Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021565.1 Corchorus olitorius cultivar O-4 contig21598, 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: 27780
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:3277 original size:101 final size:101
Alignment explanation
Indices: 3097--3298 Score: 323
Period size: 101 Copynumber: 2.0 Consensus size: 101
3087 TAATAATGTA
* *
3097 AATGTTCGTACTCATTCACTTGGTAACTTAATTATTGACTGCAAGAACTGATGAATTTTCCCTCA
1 AATGTTCATACTCATTCACTTGGTAACTTAATTATTGACTACAAGAACTGATGAATTTTCCCTCA
* *
3162 CTTGAAGATCTCCCATTGCTATAGAGAAACTAATCG
66 CTTGAAGATCTCCCATTACTAGAGAGAAACTAATCG
* * *
3198 AATGTTCATACTCATTCATTTGGTAACTTAATTATTGACTATAGGAACTGATGAATTTTCCCTCA
1 AATGTTCATACTCATTCACTTGGTAACTTAATTATTGACTACAAGAACTGATGAATTTTCCCTCA
* *
3263 CTTGAAGATTTCCCATTACTAGAGAGAAGCTAATCG
66 CTTGAAGATCTCCCATTACTAGAGAGAAACTAATCG
3299 CCTTGCAGAT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (101 bp):
AATGTTCATACTCATTCACTTGGTAACTTAATTATTGACTACAAGAACTGATGAATTTTCCCTCA
CTTGAAGATCTCCCATTACTAGAGAGAAACTAATCG
Found at i:4546 original size:3 final size:3
Alignment explanation
Indices: 4517--4566 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
4507 TACACGGGTT
* * * *
4517 GAA GAA AAA GAA GCA GAA GAA GGA GAA GAA GCA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4565 GA
1 GA
4567 GGGAAAAGGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.04, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12620 original size:11 final size:11
Alignment explanation
Indices: 12604--12668 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 11
12594 AGGGAGGAAG
*
12604 AAAGAAAGAAA
1 AAAGAAAAAAA
12615 AAAGAAAAAAA
1 AAAGAAAAAAA
12626 AAAGAAGAAGAGAA
1 AAAGAA-AA-A-AA
12640 AAATGAATAAAGAA
1 AAA-GAA-AAA-AA
12654 AAAGAATAAAAA
1 AAAGAA-AAAAA
12666 AAA
1 AAA
12669 AAGAAGAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
11 16 0.33
12 7 0.15
13 8 0.17
14 12 0.25
15 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:12655 original size:13 final size:12
Alignment explanation
Indices: 12612--12668 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 12
12602 AGAAAGAAAG
12612 AAAAAAGAA-AA
1 AAAAAAGAATAA
*
12623 AAAAAAGAAGAA
1 AAAAAAGAATAA
12635 GAGAAAAATGAATAA
1 -A-AAAAA-GAATAA
12650 AGAAAAAGAATAA
1 A-AAAAAGAATAA
12663 AAAAAA
1 AAAAAA
12669 AAGAAGAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 9 0.22
12 7 0.17
13 8 0.20
14 12 0.29
15 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (12 bp):
AAAAAAGAATAA
Found at i:12656 original size:28 final size:25
Alignment explanation
Indices: 12609--12673 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
12599 GGAAGAAAGA
12609 AAGAAAAAAGAAAAAAAAAAGAAGA
1 AAGAAAAAAGAAAAAAAAAAGAAGA
* *
12634 AGAGAAAAATGAATAAAGAAAAAGAATA
1 A-AGAAAAAAGAA-AAA-AAAAAGAAGA
*
12662 AAAAAAAAAGAA
1 AAGAAAAAAGAA
12674 GAGAACACGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 10 0.30
27 12 0.36
28 10 0.30
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (25 bp):
AAGAAAAAAGAAAAAAAAAAGAAGA
Found at i:12675 original size:23 final size:21
Alignment explanation
Indices: 12604--12701 Score: 62
Period size: 23 Copynumber: 4.5 Consensus size: 21
12594 AGGGAGGAAG
12604 AAAGAAAGAAAAAAG-AAAAAAA
1 AAAG-AAG-AAAAAGTAAAAAAA
*
12626 AAAGAAG-AAGAG-AAAAATGAA
1 AAAGAAGAAAAAGTAAAAA--AA
12647 TAAAGAA-AAAGAA-TAAAAAAA
1 -AAAGAAGAAA-AAGTAAAAAAA
* *
12668 AAAGAAGAGAACACGTTAAAAAA
1 AAAGAAGA-AA-AAGTAAAAAAA
12691 AAAGAAGAAAA
1 AAAGAAGAAAA
12702 CACGTTATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
19 9 0.15
20 6 0.10
21 9 0.15
22 17 0.27
23 21 0.34
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAGAAGAAAAAGTAAAAAAA
Found at i:12693 original size:37 final size:39
Alignment explanation
Indices: 12612--12701 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
12602 AGAAAGAAAG
*
12612 AAAAAAGAAAAAAAAAAGAAGAAGAGAAAAATGAATAAA
1 AAAAAAGAAAAAAAAAAGAAGAAGAGAAAAACGAATAAA
* * *
12651 GAAAAAGAATAAAAAAAA-AAGAAGAG-AACACG-TTAAA
1 AAAAAAGAA-AAAAAAAAGAAGAAGAGAAAAACGAATAAA
*
12688 AAAAAAGAAGAAAA
1 AAAAAAGAAAAAAA
12702 CACGTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 4 0.09
37 12 0.27
38 4 0.09
39 16 0.36
40 8 0.18
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.06
Consensus pattern (39 bp):
AAAAAAGAAAAAAAAAAGAAGAAGAGAAAAACGAATAAA
Found at i:12703 original size:23 final size:23
Alignment explanation
Indices: 12662--12708 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
12652 AAAAAGAATA
*
12662 AAAAAAAAAGAAGAGAACACGTT
1 AAAAAAAAAGAAGAAAACACGTT
12685 AAAAAAAAAGAAGAAAACACGTT
1 AAAAAAAAAGAAGAAAACACGTT
12708 A
1 A
12709 TTTACTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (23 bp):
AAAAAAAAAGAAGAAAACACGTT
Found at i:20155 original size:72 final size:72
Alignment explanation
Indices: 20069--20207 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
20059 AAAGACAAGC
20069 CAAGGTGTGAACATTGTCAAAAGATCGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTGTCAAAAGATCGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
20134 CCTGCTA
66 CCTGCTA
* * * *
20141 CAAGGTGTGGACATTGTCAAAAGATGGGGCACACGAAAGATCAGTGTTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTGTCAAAAGATCGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
20206 CC
66 CC
20208 CTCAGGGTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (72 bp):
CAAGGTGTGAACATTGTCAAAAGATCGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
CCTGCTA
Found at i:23952 original size:20 final size:20
Alignment explanation
Indices: 23909--23946 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23899 ACTTACCAAA
*
23909 TATAGCCTTACCGCAGGAAC
1 TATAACCTTACCGCAGGAAC
*
23929 TATAACCTTACTGCAGGA
1 TATAACCTTACCGCAGGA
23947 TGTATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
TATAACCTTACCGCAGGAAC
Done.