Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021600.1 Corchorus olitorius cultivar O-4 contig21633, 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: 53900
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:142 original size:21 final size:21
Alignment explanation
Indices: 104--171 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
94 CTTAGACAAT
104 TCCAATGAGCTT-GAACCTTC
1 TCCAATGAGCTTGGAACCTTC
124 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
145 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
166 TCCAAT
1 TCCAAT
172 AATCTCCTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
20 15 0.33
21 31 0.67
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:541 original size:9 final size:8
Alignment explanation
Indices: 504--540 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
494 CAACAATGTG
504 TTTTGTTTT
1 TTTTG-TTT
513 TTTTGTTT
1 TTTTGTTT
521 TTTTGTTT
1 TTTTGTTT
529 TTTTGTTT
1 TTTTGTTT
537 TTTT
1 TTTT
541 TTTGCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 23 0.82
9 5 0.18
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTGTTT
Found at i:669 original size:2 final size:2
Alignment explanation
Indices: 662--699 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
652 TGGATGCAAT
662 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
700 TACATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1768 original size:19 final size:21
Alignment explanation
Indices: 1723--1770 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
1713 CTATGTTTGT
*
1723 GAAAAAAGAAAGAAGGAAAAGA
1 GAAAAAAGAAACAA-GAAAAGA
1745 TGAAAAAAGAAACAA-AAAAG-
1 -GAAAAAAGAAACAAGAAAAGA
1765 GAAAAA
1 GAAAAA
1771 TAAAAGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
21 5 0.21
23 13 0.54
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (21 bp):
GAAAAAAGAAACAAGAAAAGA
Found at i:2374 original size:26 final size:26
Alignment explanation
Indices: 2339--2388 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2329 ACCCGAGACC
*
2339 GAACCTGAAAATACCCAAACCCGACT
1 GAACCCGAAAATACCCAAACCCGACT
*
2365 GAACCCGAAAATACCCGAACCCGA
1 GAACCCGAAAATACCCAAACCCGA
2389 ACCCGCCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.36, G:0.14, T:0.08
Consensus pattern (26 bp):
GAACCCGAAAATACCCAAACCCGACT
Found at i:4387 original size:5 final size:5
Alignment explanation
Indices: 4377--4438 Score: 81
Period size: 5 Copynumber: 12.4 Consensus size: 5
4367 AGCGGGAAAG
* **
4377 AAGAA AAGAA AAAAA AAGAA AA-AA GGGAAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA
4427 AAGAA AAGAA AA
1 AAGAA AAGAA AA
4439 AGGAAAAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
4 2 0.04
5 44 0.90
6 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:4452 original size:15 final size:16
Alignment explanation
Indices: 4372--4485 Score: 96
Period size: 15 Copynumber: 7.4 Consensus size: 16
4362 GGCCCAGCGG
4372 GAAAGAAGAAAAGAAAA
1 GAAA-AAGAAAAGAAAA
**
4389 -AAAAAGAAAA-AAGG
1 GAAAAAGAAAAGAAAA
4403 GAAAAAGAAAAGAAAA
1 GAAAAAGAAAAGAAAA
4419 G-AAAAGAAAAGAAAA
1 GAAAAAGAAAAGAAAA
* **
4434 GAAAAAGGAAA-AAGG
1 GAAAAAGAAAAGAAAA
*
4449 GAAACAAGAAAAGTAAA
1 GAAA-AAGAAAAGAAAA
* *
4466 G-GAAAGAAAA-AAAT
1 GAAAAAGAAAAGAAAA
4480 GAAAAA
1 GAAAAA
4486 AGAGGAAATA
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
14 5 0.07
15 48 0.63
16 21 0.28
17 2 0.03
ACGTcount: A:0.75, C:0.01, G:0.22, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAAAGAAAA
Found at i:4452 original size:20 final size:18
Alignment explanation
Indices: 4373--4447 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 18
4363 GCCCAGCGGG
*
4373 AAAGAAGAAAAGAAAAA-A
1 AAAGAA-AAAGGAAAAAGA
4391 AAAGAAAAAAGGGAAAAAGA
1 AAAG-AAAAA-GGAAAAAGA
**
4411 AAAGAAAAGAAAAGAAAAGA
1 AAAGAAAA-AGGA-AAAAGA
4431 AAAGAAAAAGGAAAAAG
