Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012851.1 Corchorus capsularis cultivar CVL-1 contig12872, 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: 19223
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:5715 original size:11 final size:11
Alignment explanation
Indices: 5699--5724 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5689 TATTAAAAAT
5699 ATAAAATATAA
1 ATAAAATATAA
5710 ATAAAATATAA
1 ATAAAATATAA
5721 ATAA
1 ATAA
5725 TATTTTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:15202 original size:21 final size:22
Alignment explanation
Indices: 15177--15218 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
15167 CCATACATGA
*
15177 TTTGGGGTTTGA-CCATTACGT
1 TTTGGGATTTGACCCATTACGT
15198 TTTGGGATTTGATCCCATTAC
1 TTTGGGATTTGA-CCCATTAC
15219 TAGTAGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (22 bp):
TTTGGGATTTGACCCATTACGT
Found at i:15293 original size:21 final size:22
Alignment explanation
Indices: 15269--15311 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
15259 ACTATACATG
*
15269 ATTTGGGGTTTGA-CCATTACA
1 ATTTGGGATTTGACCCATTACA
15290 ATTTGGGATTTGATCCCATTAC
1 ATTTGGGATTTGA-CCCATTAC
15312 TAGTAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (22 bp):
ATTTGGGATTTGACCCATTACA
Found at i:15371 original size:22 final size:21
Alignment explanation
Indices: 15346--15389 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
15336 TTTAAATTTC
* *
15346 ACCATACATGATTTGGGGTTTG
1 ACCAT-CAGGATTTGAGGTTTG
*
15368 ACCATTAGGATTTGAGGTTTG
1 ACCATCAGGATTTGAGGTTTG
15389 A
1 A
15390 TCCCATTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (21 bp):
ACCATCAGGATTTGAGGTTTG
Found at i:15468 original size:21 final size:22
Alignment explanation
Indices: 15442--15485 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
15432 CACCATACAT
*
15442 GATTTGGGGTTTGA-CCATTAC
1 GATTTGAGGTTTGACCCATTAC
15463 GATTTGAGGTTTGATCCCATTAC
1 GATTTGAGGTTTGA-CCCATTAC
15486 TAGTAGGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (22 bp):
GATTTGAGGTTTGACCCATTAC
Found at i:15556 original size:21 final size:22
Alignment explanation
Indices: 15532--15573 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
15522 CCATACATGA
15532 TTTGGGATTTGA-CCATTACAC
1 TTTGGGATTTGACCCATTACAC
*
15553 TTTGGGGTTTGATCCCATTAC
1 TTTGGGATTTGA-CCCATTAC
15574 TAATAGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (22 bp):
TTTGGGATTTGACCCATTACAC
Found at i:15562 original size:88 final size:86
Alignment explanation
Indices: 15123--15639 Score: 660
Period size: 87 Copynumber: 5.8 Consensus size: 86
15113 ATTATTTAAA
* * *
15123 CCCATTGCTAGTAGGGATTTGCCTAATCATACTTTACAATTTAACCATACATGATTTGGGGTTTG
1 CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTA-AATTTCACCATACATGATTTGGGGTTTG
* *
15188 ACCATTACGTTTTGGGATTTGAT
65 ACCATTAC-ATTTGGGGTTTGAT
15211 CCCATTACTAGTAGGGG-TTGCCTAATCATACTTTAAATTTCACTTGTAACTATACATGATTTGG
1 CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTAAATTTCAC------C-ATACATGATTTGG
