Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003724.1 Corchorus capsularis cultivar CVL-1 contig03732, 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, 621
Length: 1036
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Found at i:384 original size:22 final size:22
Alignment explanation
Indices: 356--714 Score: 118
Period size: 22 Copynumber: 17.0 Consensus size: 22
346 CTTTCTAATA
*
356 ACCATTTTTGCTTTTACTGATT
1 ACCATTTTTACTTTTACTGATT
*
378 ACTA-TTTTACCTTTTACTGATT
1 ACCATTTTTA-CTTTTACTGATT
**
400 A-C-TTTTTACTATTTTACTCTTT
1 ACCATTTTTAC--TTTTACTGATT
*
422 ACTGATAACCTTCTTACTTTTTACTGATT
1 AC-CAT----TT-TTAC-TTTTACTGATT
*
451 ACTA-TTTTACTCTTTACTGATT
1 ACCATTTTTACT-TTTACTGATT
* *
473 ACCA-TTTTGCTCTTACTGATT
1 ACCATTTTTACTTTTACTGATT
* *
494 ACC--TTTTACCCTTTACTGGTT
1 ACCATTTTTA-CTTTTACTGATT
* *
515 ACCA-TTTTGCTCTTACTGATT
1 ACCATTTTTACTTTTACTGATT
536 ACCA-TTTTACCTTTTACTGATT
1 ACCATTTTTA-CTTTTACTGATT
* *
558 ---ATTATCAC-TTT--T---T
1 ACCATTTTTACTTTTACTGATT
*
571 ACGA-TTTTACTCTTTACTGATT
1 ACCATTTTTACT-TTTACTGATT
* * *
593 ACCA-TTTTGCTCTTATTGATT
1 ACCATTTTTACTTTTACTGATT
614 ACCA-TTTTACCTTTTACTGATT
1 ACCATTTTTA-CTTTTACTGATT
* *
636 ---ATTATCAC-TTT--T---T
1 ACCATTTTTACTTTTACTGATT
* *
649 ACGA-TTTTACTCTTTACTAATT
1 ACCATTTTTACT-TTTACTGATT
* *
671 ACCA-TTTTGCTCTTACTGATT
1 ACCATTTTTACTTTTACTGATT
692 ACCA-TTTTACCTTTTACTGATT
1 ACCATTTTTA-CTTTTACTGATT
714 A
1 A
715 TTATCACTTT
Statistics
Matches: 253, Mismatches: 44, Indels: 80
0.67 0.12 0.21
Matches are distributed among these distances:
13 2 0.01
15 8 0.03
16 4 0.02
17 6 0.02
18 6 0.02
19 6 0.02
20 11 0.04
21 83 0.33
22 106 0.42
23 2 0.01
25 1 0.00
28 1 0.00
29 13 0.05
30 4 0.02
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (22 bp):
ACCATTTTTACTTTTACTGATT
Found at i:402 original size:29 final size:29
Alignment explanation
Indices: 369--427 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
359 ATTTTTGCTT
369 TTACTGATTACTATTTTAC-CTTTTACTGA
1 TTACTGATTACTATTTTACTC-TTTACTGA
**
398 TTACTTTTTACTATTTTACTCTTTACTGA
1 TTACTGATTACTATTTTACTCTTTACTGA
427 T
1 T
428 AACCTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (29 bp):
TTACTGATTACTATTTTACTCTTTACTGA
Found at i:408 original size:7 final size:7
Alignment explanation
Indices: 376--468 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
366 CTTTTACTGA
376 TTACTATT
1 TTACT-TT
*
384 TTACCTT
1 TTACTTT
**
391 TTACTGA
1 TTACTTT
398 TTACTTT
1 TTACTTT
405 TTACTATT
1 TTACT-TT
*
413 TTACTCT
1 TTACTTT
**
420 TTACTGA
1 TTACTTT
* *
427 TAACCTTC
1 TTA-CTTT
435 TTACTTT
1 TTACTTT
**
442 TTACTGA
1 TTACTTT
449 TTACTATT
1 TTACT-TT
*
457 TTACTCT
1 TTACTTT
464 TTACT
1 TTACT
469 GATTACCATT
Statistics
Matches: 63, Mismatches: 19, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
7 43 0.68
8 20 0.32
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTTT
Found at i:424 original size:44 final size:44
Alignment explanation
Indices: 386--556 Score: 140
Period size: 42 Copynumber: 4.0 Consensus size: 44
376 TTACTATTTT
**
386 ACCTT-TTACTGATTACTTTTTACTATTTTACTCTTTACTGATA
1 ACCTTCTTACTGATTACTGATTACTATTTTACTCTTTACTGATA
** *
429 ACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTGATT
1 ACCTTCTTACTGATTACTGATTACTATTTTACTCTTTACTGATA
* * * * * *
473 ACCATT-TTGCT-CTTACTGATTAC-CTTTTACCCTTTACTGGTT
1 ACC-TTCTTACTGATTACTGATTACTATTTTACTCTTTACTGATA
* * *
515 ACCATT-TTGCT-CTTACTGATTACCATTTTAC-CTTTTACTGAT
1 ACC-TTCTTACTGATTACTGATTACTATTTTACTC-TTTACTGAT
557 TATTATCACT
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
42 40 0.36
43 30 0.27
44 40 0.36
45 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.51
Consensus pattern (44 bp):
ACCTTCTTACTGATTACTGATTACTATTTTACTCTTTACTGATA
Found at i:443 original size:29 final size:30
Alignment explanation
Indices: 376--446 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
366 CTTTTACTGA
* *
376 TTACTATTTTAC-CTTTTACTGATTACTTT
1 TTACTATTTTACTCTTTTACTGATAACTTC
405 TTACTATTTTACTC-TTTACTGATAACCTTC
1 TTACTATTTTACTCTTTTACTGATAA-CTTC
435 TTACT-TTTTACT
1 TTACTATTTTACT
447 GATTACTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 29 0.76
30 9 0.24
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (30 bp):
TTACTATTTTACTCTTTTACTGATAACTTC
Found at i:517 original size:42 final size:42
Alignment explanation
Indices: 411--558 Score: 181
Period size: 42 Copynumber: 3.5 Consensus size: 42
401 CTTTTTACTA
* * * * *
411 TTTTACTCTTTACTGATAACC-TTCTTACTTTTTACTGATTACTA
1 TTTTACCCTTTACTGATTACCATT-TTGC-TCTTACTGATTAC-C
*
455 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACC
1 TTTTACCCTTTACTGATTACCATTTTGCTCTTACTGATTACC
*
497 TTTTACCCTTTACTGGTTACCATTTTGCTCTTACTGATTACC
1 TTTTACCCTTTACTGATTACCATTTTGCTCTTACTGATTACC
*
539 ATTTTACCTTTTACTGATTA
1 -TTTTACCCTTTACTGATTA
559 TTATCACTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
42 40 0.43
43 29 0.31
44 23 0.24
45 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (42 bp):
TTTTACCCTTTACTGATTACCATTTTGCTCTTACTGATTACC
Found at i:595 original size:78 final size:78
Alignment explanation
Indices: 497--770 Score: 485
Period size: 78 Copynumber: 3.5 Consensus size: 78
487 ACTGATTACC
* *
497 TTTTACCCTTTACTGGTTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
562 TCACTTTTTACGA
66 TCACTTTTTACGA
*
575 TTTTACTCTTTACTGATTACCATTTTGCTCTTATTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
640 TCACTTTTTACGA
66 TCACTTTTTACGA
*
653 TTTTACTCTTTACTAATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
718 TCACTTTTTACGA
66 TCACTTTTTACGA
* *
731 TTTTACTCTTTACTGATTACCATTTTACTTTTTACTGATT
1 TTTTACTCTTTACTGATTACCATTTTGC-TCTTACTGATT
771 TTTACTCTTT
Statistics
Matches: 187, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 177 0.95
79 10 0.05
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (78 bp):
TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGATTATTA
TCACTTTTTACGA
Found at i:614 original size:21 final size:22
Alignment explanation
Indices: 569--770 Score: 110
Period size: 22 Copynumber: 10.1 Consensus size: 22
559 TTATCACTTT
*
569 TTACGATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
* *
591 TTACCATTTTGCTC-TTATTGA
1 TTACCATTTTACTCTTTACTGA
612 TTACCATTTTAC-CTTTTACTGA
1 TTACCATTTTACTC-TTTACTGA
* *
634 TT---ATTATCACTTTTTAC-GA
1 TTACCATT-TTACTCTTTACTGA
*
653 TT----T--TACTCTTTACTAA
1 TTACCATTTTACTCTTTACTGA
*
