Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009856.1 Corchorus capsularis cultivar CVL-1 contig09877, 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: 30557
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3314 original size:15 final size:15
Alignment explanation
Indices: 3294--3322 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3284 GGGAATATAT
3294 AGAAAAAGAAAAAAA
1 AGAAAAAGAAAAAAA
3309 AGAAAAAGAAAAAA
1 AGAAAAAGAAAAAA
3323 GAAAGAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAAAA
Found at i:3334 original size:16 final size:16
Alignment explanation
Indices: 3294--3329 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
3284 GGGAATATAT
3294 AGAAAAAG-AAAAAAA
1 AGAAAAAGAAAAAAAA
3309 AGAAAAAGAAAAAAGAA
1 AGAAAAAGAAAAAA-AA
3326 AGAA
1 AGAA
3330 CAGAAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 5 0.26
17 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAA
Found at i:5903 original size:54 final size:54
Alignment explanation
Indices: 5844--5948 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
5834 TTTACATCTT
* *
5844 TTTAATTGGGCCATAACCCAAAGCCTTTTTAAAACTTGTCCTTCAAAACGGTTC
1 TTTAATTGGGCCATAACCCAAAGCCTATTTAAAACTTGTCCTCCAAAACGGTTC
* * *
5898 TTTAATTGGGCCATGACCCAAAGCCTATTTAACATTTGTCCTCCAAAACGG
1 TTTAATTGGGCCATAACCCAAAGCCTATTTAAAACTTGTCCTCCAAAACGG
5949 CAAGCAGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (54 bp):
TTTAATTGGGCCATAACCCAAAGCCTATTTAAAACTTGTCCTCCAAAACGGTTC
Found at i:7831 original size:16 final size:16
Alignment explanation
Indices: 7801--7830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7791 GAACACGGGA
7801 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTTTTTC
7817 TTTTTTTT-TTTTTT
1 TTTTTTTTCTTTTTT
7831 TTGGTGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTC
Found at i:10437 original size:22 final size:21
Alignment explanation
Indices: 10399--10441 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
10389 TCACTCGGTC
* *
10399 TCTACAAATCAATCAATCACA
1 TCTACAAAGCAAACAATCACA
10420 TCTACCAAAGCAAACAATCACA
1 TCTA-CAAAGCAAACAATCACA
10442 CGCACACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (21 bp):
TCTACAAAGCAAACAATCACA
Found at i:11946 original size:18 final size:17
Alignment explanation
Indices: 11920--11953 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11910 TTTGACCTTT
11920 AATTATAAAAAAATTATA
1 AATTAT-AAAAAATTATA
*
11938 AATTTTAAAAAATTAT
1 AATTATAAAAAATTAT
11954 GTTTTGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTATAAAAAATTATA
Found at i:14518 original size:12 final size:12
Alignment explanation
Indices: 14501--14535 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
14491 AGAGTAGCTT
14501 TCTCAACATCGG
1 TCTCAACATCGG
*
14513 TCTCAACATTGG
1 TCTCAACATCGG
14525 TCTCAAGCATC
1 TCTCAA-CATC
14536 ACTTTCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (12 bp):
TCTCAACATCGG
Found at i:15894 original size:140 final size:139
Alignment explanation
Indices: 15636--15917 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 139
15626 TATTAATGAG
15636 ACTAACAATTCATTTATATTTCATGACAGATGGAAAAAGTTTGAAGATCTACCTTGTCTTAGTCA
1 ACTAACAATTCATTTATATTTCATGACAGATGGAAAAAGTTTGAAGATCTACCTTGTCTTAG--A
15701 TCATCTATTAAAGAATCCATACAAATCGACAAATCGTAACACTAGAAAGAATGAATTACTTTATT
64 TCATCTATTAAAGAATCCATACAAATCGACAAATCGTAACACTAGAAAGAATGAATTACTTTATT
15766 CTTTATCAATA
129 CTTTATCAATA
15777 ACTAACAATTCATTTATATTTCATGACAGATGGAAAAAGTTTTCGAAGATCTACCTTGTCTTAG-
1 ACTAACAATTCATTTATATTTCATGACAGATGGAAAAAG-TTT-GAAGATCTACCTTGTCTTAGA
* *
15841 TCATCTATTAAAGAATTCATACAAATCGACAAATCGTAACACTAGAAATAATGAATTACTTTATT
64 TCATCTATTAAAGAATCCATACAAATCGACAAATCGTAACACTAGAAAGAATGAATTACTTTATT
15906 CTTTATCAATA
129 CTTTATCAATA
15917 A
1 A
15918 AACCATATAA
Statistics
Matches: 137, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
140 75 0.55
141 39 0.28
142 3 0.02
143 20 0.15
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (139 bp):
ACTAACAATTCATTTATATTTCATGACAGATGGAAAAAGTTTGAAGATCTACCTTGTCTTAGATC
ATCTATTAAAGAATCCATACAAATCGACAAATCGTAACACTAGAAAGAATGAATTACTTTATTCT
TTATCAATA
Found at i:16705 original size:33 final size:33
Alignment explanation
Indices: 16667--16731 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
16657 AGTTTATTCC
*
16667 CTTTTTTTTTTCT-CATATCA-AAAATCAATTTG
1 CTTTTTTTTTTTTGCAT-TCACAAAATCAATTTG
*
16699 CTTTTTTTTTTTTGCATTTACAAAATCAATTTG
1 CTTTTTTTTTTTTGCATTCACAAAATCAATTTG
16732 TTTAGATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (33 bp):
CTTTTTTTTTTTTGCATTCACAAAATCAATTTG
Found at i:16920 original size:90 final size:90
Alignment explanation
Indices: 16767--16946 Score: 342
Period size: 90 Copynumber: 2.0 Consensus size: 90
16757 CATCATCATT
16767 CATTTTTGGAGGGGCTTTCTTACATTAAGCAAATATTTTCCAATATAACCATTAAACTCAAAAGG
1 CATTTTTGGAGGGGCTTTCTTACATTAAGCAAATATTTTCCAATATAACCATTAAACTCAAAAGG
16832 AAGAAAAATTAATTTATAAAGAAAA
66 AAGAAAAATTAATTTATAAAGAAAA
* *
16857 CATTTTTGGATGGGCTTTCTTACATTAAGCAAATATTTTCCGATATAACCATTAAACTCAAAAGG
1 CATTTTTGGAGGGGCTTTCTTACATTAAGCAAATATTTTCCAATATAACCATTAAACTCAAAAGG
16922 AAGAAAAATTAATTTATAAAGAAAA
66 AAGAAAAATTAATTTATAAAGAAAA
16947 AGTTAAAAAG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (90 bp):
CATTTTTGGAGGGGCTTTCTTACATTAAGCAAATATTTTCCAATATAACCATTAAACTCAAAAGG
AAGAAAAATTAATTTATAAAGAAAA
Found at i:17610 original size:14 final size:14
Alignment explanation
Indices: 17591--17624 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17581 CCTTATTAAA
* *
17591 TTATTATTGATATT
1 TTATTATTAATATG
17605 TTATTATTAATATG
1 TTATTATTAATATG
17619 TTATTA
1 TTATTA
17625 AAATGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TTATTATTAATATG
Done.