Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000207.1 Corchorus capsularis cultivar CVL-1 contig00207, 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, 602
Length: 1004
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Found at i:482 original size:21 final size:21
Alignment explanation
Indices: 425--482 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
415 TTTACTGAAT
* *
425 TACTGATTACCATTACTATTT
1 TACTGATTACTATTACTATTG
* *
446 TACTGATTATTTTTACT-TTG
1 TACTGATTACTATTACTATTG
466 TACTGATTACTAGTTAC
1 TACTGATTACTA-TTAC
483 CATTTTATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.50
Consensus pattern (21 bp):
TACTGATTACTATTACTATTG
Found at i:570 original size:7 final size:7
Alignment explanation
Indices: 558--785 Score: 99
Period size: 7 Copynumber: 33.6 Consensus size: 7
548 CTTTACTGGA
558 TTACTCT
1 TTACTCT
565 TTACTCT
1 TTACTCT
* *
572 TCAC-CA
1 TTACTCT
578 TT-CTTCT
1 TTAC-TCT
585 TTACTGAC-
1 TTACT--CT
593 TT-CTCT
1 TTACTCT
*
599 TCACTCT
1 TTACTCT
*
606 TTACTAT
1 TTACTCT
**
613 TTTTTCT
1 TTACTCT
**
620 TTACTGA
1 TTACTCT
627 TTACTCT
1 TTACTCT
634 TTACTC-
1 TTACTCT
640 -TACTCT
1 TTACTCT
646 TTACTCT
1 TTACTCT
653 TTAC-CAT
1 TTACTC-T
**
660 TTTTTCT
1 TTACTCT
**
667 TTACTGA
1 TTACTCT
674 TTACTC-
1 TTACTCT
680 TT-CTCT
1 TTACTCT
686 TTACTCT
1 TTACTCT
693 TTACTCT
1 TTACTCT
*
700 TTACCCT
1 TTACTCT
*
707 TT-TTCT
1 TTACTCT
**
713 TTACTGA
1 TTACTCT
720 TTACTCTT
1 TTACTC-T
*
728 TTACTTT
1 TTACTCT
*
735 TTACCATTT
1 TTA-C-TCT
744 TTACT-T
1 TTACTCT
**
750 TGT--TGA
1 T-TACTCT
756 TTACTCT
1 TTACTCT
763 TTA--CT
1 TTACTCT
768 TTACTCT
1 TTACTCT
775 TTACTCT
1 TTACTCT
782 TTAC
1 TTAC
786 CATTTTTCTT
Statistics
Matches: 163, Mismatches: 35, Indels: 46
0.67 0.14 0.19
Matches are distributed among these distances:
5 17 0.10
6 15 0.09
7 113 0.69
8 11 0.07
9 7 0.04
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:620 original size:35 final size:35
Alignment explanation
Indices: 513--767 Score: 175
Period size: 35 Copynumber: 7.6 Consensus size: 35
503 GCCATTACTT
* *
513 TTTACTGATTAATATTTTACTCTTTACCATTTTTTC
1 TTTACTGATTACT-CTTTACTCTTTACCATTTTTTC
* *
549 TTTACTGGATTACTCTTTACTCTTCACCA-TTCTTC
1 TTTACT-GATTACTCTTTACTCTTTACCATTTTTTC
* *
584 TTTACTGACTT-CTCTTCACTCTTTACTATTTTTTC
1 TTTACTGA-TTACTCTTTACTCTTTACCATTTTTTC
**
619 TTTACTGATTACTCTTTACTC--TACTC-TTTACTC
1 TTTACTGATTACTCTTTACTCTTTAC-CATTTTTTC
* * **
652 TTTAC-CA-T--T-TTT--TCTTTACTGA-TTACTC
1 TTTACTGATTACTCTTTACTCTTTAC-CATTTTTTC
*
680 TTCT-CT--TTACTCTTTACTCTTTACC-CTTTTTC
1 TT-TACTGATTACTCTTTACTCTTTACCATTTTTTC
* *
712 TTTACTGATTACTCTTTTACTTTTTACCATTTTTAC
1 TTTACTGATTACTC-TTTACTCTTTACCATTTTTTC
**
748 TTTGTTGATTACTCTTTACT
1 TTTACTGATTACTCTTTACT
768 TTACTCTTTA
Statistics
Matches: 175, Mismatches: 22, Indels: 45
0.72 0.09 0.19
Matches are distributed among these distances:
26 2 0.01
28 17 0.10
29 2 0.01
30 1 0.01
31 5 0.03
32 9 0.05
33 20 0.11
34 24 0.14
35 53 0.30
36 36 0.21
37 6 0.03
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACCATTTTTTC
Found at i:645 original size:12 final size:12
Alignment explanation
Indices: 628--652 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
