Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008438.1 Corchorus capsularis cultivar CVL-1 contig08459, 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: 4139
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Found at i:2582 original size:22 final size:21
Alignment explanation
Indices: 2542--2857 Score: 119
Period size: 22 Copynumber: 14.3 Consensus size: 21
2532 GGAATCACTA
2542 TTTTACTGATTA-TATTTTAC
1 TTTTACTGATTACTATTTTAC
2562 TTTGTACTGATTACTATTTTAC
1 TTT-TACTGATTACTATTTTAC
*
2584 TCTTT-CAGA-TACCT-TTTTAC
1 T-TTTACTGATTA-CTATTTTAC
*
2604 TTTTTACTGATTACCATTTTACTC
1 -TTTTACTGATTACTATTTTA--C
** **
2628 TTTTACTTTTTACTGA-TTGCC
1 TTTTACTGATTACT-ATTTTAC
* **
2649 TTTTTGCTTTTTACTGATTACCTTTTTAC
1 -TTTTACTGATTAC----TA---TTTTAC
* ***
2678 TTCTTGCTGATTAGCCTTTTAC
1 TT-TTACTGATTACTATTTTAC
*
2700 TCTTTACTGATCACCT-TTTTAC
1 T-TTTACTGATTA-CTATTTTAC
* * *
2722 TCTTACTGATTTC-CTTTTAC
1 TTTTACTGATTACTATTTTAC
* *
2742 TTCTTACTTATTACTTTTTTTAC
1 TT-TTACTGATTAC-TATTTTAC
* *
2765 TCTTACTGATTATTA-TTTAC
1 TTTTACTGATTACTATTTTAC
* *
2785 TTTTTACTGACTATTATTTTAC
1 -TTTTACTGATTACTATTTTAC
* * *
2807 TCTTATTGATTACCT-TCTTAC
1 TTTTACTGATTA-CTATTTTAC
2828 TTTTTACTGATTACTATTTTAC
1 -TTTTACTGATTACTATTTTAC
2850 TCTTTACT
1 T-TTTACT
2858 AATTTACCAT
Statistics
Matches: 222, Mismatches: 41, Indels: 64
0.68 0.13 0.20
Matches are distributed among these distances:
20 27 0.12
21 68 0.31
22 87 0.39
23 23 0.10
24 2 0.01
25 1 0.00
26 1 0.00
28 2 0.01
29 11 0.05
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTACTGATTACTATTTTAC
Found at i:2631 original size:8 final size:7
Alignment explanation
Indices: 2596--2679 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
2586 TTTCAGATAC
2596 CTTTTTA
1 CTTTTTA
2603 CTTTTTA
1 CTTTTTA
**
2610 CTGATTA
1 CTTTTTA
*
2617 CCATTTTA
1 -CTTTTTA
2625 CTCTTTTA
1 CT-TTTTA
2633 CTTTTTA
1 CTTTTTA
* **
2640 CTGATTGC
1 CT-TTTTA
*
2648 CTTTTTG
1 CTTTTTA
2655 CTTTTTA
1 CTTTTTA
**
2662 CTGATTA
1 CTTTTTA
2669 CCTTTTTA
1 -CTTTTTA
2677 CTT
1 CTT
2680 CTTGCTGATT
Statistics
Matches: 56, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
7 36 0.64
8 20 0.36
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (7 bp):
CTTTTTA
Found at i:2634 original size:30 final size:29
Alignment explanation
Indices: 2596--2663 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
2586 TTTCAGATAC
2596 CTTTTTACTTTTTACTGATTACCATTTTA
1 CTTTTTACTTTTTACTGATTACCATTTTA
* * *
2625 CTCTTTTACTTTTTACTGATTGCCTTTTTG
1 CT-TTTTACTTTTTACTGATTACCATTTTA
2655 CTTTTTACT
1 CTTTTTACT
2664 GATTACCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (29 bp):
CTTTTTACTTTTTACTGATTACCATTTTA
Found at i:2638 original size:15 final size:14
Alignment explanation
Indices: 2596--2679 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 14
2586 TTTCAGATAC
2596 CTTTTTACTTTTTA
1 CTTTTTACTTTTTA
** *
2610 CTGATTACCATTTTA
1 CTTTTTA-CTTTTTA
2625 CTCTTTTACTTTTTA
1 CT-TTTTACTTTTTA
* ** *
2640 CTGATTGCCTTTTTG
1 CT-TTTTACTTTTTA
**
2655 CTTTTTACTGATTA
1 CTTTTTACTTTTTA
