Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006113.1 Corchorus capsularis cultivar CVL-1 contig06131, 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: 20670
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3216 original size:84 final size:82
Alignment explanation
Indices: 3071--3231 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 82
3061 TTTGCTTGTG
* ** * * * *
3071 AGTTCAATCAAAATGCTAATTTTTCCTTTTTCTTAATTTTACACCAGCAACTTTTTTACATTTTA
1 AGTTCAATCAAAATGCTAATTTTTCATTTTTCTTAATTCCACACCAACAACTTCTTAACATTGTA
3136 TATAAACTTACTTTGCA
66 TATAAACTTACTTTGCA
3153 AGTTCAATCAAAATGCTAATCTTTTACATTTTTCTTAATTCCACACCAACAACTTCTTAACATTG
1 AGTTCAATCAAAATGCTAAT-TTTT-CATTTTTCTTAATTCCACACCAACAACTTCTTAACATTG
*
3218 TATATATACTTACT
64 TATATAAACTTACT
3232 CGTTTGTCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 20 0.29
83 4 0.06
84 45 0.65
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.43
Consensus pattern (82 bp):
AGTTCAATCAAAATGCTAATTTTTCATTTTTCTTAATTCCACACCAACAACTTCTTAACATTGTA
TATAAACTTACTTTGCA
Found at i:3433 original size:14 final size:14
Alignment explanation
Indices: 3414--3441 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3404 AGTTAAAAAA
3414 ATCTTCTAAGTTAT
1 ATCTTCTAAGTTAT
3428 ATCTTCTAAGTTAT
1 ATCTTCTAAGTTAT
3442 TTTAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
ATCTTCTAAGTTAT
Found at i:4776 original size:17 final size:18
Alignment explanation
Indices: 4751--4784 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4741 AGTGTCCTTG
4751 TTTTGCCA-TTTTCTTTA
1 TTTTGCCATTTTTCTTTA
*
4768 TTTTTCCATTTTTCTTT
1 TTTTGCCATTTTTCTTT
4785 GTTTCTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTGCCATTTTTCTTTA
Found at i:6311 original size:13 final size:13
Alignment explanation
Indices: 6286--6322 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
6276 TTGCCTCTGA
6286 ATTCTGATTGTAAT
1 ATTCTG-TTGTAAT
6300 ATTCTGTTGTAAT
1 ATTCTGTTGTAAT
6313 ATTCTGTTGT
1 ATTCTGTTGT
6323 CCTTTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (13 bp):
ATTCTGTTGTAAT
Found at i:6356 original size:8 final size:7
Alignment explanation
Indices: 6325--6380 Score: 76
Period size: 7 Copynumber: 7.6 Consensus size: 7
6315 TCTGTTGTCC
6325 TTTTGAT
1 TTTTGAT
6332 TTTTGAT
1 TTTTGAT
6339 TTTTGAT
1 TTTTGAT
*
6346 TTTGGAT
1 TTTTGAT
6353 TTTTGAT
1 TTTTGAT
6360 TTTTCAGAT
1 TTTT--GAT
6369 TTTTGAAT
1 TTTTG-AT
6377 TTTT
1 TTTT
6381 TTTAAAGGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
7 31 0.70
8 6 0.14
9 7 0.16
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (7 bp):
TTTTGAT
Found at i:6689 original size:29 final size:30
Alignment explanation
Indices: 6630--6691 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
6620 GAGTTTTTGA
*
6630 CCAAACCATTGTGGTTTATAAAAATAATTC
1 CCAAACCATTGTGATTTATAAAAATAATTC
* *
6660 CCAAACCATTGT-ATTTTTAAAACTAATTC
1 CCAAACCATTGTGATTTATAAAAATAATTC
6689 CCA
1 CCA
6692 TTCCCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (30 bp):
CCAAACCATTGTGATTTATAAAAATAATTC
Found at i:11647 original size:29 final size:29
Alignment explanation
Indices: 11615--11671 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
11605 ATGTGGCAAG
11615 AAATACAAGGGAATGGGAATTAGTTTTAA
1 AAATACAAGGGAATGGGAATTAGTTTTAA
* ** *
11644 AAATACAATGGTTTGGGAATTATTTTTA
1 AAATACAAGGGAATGGGAATTAGTTTTA
11672 TAAACCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (29 bp):
AAATACAAGGGAATGGGAATTAGTTTTAA
Found at i:11684 original size:30 final size:29
Alignment explanation
Indices: 11628--11689 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
11618 TACAAGGGAA
*
11628 TGGGAATTAGTTTTAAAAATACAATGGTT
1 TGGGAATTAGTTTTAAAAACACAATGGTT
* *
11657 TGGGAATTATTTTTATAAACCACAATGGTT
1 TGGGAATTAGTTTTA-AAAACACAATGGTT
11687 TGG
1 TGG
11690 TCAAAAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (29 bp):
TGGGAATTAGTTTTAAAAACACAATGGTT
Found at i:16429 original size:11 final size:10
Alignment explanation
Indices: 16390--16450 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
16380 ACAGAAGAGG
16390 AAAAAAAGGA
1 AAAAAAAGGA
*
16400 AAATAAAAAGA
1 AAA-AAAAGGA
*
16411 AGAAAAAGGGA
1 A-AAAAAAGGA
16422 AAAAAAAGGA
1 AAAAAAAGGA
*
16432 AAAGGAAAATGA
1 AAA--AAAAGGA
16444 AAAAAAA
1 AAAAAAA
16451 AAAAAGCCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 18 0.43
11 13 0.31
12 11 0.26
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (10 bp):
AAAAAAAGGA
Done.