Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000548.1 Corchorus capsularis cultivar CVL-1 contig00548, 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: 12294
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Found at i:10399 original size:2 final size:2
Alignment explanation
Indices: 10392--10423 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10382 ATGCATGAAC
10392 TA TA 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
10424 GTGTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11209 original size:7 final size:7
Alignment explanation
Indices: 11197--11265 Score: 56
Period size: 7 Copynumber: 10.3 Consensus size: 7
11187 CCTTTGCTGA
11197 TTACTCT
1 TTACTCT
11204 TTACTCT
1 TTACTCT
11211 TTAC-CAT
1 TTACTC-T
*
11218 TT-TTCT
1 TTACTCT
**
11224 TTACTGA
1 TTACTCT
11231 TTACT-T
1 TTACTCT
*
11237 TT-CTAT
1 TTACTCT
11243 TTACTCT
1 TTACTCT
11250 TTACTCT
1 TTACTCT
*
11257 TTACCCT
1 TTACTCT
11264 TT
1 TT
11266 TTCTTTGCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
5 2 0.04
6 9 0.18
7 39 0.78
ACGTcount: A:0.16, C:0.25, G:0.01, T:0.58
Consensus pattern (7 bp):
TTACTCT
Found at i:11210 original size:34 final size:34
Alignment explanation
Indices: 11084--11235 Score: 157
Period size: 34 Copynumber: 4.4 Consensus size: 34
11074 GCCATTATTT
* * * *
11084 TTTACTGATTAATATTTTATTCTTTACCATTTTTTC
1 TTTACTGATTACT-CTTTACTCTTTACCA-TTTTCC
11120 TTTACTGGATTACTCTTTACT-TTTCACCATTCTT-C
1 TTTACT-GATTACTCTTTACTCTTT-ACCATT-TTCC
* *
11155 TTTACTGACTT-TTCTTCACTCTTTACCATTTTCC
1 TTTACTGA-TTACTCTTTACTCTTTACCATTTTCC
* *
11189 TTTGCTGATTACTCTTTACTCTTTACCATTTTTC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTCC
11223 TTTACTGATTACT
1 TTTACTGATTACT
11236 TTTCTATTTA
Statistics
Matches: 99, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
33 4 0.04
34 55 0.56
35 17 0.17
36 17 0.17
37 6 0.06
ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTACTGATTACTCTTTACTCTTTACCATTTTCC
Found at i:11253 original size:19 final size:18
Alignment explanation
Indices: 11203--11259 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
11193 CTGATTACTC
*
11203 TTTACTCTTTACCATTTTTC
1 TTTACTCTTTA-C-TTTTTA
**
11223 TTTACTGATTACTTTTCTA
1 TTTACTCTTTACTTTT-TA
*
11242 TTTACTCTTTACTCTTTA
1 TTTACTCTTTACTTTTTA
11260 CCCTTTTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 6 0.20
19 15 0.50
20 9 0.30
ACGTcount: A:0.18, C:0.21, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTACTCTTTACTTTTTA
Found at i:11295 original size:35 final size:35
Alignment explanation
Indices: 11243--11320 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
11233 ACTTTTCTAT
* *
11243 TTACTC-TTTACTCTTTACCCTTTTTCTTTGCTGA
1 TTACTCTTTTACTCTTTACCATTTTACTTTGCTGA
*
11277 TTACTCTTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTCTTTTACTCTTTACCATTTTACTTTGCTGA
11312 TTACTCTTT
1 TTACTCTTT
11321 ACTGATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 6 0.15
35 34 0.85
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (35 bp):
TTACTCTTTTACTCTTTACCATTTTACTTTGCTGA
Found at i:11325 original size:14 final size:15
Alignment explanation
Indices: 11301--11338 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
11291 TTTACCATTT
*
11301 TACTTTGCTGATTAC
1 TACTTTACTGATTAC
*
11316 T-CTTTACTGATTAT
1 TACTTTACTGATTAC
11330 TACTTTACT
1 TACTTTACT
11339 CTTTCCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.53
Consensus pattern (15 bp):
TACTTTACTGATTAC
Found at i:11421 original size:20 final size:20
Alignment explanation
Indices: 11378--11438 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