618 CTTTACTGAT
628 TACTCTTTACTC
1 TACTCTTTACTC
640 TACTCTTTACTC
1 TACTCTTTACTC
652 T
1 T
653 TTACCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTCTTTACTC
Found at i:649 original size:19 final size:19
Alignment explanation
Indices: 627--700 Score: 85
Period size: 19 Copynumber: 3.8 Consensus size: 19
617 TCTTTACTGA
*
627 TTACTCTTTACTCTACTCT
1 TTACTCTTTACTCTTCTCT
* *
646 TTACTCTTTACCATTTTTTCT
1 TTACTCTTTA-C-TCTTCTCT
**
667 TTACTGATTACTCTTCTCT
1 TTACTCTTTACTCTTCTCT
686 TTACTCTTTACTCTT
1 TTACTCTTTACTCTT
701 TACCCTTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 29 0.66
20 2 0.05
21 13 0.30
ACGTcount: A:0.15, C:0.27, G:0.01, T:0.57
Consensus pattern (19 bp):
TTACTCTTTACTCTTCTCT
Found at i:650 original size:40 final size:40
Alignment explanation
Indices: 601--779 Score: 125
Period size: 40 Copynumber: 4.2 Consensus size: 40
591 ACTTCTCTTC
601 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
1 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
641 ACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTTT
1 ACTCTTTA--C--T---ATTTTTTCTTTACTGATTA-----CTCTTTACTC--T
**
695 ACTCTTTAC-CCTTTTTCTTTACTGATTACTC-TT--T-T
1 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
* * * ** *
730 ACTTTTTACCATTTTTACTTTGTTGATTACTCTTTACTTT
1 ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
770 ACTCTTTACT
1 ACTCTTTACT
780 CTTTACCATT
Statistics
Matches: 110, Mismatches: 10, Indels: 38
0.70 0.06 0.24
Matches are distributed among these distances:
35 9 0.08
36 17 0.15
37 2 0.02
38 1 0.01
39 1 0.01
40 19 0.17
41 3 0.03
42 1 0.01
44 1 0.01
46 17 0.15
47 19 0.17
52 11 0.10
54 9 0.08
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.58
Consensus pattern (40 bp):
ACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCT
Found at i:652 original size:47 final size:45
Alignment explanation
Indices: 595--809 Score: 225
Period size: 47 Copynumber: 4.9 Consensus size: 45
585 TTACTGACTT
*
595 CTCTTCACTCTTTACTATTTTTTCTTTACTGATTACTCTTTACTCTA
1 CTCTTTACTCTTTAC-ATTTTTTCTTTACTGATTACTCTTT-CTCTA
*
642 CTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTA
1 CTCTTTACTCTTTA-CATTTTTTCTTTACTGATTACTCTT-TCTCTA
**
689 CTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTC-TT-T-TA
1 CTCTTTACTCTTTACATTTTTTCTTTACTGATTACTCTTTCTCTA
* * ** *
731 CTTTTTA--C----CATTTTTACTTTGTTGATTACTCTTTACTTTA
1 CTCTTTACTCTTTACATTTTTTCTTTACTGATTACTCTTT-CTCTA
771 CTCTTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTT
1 CTCTTTACTCTTTA-CATTTTTTCTTTACTGATTACTCTT
810 GTCTGAATAC
Statistics
Matches: 141, Mismatches: 14, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
36 18 0.13
37 2 0.01
39 1 0.01
40 9 0.06
42 9 0.06
43 1 0.01
44 1 0.01
45 1 0.01
46 40 0.28
47 57 0.40
48 2 0.01
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (45 bp):
CTCTTTACTCTTTACATTTTTTCTTTACTGATTACTCTTTCTCTA
Found at i:736 original size:27 final size:26
Alignment explanation
Indices: 674--736 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
664 TCTTTACTGA
* * *
674 TTACTCTTCTCTTTACTCTTTACTCT
1 TTACTTTTTTCTTTACTCATTACTCT
