Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013339.1 Corchorus capsularis cultivar CVL-1 contig13360, 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: 41961
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3215 original size:13 final size:13
Alignment explanation
Indices: 3197--3221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3187 TGGTCGAATT
3197 TTTTTTTATTTTA
1 TTTTTTTATTTTA
3210 TTTTTTTATTTT
1 TTTTTTTATTTT
3222 TTTGATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:4315 original size:30 final size:30
Alignment explanation
Indices: 4253--4318 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
4243 AAAGGGTCAA
* *
4253 ATGGCCGGTTGTGCCCGGATGGCCCATGCG
1 ATGGCCGGTTGTGCCCGGATGGCCAATCCG
* *
4283 ATGGCCGGTTGTGGCCGG-TTGCTCAATCCG
1 ATGGCCGGTTGTGCCCGGATGGC-CAATCCG
4313 ATGGCC
1 ATGGCC
4319 CATGCGATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.11, C:0.29, G:0.38, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTGCCCGGATGGCCAATCCG
Found at i:4705 original size:15 final size:15
Alignment explanation
Indices: 4685--4715 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4675 TTAAAGAAGT
4685 TATTAATTTATCGAG
1 TATTAATTTATCGAG
*
4700 TATTAATTTATGGAG
1 TATTAATTTATCGAG
4715 T
1 T
4716 TTATTAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.48
Consensus pattern (15 bp):
TATTAATTTATCGAG
Found at i:5547 original size:16 final size:15
Alignment explanation
Indices: 5528--5588 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
5518 GTTTGAGTCA
5528 GGTTAGGTTCAATTTG
1 GGTTAGGTT-AATTTG
5544 GGTTAGGTTAATTTG
1 GGTTAGGTTAATTTG
* *
5559 GGTTCGGGTTGAATTTT
1 GGTT-AGGTT-AATTTG
*
5576 GGTCAGGTTAATT
1 GGTTAGGTTAATT
5589 CGTGTTGGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
15 14 0.36
16 17 0.44
17 8 0.21
ACGTcount: A:0.18, C:0.05, G:0.33, T:0.44
Consensus pattern (15 bp):
GGTTAGGTTAATTTG
Found at i:5558 original size:15 final size:16
Alignment explanation
Indices: 5528--5562 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5518 GTTTGAGTCA
5528 GGTTAGGTTCAATTTG
1 GGTTAGGTTCAATTTG
5544 GGTTAGGTT-AATTTG
1 GGTTAGGTTCAATTTG
5559 GGTT
1 GGTT
5563 CGGGTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.17, C:0.03, G:0.34, T:0.46
Consensus pattern (16 bp):
GGTTAGGTTCAATTTG
Found at i:5600 original size:32 final size:32
Alignment explanation
Indices: 5533--5608 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
5523 AGTCAGGTTA
* *
5533 GGTTCAATTTGGGTTAGGTTAATTTGGGTTCG
1 GGTTCAATTTGGGTCAGGTTAATTCGGGTTCG
* * * *
5565 GGTTGAATTTTGGTCAGGTTAATTCGTGTTGG
1 GGTTCAATTTGGGTCAGGTTAATTCGGGTTCG
*
5597 GGTTCAGTTTGG
1 GGTTCAATTTGG
5609 CTTTTGGCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (32 bp):
GGTTCAATTTGGGTCAGGTTAATTCGGGTTCG
Found at i:5798 original size:16 final size:16
Alignment explanation
Indices: 5762--5818 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
5752 TGGATTGGGG
* *
5762 TTTTTTCGGGTTTCAG
1 TTTTTTCGGGTTTGAA
5778 TTTTTTCGGGTTTGAA
1 TTTTTTCGGGTTTGAA
* * *
5794 CTTTTTCGGATTTGGA
1 TTTTTTCGGGTTTGAA
5810 TTTTTTCGG
1 TTTTTTCGG
5819 ATTCGGGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.09, C:0.11, G:0.25, T:0.56
Consensus pattern (16 bp):
TTTTTTCGGGTTTGAA
Found at i:5819 original size:16 final size:16
Alignment explanation
Indices: 5748--5821 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 16
5738 TTTTCATAAA
* *
5748 TTTTT-GGATTGGGGT
1 TTTTTCGGATTTGGAT
* *
5763 TTTTTCGGGTTT-CAGT
1 TTTTTCGGATTTGGA-T
* * *
5779 TTTTTCGGGTTTGAAC
1 TTTTTCGGATTTGGAT
5795 TTTTTCGGATTTGGAT
1 TTTTTCGGATTTGGAT
5811 TTTTTCGGATT
1 TTTTTCGGATT
5822 CGGGTTTTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
15 5 0.11
16 41 0.87
17 1 0.02
ACGTcount: A:0.09, C:0.08, G:0.27, T:0.55
Consensus pattern (16 bp):
TTTTTCGGATTTGGAT
Found at i:5829 original size:16 final size:16
Alignment explanation
Indices: 5795--5830 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5785 GGGTTTGAAC
*
5795 TTTTTCGGATTTGGAT
1 TTTTTCGGATTCGGAT
*
5811 TTTTTCGGATTCGGGT
