Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013817.1 Corchorus capsularis cultivar CVL-1 contig13838, 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: 21533
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:154 original size:35 final size:34
Alignment explanation
Indices: 110--218 Score: 112
Period size: 35 Copynumber: 3.1 Consensus size: 34
100 GTAATTGGAT
*
110 AATAGTAATCAGTAAAAAGTAATCGGTAAGAGTAA
1 AATAATAATCAGTAAAAAGTAAT-GGTAAGAGTAA
* * *
145 AATAATAATCAGT-AAGAGCAAAGTGGTAATAGTAA
1 AATAATAATCAGTAAAAAG-TAA-TGGTAAGAGTAA
* * *
180 AATATTAATCAGTAAAAGGTAATTAGTAAGAGTAA
1 AATAATAATCAGTAAAAAGTAA-TGGTAAGAGTAA
215 AATA
1 AATA
219 GTAAAGAGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
34 4 0.07
35 52 0.87
36 4 0.07
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (34 bp):
AATAATAATCAGTAAAAAGTAATGGTAAGAGTAA
Found at i:229 original size:35 final size:35
Alignment explanation
Indices: 110--324 Score: 107
Period size: 35 Copynumber: 6.0 Consensus size: 35
100 GTAATTGGAT
* * ***
110 AATAGTAATCAGTAAAAAGTAATCGGTAAGAGTAA
1 AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
* * * * ** *
145 AATAATAATCAGTAAGA-GCAAAGTGGTAATAGTAA
1 AATAGTAAACAGTAAAAGGTAAA-AAGTAAGAGTAA
* * **
180 AATATTAATCAGTAAAAGGTAATTAGTAAGAGTAA
1 AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
* * *
215 AATAGTAAAGAGTAAGATGATAAAAAGTAAAGAGT--
1 AATAGTAAACAGTAA-AAGGTAAAAAGT-AAGAGTAA
*
250 AATCAGTAAAGAGTAAAATGGTAAAAAGTAA-AG-AA
1 AAT-AGTAAACAGTAAAA-GGTAAAAAGTAAGAGTAA
* *
285 TAATCAGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAA
1 -AAT-AGT-AAACAGTAAAA-GGTAAAAAGT-AAGAGTAA
325 TCAGTAAAGA
Statistics
Matches: 145, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
34 5 0.03
35 68 0.47
36 39 0.27
37 27 0.19
38 2 0.01
39 2 0.01
40 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.22
Consensus pattern (35 bp):
AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
Found at i:245 original size:7 final size:7
Alignment explanation
Indices: 210--324 Score: 52
Period size: 7 Copynumber: 15.7 Consensus size: 7
200 AATTAGTAAG
210 AGTAAAA
1 AGTAAAA
*
217 TAGTAAAG
1 -AGTAAAA
*
225 AGTAAGA
1 AGTAAAA
*
232 TGATAAAA
1 AG-TAAAA
*
240 AGTAAAG
1 AGTAAAA
**
247 AGTAATC
1 AGTAAAA
*
254 AGTAAAG
1 AGTAAAA
261 AGTAAAA
1 AGTAAAA
*
268 TGGTAAAA
1 -AGTAAAA
276 AGTAAAGA
1 AGTAAA-A
**
284 A-TAATC
1 AGTAAAA
290 AGTAAAA
1 AGTAAAA
297 GAGTAAAA
1 -AGTAAAA
*
305 TGGTAAAA
1 -AGTAAAA
* *
313 GGTAAAG
1 AGTAAAA
320 AGTAA
1 AGTAA
325 TCAGTAAAGA
Statistics
Matches: 80, Mismatches: 22, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
6 1 0.01
7 47 0.59
8 32 0.40
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (7 bp):
AGTAAAA
Found at i:307 original size:37 final size:36
Alignment explanation
Indices: 218--349 Score: 201
Period size: 36 Copynumber: 3.6 Consensus size: 36
208 AGAGTAAAAT
* *
218 AGTAAAGAGTAAGATGATAAAAAGTAAAGAGTAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
*
254 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAATAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
*
290 AGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAATC
1 AGT-AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
* *
327 AGTAAAGAGAAAAATGGCAAAAA
1 AGTAAAGAGTAAAATGGTAAAAA
350 TATATATATA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 53 0.61
37 34 0.39
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (36 bp):
AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
Found at i:4177 original size:23 final size:22
Alignment explanation
Indices: 4136--4185 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
4126 ATGAAAATTC
4136 TTTTTGTATTTTTGTTATTTCATT
1 TTTTTGTATTTTTGTTA-TT-ATT
4160 TTTTTGTATTTTTG-TATTATT
1 TTTTTGTATTTTTGTTATTATT
4181 TTTTT
1 TTTTT
4186 AATAACAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
23 2 0.08
24 14 0.54
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTTGTATTTTTGTTATTATT
Found at i:18528 original size:28 final size:28
Alignment explanation
Indices: 18493--18569 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
18483 AAAATGGACT
*
18493 AAAAATGACCAAAATGCCCCTTTAATGC