*
15275 GGTTTGACCATTACAATTTGGGATTTGAT
59 GGTTTGACCATTAC-ATTTGGGGTTTGAT
* * *
15304 CCCATTACTAGTAAGGTTTTGCCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
1 CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTAAATTTCACCATACATGATTTGGGGTTTGA
* *
15369 CCATTAGGATTTGAGGTTTGAT
66 CCATTA-CATTTGGGGTTTGAT
* * * *
15391 CCCATTACTAATAAGGTTTTGCCTAATCATATTTTAAATTTCACCATACATGATTTGGGGTTTGA
1 CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTAAATTTCACCATACATGATTTGGGGTTTGA
*
15456 CCATTACGATTTGAGGTTTGAT
66 CCATTAC-ATTTGGGGTTTGAT
* *
15478 CCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTACAGA-TTCACCATACATGATTTGGGATTT
1 CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTA-A-ATTTCACCATACATGATTTGGGGTTT
15542 GACCATTACACTTTGGGGTTTGAT
64 GACCATTACA-TTTGGGGTTTGAT
* * * **
15566 CCCATTACTAATAGGGGTTTGCCTGATCATGCTTTAAATTTCATTATACATGATTTGGGGTTTGA
1 CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTAAATTTCACCATACATGATTTGGGGTTTGA
15631 TCTCATTAC
66 -C-CATTAC
15640 TAGTAAGTGT
Statistics
Matches: 386, Mismatches: 27, Indels: 31
0.87 0.06 0.07
Matches are distributed among these distances:
86 8 0.02
87 194 0.50
88 96 0.25
89 7 0.02
92 1 0.00
93 55 0.14
94 25 0.06
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (86 bp):
CCCATTACTAGTAGGGGTTTGCCTAATCATACTTTAAATTTCACCATACATGATTTGGGGTTTGA
CCATTACATTTGGGGTTTGAT
Found at i:15604 original size:175 final size:174
Alignment explanation
Indices: 15123--15639 Score: 700
Period size: 175 Copynumber: 2.9 Consensus size: 174
15113 ATTATTTAAA
* * *
15123 CCCATTGCTAGTAGGGATTTGCCTAATCATACTTTACAATTTAACCATACATGATTTGGGGTTTG
1 CCCATTACTAGTAGGGATTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGGTTTG
* * *
15188 ACCATTACGTTTTGGGATTTGATCCCATTACTAGTAGGGG-TTGCCTAATCATACTTTAAATTTC
66 ACCATTAC-ATTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTAATCATACTTTAAATTTC
15252 ACTTGTAACTATACATGATTTGGGGTTTGACCATTACAATTTGGGATTTGAT
130 AC------C-ATACATGATTTGGGGTTTGACCATTACAATTTGGGATTTGAT
* *
15304 CCCATTACTAGTAAGGTTTTGCCTAATCATGCTTTA-AATTTCACCATACATGATTTGGGGTTTG
1 CCCATTACTAGTAGGGATTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGGTTTG
* * * * *
15368 ACCATTAGGATTTGAGGTTTGATCCCATTACTAATAAGGTTTTGCCTAATCATATTTTAAATTTC
66 ACCATTA-CATTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTAATCATACTTTAAATTTC
*
15433 ACCATACATGATTTGGGGTTTGACCATTACGATTTGAGG-TTTGAT
130 ACCATACATGATTTGGGGTTTGACCATTACAATTTG-GGATTTGAT
* *
15478 CCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTACAGA-TTCACCATACATGATTTGGGATTT
1 CCCATTACTAGTAGGGATTTGCCTAATCATGCTTTACA-ATTTCACCATACATGATTTGGGGTTT
* *
15542 GACCATTACACTTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTGATCATGCTTTAAATTT
65 GACCATTACA-TTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTAATCATACTTTAAATTT
**
15607 CATTATACATGATTTGGGGTTTGATCTCATTAC
129 CACCATACATGATTTGGGGTTTGA-C-CATTAC
15640 TAGTAAGTGT
Statistics
Matches: 302, Mismatches: 26, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
