Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018683.1 Corchorus olitorius cultivar O-4 contig18716, 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: 46386
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:88 original size:14 final size:14
Alignment explanation
Indices: 69--99 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59 CGACCCGCTA
*
69 TTTCTGGGTTTTTT
1 TTTCTGCGTTTTTT
83 TTTCTGCGTTTTTT
1 TTTCTGCGTTTTTT
97 TTT
1 TTT
100 AATCTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.74
Consensus pattern (14 bp):
TTTCTGCGTTTTTT
Found at i:4301 original size:45 final size:48
Alignment explanation
Indices: 4213--4308 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 48
4203 TTGGTAACTT
*
4213 ACTAAAATCTTTTACTAATTTTACTAACTTTTGTATTGTAGTAGCTTGTA
1 ACTAAAATCTTTTACTAATCTTACTAAC--TTGTATTGTAGTAGCTTGTA
4263 ACTAAAATCTTTTACTAATCTTACTAAC-T-T-TTGTAGTAGCTTGTA
1 ACTAAAATCTTTTACTAATCTTACTAACTTGTATTGTAGTAGCTTGTA
4308 A
1 A
4309 AGACTTTAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 16 0.36
46 1 0.02
47 1 0.02
50 27 0.60
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (48 bp):
ACTAAAATCTTTTACTAATCTTACTAACTTGTATTGTAGTAGCTTGTA
Found at i:8344 original size:17 final size:16
Alignment explanation
Indices: 8319--8365 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
8309 ATTGTGAAAT
*
8319 AAAAGAAAGAAATGAGA
1 AAAAAAAAGAAAT-AGA
8336 AAAAAAAAGAAA-AGA
1 AAAAAAAAGAAATAGA
*
8351 AAAAGAAAAGGAATA
1 AAAA-AAAAGAAATA
8366 AGGAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAAAAAAGAAATAGA
Found at i:8353 original size:11 final size:11
Alignment explanation
Indices: 8319--8360 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
8309 ATTGTGAAAT
8319 AAAAG-AAAGA
1 AAAAGAAAAGA
*
8329 AATGAGAAAA-A
1 AA-AAGAAAAGA
8340 AAAAGAAAAGA
1 AAAAGAAAAGA
8351 AAAAGAAAAG
1 AAAAGAAAAG
8361 GAATAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.30
11 16 0.59
12 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:8357 original size:21 final size:21
Alignment explanation
Indices: 8319--8359 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8309 ATTGTGAAAT
*
8319 AAAAGAAAGAAATGAGAAAAA
1 AAAAGAAAGAAATAAGAAAAA
8340 AAAAGAAAAGAAA-AAGAAAA
1 AAAAG-AAAGAAATAAGAAAA
8360 GGAATAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAGAAAGAAATAAGAAAAA
Found at i:9567 original size:34 final size:33
Alignment explanation
Indices: 9529--9598 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
9519 TTTGAAAACT
9529 AAAACTGAAAA-TGACGGGAACTTTCCCTAAATTG
1 AAAACT-AAAACTGACGGGAACTTTCCC-AAATTG
* *
9563 AAAACTAAAACTGATGGGAACTTTCCCAATTTG
1 AAAACTAAAACTGACGGGAACTTTCCCAAATTG
9596 AAA
1 AAA
9599 TAGAGCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (33 bp):
AAAACTAAAACTGACGGGAACTTTCCCAAATTG
Found at i:9633 original size:52 final size:52
Alignment explanation
Indices: 9569--9703 Score: 227
Period size: 52 Copynumber: 2.6 Consensus size: 52
9559 ATTGAAAACT
*
9569 AAAACTGATGGGAACTTTCCCAATTTGAAATA-GAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAA-AGGAGCTAAATTGAATACATTG
*
9621 AAAACTGGTGGGAACTTTCCCAATTTGAAAAGGAGCTAAATTGAATACATTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAGGAGCTAAATTGAATACATTG
*
9673 AAAACTAATGGGAACTTTCCCAATTTGAAAA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAA
9704 CTTAAACCTG
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 1 0.01
