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
2624 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
2649 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
*
2674 TATCGACGGATATATCG-ACAGATA
1 TATCGACGGATATATCGAACGGATA
*
2698 TATCGAGGGATATATCGA
1 TATCGACGGATATATCGA
2716 GGTATCGATG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
24 22 0.25
25 67 0.75
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (25 bp):
TATCGACGGATATATCGAACGGATA
Found at i:2717 original size:12 final size:12
Alignment explanation
Indices: 2599--2715 Score: 189
Period size: 12 Copynumber: 9.5 Consensus size: 12
2589 TTAATACAGG
2599 TATCGACGGATA
1 TATCGACGGATA
2611 TATCGAACGGATA
1 TATCG-ACGGATA
2624 TATCGACGGATA
1 TATCGACGGATA
2636 TATCGAACGGATA
1 TATCG-ACGGATA
2649 TATCGACGGATA
1 TATCGACGGATA
2661 TATCGAACGGATA
1 TATCG-ACGGATA
2674 TATCGACGGATA
1 TATCGACGGATA
*
2686 TATCGACAGATA
1 TATCGACGGATA
*
2698 TATCGAGGGATA
1 TATCGACGGATA
2710 TATCGA
1 TATCGA
2716 GGTATCGATG
Statistics
Matches: 99, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
12 63 0.64
13 36 0.36
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:4616 original size:20 final size:21
Alignment explanation
Indices: 4598--4656 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
4588 ATTGAGATAT
4598 CGATAAATATCGACGGATACA
1 CGATAAATATCGACGGATACA
*
4619 CG-GAAATATCGACGGATACA
1 CGATAAATATCGACGGATACA
4639 CGGAT--ATATCGACGGATA
1 C-GATAAATATCGACGGATA
4657 TCCCGTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (21 bp):
CGATAAATATCGACGGATACA
Found at i:4973 original size:12 final size:11
Alignment explanation
Indices: 4964--4994 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4954 GTAAAAAATC
4964 TTTAAAAAAAA
1 TTTAAAAAAAA
4975 TTTAAAAAAAA
1 TTTAAAAAAAA
4986 -TTAAAAAAA
1 TTTAAAAAAA
4995 TGGCCTAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
TTTAAAAAAAA
Found at i:5150 original size:15 final size:15
Alignment explanation
Indices: 5126--5176 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
5116 AAATTACTTA
5126 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
5140 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
5152 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
5166 GATTAATTAGT
1 GTTTAATTAGT
5177 ATTGGATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
11 9 0.29
13 4 0.13
14 4 0.13
15 14 0.45
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:5159 original size:26 final size:26
Alignment explanation
Indices: 5130--5223 Score: 152
Period size: 26 Copynumber: 3.6 Consensus size: 26
5120 TACTTAGTTT
*
5130 ATTAGTTTATGTTTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
**
5156 ATTAGTTTATGATTAATTAGTATTGG
1 ATTAGTTTATGATTAATTAGTATTTA
*
5182 ATTAGTTTATGATTAATAAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
5208 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
5224 AATGAAGGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATTTA
Found at i:5162 original size:52 final size:52
Alignment explanation
Indices: 5094--5215 Score: 144
Period size: 52 Copynumber: 2.4 Consensus size: 52
5084 TTAGTTTATG
* *
5094 ATTAGT-TTTAATTAGTTAATTAAAATTACTTAGT-TT-ATTAGTTTATGTTTA
1 ATTAGTATTTAATTAGTT--TTAAAATTAATTAGTATTGATTAGTTTATGATTA
**
5145 ATTAGTATTTAATTAG-TTTATGATTAATTAGTATTGGATTAGTTTATGATTA
1 ATTAGTATTTAATTAGTTTTAAAATTAATTAGTATT-GATTAGTTTATGATTA
*
5197 ATAAGTATTTAATTAGTTT
1 ATTAGTATTTAATTAGTTT
5216 ATGATTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
49 12 0.20
50 2 0.03
51 7 0.11
52 38 0.62
53 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (52 bp):
ATTAGTATTTAATTAGTTTTAAAATTAATTAGTATTGATTAGTTTATGATTA
Found at i:6012 original size:13 final size:13
Alignment explanation
Indices: 5969--6012 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5959 GAAGAAAAGG
*
5969 AAAAGAAATAAAA
1 AAAAGAAATAGAA
**
5982 AAAAGGAAATAGGG
1 AAAA-GAAATAGAA
5996 AAAAGAAATAGAA
1 AAAAGAAATAGAA
6009 AAAA
1 AAAA
6013 CGTAGAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (13 bp):
AAAAGAAATAGAA
Found at i:8327 original size:27 final size:27
Alignment explanation
Indices: 8287--8341 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
8277 TTTATATGAT
8287 TAATTGTTTATGACAATCACACTGCCA
1 TAATTGTTTATGACAATCACACTGCCA
* * *
8314 TAATTGTTTTTGACGATGACACTGCCA
1 TAATTGTTTATGACAATCACACTGCCA
8341 T
1 T
8342 TTCCATGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (27 bp):
TAATTGTTTATGACAATCACACTGCCA
Found at i:9027 original size:1 final size:1
Alignment explanation
Indices: 9021--9058 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
9011 TTTGCTTAAG
9021 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9059 GAAATCTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16524 original size:33 final size:35
Alignment explanation
Indices: 16482--16572 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 35
16472 TAAAATTAAA
*
16482 TACTAATATATGGGTCTCTACGATAT-G-TACAAG
1 TACTAATATATAGGTCTCTACGATATGGATACAAG
* *
16515 TACTAATATATAGGTGTCTACTATATAGGGCATACAAG
1 TACTAATATATAGGTCTCTACGATAT--GG-ATACAAG
*
16553 TACTTATATATAGGTCTCTA
1 TACTAATATATAGGTCTCTA
16573 TTATAAAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
33 23 0.48
36 1 0.02
38 24 0.50
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (35 bp):
TACTAATATATAGGTCTCTACGATATGGATACAAG
Done.