Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016471.1 Corchorus capsularis cultivar CVL-1 contig16492, 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: 11510
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Found at i:2722 original size:21 final size:22
Alignment explanation
Indices: 2698--2753 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
2688 TTTTACTGAA
2698 TTACTGATTACTATCACTA-TT
1 TTACTGATTACTATCACTATTT
**
2719 TTACTGATTA-T-TCTTTATTT
1 TTACTGATTACTATCACTATTT
2739 TGTACTGATTACTAT
1 T-TACTGATTACTAT
2754 TCTACTCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 19 0.66
22 1 0.03
23 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (22 bp):
TTACTGATTACTATCACTATTT
Found at i:2792 original size:22 final size:22
Alignment explanation
Indices: 2717--3121 Score: 277
Period size: 22 Copynumber: 18.5 Consensus size: 22
2707 ACTATCACTA
2717 TTTTACTGATTA--TTCTTTA-T
1 TTTTACTGATTACCTT-TTTACT
*
2737 TTTGTACTGATTA-CTATTCTAC-
1 TTT-TACTGATTACCT-TTTTACT
* * *
2759 TCTTATTGATTACCTTCTTACT
1 TTTTACTGATTACCTTTTTACT
*
2781 TTTTACTGATTACCATTTTACT
1 TTTTACTGATTACCTTTTTACT
* * *
2803 CATTTACTGATTACTATTTTCTGCTCCTT
1 -TTTTACTGATTAC--CTTT-T--TAC-T
2832 TTTTACTGATTA-CTCTTTTACT
1 TTTTACTGATTACCT-TTTTACT
* *
2854 TTTTACTGATTGCC-TTTTGCT
1 TTTTACTGATTACCTTTTTACT
2875 TTTTACTGATTACCTTTTTACT
1 TTTTACTGATTACCTTTTTACT
* * *
2897 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTACCTTTTTACT
* *
2919 CTTTACTGATCACCTTTTTAC-
1 TTTTACTGATTACCTTTTTACT
* *
2940 TCTTACTGATTTCC-TTTTACT
1 TTTTACTGATTACCTTTTTACT
* * *
2961 TCTTACTTATTACTTTTTTAC-
1 TTTTACTGATTACCTTTTTACT
*
2982 TCTTACTGATTA-CTATTTTACT
1 TTTTACTGATTACCT-TTTTACT
* *
3004 TTTTACTGACTA-TTATTTTACT
1 TTTTACTGATTACCT-TTTTACT
* *
3026 CTTGT--TGATTACCTTCTTACT
1 -TTTTACTGATTACCTTTTTACT
3047 TTTTACTGATTA-CTATTTTACT
1 TTTTACTGATTACCT-TTTTACT
* * * *
3069 CTTTACTAATTACCATTTTACC
1 TTTTACTGATTACCTTTTTACT
* *
3091 CTTT-CCGA-TACCTTTTTACT
1 TTTTACTGATTACCTTTTTACT
3111 TTTTACTGATT
1 TTTTACTGATT
3122 GCACGCTATT
Statistics
Matches: 301, Mismatches: 56, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
20 26 0.09
21 96 0.32
22 138 0.46
23 20 0.07
25 4 0.01
26 3 0.01
28 13 0.04
29 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTACTGATTACCTTTTTACT
Found at i:2803 original size:43 final size:43
Alignment explanation
Indices: 2719--3082 Score: 292
Period size: 43 Copynumber: 8.3 Consensus size: 43
2709 TATCACTATT
* *
2719 TTACTGATTA--TTCTTTA-TTTTGTACTGATTACTATTCTACTC
1 TTACTGATTACCTTC-TTACTTTT-TACTGATTACCATTTTACTC
*
2761 TTATTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
1 TTACTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
* * *
2804 ATTTACTGATTACTATTTTCTGCTCCTTTTTTACTGATTACTC-TTTTACTTT
1 --TTACTGATTAC---CTTCT--TAC-TTTTTACTGATTAC-CATTTTAC-TC
* * *
2856 TTACTGATTGCCTT-TTGCTTTTTACTGATTACCTTTTTACTTC
1 TTACTGATTACCTTCTTACTTTTTACTGATTACCATTTTAC-TC
* * * * * *
2899 TTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTC
1 TTACTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
* * * **
