Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015508.1 Corchorus capsularis cultivar CVL-1 contig15529, 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: 13394
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:241 original size:22 final size:22
Alignment explanation
Indices: 216--705 Score: 126
Period size: 20 Copynumber: 23.2 Consensus size: 22
206 TAATTACCAC
*
216 TTACTGATTGCTATTTTACTCT
1 TTACTGATTACTATTTTACTCT
*
238 TTACTGATTACT-CTTTACTCTT
1 TTACTGATTACTATTTTACTC-T
* * *
260 TTACTGATTAATATTTTATTCC
1 TTACTGATTACTATTTTACTCT
* * *
282 TTACTGATTGC--CTTTACTTT
1 TTACTGATTACTATTTTACTCT
*
302 TTACTGATTAATATTTTACTCT
1 TTACTGATTACTATTTTACTCT
* * * ** **
324 CTAC-CATT-TTCCTTTACTGA
1 TTACTGATTACTATTTTACTCT
* ** **
344 TTACT-CTTTGTCCTTTAC-CATT
1 TTACTGATTACTATTTTACTC--T
*
366 TTACTGATTTA-T-TTTCACT-T
1 TTACTGA-TTACTATTTTACTCT
* * **
386 CTTACT-ATT-TTTTCTTTACTGA
1 -TTACTGATTACTAT-TTTACTCT
* *
408 TTACT-TTTCACTCTT-TACTCT
1 TTACTGATT-ACTATTTTACTCT
* *
429 TTACTGATTACT-CTTTACTTT
1 TTACTGATTACTATTTTACTCT
* * *
450 TTACTAATTACCATTTTACTTT
1 TTACTGATTACTATTTTACTCT
*
472 TTACTGATTAC--CTTTACTCT
1 TTACTGATTACTATTTTACTCT
* * *
492 TTTCTAATTACCATTTTTACT-T
1 TTACTGATTACTA-TTTTACTCT
* *
514 TTCACTGATTAC--CTTTACTTT
1 TT-ACTGATTACTATTTTACTCT
* * *
535 TTATTGATTACCATTTTACTTT
1 TTACTGATTACTATTTTACTCT
* * * * *
557 TTATTAATTACCTTTTTTAATTT
1 TTACTGATTA-CTATTTTACTCT
* *
580 TTACTGATTGCCA--TTACT-T
1 TTACTGATTACTATTTTACTCT
*
599 CTTACTGATCACTA--TTACTCT
1 -TTACTGATTACTATTTTACTCT
*
620 TTACTGATTACCATATTT--TCT
1 TTACTGATTACTAT-TTTACTCT
641 TTACTGATTACT-TTTTA--CT
1 TTACTGATTACTATTTTACTCT
** *
660 TTACTTTTTACCATTTT-CT-T
1 TTACTGATTACTATTTTACTCT
* * * *
680 TCACTGATTACTCTATTACTCC
1 TTACTGATTACTATTTTACTCT
702 TTAC
1 TTAC
706 CATTTCTGTT
Statistics
Matches: 345, Mismatches: 83, Indels: 80
0.68 0.16 0.16
Matches are distributed among these distances:
19 18 0.05
20 107 0.31
21 82 0.24
22 96 0.28
23 40 0.12
24 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.54
Consensus pattern (22 bp):
TTACTGATTACTATTTTACTCT
Found at i:275 original size:44 final size:42
Alignment explanation
Indices: 216--323 Score: 153
Period size: 44 Copynumber: 2.5 Consensus size: 42
206 TAATTACCAC
**
216 TTACTGATTGCTATTTTACTCTTTACTGATTACTCTTTACTCTT
1 TTACTGATTAATATTTTACTCTTTACTGATTAC-CTTTACT-TT
* * *
260 TTACTGATTAATATTTTATTCCTTACTGATTGCCTTTACTTT
1 TTACTGATTAATATTTTACTCTTTACTGATTACCTTTACTTT
302 TTACTGATTAATATTTTACTCT
1 TTACTGATTAATATTTTACTCT
324 CTACCATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 22 0.39
43 7 0.12
44 28 0.49
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (42 bp):
TTACTGATTAATATTTTACTCTTTACTGATTACCTTTACTTT
Found at i:348 original size:42 final size:42