1 AAAGAAAAAGGAAAAAG
4448 GGAAACAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 12 0.26
19 15 0.32
20 20 0.43
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGGAAAAAGA
Found at i:4486 original size:47 final size:47
Alignment explanation
Indices: 4377--4488 Score: 151
Period size: 47 Copynumber: 2.4 Consensus size: 47
4367 AGCGGGAAAG
4377 AAGAAAAG-AAA-AAAAAAGAAAAAAGGGAAAAAGAAAAGAAAAGAA
1 AAGAAAAGAAAAGAAAAAAGAAAAAAGGGAAAAAGAAAAGAAAAGAA
* * *
4422 AAGAAAAGAAAAG-AAAAAGGAAAAAGGGAAACAAGAAAAGTAAAGGA
1 AAGAAAAGAAAAGAAAAAAGAAAAAAGGGAAA-AAGAAAAGAAAAGAA
*
4469 AAGAAAA-AAATGAAAAAAGA
1 AAGAAAAGAAAAGAAAAAAGA
4489 GGAAATAGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
45 8 0.14
46 24 0.41
47 26 0.45
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.02
Consensus pattern (47 bp):
AAGAAAAGAAAAGAAAAAAGAAAAAAGGGAAAAAGAAAAGAAAAGAA
Found at i:18363 original size:14 final size:14
Alignment explanation
Indices: 18308--18356 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
18298 TTCCTAAAAC
*
18308 TAGAGAAAAA-A-C
1 TAGAGAAAAAGATG
18320 TAGA-AAAATAGATG
1 TAGAGAAAA-AGATG
*
18334 AAGAGAAAAAGATG
1 TAGAGAAAAAGATG
18348 TAGAGAAAA
1 TAGAGAAAA
18357 GATTGTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 1 0.03
14 16 0.53
15 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.12
Consensus pattern (14 bp):
TAGAGAAAAAGATG
Found at i:22626 original size:20 final size:20
Alignment explanation
Indices: 22601--22640 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
22591 AATTACAAAC
22601 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
22621 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
22641 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:29326 original size:31 final size:31
Alignment explanation
Indices: 29291--29351 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
29281 ATAGAACAAT
*
29291 CAAGCCTCAAATTGAAACAAATCAACATAAA
1 CAAGCCTCAAATTGAAACAAATAAACATAAA
* * *
29322 CAAGCGTCAAATTGCAACAATTAAACATAA
1 CAAGCCTCAAATTGAAACAAATAAACATAA
29352 TAAATCTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.18
Consensus pattern (31 bp):
CAAGCCTCAAATTGAAACAAATAAACATAAA
Found at i:32062 original size:28 final size:28
Alignment explanation
Indices: 32022--32173 Score: 216
Period size: 28 Copynumber: 5.5 Consensus size: 28
32012 ATGGTACTTG
* *
32022 AAATGACTAAAATGCCCCTGGATGTGCA
1 AAATGACCAAAATGCCCCTGGACGTGCA
* *
32050 AAATAACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACGTGCA
* * **
32078 AAATGACCAAAATGCCCCTGAACATGTG
1 AAATGACCAAAATGCCCCTGGACGTGCA
32106 AAATGACCAAAATGCCCCTGGACGTGCA
1 AAATGACCAAAATGCCCCTGGACGTGCA
*
32134 AAATGACCAAAATGCCCCT-GACATGCA
1 AAATGACCAAAATGCCCCTGGACGTGCA
32161 AAATGACCAAAAT
1 AAATGACCAAAAT
32174 AAGAAATAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 20 0.18
28 91 0.82
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACGTGCA
Found at i:33274 original size:14 final size:14
Alignment explanation
Indices: 33252--33281 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33242 TCCAATCCCG
33252 AAATCTGATTTTTC
1 AAATCTGATTTTTC
*
33266 AAATTTGATTTTTC
1 AAATCTGATTTTTC
33280 AA
1 AA
33282 GCTCCTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (14 bp):
AAATCTGATTTTTC
Found at i:33803 original size:6 final size:6
Alignment explanation
Indices: 33792--33817 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
33782 AGATAGTTTA
33792 TGGGTT TGGGTT TGGGTT TGGGTT TG
1 TGGGTT TGGGTT TGGGTT TGGGTT TG
33818 AATGTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TGGGTT
Found at i:34015 original size:23 final size:23
Alignment explanation
Indices: 33989--34037 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33979 ATTTATAGCA
* *
33989 ATAATAATAATAATTATTATTAT
1 ATAATAATAATAATTAGTATAAT
