Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008404.1 Corchorus capsularis cultivar CVL-1 contig08425, 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: 29645
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2305 original size:22 final size:21
Alignment explanation
Indices: 2280--2322 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2270 TTATGAACAT
2280 ATAG-GCAATAACCTTTCAATCG
1 ATAGTGCAATAA-C-TTCAATCG
*
2302 ATAGTTCAATAACTTCAATCG
1 ATAGTGCAATAACTTCAATCG
2323 GACACATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (21 bp):
ATAGTGCAATAACTTCAATCG
Found at i:3263 original size:10 final size:10
Alignment explanation
Indices: 3248--3283 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
3238 TCAACTTTAA
3248 TATATGTTAT
1 TATATGTTAT
3258 TATATGTTAT
1 TATATGTTAT
3268 TATATGTTA-
1 TATATGTTAT
3277 TATATGT
1 TATATGT
3284 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (10 bp):
TATATGTTAT
Found at i:7023 original size:32 final size:32
Alignment explanation
Indices: 6987--7050 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
6977 AATGACCTAC
* * **
6987 AACCCAGATGACTTGAGAGTCGAATGACCCGT
1 AACCCAAATGACCTGAGACCCGAATGACCCGT
7019 AACCCAAATGACCTGAGACCCGAATGACCCGT
1 AACCCAAATGACCTGAGACCCGAATGACCCGT
7051 GACCAAAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.16
Consensus pattern (32 bp):
AACCCAAATGACCTGAGACCCGAATGACCCGT
Found at i:7028 original size:16 final size:16
Alignment explanation
Indices: 7009--7065 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
6999 TTGAGAGTCG
7009 AATGACCCGTAACCCA
1 AATGACCCGTAACCCA
* *
7025 AATGACCTG-AGACCCG
1 AATGACCCGTA-ACCCA
*
7041 AATGACCCGTGA-CCA
1 AATGACCCGTAACCCA
7056 AA-GACCCGTA
1 AATGACCCGTA
7066 TGACCCGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 7 0.21
15 5 0.15
16 21 0.64
ACGTcount: A:0.35, C:0.33, G:0.19, T:0.12
Consensus pattern (16 bp):
AATGACCCGTAACCCA
Found at i:7071 original size:32 final size:32
Alignment explanation
Indices: 7007--7074 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
6997 ACTTGAGAGT
*
7007 CGAATGACCCGTAACCCAAATGACCTGAGACC
1 CGAATGACCCGTAACCCAAATGACCCGAGACC
*
7039 CGAATGACCCGTGA-CCAAA-GACCCGTATGACC
1 CGAATGACCCGTAACCCAAATGACCCG-A-GACC
7071 CGAA
1 CGAA
7075 ACCCAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 5 0.16
31 6 0.19
32 21 0.66
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.12
Consensus pattern (32 bp):
CGAATGACCCGTAACCCAAATGACCCGAGACC
Found at i:8570 original size:17 final size:17
Alignment explanation
Indices: 8548--8580 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8538 GGGTTTTATC
8548 TTTCAATTAAATTAGGG
1 TTTCAATTAAATTAGGG
*
8565 TTTCAATTAGATTAGG
1 TTTCAATTAAATTAGG
8581 TTTTTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (17 bp):
TTTCAATTAAATTAGGG
Found at i:8695 original size:40 final size:41
Alignment explanation
Indices: 8651--8727 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
8641 GTTTTCGATG
*
8651 AAATAAATTTGGGTATTTGTGAAATGTT-GGGTTTCTTATT
1 AAATAAATTTGGGGATTTGTGAAATGTTAGGGTTTCTTATT
* * *
8691 AAATAAATTTGGGGGTTTGTTAAATTTTAGGGTTTCT
1 AAATAAATTTGGGGATTTGTGAAATGTTAGGGTTTCT
8728 GATGTAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (41 bp):
AAATAAATTTGGGGATTTGTGAAATGTTAGGGTTTCTTATT
Found at i:9729 original size:17 final size:17
Alignment explanation
Indices: 9709--9756 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
9699 GTGATCTAAG
9709 ATCACCAGTAATCTTAC
1 ATCACCAGTAATCTTAC
*
9726 ATCACC-GTTAATCTTAG
1 ATCACCAG-TAATCTTAC
*
9743 ATCACCAGTGATCT
1 ATCACCAGTAATCT
9757 GAGGGGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (17 bp):
ATCACCAGTAATCTTAC
Found at i:22661 original size:34 final size:34
Alignment explanation
Indices: 22607--22674 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
22597 CCTTTATTGT
*
22607 CTCTCTCTCTCTGGGTGGTGGGTGTACAATTTGG
1 CTCTCTCTCTCTGGGGGGTGGGTGTACAATTTGG
* *
22641 CTCTCTCTGTTTGGGGGGTGGGTGTACAATTTGG
1 CTCTCTCTCTCTGGGGGGTGGGTGTACAATTTGG
22675 GAATTGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.09, C:0.18, G:0.35, T:0.38
Consensus pattern (34 bp):
CTCTCTCTCTCTGGGGGGTGGGTGTACAATTTGG
Done.