1 AAAAATGACCAAAATGCCCCTATAATGC
* *
18521 AAAAATGACCAAAATGCCCCTATGATGT
1 AAAAATGACCAAAATGCCCCTATAATGC
*
18549 GAAAATGACCAAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
18570 GGATGACCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.19
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTATAATGC
Found at i:19078 original size:123 final size:123
Alignment explanation
Indices: 18776--19200 Score: 454
Period size: 123 Copynumber: 3.5 Consensus size: 123
18766 AACTCTCGAG
* * *
18776 CAAGATTTTAGATTGAAACAGAAACTCTCGGCTAGAGACCTCAAGCAGGATTTAAAATGAAACAA
1 CAAGATTTAAAATTGAAACAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAA
* *
18841 GATTTTGGGTTG----A-AAACTCTCGATTAGAGACCTCGAGTT-GGATTTGAAAATGAAA
66 GATTTTGGATTGAAAAAGAAACTCTCGACTAGAGACCTCGA-TTAGGATTTG-AAATG-AA
* * * *
18896 CAGGACTTAGAATTG----A-TAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAA
1 CAAGATTTAAAATTGAAACAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAA
*
18956 GATTTTGGATTGAAATAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G-A
66 GATTTTGGATTGAAA-AAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAA
*
19013 CAAGATTTAAAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACA
1 CAAGATTTAAAATTGAAAC-AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACA
* * **
19078 AGA-----CATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAA
65 AGATTTTGGATTGAAA-AAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAA
* ** *
19133 CATGATATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTTGAAATGA
1 CA--AGA-TTTAAAATTGAAAC-AGAAACTCTCGACTAGAGACCTCAAGCAGGA-TTTAAAATGA
19198 AAC
61 AAC
19201 TCTCCAACAG
Statistics
Matches: 262, Mismatches: 24, Indels: 34
0.82 0.08 0.11
Matches are distributed among these distances:
115 53 0.20
116 1 0.00
117 13 0.05
118 42 0.16
119 2 0.01
120 18 0.07
121 29 0.11
122 3 0.01
123 88 0.34
124 13 0.05
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (123 bp):
CAAGATTTAAAATTGAAACAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAA
GATTTTGGATTGAAAAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAA
Found at i:19186 original size:65 final size:62
Alignment explanation
Indices: 18787--19198 Score: 382
Period size: 58 Copynumber: 6.8 Consensus size: 62
18777 AAGATTTTAG
* *
18787 ATTGAAAC-AGAAACTCTCGGCTAGAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGG-
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGA-TTTGGA
* * * ** * * *
18849 GTTG-----A-AAACTCTCGATTAGAGACCTCGAGTTGGATTTGAAAATGAAACAGGACTTAGA
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATG-AACAAGATTTGGA
* *
18907 ATTG-----A-TAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGG-
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGA-TTTGGA
* * ** * **
18964 ATTGAAATAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G-ACAAGATTTAAA
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTGGA
*
19024 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGA-----C
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGATTTGGA
*
19082 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACATGATATTTTGGA
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACA--AGA-TTTGGA
19147 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTTGAAATGAA
1 ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGA-TTTGAAATGAA
19199 ACTCTCCAAC
Statistics
Matches: 292, Mismatches: 36, Indels: 40
0.79 0.10 0.11
Matches are distributed among these distances:
57 50 0.17
58 96 0.33
59 5 0.02
60 48 0.16
61 1 0.00
62 5 0.02
63 36 0.12
65 40 0.14
66 11 0.04
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (62 bp):
ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTGGA
Found at i:19505 original size:70 final size:69
Alignment explanation
Indices: 19414--19552 Score: 179
Period size: 70 Copynumber: 2.0 Consensus size: 69
19404 TAGACCACCC
* * * *
19414 TGGATCAACTGGAAACAACTGATGAAAAACCGCCCTGGGTCAACTGAATCGATCACTCTAACATA
1 TGGATAAACTGGAAACAACTGAAGAAAAACCACCCTGGGTCAACCGAATCGATCACTCTAACATA
19479 AACT
66 AACT
* * * * *
19483 TGGATAAACGTGGAAACTACTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACAT
1 TGGATAAAC-TGGAAACAACTGAAGAAAAACCACCCTGGGTCAACCGAATCGATCACTCTAACAT