52 77 0.99
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAGGAGCTAAATTGAATACATTG
Found at i:9718 original size:34 final size:34
Alignment explanation
Indices: 9680--9842 Score: 245
Period size: 34 Copynumber: 4.8 Consensus size: 34
9670 TTGAAAACTA
9680 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTG
1 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTG
*
9714 ATGGGAACTTTCCCAATTTTGAAAACGTAAACCTG
1 ATGGGAACTTTCCCAA-TTTGAAAACTTAAACCTG
*
9749 ATGGGAACTTTCCCAATTTGAAAACCTAAACCTG
1 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTG
** * *
9783 ATGAAAACTTTCCCAATTTGAAAACTAAAATCTG
1 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTG
* *
9817 GTGGGAAATTTCCCAATTTGAAAACT
1 ATGGGAACTTTCCCAATTTGAAAACT
9843 ATGAAGACTT
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 84 0.72
35 33 0.28
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (34 bp):
ATGGGAACTTTCCCAATTTGAAAACTTAAACCTG
Found at i:9757 original size:69 final size:68
Alignment explanation
Indices: 9680--9842 Score: 247
Period size: 69 Copynumber: 2.4 Consensus size: 68
9670 TTGAAAACTA
**
9680 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTGATGGGAACTTTCCCAATTTTGAAAACGT-AA
1 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTGATGAAAACTTTCCCAA-TTTGAAAAC-TAAA
9744 ACCTG
64 ACCTG
* *
9749 ATGGGAACTTTCCCAATTTGAAAACCTAAACCTGATGAAAACTTTCCCAATTTGAAAACTAAAAT
1 ATGGGAACTTTCCCAATTTGAAAACTTAAACCTGATGAAAACTTTCCCAATTTGAAAACTAAAAC
9814 CTG
66 CTG
* *
9817 GTGGGAAATTTCCCAATTTGAAAACT
1 ATGGGAACTTTCCCAATTTGAAAACT
9843 ATGAAGACTT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
67 1 0.01
68 38 0.44
69 47 0.55
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (68 bp):
ATGGGAACTTTCCCAATTTGAAAACTTAAACCTGATGAAAACTTTCCCAATTTGAAAACTAAAAC
CTG
Found at i:13205 original size:2 final size:2
Alignment explanation
Indices: 13200--13240 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13190 TTTCTCTCTC
13200 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13241 GACTCCACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14031 original size:13 final size:13
Alignment explanation
Indices: 14015--14048 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
14005 CTGACTGTTT
*
14015 TGGTTTATTATTC
1 TGGTTTATTACTC
14028 TGGTTTATTACTC
1 TGGTTTATTACTC
14041 TGGTTTAT
1 TGGTTTAT
14049 GACTTTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.18, T:0.59
Consensus pattern (13 bp):
TGGTTTATTACTC
Found at i:31733 original size:3 final size:3
Alignment explanation
Indices: 31725--31749 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31715 CTAGACTTTT
31725 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
31750 ATATAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31781 original size:12 final size:12
Alignment explanation
Indices: 31766--31806 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
31756 TACATATTAT
31766 AAAAAATAAAT-
1 AAAAAATAAATA
31777 AAAAAATAAAATA
1 AAAAAAT-AAATA
31790 AAAATAAT-AATA
1 AAAA-AATAAATA
31802 AAAAA
1 AAAAA
31807 TAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.30
12 12 0.44
13 4 0.15
14 3 0.11
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:31813 original size:13 final size:12
Alignment explanation
Indices: 31764--31809 Score: 69
Period size: 11 Copynumber: 3.9 Consensus size: 12
31754 AATACATATT
31764 ATAAAAAAT-AA
1 ATAAAAAATAAA