Alignment explanation
Indices: 216--348 Score: 108
Period size: 42 Copynumber: 3.1 Consensus size: 42
206 TAATTACCAC
** * * * **
216 TTACTGATTGCTATTTTACTCTTTACTGATTACTCTTTACTCTT
1 TTACTGATTAATATTTTACTCCTTACTCATTGC-CTTTACT-GA
* * **
260 TTACTGATTAATATTTTATTCCTTACTGATTGCCTTTACTTT
1 TTACTGATTAATATTTTACTCCTTACTCATTGCCTTTACTGA
*
302 TTACTGATTAATATTTTACT-CTCTAC-CATTTTCCTTTACTGA
1 TTACTGATTAATATTTTACTCCT-TACTCA-TTGCCTTTACTGA
344 TTACT
1 TTACT
349 CTTTGTCCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
41 3 0.04
42 39 0.51
43 7 0.09
44 28 0.36
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (42 bp):
TTACTGATTAATATTTTACTCCTTACTCATTGCCTTTACTGA
Found at i:368 original size:64 final size:63
Alignment explanation
Indices: 292--437 Score: 158
Period size: 64 Copynumber: 2.3 Consensus size: 63
282 TTACTGATTG
*
292 CCTTTACTTTTTACTGATTAATATTTT-AC-TCTCTACCA-TTTTCCTTTACTGATTACTCTTTG
1 CCTTTACATTTTACTGATT--TATTTTCACTTCT-TACCATTTTTCCTTTACTGATTACTCTTTG
354 T
63 T
* * **
355 CCTTTACCATTTTACTGATTTATTTTCACTTCTTACTATTTTTTCTTTACTGATTACT-TTTCA
1 CCTTTA-CATTTTACTGATTTATTTTCACTTCTTACCATTTTTCCTTTACTGATTACTCTTTGT
418 CTCTTTAC-TCTTTACTGATT
1 C-CTTTACAT-TTTACTGATT
438 ACTCTTTACT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
62 7 0.10
63 27 0.38
64 38 0.53
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.55
Consensus pattern (63 bp):
CCTTTACATTTTACTGATTTATTTTCACTTCTTACCATTTTTCCTTTACTGATTACTCTTTGT
Found at i:427 original size:7 final size:7
Alignment explanation
Indices: 398--493 Score: 54
Period size: 7 Copynumber: 13.7 Consensus size: 7
388 TACTATTTTT
398 TCTTTAC
1 TCTTTAC
**
405 TGATTAC
1 TCTTTAC
412 T-TTTCAC
1 TCTTT-AC
419 TCTTTAC
1 TCTTTAC
426 TCTTTAC
1 TCTTTAC
**
433 TGATTAC
1 TCTTTAC
440 TCTTTAC
1 TCTTTAC
*
447 TTTTTAC
1 TCTTTAC
**
454 TAATTAC
1 TCTTTAC
461 -CATTTTAC
1 TC--TTTAC
*
469 TTTTTAC
1 TCTTTAC
**
476 TGATTAC
1 TCTTTAC
483 -CTTTAC
1 TCTTTAC
489 TCTTT
1 TCTTT
494 TCTAATTACC
Statistics
Matches: 66, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
6 6 0.09
7 53 0.80
8 7 0.11
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (7 bp):
TCTTTAC
Found at i:439 original size:14 final size:14
Alignment explanation
Indices: 398--447 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
388 TACTATTTTT
398 TCTTTACTGATTAC
1 TCTTTACTGATTAC
**
412 T-TTTCACTCTTTAC
1 TCTTT-ACTGATTAC
426 TCTTTACTGATTAC
1 TCTTTACTGATTAC
440 TCTTTACT
1 TCTTTACT
448 TTTTACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 3 0.10
14 24 0.80
15 3 0.10
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:477 original size:43 final size:43
Alignment explanation
Indices: 421--699 Score: 249
Period size: 43 Copynumber: 6.6 Consensus size: 43
411 CTTTTCACTC
* *
