Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007609.1 Corchorus capsularis cultivar CVL-1 contig07630, 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: 14543
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:361 original size:2 final size:2
Alignment explanation
Indices: 354--383 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
344 TCCAGCTTAA
354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
384 GTTTGGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2973 original size:21 final size:21
Alignment explanation
Indices: 2930--2973 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2920 TAGGGTTTAG
*
2930 AAACAATTAATTAAAAACCTT
1 AAACAATTAATTAAAAACATT
2951 AAAC-ATTAATTAAAAACAATT
1 AAACAATTAATTAAAAAC-ATT
2972 AA
1 AA
2974 GGAATGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (21 bp):
AAACAATTAATTAAAAACATT
Found at i:5687 original size:34 final size:34
Alignment explanation
Indices: 5644--5712 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5634 CGGATGGTAA
5644 GGAAATTAGATATTGAATCCAATGGTCAGAAATC
1 GGAAATTAGATATTGAATCCAATGGTCAGAAATC
5678 GGAAATTAGATATTGAATCCAATGGTCAGAAATC
1 GGAAATTAGATATTGAATCCAATGGTCAGAAATC
5712 G
1 G
5713 TTGGGAGCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (34 bp):
GGAAATTAGATATTGAATCCAATGGTCAGAAATC
Found at i:6493 original size:20 final size:21
Alignment explanation
Indices: 6458--6497 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6448 TCTGGATTGT
6458 TAAACACCGCCCCCCTTTTGC
1 TAAACACCGCCCCCCTTTTGC
* *
6479 TAAATACCGCCCCCTTTTT
1 TAAACACCGCCCCCCTTTT
6498 ACACTTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.42, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAACACCGCCCCCCTTTTGC
Found at i:6601 original size:25 final size:24
Alignment explanation
Indices: 6567--6626 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
6557 TTCAAACCCT
*
6567 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
6592 AAACTTCATTGTCTAACAAATCTTG
1 AAACTTCATT-TCTAACAAATCTTC
6617 AAA-TTCATTT
1 AAACTTCATTT
6627 TCCTTCACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.03
24 6 0.19
25 17 0.53
26 8 0.25
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:10636 original size:21 final size:21
Alignment explanation
Indices: 10589--10628 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
10579 GAACTGAGTA
10589 ATTGTTGCTTTAGAATCTGTC
1 ATTGTTGCTTTAGAATCTGTC
10610 ATTGTTGCTTTAGAATCTG
1 ATTGTTGCTTTAGAATCTG
10629 ATGTTGTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (21 bp):
ATTGTTGCTTTAGAATCTGTC
Found at i:11391 original size:48 final size:47
Alignment explanation
Indices: 11339--11430 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 47
11329 GTTTGAAGTC
11339 TATATATTGGTATAAATGAAATAAGCAGGATTAATT-GGAAAAAAAG
1 TATATATTGGTATAAATGAAATAAGCAGGATTAATTGGGAAAAAAAG
* *
11385 TATATATTGGTCTATATGAAATAAGCAGGATTAATTGGGAAAAAAA
1 TATATATTGGTATAAATGAAATAAGCAGGATTAATTGGGAAAAAAA
11431 AAAATGGACA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
46 34 0.79
47 9 0.21
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.29
Consensus pattern (47 bp):
TATATATTGGTATAAATGAAATAAGCAGGATTAATTGGGAAAAAAAG
Found at i:12619 original size:2 final size:2
Alignment explanation
Indices: 12612--12640 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12602 CTCCTAACCT
12612 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12641 TGTCGAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13278 original size:21 final size:21
Alignment explanation
Indices: 13254--13302 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
13244 TCTCACTAAG
*
13254 TCTGATTTGAAT-TTGAAAACC
1 TCTGATTTAAATCTTGAAAA-C
13275 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
13295 TCTTGATT
1 TC-TGATT
13303 ACCAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Found at i:13464 original size:13 final size:14
Alignment explanation
Indices: 13441--13469 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13431 CTTCTACTTT
13441 AATGCATGGATGCA
1 AATGCATGGATGCA
13455 AATG-ATGGATGCA
1 AATGCATGGATGCA
13468 AA
1 AA
13470 GTCTGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (14 bp):
AATGCATGGATGCA
Done.