174 73 0.24
175 105 0.35
176 2 0.01
177 6 0.02
180 59 0.20
181 57 0.19
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (174 bp):
CCCATTACTAGTAGGGATTTGCCTAATCATGCTTTACAATTTCACCATACATGATTTGGGGTTTG
ACCATTACATTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTAATCATACTTTAAATTTCA
CCATACATGATTTGGGGTTTGACCATTACAATTTGGGATTTGAT
Found at i:15617 original size:262 final size:263
Alignment explanation
Indices: 15140--15630 Score: 749
Period size: 262 Copynumber: 1.9 Consensus size: 263
15130 CTAGTAGGGA
*
15140 TTTGCCTAATCATACTTTACAATTTAACCATACATGATTTGGGGTTTGACCATTACGTTTTGGGA
1 TTTGCCTAATCATACTTTACAATTTAACCATACATGATTTGGGGTTTGACCATTACGATTTGGGA
15205 TTTGATCCCATTACTAGTAGGGGTTGCCTAATCATACTTTAAATTTCACTTGTAACTATACATGA
66 TTTGATCCCATTACTAGTAGGGGTTGCCTAATCATACTTTAAATTTCAC---T--CTATACATGA
* * *
15270 TTTGGGGTTTGACCATTACAATTTGGGATTTGATCCCATTACTAGTAAGGTTTTGCCTAATCATG
126 TTTGGGATTTGACCATTACAATTTGGGATTTGATCCCATTACTAATAAGGGTTTGCCTAATCATG
15335 CTTTAAATTTCACCATACATGATTTGGGGTTTGACCATTAGGATTTGAGGTTTGATCCCATTACT
191 CTTTAAATTTCACCATACATGATTTGGGGTTTGACCATTAGGATTTGAGGTTTGATCCCATTACT
15400 AATAAGGT
256 AATAAGGT
* *
15408 TTTGCCTAATCATATTTTA-AATTTCACCATACATGATTTGGGGTTTGACCATTACGATTTGAGG
1 TTTGCCTAATCATACTTTACAATTTAACCATACATGATTTGGGGTTTGACCATTACGATTTG-GG
*
15472 -TTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTACAGA-TTCAC-C-ATACATGAT
65 ATTTGATCCCATTACTAGTAGGGG-TTGCCTAATCATACTTTA-A-ATTTCACTCTATACATGAT
* * * *
15533 TTGGGATTTGACCATTACACTTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTGATCATGC
127 TTGGGATTTGACCATTACAATTTGGGATTTGATCCCATTACTAATAAGGGTTTGCCTAATCATGC
**
15598 TTTAAATTTCATTATACATGATTTGGGGTTTGA
192 TTTAAATTTCACCATACATGATTTGGGGTTTGA
15631 TCTCATTACT
Statistics
Matches: 206, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
262 98 0.48
263 1 0.00
267 63 0.31
268 37 0.18
269 6 0.03
270 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (263 bp):
TTTGCCTAATCATACTTTACAATTTAACCATACATGATTTGGGGTTTGACCATTACGATTTGGGA
TTTGATCCCATTACTAGTAGGGGTTGCCTAATCATACTTTAAATTTCACTCTATACATGATTTGG
GATTTGACCATTACAATTTGGGATTTGATCCCATTACTAATAAGGGTTTGCCTAATCATGCTTTA
AATTTCACCATACATGATTTGGGGTTTGACCATTAGGATTTGAGGTTTGATCCCATTACTAATAA
GGT
Found at i:15627 original size:66 final size:63
Alignment explanation
Indices: 15553--15693 Score: 183
Period size: 66 Copynumber: 2.2 Consensus size: 63
15543 ACCATTACAC
* * *
15553 TTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTGATCATGCTTTAAATTTCATTATACATG
1 TTTGGGGTTTGATCCCATTACTAATAAGGGTTTGCCTAATCATGCTTTAAA--T-ACTATACATG
15618 A
63 A
* * * *
15619 TTTGGGGTTTGATCTCATTACTAGTAAGTGTTTGCCTAATCATGTTTTAAATACTATACATGA
1 TTTGGGGTTTGATCCCATTACTAATAAGGGTTTGCCTAATCATGCTTTAAATACTATACATGA
*
15682 TTTGGGATTTGA
1 TTTGGGGTTTGA
15694 CCATTATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 21 0.31
64 1 0.01
66 45 0.67
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.43
Consensus pattern (63 bp):
TTTGGGGTTTGATCCCATTACTAATAAGGGTTTGCCTAATCATGCTTTAAATACTATACATGA