* *
34012 ATAATTATCATAATTAGTATAAT
1 ATAATAATAATAATTAGTATAAT
34035 ATA
1 ATA
34038 TTAAGTATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAATAATAATAATTAGTATAAT
Found at i:40370 original size:21 final size:21
Alignment explanation
Indices: 40331--40371 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40321 TTGGTTAATA
*
40331 AGTTGTTGTTAATGGTATTTG
1 AGTTGTTGTTAATAGTATTTG
* *
40352 AGTTGTTGTTGATATTATTT
1 AGTTGTTGTTAATAGTATTT
40372 CTTTGATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
AGTTGTTGTTAATAGTATTTG
Found at i:40687 original size:14 final size:15
Alignment explanation
Indices: 40670--40698 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40660 TCCAACCTGG
40670 TTGA-TCAAACCAGA
1 TTGACTCAAACCAGA
40684 TTGACTCAAACCAGA
1 TTGACTCAAACCAGA
40699 CCGAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (15 bp):
TTGACTCAAACCAGA
Found at i:41804 original size:13 final size:13
Alignment explanation
Indices: 41786--41810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41776 TGGTTTTGTT
41786 ATAAATTGTTTTA
1 ATAAATTGTTTTA
41799 ATAAATTGTTTT
1 ATAAATTGTTTT
41811 GGTTGTGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATAAATTGTTTTA
Found at i:45202 original size:10 final size:10
Alignment explanation
Indices: 45187--45213 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
45177 ATGGATCCAA
45187 AAAGCCCTAC
1 AAAGCCCTAC
45197 AAAGCCCTAC
1 AAAGCCCTAC
45207 AAAGCCC
1 AAAGCCC
45214 ATATTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.41, G:0.11, T:0.07
Consensus pattern (10 bp):
AAAGCCCTAC
Found at i:45396 original size:17 final size:18
Alignment explanation
Indices: 45374--45412 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
45364 AGGGCATTGT
*
45374 TTCATT-AAAGCCCATTA
1 TTCATTAAAAGCCAATTA
45391 TTCATTAAAAGCCAATTA
1 TTCATTAAAAGCCAATTA
45409 TTCA
1 TTCA
45413 CAAATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (18 bp):
TTCATTAAAAGCCAATTA
Found at i:47300 original size:2 final size:2
Alignment explanation
Indices: 47295--47320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47285 TACATAAAAG
47295 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
47321 ACACTAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:49306 original size:18 final size:18
Alignment explanation
Indices: 49283--49321 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
49273 CAAACCTCTC
**
49283 TTACTATTTCCTTTATTA
1 TTACTATTTCCCATATTA
49301 TTACTATTTCCCATATTA
1 TTACTATTTCCCATATTA
49319 TTA
1 TTA
49322 TTATCTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (18 bp):
TTACTATTTCCCATATTA
Found at i:49748 original size:22 final size:22
Alignment explanation
Indices: 49723--49775 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
49713 AAATCAAACT
** *
49723 AACAATTAAGACTATTTAAGAA
1 AACAATTAAGAAAATTAAAGAA
*
49745 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAATTAAAGAA
49767 AACAATTAA
1 AACAATTAA
49776 TCAGAAAGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.21
Consensus pattern (22 bp):
AACAATTAAGAAAATTAAAGAA
Found at i:51085 original size:19 final size:18
Alignment explanation
Indices: 51052--51087 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51042 TTGAAATTAT
*
51052 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
51070 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
51088 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:52648 original size:30 final size:29
Alignment explanation
Indices: 52609--52665 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
52599 GTTTATTAAT
52609 GAAACTTGAAAATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
52640 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
52666 CTAATCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Done.