Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013481.1 Corchorus capsularis cultivar CVL-1 contig13502, 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: 12294
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3313 original size:21 final size:21
Alignment explanation
Indices: 3255--3314 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
3245 GCATCTGCCG
* *
3255 TGCCGCCTGCCCGGCCCAGCTA
1 TGCCGCCTGCCCGG-CCATCCA
* *
3277 GGCC-ACTG-CCGCGCCATCCA
1 TGCCGCCTGCCCG-GCCATCCA
3297 TGCCGCCTGCCCGGCCAT
1 TGCCGCCTGCCCGGCCAT
3315 GCTCGGCCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
20 11 0.38
21 12 0.41
22 6 0.21
ACGTcount: A:0.10, C:0.50, G:0.27, T:0.13
Consensus pattern (21 bp):
TGCCGCCTGCCCGGCCATCCA
Found at i:4136 original size:10 final size:11
Alignment explanation
Indices: 4109--4136 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4099 AAATTGGAAT
4109 AATTTTTCGAA
1 AATTTTTCGAA
4120 AATTTTTCGAA
1 AATTTTTCGAA
4131 AATTTT
1 AATTTT
4137 GATTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (11 bp):
AATTTTTCGAA
Found at i:5732 original size:10 final size:10
Alignment explanation
Indices: 5717--5741 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5707 GTTGCTGCAC
5717 AATTCCAGAA
1 AATTCCAGAA
5727 AATTCCAGAA
1 AATTCCAGAA
5737 AATTC
1 AATTC
5742 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:6676 original size:6 final size:6
Alignment explanation
Indices: 6661--6693 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
6651 TGCTTTATTA
6661 ATTT-G ATTTAG ATTTAG ATTTAG ATTTAG ATTT
1 ATTTAG ATTTAG ATTTAG ATTTAG ATTTAG ATTT
6694 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
ATTTAG
Found at i:8039 original size:18 final size:18
Alignment explanation
Indices: 8003--8040 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7993 AATAACCCGG
*
8003 CTCTCTCTGGAGCTGTCT
1 CTCTCTCTGGAGCTCTCT
8021 CTCTCTCT-GAGC-CTCT
1 CTCTCTCTGGAGCTCTCT
8037 CTCT
1 CTCT
8041 GAAGCTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.05, C:0.39, G:0.16, T:0.39
Consensus pattern (18 bp):
CTCTCTCTGGAGCTCTCT
Found at i:8039 original size:30 final size:30
Alignment explanation
Indices: 8003--8120 Score: 155
Period size: 30 Copynumber: 3.9 Consensus size: 30
7993 AATAACCCGG
* * *
8003 CTCTCTCTGGAGCTGTCTCTCTCTCTGAGC
1 CTCTCTCTGAAGCTCTCTCTCCCTCTGAGC
* *
8033 CTCTCTCTGAAGCTCTTTCTCCCTCTGATC
1 CTCTCTCTGAAGCTCTCTCTCCCTCTGAGC
* *
8063 CTCTCTTTGAAGCTCTCTCCCCCTCTGAGC
1 CTCTCTCTGAAGCTCTCTCTCCCTCTGAGC
* *
8093 CTTTCTTTGAAGCTCTCTCTCCCTCTGA
1 CTCTCTCTGAAGCTCTCTCTCCCTCTGA
8121 AACTGAGCCT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.09, C:0.39, G:0.14, T:0.38
Consensus pattern (30 bp):
CTCTCTCTGAAGCTCTCTCTCCCTCTGAGC
Found at i:8307 original size:18 final size:18
Alignment explanation
Indices: 8257--8313 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
8247 ATTAATCATA
*
8257 AATAAACTAATTAAAACT
1 AATAAACTAATTAACACT
* *
8275 AATAAAATAATTAACCCT
1 AATAAACTAATTAACACT
* *
8293 AATAAACTATTTAACAAT
1 AATAAACTAATTAACACT
8311 AAT
1 AAT
8314 TAATTTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAACTAATTAACACT
Found at i:8347 original size:21 final size:21
Alignment explanation
Indices: 8323--8364 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8313 TTAATTTTAA
8323 TTAAATTTCAAAATTCAAAAT
1 TTAAATTTCAAAATTCAAAAT
*
8344 TTAAATTTTAAAATTCAAAAT
1 TTAAATTTCAAAATTCAAAAT
8365 AGATCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATTTCAAAATTCAAAAT
Found at i:10335 original size:15 final size:15
Alignment explanation
Indices: 10315--10356 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
10305 CGTTCAAATG
10315 TCGGGTCATTTGGGT
1 TCGGGTCATTTGGGT
10330 TCGGGTCAATTTTGGGT
1 TCGGGTC-A-TTTGGGT
*
10347 T-GGTTCATTT
1 TCGGGTCATTT
10357 TTGGTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 5 0.21
17 8 0.33
ACGTcount: A:0.10, C:0.12, G:0.33, T:0.45
Consensus pattern (15 bp):
TCGGGTCATTTGGGT
Found at i:10358 original size:16 final size:17
Alignment explanation
Indices: 10315--10360 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
10305 CGTTCAAATG
10315 TCGGGTC-A-TTTGGGT
1 TCGGGTCAATTTTGGGT
10330 TCGGGTCAATTTTGGGT
1 TCGGGTCAATTTTGGGT
* *
10347 T-GGTTCATTTTTGG
1 TCGGGTCAATTTTGG
10361 TTTTAGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
17 8 0.30
ACGTcount: A:0.09, C:0.11, G:0.35, T:0.46
Consensus pattern (17 bp):
TCGGGTCAATTTTGGGT
Done.