Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015503.1 Corchorus olitorius cultivar O-4 contig15536, 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: 37964
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:3047 original size:19 final size:19
Alignment explanation
Indices: 3023--3068 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3013 TGGACCGGGT
*
3023 CAAACCGGTTCGGTCCGAC
1 CAAACCGGTTCGGACCGAC
*
3042 CAAACCGGTTCGGACCGGC
1 CAAACCGGTTCGGACCGAC
*
3061 CAAGCCGG
1 CAAACCGG
3069 CTGGCTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.30, T:0.11
Consensus pattern (19 bp):
CAAACCGGTTCGGACCGAC
Found at i:4763 original size:1 final size:1
Alignment explanation
Indices: 4759--4783 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4749 AAGTTTAATT
4759 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4784 CACTACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7327 original size:11 final size:10
Alignment explanation
Indices: 7299--7325 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
7289 AAAGATTAAC
7299 AAAAAAACTA
1 AAAAAAACTA
7309 AAAAAAACTA
1 AAAAAAACTA
7319 AAAAAAA
1 AAAAAAA
7326 ACCTATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAACTA
Found at i:12633 original size:35 final size:36
Alignment explanation
Indices: 12582--12651 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
12572 ATTGTGGATG
*
12582 TAGTTTGAATAGTATTGTTGAGA-TATGTAATCCTA
1 TAGTTTAAATAGTATTGTTGAGATTATGTAATCCTA
*
12617 TAGTTTAAATATTATTGTTGAGATTATGTAATCCT
1 TAGTTTAAATAGTATTGTTGAGATTATGTAATCCT
12652 TGTCACGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 21 0.66
36 11 0.34
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (36 bp):
TAGTTTAAATAGTATTGTTGAGATTATGTAATCCTA
Found at i:22569 original size:14 final size:15
Alignment explanation
Indices: 22549--22583 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22539 GTTTGATAAA
22549 ACTGAAA-ATTAAGT
1 ACTGAAAGATTAAGT
*
22563 GCTGAAAGATTAAGT
1 ACTGAAAGATTAAGT
22578 ACTGAA
1 ACTGAA
22584 TTTTTAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (15 bp):
ACTGAAAGATTAAGT
Found at i:22612 original size:16 final size:15
Alignment explanation
Indices: 22573--22617 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
22563 GCTGAAAGAT
**
22573 TAAGTACTGAATTTT
1 TAAGTACTGAATTCA
22588 TAA-TACTGAATCTCA
1 TAAGTACTGAAT-TCA
22603 TAAGTACTGAATTCA
1 TAAGTACTGAATTCA
22618 AACTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (15 bp):
TAAGTACTGAATTCA
Found at i:26153 original size:60 final size:61
Alignment explanation
Indices: 26040--26154 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 61
26030 TTATTTGACC
* * * * *
26040 AATTGAAAAGCATGGGCCCTTATTTGAACATTTCCGCATACCTTAGGACCCTATTTAACTA
1 AATTGAAAAGCATGGGCCCTAAATTGAACATTTCCACATACATTAAGACCCTATTTAACTA
*
26101 AATT-AAAAGCATGAGG-CCTAAATTGAACATTTTCACATACATTAAAGA-CCTATT
1 AATTGAAAAGCATG-GGCCCTAAATTGAACATTTCCACATACATT-AAGACCCTATT
26155 CAAGCAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
60 37 0.80
61 9 0.20
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (61 bp):
AATTGAAAAGCATGGGCCCTAAATTGAACATTTCCACATACATTAAGACCCTATTTAACTA
Found at i:26770 original size:5 final size:6
Alignment explanation
Indices: 26755--26789 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
26745 TGAAAATAGA
26755 AAAAAC AAAAAC -AAAAC AAAAAC AAAAAC AGAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC A-AAAA
26790 AGAAGGCGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 18 0.67
7 4 0.15
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:26772 original size:11 final size:11
Alignment explanation
Indices: 26756--26781 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26746 GAAAATAGAA
26756 AAAACAAAAAC
1 AAAACAAAAAC
26767 AAAACAAAAAC
1 AAAACAAAAAC
26778 AAAA
1 AAAA
26782 ACAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:29648 original size:22 final size:21
Alignment explanation
Indices: 29590--29649 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
29580 TAAAATTACT
* *
29590 TAAAGAATAATTAAATATTTC
1 TAAAAAATAATTAAATATTTA
*
29611 TAAAAAACT-ATAAAAT-TTATGA
1 TAAAAAA-TAATTAAATATT-T-A
29633 TAAAAAATAATTAAATA
1 TAAAAAATAATTAAATA
29650 AACTCAATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.07
21 14 0.47
22 14 0.47
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAAAAATAATTAAATATTTA
Done.