421 TTTACTCTTTACTGATTACTCTTTACTTTTTACTAATTACCAT
1 TTTACTTTTTACTGATTACTCTTTACTTTTTACTGATTACCAT
*
464 TTTACTTTTTACTGATTAC-CTTTACTCTTTT-CTAATTACCATT
1 TTTACTTTTTACTGATTACTCTTTACT-TTTTACTGATTACCA-T
* *
507 TTTACTTTTCACTGATTAC-CTTTACTTTTTATTGATTACCAT
1 TTTACTTTTTACTGATTACTCTTTACTTTTTACTGATTACCAT
* * * * *
549 TTTACTTTTTATTAATTACCTTTTTTAATTTTTACTGATTGCCA-
1 TTTACTTTTTACTGATTA-C-TCTTTACTTTTTACTGATTACCAT
* * * *
593 -TTACTTCTTACTGATCACT-ATTACTCTTTACTGATTACCAT
1 TTTACTTTTTACTGATTACTCTTTACTTTTTACTGATTACCAT
* * **
634 ATTT--TCTTTACTGATTACTTTTTAC--TTTACTTTTTACCAT
1 -TTTACTTTTTACTGATTACTCTTTACTTTTTACTGATTACCAT
*
674 TTT-C-TTTCACTGATTACTCTATTACT
1 TTTACTTTTTACTGATTACTCT-TTACT
700 CCTTACCATT
Statistics
Matches: 195, Mismatches: 28, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
39 16 0.08
40 34 0.17
41 13 0.07
42 42 0.22
43 72 0.37
45 18 0.09
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.55
Consensus pattern (43 bp):
TTTACTTTTTACTGATTACTCTTTACTTTTTACTGATTACCAT
Found at i:565 original size:65 final size:64
Alignment explanation
Indices: 421--661 Score: 219
Period size: 65 Copynumber: 3.8 Consensus size: 64
411 CTTTTCACTC
* * * *
421 TTTACTCTTTACTGATTA-C-TCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGATTACC
1 TTTACTTTTTACTAATTACCATTTTTACTTTTTACTGATTACC--TTTACTTTTTACTGATTACC
484 -
64 T
* *
484 TTTACTCTTTT-CTAATTACCATTTTTACTTTTCACTGATTACCTTTACTTTTTATTGATTACCA
1 TTTACT-TTTTACTAATTACCATTTTTACTTTTTACTGATTACCTTTACTTTTTACTGATTACC-
548 T
64 T
* * * * * * *
549 TTTACTTTTTATTAATTACCTTTTTTAATTTTTACTGATTGCCATTACTTCTTACTGATCA-CT
1 TTTACTTTTTACTAATTACCATTTTTACTTTTTACTGATTACCTTTACTTTTTACTGATTACCT
* * * *
612 ATTACTCTTTACTGATTACCATATTTT-C--TTTACTGATTACTTTTTACTTT
1 TTTACTTTTTACTAATTACCAT-TTTTACTTTTTACTGATTAC-CTTTACTTT
662 ACTTTTTACC
Statistics
Matches: 145, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
61 11 0.08
62 6 0.04
63 49 0.34
64 13 0.09
65 66 0.46
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (64 bp):
TTTACTTTTTACTAATTACCATTTTTACTTTTTACTGATTACCTTTACTTTTTACTGATTACCT
Found at i:597 original size:85 final size:82
Alignment explanation
Indices: 421--699 Score: 228
Period size: 85 Copynumber: 3.3 Consensus size: 82
411 CTTTTCACTC
* *
421 TTTACTCTTTACTGATTACTCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGATTACCTT
1 TTTACT-TTTACTGATTAC-CTTTACTTTTTACTGATTACCATTTTACTTTTTACTAATTACCTT
*
486 TACTCTTTTCTAATTACCA
64 TAATCTTTTCTAATTACCA
* *
505 TTTTTACTTTTCACTGATTACCTTTACTTTTTATTGATTACCATTTTACTTTTTATTAATTACCT
1 --TTTACTTTT-ACTGATTACCTTTACTTTTTACTGATTACCATTTTACTTTTTACTAATTACC-
* *
570 TTTTTAAT-TTTTACTGATTGCCA
62 --TTTAATCTTTT-CTAATTACCA
* * * * *
593 -TTACTTCTTACTGATCA-CTATTACTCTTTACTGATTACCATATTT--TCTTTACTGATTACTT
1 TTTACTT-TTACTGATTACCT-TTACTTTTTACTGATTACCAT-TTTACTTTTTACTAATTACCT