11368 GACTACCTTT
* *
11378 TTACTTTTTACTGATTACCG
1 TTACTTCTTACTGATTACCA
*
11398 TTACTTCTTACTGATTACTA
1 TTACTTCTTACTGATTACCA
*
11418 TTAC-TCTCTACTAATTACCA
1 TTACTTCT-TACTGATTACCA
11438 T
1 T
11439 ATTGCTCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.48
Consensus pattern (20 bp):
TTACTTCTTACTGATTACCA
Found at i:11446 original size:22 final size:22
Alignment explanation
Indices: 11416--11465 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
11406 TACTGATTAC
11416 TATTACTCTCTACTAATTACCA
1 TATTACTCTCTACTAATTACCA
* *
11438 TATTGCTCTTTACTAATTACCA
1 TATTACTCTCTACTAATTACCA
*
11460 TTTTAC
1 TATTAC
11466 CTTTTACTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (22 bp):
TATTACTCTCTACTAATTACCA
Found at i:11464 original size:84 final size:85
Alignment explanation
Indices: 11328--11505 Score: 200
Period size: 84 Copynumber: 2.1 Consensus size: 85
11318 TTTACTGATT
* * * * *
11328 ATTACT-TTACTCTTTCCTAATTACCATTGTACCCATTACTGACTACCTTTTTACTTTTTACTGA
1 ATTACTATTACTCTCTACTAATTACCATTGTACCCATTACTAACTACCATTTTACCTTTTACTGA
*
11392 TTACCGTTA-CTTCTTACTG
66 TTACCATTATCTTCTTACTG
* * * *
11411 ATTACTATTACTCTCTACTAATTACCATAT-TGCTCTTTACTAATTACCATTTTACCTTTTACTG
1 ATTACTATTACTCTCTACTAATTACCAT-TGTACCCATTACTAACTACCATTTTACCTTTTACTG
* * *
11475 ATTATCATTATTTTTTTTACTG
65 ATTACCATTA-TCTTCTTACTG
11497 ATTACTATT
1 ATTACTATT
11506 TTACTATTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 6 0.08
84 54 0.69
85 1 0.01
86 17 0.22
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.49
Consensus pattern (85 bp):
ATTACTATTACTCTCTACTAATTACCATTGTACCCATTACTAACTACCATTTTACCTTTTACTGA
TTACCATTATCTTCTTACTG
Found at i:11471 original size:22 final size:21
Alignment explanation
Indices: 11426--11507 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
11416 TATTACTCTC
* *
11426 TACTAATTACCATATTGCTCTT
1 TACTAATTACCATTTTCCT-TT
11448 TACTAATTACCATTTTACCTTT
1 TACTAATTACCATTTT-CCTTT
* * **
11470 TACTGATTATCATTATTTTTTT
1 TACTAATTACCATT-TTCCTTT
* *
11492 TACTGATTACTATTTT
1 TACTAATTACCATTTT
11508 ACTATTTGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.04
22 44 0.88
23 4 0.08
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.54
Consensus pattern (21 bp):
TACTAATTACCATTTTCCTTT
Found at i:11585 original size:30 final size:30
Alignment explanation
Indices: 11549--11645 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 30
11539 TTTTCTCTTT
11549 ACTGATTGCTTTTTCTTATTGAACTTAATC
1 ACTGATTGCTTTTTCTTATTGAACTTAATC
* *
11579 ACTGATTACTTTTTCTTATTGAACTTAATT
1 ACTGATTGCTTTTTCTTATTGAACTTAATC
* *
11609 ATTGATTGCCCTTTTTACTTTTTGGAACTTAATC
1 ACTGATTG--CTTTTT-CTTATT-GAACTTAATC
11643 ACT
1 ACT
11646 CTGATCACCC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 34 0.61
32 6 0.11
33 5 0.09
34 11 0.20
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (30 bp):
ACTGATTGCTTTTTCTTATTGAACTTAATC
Found at i:11638 original size:34 final size:35
Alignment explanation
Indices: 11557--11665 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 35
11547 TTACTGATTG
* *
11557 CTTTTT-CTTATTGAACTTAATCA--CTGATTA--
1 CTTTTTACTTTTTGAACTTAATCACTCTGATCACC
* * **
11587 CTTTTT-CTTATTGAACTTAATTA-T-TGATTGCC
1 CTTTTTACTTTTTGAACTTAATCACTCTGATCACC
11619 CTTTTTACTTTTTGGAACTTAATCACTCTGATCACC
1 CTTTTTACTTTTT-GAACTTAATCACTCTGATCACC
11655 CTTTTTACTTT
1 CTTTTTACTTT
11666 CCTGACTGAC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
30 27 0.41
32 6 0.09
33 5 0.08
34 10 0.15
35 1 0.02
36 17 0.26
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.51
Consensus pattern (35 bp):
CTTTTTACTTTTTGAACTTAATCACTCTGATCACC
Done.