669 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
690 TTACCATTTTAC-CTTTTACTGA
1 TTACCATTTTACTC-TTTACTGA
* *
712 TT---ATTATCACTTTTTAC-GA
1 TTACCATT-TTACTCTTTACTGA
731 TT----T--TACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
747 TTACCATTTTACTTTTTACTGA
1 TTACCATTTTACTCTTTACTGA
769 TT
1 TT
771 TTTACTCTTT
Statistics
Matches: 140, Mismatches: 18, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
15 16 0.11
16 7 0.05
18 2 0.01
19 14 0.10
20 20 0.14
21 34 0.24
22 47 0.34
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.52
Consensus pattern (22 bp):
TTACCATTTTACTCTTTACTGA
Found at i:622 original size:43 final size:38
Alignment explanation
Indices: 449--787 Score: 211
Period size: 35 Copynumber: 8.6 Consensus size: 38
439 TTTTTACTGA
* *
449 TTACTATTTTACTCTTTACTGATTACCATTTTGCTCTTACT
1 TTACGATTTTACTCTTTACTGATTACCATTTT-CACTT--T
* * * *
490 GATTAC-CTTTTACCCTTTACTGGTTACCATTTTGCTCTTACT
1 --TTACGATTTTACTCTTTACTGATTACCATTTT-CACTT--T
* *
532 GATTACCATTTTAC-CTTTTACTGATT---ATTATCACTTT
1 --TTACGATTTTACTC-TTTACTGATTACCATTTTCACTTT
*
569 TTACGATTTTACTCTTTACTGATTACCATTTTGCTCTTATT
1 TTACGATTTTACTCTTTACTGATTACCATTTT-CAC-T-TT
* *
610 GATTACCATTTTAC-CTTTTACTGATT---ATTATCACTTT
1 --TTACGATTTTACTC-TTTACTGATTACCATTTTCACTTT
* *
647 TTACGATTTTACTCTTTACTAATTACCATTTTGCTCTTACT
1 TTACGATTTTACTCTTTACTGATTACCATTTT-CACTT--T
* *
688 GATTACCATTTTAC-CTTTTACTGATT---ATTATCACTTT
1 --TTACGATTTTACTC-TTTACTGATTACCATTTTCACTTT
725 TTACGATTTTACTCTTTACTGATTACCATTTT-ACTTT
1 TTACGATTTTACTCTTTACTGATTACCATTTTCACTTT
*
762 TTACTGATTTTTACTCTTTACCGATT
1 TTAC-GA-TTTTACTCTTTACTGATT
788 TACTGATTAC
Statistics
Matches: 244, Mismatches: 24, Indels: 60
0.74 0.07 0.18
Matches are distributed among these distances:
35 62 0.25
36 3 0.01
37 13 0.05
38 15 0.06
39 33 0.14
40 13 0.05
41 3 0.01
42 42 0.17
43 60 0.25
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (38 bp):
TTACGATTTTACTCTTTACTGATTACCATTTTCACTTT
Found at i:657 original size:28 final size:28
Alignment explanation
Indices: 616--737 Score: 73
Period size: 28 Copynumber: 4.6 Consensus size: 28
606 TATTGATTAC
*
616 CATTTTAC-CTTTTACTGATTATTATCA
1 CATTTTACGATTTTACTGATTATTATCA
* ** * *
643 CTTTTTACGATTTTACTCTTTACTAATTA
1 CATTTTACGATTTTACTGATTA-TTATCA
* *
672 CCATTTT--GCTCTTACTG---ATTA-C-
1 -CATTTTACGATTTTACTGATTATTATCA
*
694 CATTTTAC-CTTTTACTGATTATTATCA
1 CATTTTACGATTTTACTGATTATTATCA
*
721 CTTTTTACGATTTTACT
1 CATTTTACGATTTTACT
738 CTTTACTGAT
Statistics
Matches: 69, Mismatches: 15, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
21 6 0.09
22 8 0.12
24 2 0.03
25 5 0.07
26 1 0.01
27 14 0.20
28 24 0.35
29 4 0.06
30 5 0.07
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (28 bp):
CATTTTACGATTTTACTGATTATTATCA
Found at i:682 original size:156 final size:160
Alignment explanation
Indices: 332--770 Score: 546
Period size: 156 Copynumber: 2.8 Consensus size: 160
322 CTCTTTACAG
* * * *
332 ATTACTATCTTACTCTTT-CTAATAACCATTTTTGCTTTTACTGATTACTATTTTACCTTTTACT
1 ATTAC-ATTTTACTCTTTACTAATTACCA-TTTTGCTCTTACTGATTACCATTTTACCTTTTACT
* * * *
396 G---A-T-T-ACTTTTTACTATTTTACTCTTTACTGATAACC-TTCTTACTTTTTACTGATTACT