2942 TTACTGATTTCCTT-TTACTTCTTACTTATTACTTTTTTACTC
1 TTACTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
* * **
2984 TTACTGATTA-CTATTTTACTTTTTACTGACTATTATTTTACTC
1 TTACTGATTACCT-TCTTACTTTTTACTGATTACCATTTTACTC
** *
3027 TTGTTGATTACCTTCTTACTTTTTACTGATTACTATTTTACTC
1 TTACTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
*
3070 TTTACTAATTACC
1 -TTACTGATTACC
3083 ATTTTACCCT
Statistics
Matches: 264, Mismatches: 39, Indels: 36
0.78 0.12 0.11
Matches are distributed among these distances:
41 2 0.01
42 43 0.16
43 125 0.47
44 43 0.16
45 10 0.04
46 1 0.00
47 2 0.01
48 4 0.02
50 12 0.05
51 20 0.08
52 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (43 bp):
TTACTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
Found at i:3108 original size:150 final size:149
Alignment explanation
Indices: 2834--3117 Score: 342
Period size: 150 Copynumber: 1.9 Consensus size: 149
2824 TGCTCCTTTT
* * * * *
2834 TTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTGCTTTTTACTGATTACCTTTTTACTTC
1 TTACTGATTACTATTTTACTTTTTACTGATTGCATTTTACTTTGTA-TGATTACCTTCTTACTTC
* * * * * *
2899 TTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTTCCTTTTACTTCT
65 TTACTGATTAGCTTTTTACTCTTTACTAATCACCATTTTACCCTTACCGATTACCTTTTACTTCT
2964 TACTTATTACTTTTTTACTC
130 TACTTATTACTTTTTTACTC
*
2984 TTACTGATTACTATTTTACTTTTTACTGACTAT-TATTTTACTCTTGT-TGATTACCTTCTTACT
1 TTACTGATTACTATTTTACTTTTTACTGA-T-TGCATTTTACT-TTGTATGATTACCTTCTTACT
* * *
3047 TTTTACTGATTA-CTATTTTACTCTTTACTAATTACCATTTTACCCTTTCCGA-TACCTTTTTAC
63 TCTTACTGATTAGCT-TTTTACTCTTTACTAATCACCATTTTACCCTTACCGATTACC-TTTTAC
*
3110 TTTTTACT
126 TTCTTACT
3118 GATTGCACGC
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
149 5 0.04
150 97 0.86
151 7 0.06
152 4 0.04
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (149 bp):
TTACTGATTACTATTTTACTTTTTACTGATTGCATTTTACTTTGTATGATTACCTTCTTACTTCT
TACTGATTAGCTTTTTACTCTTTACTAATCACCATTTTACCCTTACCGATTACCTTTTACTTCTT
ACTTATTACTTTTTTACTC
Found at i:3344 original size:55 final size:55
Alignment explanation
Indices: 3275--3956 Score: 1058
Period size: 55 Copynumber: 12.5 Consensus size: 55
3265 CATTTTAACT
*
3275 CTTAATTA-TCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
**
3330 CTTAATTACTGATTTACTGATTACTACCACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
** *
3385 CTTAATTACTGATTTACTGATTACTACCACTTTGACTCTGATTAATCTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3440 CTTAATTACTGATTTACTGATTTCTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3495 CTTAATTACTGATTTACTGATTTCTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
3550 CTTAATTACCGATTCACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3605 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
3660 CTTAATTACTGATTTACTGATTACTGTTACTTTGACTCTGATTTACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
3715 CTTAATTACTGATTTACTGATTAATGTTACTTTGACTCTGATTAACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
3770 CTTAATTACTGATTTACTGATTACTGTTACTTTGACTCTGATTTACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