31775 ATAAAAAATAAA
1 ATAAAAAATAAA
31787 AT-AAAAATAATA
1 ATAAAAAATAA-A
31799 ATAAAAAATAA
1 ATAAAAAATAA
31810 TAATTATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 17 0.53
12 7 0.22
13 8 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:32558 original size:179 final size:178
Alignment explanation
Indices: 32288--32618 Score: 486
Period size: 179 Copynumber: 1.9 Consensus size: 178
32278 CCGATTAAAG
*
32288 TGATTTAAGTGTCTATTAAAAGATTGTCCCATGATCTACAACTTTCATAAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTCCCATGATCTACAACTTTCATAAAGGACTCGAAAACTA
* * * *
32353 AATTTGATGTTTCAAATATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAACGGGAATAG
66 AATTTAATGTTTCAAATATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAACGGAAATAG
* *
32417 ATGGTCCACTTAATATTATATAACTTTTGCTCTATATGTCTGATTGAGA
130 ACGGTCCACTTAATATTACATAACTTTTGCTCTATATGTCTGATTGAGA
* * * * *
32466 TGATTCAAGTGTCTCTTGAAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGACAACT
1 TGATTCAAGTGTCTATT-AAAAGATTGTCCCATGATCTACAACTTTCATAAAGGACTCGAAAACT
* *
32531 TAATTTAATG-TTCAATGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATA
65 AAATTTAATGTTTCAA-ATATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATA
*
32595 GACGGTCTACTTAATATTACATAA
129 GACGGTCCACTTAATATTACATAA
32619 TTTGTGTTTA
Statistics
Matches: 135, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
178 23 0.17
179 112 0.83
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTCCCATGATCTACAACTTTCATAAAGGACTCGAAAACTA
AATTTAATGTTTCAAATATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTCTATATGTCTGATTGAGA
Found at i:35452 original size:86 final size:86
Alignment explanation
Indices: 35335--35506 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
35325 GAATGCCTAA
*
35335 TTTTTTGTAGTCAAGGAGTATGTATAGTTGTCGTAGGAAAATTGAATTAGTTGAGAACATTTGTA
1 TTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGTTGAGAACATTTGTA
35400 GGAGCATATTACACAATGCAT
66 GGAGCATATTACACAATGCAT
35421 TTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGTTGAGAACATTTGTA
1 TTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGTTGAGAACATTTGTA
35486 GGAGCATATTACACAATGCAT
66 GGAGCATATTACACAATGCAT
35507 CACAAAATGA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (86 bp):
TTTTTTGTAGTCAAGGAGCATGTATAGTTGTCGTAGGAAAATTGAATTAGTTGAGAACATTTGTA
GGAGCATATTACACAATGCAT
Found at i:36504 original size:22 final size:23
Alignment explanation
Indices: 36474--36520 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
36464 TTTTAGTTTA
* *
36474 TAATATTCTTGGGTCATTTGGGT
1 TAATATTCTCGGGTCATTCGGGT
36497 TAAT-TTCTCGGGTCATTCGGGT
1 TAATATTCTCGGGTCATTCGGGT
36519 TA
1 TA
36521 CGGGTTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.45
Consensus pattern (23 bp):
TAATATTCTCGGGTCATTCGGGT
Found at i:36871 original size:60 final size:60
Alignment explanation
Indices: 36802--36920 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
36792 GTTGCTTTGT
* * *
36802 TAGTTTGTGTTTAATTAATCTCATGTAGATCAATAAAAAGGAATCAATGTTATGTGAAGG
1 TAGTTTGTGTTTAATTAATCTCATGGAGATCAACAAAAAGGAACCAATGTTATGTGAAGG
* *
36862 TAGTTTGTGTTTAATTGATCTCATGGAGATCAACAAGAAGGAACCAATGTTATGTGAAG
1 TAGTTTGTGTTTAATTAATCTCATGGAGATCAACAAAAAGGAACCAATGTTATGTGAAG
36921 ATGCTTGATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.34
Consensus pattern (60 bp):
TAGTTTGTGTTTAATTAATCTCATGGAGATCAACAAAAAGGAACCAATGTTATGTGAAGG
Done.