Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008631.1 Corchorus capsularis cultivar CVL-1 contig08652, 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: 58594
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3588 original size:31 final size:32
Alignment explanation
Indices: 3541--3637 Score: 112
Period size: 31 Copynumber: 3.1 Consensus size: 32
3531 AAAAGAGATC
*
3541 AATTTAGTCCC-TCTACTCATAAGATTGAGTT
1 AATTCAGTCCCTTCTACTCATAAGATTGAGTT
* *
3572 AATTCAGT-CTTTCTACTTATAAGATTGAGTT
1 AATTCAGTCCCTTCTACTCATAAGATTGAGTT
* *
3603 AATTTAGTCCCTT-TACTCACAAGATTG-GATT
1 AATTCAGTCCCTTCTACTCATAAGATTGAG-TT
3634 AATT
1 AATT
3638 GAATCCTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
30 2 0.04
31 51 0.91
32 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (32 bp):
AATTCAGTCCCTTCTACTCATAAGATTGAGTT
Found at i:5267 original size:83 final size:83
Alignment explanation
Indices: 5129--5375 Score: 433
Period size: 83 Copynumber: 3.0 Consensus size: 83
5119 AACATAAACA
5129 CATAGATCATATGA-TAAAAAAAAAAAAGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGTG
1 CATAGATCATATGATTAAAAAAAAAAAAGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGTG
*
5193 CCACTGAAAAGAGAAGCC
66 CCACTAAAAAGAGAAGCC
*
5211 CATAGATCATATGATTAAAAAAAAAAATGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGTG
1 CATAGATCATATGATTAAAAAAAAAAAAGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGTG
5276 CCACTAAAAAGAGAAGCC
66 CCACTAAAAAGAGAAGCC
*
5294 CATAGATCATATGATAAAAAAAAAATAAAGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGT
1 CATAGATCATATGATTAAAAAAAAA-AAAGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGT
* *
5359 GCCACTCAGAAGAGAAG
65 GCCACTAAAAAGAGAAG
5376 ACCAGTAATG
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 14 0.09
83 90 0.57
84 53 0.34
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (83 bp):
CATAGATCATATGATTAAAAAAAAAAAAGGATATGCAGCATTGGATCAATCTTGTAGTTCTGGTG
CCACTAAAAAGAGAAGCC
Found at i:6279 original size:22 final size:21
Alignment explanation
Indices: 6245--6285 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
6235 TTCGTGGTAG
6245 TTTTTTTTAAA-TTGATAGTT
1 TTTTTTTTAAATTTGATAGTT
6265 TTTTTTTTATCAATTTGATAG
1 TTTTTTTTA--AATTTGATAG
6286 AATGAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (21 bp):
TTTTTTTTAAATTTGATAGTT
Found at i:16167 original size:18 final size:18
Alignment explanation
Indices: 16133--16165 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16123 AGGAACATTG
16133 TTTTCATTTTTTCTTTTC
1 TTTTCATTTTTTCTTTTC
16151 TTTTC-TTTTTT-TTTT
1 TTTTCATTTTTTCTTTT
16166 TTAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTCATTTTTTCTTTTC
Found at i:19998 original size:28 final size:28
Alignment explanation
Indices: 19958--20015 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19948 TCCAGCTCCT
19958 TAAGGCTATATATCAGAAAAATGAAGCG
1 TAAGGCTATATATCAGAAAAATGAAGCG
19986 TAAGGCTATATATCAGAAAAATGAAGCG
1 TAAGGCTATATATCAGAAAAATGAAGCG
20014 TA
1 TA
20016 TGTACACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (28 bp):
TAAGGCTATATATCAGAAAAATGAAGCG
Found at i:26154 original size:22 final size:21
Alignment explanation
Indices: 26121--26166 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
26111 AAACAAAGAA
* *
26121 CTTTCTTTCTTTTCCCTTTTT
1 CTTTCTTCCTTTTCCCTTTCT
*
26142 CTTTACTTCCTTTTTCCTTTCT
1 CTTT-CTTCCTTTTCCCTTTCT
26164 CTT
1 CTT
26167 CAATTCAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTTCTTCCTTTTCCCTTTCT
Found at i:28177 original size:12 final size:12
Alignment explanation
Indices: 28160--28186 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28150 ACTTTTCAAC
28160 TTGTATAAATTG
1 TTGTATAAATTG
28172 TTGTATAAATTG
1 TTGTATAAATTG
28184 TTG
1 TTG
28187 CTTTTAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (12 bp):
TTGTATAAATTG
Found at i:39514 original size:3 final size:3
Alignment explanation
Indices: 39508--39549 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39498 ATCATCATAA
39508 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39550 ATATACCGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40066 original size:2 final size:2
Alignment explanation
Indices: 40059--40089 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40049 ATGGATAATT
40059 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 T
40090 TTCTTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44293 original size:26 final size:25
Alignment explanation
Indices: 44264--44330 Score: 116
Period size: 25 Copynumber: 2.6 Consensus size: 25
44254 TGACATCATG
*
44264 AAAAATATGAGACTTTTCACCAAAA
1 AAAAATATGAGACTTATCACCAAAA
44289 AAAAATATGAGACTTATCACCAAAA
1 AAAAATATGAGACTTATCACCAAAA
44314 AAAATATATGAGACTTA
1 AAAA-ATATGAGACTTA
44331 ACAATTTCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 28 0.70
26 12 0.30
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (25 bp):
AAAAATATGAGACTTATCACCAAAA
Found at i:45291 original size:2 final size:2
Alignment explanation
Indices: 45284--45318 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45274 ATAGTTAAGC
45284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45319 ATAGTAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51018 original size:32 final size:33
Alignment explanation
Indices: 50957--51058 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
50947 CTTTTACACT
** *
50957 GAGCCTCCCCACTAAGACGGCTCAGCCACGGCG
1 GAGCCTCCCCACTGGGACGGCTCAACCACGGCG
*
50990 GAGTCTCCCCACTGGGA-GGCTCAACCACGGCG
1 GAGCCTCCCCACTGGGACGGCTCAACCACGGCG
* ***
51022 GAGCCTCCCCACTGGGGCGGCTTTGCCACGGCG
1 GAGCCTCCCCACTGGGACGGCTCAACCACGGCG
51055 GAGC
1 GAGC
51059 GCCCCGGTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 29 0.49
33 30 0.51
ACGTcount: A:0.17, C:0.39, G:0.32, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTGGGACGGCTCAACCACGGCG
Found at i:51033 original size:16 final size:16
Alignment explanation
Indices: 50982--51033 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
50972 GACGGCTCAG
*
50982 CCACGGCGGAGTCTCC
1 CCACGGCGGAGCCTCC
* * *
50998 CCACTG-GGAGGCTCAA
1 CCACGGCGGAGCCTC-C
51014 CCACGGCGGAGCCTCC
1 CCACGGCGGAGCCTCC
51030 CCAC
1 CCAC
51034 TGGGGCGGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.17, C:0.44, G:0.29, T:0.10
Consensus pattern (16 bp):
CCACGGCGGAGCCTCC
Found at i:58565 original size:2 final size:2
Alignment explanation
Indices: 58558--58594 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
58548 CTATAGCATT
58558 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.