3825 CTTAATTACTGA-TTACTG-------TTACTTTGACTCTGATTTACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
3872 CTTAATTACTGATTTACTGATTACTGTTACTTTGACTCTGATTTACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3927 CTTAATTACTGATTTATTGATTACTATTAC
1 CTTAATTACTGATTTACTGATTACTATTAC
3957 CTTACTGATT
Statistics
Matches: 594, Mismatches: 24, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
47 41 0.07
48 6 0.01
54 6 0.01
55 540 0.91
56 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:3371 original size:29 final size:29
Alignment explanation
Indices: 3338--3427 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
3328 TACTTAATTA
3338 CTGATTTACTGATTACTACCACTTTGACT
1 CTGATTTACTGATTACTACCACTTTGACT
* * ** * *
3367 CTGATTAATCT-CTT--T-TTAC-TTAATT
1 CTGATTTA-CTGATTACTACCACTTTGACT
3392 ACTGATTTACTGATTACTACCACTTTGACT
1 -CTGATTTACTGATTACTACCACTTTGACT
3422 CTGATT
1 CTGATT
3428 AATCTCTTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 14
0.62 0.18 0.21
Matches are distributed among these distances:
25 6 0.14
26 11 0.26
27 1 0.02
28 1 0.02
29 17 0.40
30 6 0.14
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (29 bp):
CTGATTTACTGATTACTACCACTTTGACT
Found at i:3810 original size:21 final size:21
Alignment explanation
Indices: 3786--3859 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
3776 TACTGATTTA
3786 CTGATTACTGTTACTTTGACT
1 CTGATTACTGTTACTTTGACT
* * *
3807 CTGATTTACCTCTTTTTAC-TTAATT
1 CTGA-TTA---C-TGTTACTTTGACT
3832 ACTGATTACTGTTACTTTGACT
1 -CTGATTACTGTTACTTTGACT
3854 CTGATT
1 CTGATT
3860 TACCTCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 15 0.38
22 8 0.20
25 8 0.20
26 9 0.22
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (21 bp):
CTGATTACTGTTACTTTGACT
Found at i:3912 original size:29 final size:29
Alignment explanation
Indices: 3830--3917 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
3820 TTTTACTTAA
3830 TTACTGATTACTGTTACTTTGACTCTGAT
1 TTACTGATTACTGTTACTTTGACTCTGAT
* * *
3859 TTACCT-CTT--T-TTAC-TTAATTACTGAT
1 TTA-CTGATTACTGTTACTTTGACT-CTGAT
3885 TTACTGATTACTGTTACTTTGACTCTGAT
1 TTACTGATTACTGTTACTTTGACTCTGAT
3914 TTAC
1 TTAC
3918 CTCTTTTTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 6 0.13
26 14 0.30
27 1 0.02
28 1 0.02
29 18 0.39
30 6 0.13
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (29 bp):
TTACTGATTACTGTTACTTTGACTCTGAT
Found at i:4726 original size:27 final size:27
Alignment explanation
Indices: 4674--4728 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
4664 TCAAACTTCT
*
4674 AATTCAATCTTATTTACTAAACTTAAA
1 AATTCAATCTTATTTACAAAACTTAAA
* *
4701 AATTCAATCTT-TTATTCAAAAGTTAAA
1 AATTCAATCTTATT-TACAAAACTTAAA
4728 A
1 A
4729 TTTTATTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (27 bp):
AATTCAATCTTATTTACAAAACTTAAA
Found at i:4968 original size:101 final size:100
Alignment explanation
Indices: 4694--5026 Score: 533
Period size: 101 Copynumber: 3.3 Consensus size: 100
4684 TATTTACTAA
4694 ACTTAAAAATTCAATCTTTTATTCAAAAGTTAAAATTTTATTTACTAATCACTCTAAAAAATTCA
1 ACTTAAAAATTCAATCTTTTATTC-AAAGTTAAAATTTTATTTACTAATCACTCT-AAAAATTCA
*
