Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023432.1 Corchorus olitorius cultivar O-4 contig23465, 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: 13851
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:2594 original size:30 final size:30
Alignment explanation
Indices: 2531--2597 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2521 ATGCAAAGTC
* *
2531 ATGATAAAATGCAATACATAAGAAATCTAA
1 ATGATAAAATGCAAAACACAAGAAATCTAA
* *
2561 ATGATAAAATGCAAAACACATA-ACATCTTA
1 ATGATAAAATGCAAAACACA-AGAAATCTAA
2591 ATGATAA
1 ATGATAA
2598 GAGTTATCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (30 bp):
ATGATAAAATGCAAAACACAAGAAATCTAA
Found at i:6354 original size:21 final size:22
Alignment explanation
Indices: 6330--6370 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6320 TAGCTTGTTG
*
6330 GAAATGGCTCTTGC-TTCCTTT
1 GAAATCGCTCTTGCATTCCTTT
*
6351 GAAATCTCTCTTGCATTCCT
1 GAAATCGCTCTTGCATTCCT
6371 AAAGCATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.17, C:0.27, G:0.15, T:0.41
Consensus pattern (22 bp):
GAAATCGCTCTTGCATTCCTTT
Found at i:7528 original size:22 final size:22
Alignment explanation
Indices: 7502--7553 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
7492 AAGTAACTAA
*
7502 GAAAAATAAACAA-AAAGAAAAG
1 GAAAAAGAAA-AATAAAGAAAAG
* *
7524 GAAAAAGAAAAATAACGAAAAT
1 GAAAAAGAAAAATAAAGAAAAG
7546 GAAAAAGA
1 GAAAAAGA
7554 TAAAGGTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.75, C:0.04, G:0.15, T:0.06
Consensus pattern (22 bp):
GAAAAAGAAAAATAAAGAAAAG
Found at i:7558 original size:28 final size:28
Alignment explanation
Indices: 7500--7558 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
7490 AAAAGTAACT
*
7500 AAGAAAAATAAACAAAAAGAAAAGGAAA
1 AAGAAAAATAAACAAAAAGAAAAAGAAA
* *
7528 AAGAAAAAT-AACGAAAATGAAAAAGATA
1 AAGAAAAATAAAC-AAAAAGAAAAAGAAA
7556 AAG
1 AAG
7559 GTAAGAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (28 bp):
AAGAAAAATAAACAAAAAGAAAAAGAAA
Found at i:13195 original size:21 final size:21
Alignment explanation
Indices: 13171--13286 Score: 173
Period size: 21 Copynumber: 5.6 Consensus size: 21
13161 CTTAGGCAAT
* *
13171 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
13192 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
13213 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
13234 TCCAAT-AACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
13254 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
13275 TCCAATGAACTT
1 TCCAATGAACTT
13287 CTAGCATCTT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
20 23 0.26
21 65 0.74
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:13258 original size:41 final size:42
Alignment explanation
Indices: 13171--13286 Score: 182
Period size: 41 Copynumber: 2.8 Consensus size: 42
13161 CTTAGGCAAT
* *
13171 TCCAATGAGCTTGAAACCTTCTCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAACTTGGAACCTTC
*
13213 TCCAATGAACTTGGAACCTTCTCCAAT-AACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAACTTGGAACCTTC
13254 TCCAATGAGCTTGGAA-CTTGCTCCAATGAACTT
1 TCCAATGAGCTTGGAACCTT-CTCCAATGAACTT
13287 CTAGCATCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
40 3 0.04
41 35 0.51
42 30 0.44
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (42 bp):
TCCAATGAGCTTGGAACCTTCTCCAATGAACTTGGAACCTTC
Done.