* * **
654 TTTA-CTTTACTTTTTACCA
63 TTAATCTTTTCTAATTACCA
* *
673 TTTTCTTTCACTGATTACTCTATTACT
1 TTTACTTTTACTGATTAC-CT-TTACT
700 CCTTACCATT
Statistics
Matches: 159, Mismatches: 22, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
80 15 0.09
81 12 0.08
82 8 0.05
84 13 0.08
85 74 0.47
86 20 0.13
87 4 0.03
88 13 0.08
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.55
Consensus pattern (82 bp):
TTTACTTTTACTGATTACCTTTACTTTTTACTGATTACCATTTTACTTTTTACTAATTACCTTTA
ATCTTTTCTAATTACCA
Found at i:651 original size:35 final size:35
Alignment explanation
Indices: 612--733 Score: 97
Period size: 35 Copynumber: 3.4 Consensus size: 35
602 ACTGATCACT
*
612 ATTACTCTTTACTGATTACCATATTTTCTTTACTG
1 ATTACTCTTTACTCATTACCATATTTTCTTTACTG
**
647 ATTACTTTTTACTTTACTTTTTACC--ATTTTCTTTCACTG
1 ATTAC----T-CTTTACTCATTACCATATTTTCTTT-ACTG
* * *
686 ATTACTCTATTACTCCTTACCAT-TTCTGTTTACTG
1 ATTACTCT-TTACTCATTACCATATTTTCTTTACTG
*
721 ATTACTTTTTACT
1 ATTACTCTTTACT
734 ATTTCATTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
34 7 0.10
35 27 0.38
36 6 0.08
38 9 0.13
39 10 0.14
40 12 0.17
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.54
Consensus pattern (35 bp):
ATTACTCTTTACTCATTACCATATTTTCTTTACTG
Found at i:726 original size:27 final size:28
Alignment explanation
Indices: 694--754 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
684 TGATTACTCT
694 ATTACTCCTTACCATTTC-TGTTTACTG
1 ATTACTCCTTACCATTTCATGTTTACTG
** *
721 ATTACTTTTTACTATTTCATTGTTTACTG
1 ATTACTCCTTACCATTTCA-TGTTTACTG
750 ATTAC
1 ATTAC
755 CATTACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 15 0.52
29 14 0.48
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (28 bp):
ATTACTCCTTACCATTTCATGTTTACTG
Found at i:760 original size:35 final size:35
Alignment explanation
Indices: 721--787 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
711 CTGTTTACTG
* * *
721 ATTACTTTTTACTATTTCATTGTTTACTGATTACC
1 ATTACTTTTTACCATTTCACTCTTTACTGATTACC
*
756 ATTACTTTTTACCATTTTACTCTTTACTGATT
1 ATTACTTTTTACCATTTCACTCTTTACTGATT
788 GCCTTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.55
Consensus pattern (35 bp):
ATTACTTTTTACCATTTCACTCTTTACTGATTACC
Found at i:892 original size:26 final size:25
Alignment explanation
Indices: 862--993 Score: 133
Period size: 26 Copynumber: 5.0 Consensus size: 25
852 ACTATCGCGC
862 TTTTCTTACTCTTTTTACTGAATAT
1 TTTTCTTACTCTTTTTACTGAATAT
*
887 TATTTCCTACTCTTTTTACTG-ATGACT
1 T-TTTCTTACTCTTTTTACTGAAT-A-T
*
914 CTTTTCTTATTCTTTTTACTGAATAT
1 -TTTTCTTACTCTTTTTACTGAATAT
* *
940 TGTTCCTTACTCTTTTTACTG-ATGGCT
1 T-TTTCTTACTCTTTTTACTGAAT--AT
*
967 CTTTTCTTACTCTTTTTACTGATTAT
1 -TTTTCTTACTCTTTTTACTGAATAT
993 T
1 T
994 GATTACTAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