2669 CCTTTTTACTT
1 -CTTTTTACTT
2680 CTTGCTGATT
Statistics
Matches: 49, Mismatches: 18, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
14 11 0.22
15 35 0.71
16 3 0.06
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (14 bp):
CTTTTTACTTTTTA
Found at i:2659 original size:21 final size:21
Alignment explanation
Indices: 2628--2904 Score: 183
Period size: 22 Copynumber: 12.8 Consensus size: 21
2618 CATTTTACTC
*
2628 TTTTACTTTTTACTGATTGCCT
1 TTTTAC-TTTTACTGATTACCT
*
2650 TTTTGCTTTTTACTGATTACCT
1 TTTTAC-TTTTACTGATTACCT
*
2672 TTTTACTTCTTGCTGATTAGCC-
1 TTTTACTT-TTACTGATTA-CCT
*
2694 TTTTACTCTTTACTGATCACCT
1 TTTTACT-TTTACTGATTACCT
* *
2716 TTTTACTCTTACTGATTTCC-
1 TTTTACTTTTACTGATTACCT
* *
2736 TTTTACTTCTTACTTATTACTTT
1 TTTTACTT-TTACTGATTAC-CT
*
2759 TTTTACTCTTACTGATTA--T
1 TTTTACTTTTACTGATTACCT
* *
2778 TATTTACTTTTTACTGACTA-TT
1 T-TTTAC-TTTTACTGATTACCT
* *
2800 ATTTTACTCTTATTGATTACCT
1 -TTTTACTTTTACTGATTACCT
*
2822 TCTTACTTTTTACTGATTA-CT
1 TTTTAC-TTTTACTGATTACCT
*
2843 ATTTTACTCTTTACTAATTTACCAT
1 -TTTTACT-TTTACTGA-TTACC-T
* * *
2868 TTTTCCCTTT-CAGA-TACCT
1 TTTTACTTTTACTGATTACCT
*
2887 TTTTTCTTTTTACTGATT
1 TTTTAC-TTTTACTGATT
2905 GCATGCTATT
Statistics
Matches: 201, Mismatches: 33, Indels: 42
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.04
20 19 0.09
21 53 0.26
22 97 0.48
23 17 0.08
24 6 0.03
25 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTACTTTTACTGATTACCT
Found at i:2762 original size:43 final size:42
Alignment explanation
Indices: 2622--2862 Score: 218
Period size: 43 Copynumber: 5.6 Consensus size: 42
2612 GATTACCATT
* * * *
2622 TTACTCTTTTACTTTTTACTGATTGCCTTTTTGCTTTTTACTGA
1 TTACTTTTTTAC-TCTTACTGATTTCC-TTTTACTTTTTACTGA
* * * *
2666 TTACCTTTTTACTTCTTGCTGATTAGCCTTTTACTCTTTACTGA
1 TTACTTTTTTAC-TCTTACTGATT-TCCTTTTACTTTTTACTGA
* * * *
2710 TCACCTTTTTACTCTTACTGATTTCCTTTTACTTCTTACTTA
1 TTACTTTTTTACTCTTACTGATTTCCTTTTACTTTTTACTGA
2752 TTACTTTTTTTACTCTTACTGATTAT--TATTTACTTTTTACTGA
1 TTAC-TTTTTTACTCTTACTGATT-TCCT-TTTACTTTTTACTGA
* * *
2795 CTA-TTATTTTACTCTTATTGATTACCTTCTTACTTTTTACTGA
1 TTACTT-TTTTACTCTTACTGATTTCCTT-TTACTTTTTACTGA
* *
2838 TTACTATTTTACTCTTTACTAATTT
1 TTACTTTTTTACTC-TTACTGATTT
2863 ACCATTTTTC
Statistics
Matches: 163, Mismatches: 24, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
41 2 0.01
42 36 0.22
43 68 0.42
44 54 0.33
45 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (42 bp):
TTACTTTTTTACTCTTACTGATTTCCTTTTACTTTTTACTGA
Found at i:2792 original size:64 final size:62
Alignment explanation
Indices: 2655--2862 Score: 156
Period size: 64 Copynumber: 3.2 Consensus size: 62
2645 TGCCTTTTTG
* * * * *
2655 CTTTTTACTGATTACCTTTTTACTTCTTGCTGATTAGCCTTTTACTCTTTACTGATCACCTT-TT
1 CTTTTTACTGATTTCC-TTTTACTTCTTACTTATTA-CTTTTTACTC-TTACTGATTA--TTATT
2719 TA
61 TA
*
2721 C-TCTTACTGATTTCCTTTTACTTCTTACTTATTACTTTTTTTACTCTTACTGATTATTATTTA
1 CTTTTTACTGATTTCCTTTTACTTCTTACTTATTAC--TTTTTACTCTTACTGATTATTATTTA
* * * *
2784 CTTTTTACTGACTATT-ATTTTAC-TCTTA-TTGATTACCTTCTTACTTTTTACTGATTACTATT