Found at i:15731 original size:150 final size:154
Alignment explanation
Indices: 15463--15751 Score: 426
Period size: 150 Copynumber: 1.9 Consensus size: 154
15453 TGACCATTAC
*
15463 GATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTACAGATTCACCATAC
1 GATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTACAGATTCACCATAC
* * *
15528 ATGATTTGGGATTTGACCATTACACTTTGGGGTTTGATCCCATTACTAATAGGGGTTTGCCTGAT
66 ATGATTTGGGATTTGACCATTACACTTTGAGATTTGATCCCATTACTAATAGGGGTTTGCCTAAT
15593 CATGCTTTAAATTTCATTATACAT
131 CATGCTTTAAATTTCATTATACAT
* * * * *
15617 GATTTGGGGTTTGATCTCATTACTAGTAAGTGTTTGCCTAATCATGTTTTA-A-A-T-ACTATAC
1 GATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTACAGATTCACCATAC
* * *
15678 ATGATTTGGGATTTGACCATTATGA-TTTGAGATTTGATCCCATTACTAGTAGGGGTTTTCCTAA
66 ATGATTTGGGATTTGACCATTA-CACTTTGAGATTTGATCCCATTACTAATAGGGGTTTGCCTAA
15742 TCATGCTTTA
130 TCATGCTTTA
15752 TAGTTTGACC
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
150 72 0.59
151 2 0.02
152 1 0.01
153 1 0.01
154 46 0.38
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (154 bp):
GATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTACAGATTCACCATAC
ATGATTTGGGATTTGACCATTACACTTTGAGATTTGATCCCATTACTAATAGGGGTTTGCCTAAT
CATGCTTTAAATTTCATTATACAT
Found at i:16382 original size:6 final size:6
Alignment explanation
Indices: 16361--16405 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
16351 ATATATAATA
* * * *
16361 TATATG TGTGTG TATATG TATATG TATATG TATATA TTTATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
16406 GTATAATTGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (6 bp):
TATATG
Found at i:17210 original size:24 final size:24
Alignment explanation
Indices: 17157--17214 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
17147 CTAATTAGAT
17157 TTGATTTAATTTTGATTTGAAGAA
1 TTGATTTAATTTTGATTTGAAGAA
** **
17181 ACGATTTAATTTTGATATTG-ATTA
1 TTGATTTAATTTTGAT-TTGAAGAA
17205 TTGATTTAAT
1 TTGATTTAAT
17215 AACTAATTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.52
Consensus pattern (24 bp):
TTGATTTAATTTTGATTTGAAGAA
Found at i:17490 original size:26 final size:25
Alignment explanation
Indices: 17461--17517 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
17451 ATTTCTACAT
*
17461 AAATTTAGTAAC-CTCACATTCTTAGA
1 AAATTTAGAAACACT-ACATTCTTA-A
17487 AAATTTAGAAACACTACATTCTTAA
1 AAATTTAGAAACACTACATTCTTAA
17512 AAATTT
1 AAATTT
17518 CAGGTTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.24
26 20 0.69
27 2 0.07
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (25 bp):
AAATTTAGAAACACTACATTCTTAA
Found at i:19015 original size:30 final size:30
Alignment explanation
Indices: 18981--19040 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18971 ACTAATTAAT
*
18981 CAATCAATCTAAACTAATTAATATATTTCC
1 CAATCAAGCTAAACTAATTAATATATTTCC
* *
19011 CAATCAAGCTAAAGTAATTAATTTATTTCC
1 CAATCAAGCTAAACTAATTAATATATTTCC
19041 TTTTGTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (30 bp):
CAATCAAGCTAAACTAATTAATATATTTCC
Done.