* *
700 TTACCCTTTTTCTTTACTGATTACTCTT
1 TTA-CTTTTTTCTTTACTCATTACTC-T
728 TTACTTTTT
1 TTACTTTTT
737 ACCATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 22 0.76
28 4 0.14
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.60
Consensus pattern (26 bp):
TTACTTTTTTCTTTACTCATTACTCT
Found at i:738 original size:82 final size:81
Alignment explanation
Indices: 528--809 Score: 331
Period size: 82 Copynumber: 3.4 Consensus size: 81
518 TGATTAATAT
* *
528 TTTACTCTTTACCATTTTTTCTTTACTGGATTACTCTTTACTCTTCACCA-TTCTTCTTTACTGA
1 TTTACTCTTTACCA-TTTTTCTTTACT-GATTACTCTTTACTCTTTACCATTTTTTCTTTACTGA
*
592 CTT-CTCTTCACTCTTTACTA
64 -TTACTCTT--CTCTTTACTC
** * ** *
612 TTTTTTCTTTACTGATTACTCTTTACT--CTACTCTTTACTCTTTACCATTTTTTCTTTACTGAT
1 TTTACTCTTTAC-CATTTTTCTTTACTGATTACTCTTTACTCTTTACCATTTTTTCTTTACTGAT
675 TACTCTTCTCTTTACTC
65 TACTCTTCTCTTTACTC
* * * **
692 TTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTTACTTTGTTGAT
1 TTTACTCTTTACCATTTTTCTTTACTGATTACTC-TTTACTCTTTACCATTTTTTCTTTACTGAT
757 TACTCTT-TACTTTACTC
65 TACTCTTCT-CTTTACTC
774 TTTACTCTTTACCATTTTTCTTTACTGATTACTCTT
1 TTTACTCTTTACCATTTTTCTTTACTGATTACTCTT
810 GTCTGAATAC
Statistics
Matches: 170, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
79 10 0.06
80 19 0.11
81 28 0.16
82 92 0.54
84 20 0.12
85 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.56
Consensus pattern (81 bp):
TTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACCATTTTTTCTTTACTGATT
ACTCTTCTCTTTACTC
Found at i:821 original size:48 final size:49
Alignment explanation
Indices: 710--824 Score: 148
Period size: 47 Copynumber: 2.4 Consensus size: 49
700 TTACCCTTTT
* **
710 TCTTTACTGATTACTCTTTTACTTTTTACCATTTTTACTTTGTTGATTAC
1 TCTTTACTGATTACTC-TTTACTCTTTACCATTTTTACTTTACTGATTAC
760 TCTTTACT--TTACTCTTTACTCTTTACCATTTTT-CTTTACTGATTAC
1 TCTTTACTGATTACTCTTTACTCTTTACCATTTTTACTTTACTGATTAC
*
806 TCTTGT-CTGAATACTCTTT
1 TCTT-TACTGATTACTCTTT
825 TACTTTTTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
46 17 0.29
47 19 0.33
48 14 0.24
50 8 0.14
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (49 bp):
TCTTTACTGATTACTCTTTACTCTTTACCATTTTTACTTTACTGATTAC
Found at i:885 original size:59 final size:59
Alignment explanation
Indices: 801--927 Score: 227
Period size: 59 Copynumber: 2.2 Consensus size: 59
791 TTCTTTACTG
* *
801 ATTACTCTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATGACCATTTCCTTTGCTA
1 ATTACTCTTGTCTAAATACTATTTTACTTTTTCTTTACTGATGACCATTTCCTTTGCTA
*
860 ATTACTCTTGTCTAAATACTATTTTACTTTTTCTTTACTGATGACCATTTCCTTTGCTG
1 ATTACTCTTGTCTAAATACTATTTTACTTTTTCTTTACTGATGACCATTTCCTTTGCTA
919 ATTACTCTT
1 ATTACTCTT
928 TACTCTTTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.20, C:0.21, G:0.08, T:0.51
Consensus pattern (59 bp):
ATTACTCTTGTCTAAATACTATTTTACTTTTTCTTTACTGATGACCATTTCCTTTGCTA
Found at i:932 original size:7 final size:7
Alignment explanation
Indices: 920--944 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
910 CCTTTGCTGA
920 TTACTCT
1 TTACTCT
927 TTACTCT
1 TTACTCT
934 TTACTCT
1 TTACTCT
941 TTAC
1 TTAC
945 CATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
TTACTCT
Done.