1 CTTTTTACTGA-T-TTCCTTTTACTTCTTACTT-ATTA-CTTTTTAC-TCTTACTGATTATTA-T
2846 TTA
60 TTA
* *
2849 CTCTTTACTAATTT
1 CTTTTTACTGATTT
2863 ACCATTTTTC
Statistics
Matches: 119, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
62 2 0.02
63 16 0.13
64 57 0.48
65 41 0.34
66 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (62 bp):
CTTTTTACTGATTTCCTTTTACTTCTTACTTATTACTTTTTACTCTTACTGATTATTATTTA
Found at i:3160 original size:55 final size:55
Alignment explanation
Indices: 3099--3324 Score: 346
Period size: 55 Copynumber: 4.1 Consensus size: 55
3089 CTTAGTTATC
*
3099 GATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
1 GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
* *
3154 GATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTACTTAATTATT
1 GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
* *
3209 GATTTACTGATTACTACTACTTTGACTCTGATTAATCTCCTTTTTACTTAATTATT
1 GATTTACTGATTACTACTACCTTGACTCTGATTAATCT-CTTTTTACTTAATTACT
** * *
3265 GATTTACTGATTACTGTTA-CTATGACTCTGATTTACCTCTTTTTACTTAATTACT
1 GATTTACTGATTACTACTACCT-TGACTCTGATTAATCTCTTTTTACTTAATTACT
3320 GATTT
1 GATTT
3325 CTCCTTAATA
Statistics
Matches: 160, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
55 112 0.70
56 48 0.30
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (55 bp):
GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
Found at i:3184 original size:29 final size:29
Alignment explanation
Indices: 3152--3241 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
3142 TACTTAATTA
3152 CTGATTTACTGATTACTACTACTTTGACT
1 CTGATTTACTGATTACTACTACTTTGACT
* * ** *
3181 CTGATTAATCT-CTTTTTACTTA-ATT-A-T
1 CTGATTTA-CTGATTACTAC-TACTTTGACT
3208 -TGATTTACTGATTACTACTACTTTGACT
1 CTGATTTACTGATTACTACTACTTTGACT
3236 CTGATT
1 CTGATT
3242 AATCTCCTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 4 0.09
26 13 0.30
27 2 0.05
28 2 0.05
29 19 0.43
30 4 0.09
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (29 bp):
CTGATTTACTGATTACTACTACTTTGACT
Found at i:3292 original size:111 final size:110
Alignment explanation
Indices: 3089--3324 Score: 364
Period size: 111 Copynumber: 2.1 Consensus size: 110
3079 CATTTTAACT
* * *
3089 CTTAGTTATCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
1 CTTAATTATTGATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
* *
3154 GATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
66 GATTTACTGATTACTACTACTATGACTCTGATTAACCTCTTTTTA
* *
3199 CTTAATTATTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCCTTTTTACTTAATTAT
1 CTTAATTATTGATTTACTGATTACTACTACCTTGACTCTGATTAATCT-CTTTTTACTTAATTAC
** *
3264 TGATTTACTGATTACTGTTACTATGACTCTGATTTACCTCTTTTTA
65 TGATTTACTGATTACTACTACTATGACTCTGATTAACCTCTTTTTA
*
3310 CTTAATTACTGATTT
1 CTTAATTATTGATTT
3325 CTCCTTAATA
Statistics
Matches: 114, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 44 0.39
111 70 0.61
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (110 bp):
CTTAATTATTGATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACT
GATTTACTGATTACTACTACTATGACTCTGATTAACCTCTTTTTA
Done.