25 7 0.08
26 38 0.43
27 38 0.43
28 5 0.06
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.58
Consensus pattern (25 bp):
TTTTCTTACTCTTTTTACTGAATAT
Found at i:918 original size:53 final size:53
Alignment explanation
Indices: 861--994 Score: 216
Period size: 53 Copynumber: 2.5 Consensus size: 53
851 TACTATCGCG
*
861 CTTTTCTTACTCTTTTTACTGAATATTATTTCC-TACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATT-GTTCCTTACTCTTTTTACTGATGACT
* *
914 CTTTTCTTATTCTTTTTACTGAATATTGTTCCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTCCTTACTCTTTTTACTGATGACT
*
967 CTTTTCTTACTCTTTTTACTGATTATTG
1 CTTTTCTTACTCTTTTTACTGAATATTG
995 ATTACTAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
52 4 0.05
53 71 0.95
ACGTcount: A:0.16, C:0.19, G:0.07, T:0.57
Consensus pattern (53 bp):
CTTTTCTTACTCTTTTTACTGAATATTGTTCCTTACTCTTTTTACTGATGACT
Found at i:919 original size:27 final size:25
Alignment explanation
Indices: 861--989 Score: 136
Period size: 27 Copynumber: 4.9 Consensus size: 25
851 TACTATCGCG
861 CTTTTCTTACTCTTTTTACTGAATAT
1 CTTTTCTTACTCTTTTTACTG-ATAT
*
887 -TATTTCCTACTCTTTTTACTGATGACT
1 CT-TTTCTTACTCTTTTTACTGAT-A-T
*
914 CTTTTCTTATTCTTTTTACTGAATAT
1 CTTTTCTTACTCTTTTTACTG-ATAT
* *
940 -TGTTCCTTACTCTTTTTACTGATGGCT
1 CT-TTTCTTACTCTTTTTACTGAT--AT
967 CTTTTCTTACTCTTTTTACTGAT
1 CTTTTCTTACTCTTTTTACTGAT
990 TATTGATTAC
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
25 6 0.07
26 37 0.43
27 40 0.46
28 4 0.05
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.57
Consensus pattern (25 bp):
CTTTTCTTACTCTTTTTACTGATAT
Found at i:4175 original size:17 final size:17
Alignment explanation
Indices: 4150--4194 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4140 ACCAATGAGA
*
4150 AATGCAAAAATAGGATT
1 AATGAAAAAATAGGATT
*
4167 AATGAAAAAATATGATT
1 AATGAAAAAATAGGATT
*
4184 AATGAGAAAAT
1 AATGAAAAAAT
4195 GAAAATGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.24
Consensus pattern (17 bp):
AATGAAAAAATAGGATT
Found at i:5887 original size:17 final size:19
Alignment explanation
Indices: 5860--5897 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
5850 CACTAACTAA
*
5860 TTTCTTTTGTTGTTT-GCT
1 TTTCTTTTGTTCTTTCGCT
5878 TTTC-TTTGTTCTTTCGCT
1 TTTCTTTTGTTCTTTCGCT
5896 TT
1 TT
5898 GCATTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71
Consensus pattern (19 bp):
TTTCTTTTGTTCTTTCGCT
Found at i:8528 original size:16 final size:16
Alignment explanation
Indices: 8489--8533 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
8479 TTGCATTTAA
* *
8489 AAAAAATGAATGATAAT
1 AAAAAAT-AATAACAAT
*
8506 AATAAATAATAACAAT
1 AAAAAATAATAACAAT
8522 AAAAAATAATAA
1 AAAAAATAATAA
8534 AGATTTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAAATAATAACAAT
Done.