Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007606.1 Corchorus capsularis cultivar CVL-1 contig07627, 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: 24737
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:72 original size:38 final size:38
Alignment explanation
Indices: 17--129 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 38
7 AGTAATCAAA
* *
17 TTGAATTTTTTTAGTCCAATTCCAATTATGTATTACGGG
1 TTGAA-TTTATTAGTCCAATTCCAATTATATATTACGGG
*
56 TTGAATTTATTAGTCCAATTCAAATTATATATTACGGG
1 TTGAATTTATTAGTCCAATTCCAATTATATATTACGGG
* *
94 -T---TTTCTTAGTCCAATTCCAATTATATATTACAGG
1 TTGAATTTATTAGTCCAATTCCAATTATATATTACGGG
128 TT
1 TT
130 AAGTGGATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 30 0.45
35 1 0.01
37 1 0.01
38 30 0.45
39 5 0.07
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (38 bp):
TTGAATTTATTAGTCCAATTCCAATTATATATTACGGG
Found at i:252 original size:28 final size:26
Alignment explanation
Indices: 195--255 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
185 AGTAATCTTG
*
195 AAGAGGTTGGTTGAGATTAAAATTGT
1 AAGAGTTTGGTTGAGATTAAAATTGT
221 --GAGTTTGGTTGAGATTAAAATTGGTT
1 AAGAGTTTGGTTGAGATTAAAATT-G-T
247 AAGAGTTTG
1 AAGAGTTTG
256 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 21 0.70
25 1 0.03
26 1 0.03
28 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (26 bp):
AAGAGTTTGGTTGAGATTAAAATTGT
Found at i:3030 original size:80 final size:80
Alignment explanation
Indices: 2892--3055 Score: 301
Period size: 80 Copynumber: 2.0 Consensus size: 80
2882 TCTGAAGCCT
* *
2892 AAACTCCCATCCAACTTTGAAATGCACAAATCCTCCCATGCAACCCAATGAATGCCCCTGTTTCT
1 AAACCCCCATCCAACTTTGAAATGCACAAATCCTCCCATGCAACCCAATGAATGCCCCTATTTCT
2957 TCCATGACTCCACCA
66 TCCATGACTCCACCA
2972 AAACCCCCATCCAACTTTGAAATGCACAAATCCTCCCATGCAACCCAATGAATGCCCCTATTTCT
1 AAACCCCCATCCAACTTTGAAATGCACAAATCCTCCCATGCAACCCAATGAATGCCCCTATTTCT
*
3037 TCCGTGACTCCACCA
66 TCCATGACTCCACCA
3052 AAAC
1 AAAC
3056 TTTGCTAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.31, C:0.38, G:0.09, T:0.23
Consensus pattern (80 bp):
AAACCCCCATCCAACTTTGAAATGCACAAATCCTCCCATGCAACCCAATGAATGCCCCTATTTCT
TCCATGACTCCACCA
Found at i:7687 original size:22 final size:23
Alignment explanation
Indices: 7650--7693 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
7640 CACATTTTAC
*
7650 TTTCAAAATCATTTTTCAAATTA
1 TTTCAAAATCATTTTTAAAATTA
*
7673 TTTCAATAT-ATTTTTAAAATT
1 TTTCAAAATCATTTTTAAAATT
7694 TAATTGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTCAAAATCATTTTTAAAATTA
Found at i:19360 original size:22 final size:22
Alignment explanation
Indices: 19318--19361 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19308 CTGATTGAAT
*
19318 TTGTCACATATGATAATTATTA
1 TTGTCACATATGATAAATATTA
*
19340 TTGTC-CATATGCTAAGATATTA
1 TTGTCACATATGATAA-ATATTA
19362 AGGTTTGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TTGTCACATATGATAAATATTA
Found at i:24531 original size:14 final size:15
Alignment explanation
Indices: 24502--24545 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
24492 CGCCCCACTT
*
24502 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
24517 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
24531 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
24546 ACTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:24725 original size:32 final size:33
Alignment explanation
Indices: 24594--24737 Score: 209
Period size: 33 Copynumber: 4.4 Consensus size: 33
24584 GCCTCCCCAC
*
24594 TGGGGCGGCTTCGCGCAAGGCAGGCCGCACTCA
1 TGGGGCGGCTTCGCGCAAGGCAGGCCGCCCTCA
*
24627 AGGGGCGGCTTCGCGCAAGGCAGGCCGCCCTCA
1 TGGGGCGGCTTCGCGCAAGGCAGGCCGCCCTCA
* *
24660 AGGGGCGTCTTCGCGCAAGGCAGGCCGCCCTCA
1 TGGGGCGGCTTCGCGCAAGGCAGGCCGCCCTCA
* * **
24693 TGGGGCGGCTTTGC-CACGGCAAACCGCCCTCA
1 TGGGGCGGCTTCGCGCAAGGCAGGCCGCCCTCA
24725 TGGGGCGGCTTCG
1 TGGGGCGGCTTCG
Statistics
Matches: 101, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 27 0.27
33 74 0.73
ACGTcount: A:0.14, C:0.35, G:0.38, T:0.13
Consensus pattern (33 bp):
TGGGGCGGCTTCGCGCAAGGCAGGCCGCCCTCA
Done.