*
19548 GAACT
65 AAACT
19553 GAAGAAAAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
69 8 0.14
70 51 0.86
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (69 bp):
TGGATAAACTGGAAACAACTGAAGAAAAACCACCCTGGGTCAACCGAATCGATCACTCTAACATA
AACT
Found at i:19573 original size:49 final size:49
Alignment explanation
Indices: 19501--19601 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
19491 CGTGGAAACT
* * * *
19501 ACTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACATGA
1 ACTGAAGAAAAACCACCCTGGGTCAACCGAATCGATCATTCTAACATAA
*
19550 ACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAA
1 ACTGAAGAAAAACCACCCTGGGTCAACCGAATCGATCATTCTAACATAA
19599 ACT
1 ACT
19602 TGGATAAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (49 bp):
ACTGAAGAAAAACCACCCTGGGTCAACCGAATCGATCATTCTAACATAA
Found at i:19641 original size:119 final size:119
Alignment explanation
Indices: 19430--19691 Score: 425
Period size: 119 Copynumber: 2.2 Consensus size: 119
19420 AACTGGAAAC
* *
19430 AACTGATGAAAAACCGCCCTGGGTCAACTGAATCGATCACTCTAACATAAACTTGGATAAACGTG
1 AACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCACTCTAACATAAACTTGGATAAACGTG
* * *
19495 GAAACTACTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACATG
66 GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGAAATA
* *
19549 AACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
1 AACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCACTCTAACATAAACTTGGATAAACGTG
* *
19614 GAAACTACTAAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGAAATA
66 GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGAAATA
* *
19668 AAATGGAGAAAAACCACCCTGGGT
1 AACTGAAGAAAAACCACCCTGGGT
19692 TTACTGAAAT
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 132 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (119 bp):
AACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCACTCTAACATAAACTTGGATAAACGTG
GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGAAATA
Found at i:19713 original size:35 final size:35
Alignment explanation
Indices: 19660--19783 Score: 122
Period size: 35 Copynumber: 3.5 Consensus size: 35
19650 ATCGATCATT
* * **
19660 CTGAAATAAAATGGAGAAAAACCACCCTGGGTTTA
1 CTGAAATAAACTGAAGAAAAACCACCCTGGGTCAA
* * * *
19695 CTGAAATAAGCTGAAGAAAGACCATCCTAGGTCAA
1 CTGAAATAAACTGAAGAAAAACCACCCTGGGTCAA
* * * *
19730 CTGAAATAAACTCAAGAAATATCACCCTGGATCAA
1 CTGAAATAAACTGAAGAAAAACCACCCTGGGTCAA
* *
19765 TTGAAATTAACTGAAGAAA
1 CTGAAATAAACTGAAGAAA
19784 GATCGCCCTG
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAAACCACCCTGGGTCAA
Found at i:19793 original size:35 final size:35
Alignment explanation
Indices: 19696--19801 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 35
19686 CTGGGTTTAC
* * *
19696 TGAAA-TAAGCTGAAGAAAGACCATCCTAGG-TCAAC
1 TGAAATTAA-CTGAAGAAAGATCACCCT-GGATCAAT
* * *
19731 TGAAATAAACTCAAGAAATATCACCCTGGATCAAT
1 TGAAATTAACTGAAGAAAGATCACCCTGGATCAAT
* *
19766 TGAAATTAACTGAAGAAAGATCGCCCTGGATTAAT
1 TGAAATTAACTGAAGAAAGATCACCCTGGATCAAT
19801 T
1 T
19802 AACTCAAGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
34 2 0.03
35 54 0.93
36 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (35 bp):
TGAAATTAACTGAAGAAAGATCACCCTGGATCAAT
Found at i:19811 original size:29 final size:29
Alignment explanation
Indices: 19769--19825 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
19759 GATCAATTGA
* *
19769 AATTAACTGAAGAAAGATCGCCCTGGATT
1 AATTAACTCAAGAAAAATCGCCCTGGATT
*
19798 AATTAACTCAAGAAAAATCGCCTTGGAT
1 AATTAACTCAAGAAAAATCGCCCTGGAT
19826 CAATAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (29 bp):
AATTAACTCAAGAAAAATCGCCCTGGATT
Found at i:20885 original size:29 final size:29
Alignment explanation
Indices: 20831--20894 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
20821 CTAGAGCTTC
* *
20831 TTTTC-TTCATCATTAAT-TTTCTTTTTCT
1 TTTTCTTTCATCATTAATCTTCCTTTTT-G
**
20859 TTTTCTTTCATCATTTCTCTTCCTTTTTG
1 TTTTCTTTCATCATTAATCTTCCTTTTTG
20888 TTTTCTT
1 TTTTCTT
20895 GTTTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.17
29 17 0.57
30 8 0.27
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTTCTTTCATCATTAATCTTCCTTTTTG
Done.