4759 ACCTTTTACCCAAAGATGACATTTTTATTTACCAATT
64 ATCTTTTACCCAAAGATGACATTTTTATTTACCAATT
** *
4796 ACTTAAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTTATTTACTAATTACTCT-AAAATTC
1 ACTT-AAAAATTCAATCTTTTATTCAAA-GTTA-AAATTTTATTTACTAATCACTCTAAAAATTC
*
4860 AATCTTTTACCCAAACATGACATTTTTATTTACCAATT
63 AATCTTTTACCCAAAGATGACATTTTTATTTACCAATT
*
4898 ACTTGAAAATTCAATCTTTTATTCAAAGCTTAAAATTTTATTTACTAATCACTCTAAAAATTCAA
1 ACTTAAAAATTCAATCTTTTATTCAAAG-TTAAAATTTTATTTACTAATCACTCTAAAAATTCAA
*
4963 TCTTTTACCCAAAGATGACATTTTTATTTAGCAATT
65 TCTTTTACCCAAAGATGACATTTTTATTTACCAATT
*
4999 ACTCAAAAATTCAATCTTTTATTCAAAG
1 ACTTAAAAATTCAATCTTTTATTCAAAG
5027 GTTACATCTT
Statistics
Matches: 213, Mismatches: 13, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
100 21 0.10
101 94 0.44
102 54 0.25
103 24 0.11
104 20 0.09
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (100 bp):
ACTTAAAAATTCAATCTTTTATTCAAAGTTAAAATTTTATTTACTAATCACTCTAAAAATTCAAT
CTTTTACCCAAAGATGACATTTTTATTTACCAATT
Found at i:5026 original size:50 final size:50
Alignment explanation
Indices: 4683--5026 Score: 363
Period size: 51 Copynumber: 6.8 Consensus size: 50
4673 TAATTCAATC
* * * *
4683 TTATTTACTAA--ACTTAAAAATTCAATCTTTTATTCAAA-AGTTAAAATT
1 TTATTTACTAATTACTCAAAAATTCAATCTTTTATTCAAAGA-TGACATTT
* * **
4731 TTATTTACTAATCACTCTAAAAAATTCAACCTTTTACCCAAAGATGACATTT
1 TTATTTACTAATTACTC--AAAAATTCAATCTTTTATTCAAAGATGACATTT
* * * *
4783 TTATTTACCAATTACTTAAAAAATTCAATCTTTTATTCAAAGGTTACATCTT
1 TTATTTACTAATTAC-TCAAAAATTCAATCTTTTATTCAAAGATGACAT-TT
* ** *
4835 TTATTTACTAATTACTCTAAAATTCAATCTTTTACCCAAACATGACATTT
1 TTATTTACTAATTACTCAAAAATTCAATCTTTTATTCAAAGATGACATTT
* ** * * * *
4885 TTATTTACCAATTACTTGAAAATTCAATCTTTTATTCAAAGCTTAAAATT
1 TTATTTACTAATTACTCAAAAATTCAATCTTTTATTCAAAGATGACATTT
* **
4935 TTATTTACTAATCACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTT
1 TTATTTACTAATTACTC-AAAAATTCAATCTTTTATTCAAAGATGACATTT
4986 TTATTTAGC-AATTACTCAAAAATTCAATCTTTTATTCAAAG
1 TTATTTA-CTAATTACTCAAAAATTCAATCTTTTATTCAAAG
5027 GTTACATCTT
Statistics
Matches: 241, Mismatches: 46, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
48 11 0.05
50 81 0.34
51 92 0.38
52 55 0.23
53 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (50 bp):
TTATTTACTAATTACTCAAAAATTCAATCTTTTATTCAAAGATGACATTT
Found at i:5992 original size:16 final size:16
Alignment explanation
Indices: 5971--6002 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5961 TATTTTCTCT
5971 TTTTGTTTGCTTGTTC
1 TTTTGTTTGCTTGTTC
*
5987 TTTTGTTTGTTTGTTC
1 TTTTGTTTGCTTGTTC
6003 ACATAGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.19, T:0.72
Consensus pattern (16 bp):
TTTTGTTTGCTTGTTC
Found at i:9189 original size:27 final size:27
Alignment explanation
Indices: 9113--9189 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
9103 GGTGAACTTA
* * *
9113 AAAATGACTAAAATGCCCCTGAGTGTG
1 AAAATGACCAAAATGCCCCTGGGTGCG
9140 AAAATGACCAAAATGCCCCTGGGTGCG
1 AAAATGACCAAAATGCCCCTGGGTGCG
* *
9167 AAAATGACCAAAATACCCTTGGG
1 AAAATGACCAAAATGCCCCTGGG
9190 CGACCCTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGGTGCG
Done.