64 GATTATTATCACTTTTTACGATTTTACTCTTTACTGATTACCATT-TTACTTCTTACTGATTACC
* *
454 ATTTTACTCTTTACTGATTACCATTTTGCTCTTACT
128 ATTTTACTCTTTACTGATT--CATTATGCACTTA-T
* * **
490 GATTACCTTTTACCCTTTACTGGTTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTG
1 -ATTACATTTTACTCTTTACTAATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTG
* *
555 ATTATTATCACTTTTTACGATTTTACTCTTTACTGATTACCATTTTGC-TCTTATTGATTACCAT
65 ATTATTATCACTTTTTACGATTTTACTCTTTACTGATTACCATTTTACTTCTTACTGATTACCAT
619 TTTAC-CTTTTACTGATT-ATTAT-CACTT-T
130 TTTACTC-TTTACTGATTCATTATGCACTTAT
647 -TTACGATTTTACTCTTTACTAATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTG
1 ATTAC-ATTTTACTCTTTACTAATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTG
*
711 ATTATTATCACTTTTTACGATTTTACTCTTTACTGATTACCATTTTACTTTTTACTGATT
65 ATTATTATCACTTTTTACGATTTTACTCTTTACTGATTACCATTTTACTTCTTACTGATT
771 TTTACTCTTT
Statistics
Matches: 246, Mismatches: 23, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
155 4 0.02
156 102 0.41
157 10 0.04
158 43 0.17
159 16 0.07
160 4 0.02
161 1 0.00
162 2 0.01
163 29 0.12
164 33 0.13
165 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (160 bp):
ATTACATTTTACTCTTTACTAATTACCATTTTGCTCTTACTGATTACCATTTTACCTTTTACTGA
TTATTATCACTTTTTACGATTTTACTCTTTACTGATTACCATTTTACTTCTTACTGATTACCATT
TTACTCTTTACTGATTCATTATGCACTTAT
Found at i:797 original size:15 final size:16
Alignment explanation
Indices: 739--797 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 16
729 GATTTTACTC
739 TTTACTGATTACC-AT
1 TTTACTGATTACCGAT
** *
754 TTTACTTTTTACTGATT
1 TTTACTGATTACCGA-T
**
771 TTTACTCTTTACCGA-
1 TTTACTGATTACCGAT
786 TTTACTGATTAC
1 TTTACTGATTAC
798 TTCTTTTACT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 20 0.57
16 1 0.03
17 14 0.40
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTACTGATTACCGAT
Found at i:830 original size:40 final size:42
Alignment explanation
Indices: 786--878 Score: 138
Period size: 40 Copynumber: 2.3 Consensus size: 42
776 TCTTTACCGA
786 TTTACTGATTACTTCTTTTACTCTT-ACTC-TTAATTAC-CAT
1 TTTACTGATTACTTCTTTTACT-TTGACTCTTTAATTACTCAT
*
826 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTGAT
1 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
*
868 TTCACTGATTA
1 TTTACTGATTA
879 ATCTCTTACC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 2 0.04
40 26 0.54
41 8 0.17
42 12 0.25
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (42 bp):
TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTACTCAT
Found at i:893 original size:41 final size:39
Alignment explanation
Indices: 783--917 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
773 TACTCTTTAC
783 CGATTTACTGATTACTTCTTTTACTCTT-ACTCTTAATTA
1 CGATTTACTGATTACTTCTTTTAC-CTTGACTCTTAATTA
* *
822 CCATTTTACTGATTACTTCTTTTACTTTGACTCTTTAATTA
1 CGA-TTTACTGATTACTTCTTTTACCTTGACTC-TTAATTA
* * * *
863 CTGATTTCACTGATTA-ATCTCTTACCTTGACTATTGATTA
1 C-GATTT-ACTGATTACTTCTTTTACCTTGACTCTTAATTA
* *
903 TCAAATTACTGATTA
1 -CGATTTACTGATTA
918 ATCCCTTTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
39 12 0.15
40 34 0.43
41 25 0.31
42 9 0.11
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (39 bp):
CGATTTACTGATTACTTCTTTTACCTTGACTCTTAATTA
Done.