1 TTTTTCGGATTCGGAT
5827 TTTT
1 TTTT
5831 GACTTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.08, G:0.25, T:0.58
Consensus pattern (16 bp):
TTTTTCGGATTCGGAT
Found at i:6145 original size:48 final size:47
Alignment explanation
Indices: 6071--6215 Score: 166
Period size: 49 Copynumber: 3.0 Consensus size: 47
6061 AGCGTGCCAA
* * * *
6071 TCAATTTTGTCCAAAAATTGATAAAAAGTGCAATGAAAAGTAAATAT
1 TCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGGAAAAGTAAAGAT
* * *
6118 TCAATTTTGTCATAAAAATTGAGAAAAAGGTGGAAGGAAAATTAAAGGT
1 TCAATTTTGTC-TAAAAATTGAGAAAAA-GTGCAAGGAAAAGTAAAGAT
* *
6167 TCAATTTTGTTGTAAAAATTGAGAAAAAGTGC-AGGAAATGTAAGAGAT
1 TCAATTTTG-TCTAAAAATTGAGAAAAAGTGCAAGGAAAAGTAA-AGAT
6215 T
1 T
6216 GCTTTCAGTG
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
47 20 0.24
48 21 0.26
49 40 0.49
50 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (47 bp):
TCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGGAAAAGTAAAGAT
Found at i:13427 original size:21 final size:21
Alignment explanation
Indices: 13385--13429 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13375 CCCGACTCCC
* *
13385 CCTGGGCGCCCATGTCAATGG
1 CCTGGGCGCCCAGGGCAATGG
* *
13406 CCTGTGCGCCCAGGGCATTGG
1 CCTGGGCGCCCAGGGCAATGG
13427 CCT
1 CCT
13430 CAGGCCCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.36, G:0.33, T:0.20
Consensus pattern (21 bp):
CCTGGGCGCCCAGGGCAATGG
Found at i:15653 original size:35 final size:34
Alignment explanation
Indices: 15584--15682 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 34
15574 TTACGGATTG
15584 CCATTACTT-TTTACTGATTAATAT-TTTACTCTTTA
1 CCATT-CTTCTTTACTGATT-AT-TCTTTACTCTTTA
* *
15619 TCATTTTTCCTTTACTGATTATTCTTTACTCTTTA
1 CCATTCTT-CTTTACTGATTATTCTTTACTCTTTA
* *
15654 CCATTCTTCTTTCCTGATTACTCTTTACT
1 CCATTCTTCTTTACTGATTATTCTTTACT
15683 TTATTCTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
34 22 0.40
35 23 0.42
36 10 0.18
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (34 bp):
CCATTCTTCTTTACTGATTATTCTTTACTCTTTA
Found at i:15679 original size:34 final size:35
Alignment explanation
Indices: 15593--15682 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 35
15583 GCCATTACTT
* * * *
15593 TTTACTGATTAATATTTTACTCTTTATCATTTTTCC
1 TTTACTGATTACT-CTTTACTCTTTACCATTCTTCC
*
15629 TTTACTGATTATTCTTTACTCTTTACCATTCTT-C
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
*
15663 TTTCCTGATTACTCTTTACT
1 TTTACTGATTACTCTTTACT
15683 TTATTCTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
34 19 0.40
35 17 0.35
36 12 0.25
ACGTcount: A:0.19, C:0.21, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
Found at i:15734 original size:20 final size:19
Alignment explanation
Indices: 15711--15757 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
15701 CCTTTGCTGA
15711 TTACTCTTTACCACTTTTCT
1 TTACTCTTTA-CACTTTTCT
** *
15731 TTACTGATTACTCTTTTCT
1 TTACTCTTTACACTTTTCT
15750 TTACTCTT
1 TTACTCTT
15758 CATTATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (19 bp):
TTACTCTTTACACTTTTCT
Found at i:15776 original size:47 final size:48
Alignment explanation
Indices: 15725--15843 Score: 163
Period size: 47 Copynumber: 2.5 Consensus size: 48
15715 TCTTTACCAC
* * *
15725 TTTTCTTTACTGATTACTCTTTTCTTTACTCTTCATTATTT-T-ACTTT
1 TTTTCTTTACTGATTACTCTTTACTTTACTCTTCACTCTTTATCA-TTT
*
15772 TTTTCTTTACTGATTACTCTTTACTTTACTCTTTACTCTTTATCATTT
1 TTTTCTTTACTGATTACTCTTTACTTTACTCTTCACTCTTTATCATTT
*
15820 TTTT-TTTACTAATTACTCTTTACT
1 TTTTCTTTACTGATTACTCTTTACT
15844 GATTATTCTT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 56 0.86
48 8 0.12
49 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.02, T:0.62
Consensus pattern (48 bp):
TTTTCTTTACTGATTACTCTTTACTTTACTCTTCACTCTTTATCATTT
Found at i:15782 original size:67 final size:67
Alignment explanation
Indices: 15640--15782 Score: 198
Period size: 67 Copynumber: 2.1 Consensus size: 67
15630 TTACTGATTA
* *
15640 TTCTTTACTCTTTACCATTCTTCTTTCCTGATTACTCTTTACTTTATTCTTCATTATTTTACCTT
1 TTCTTTACTCTTTACCATTCTTCTTTACTGATTACTCTTTACTTTACTCTTCATTATTTTACCTT
15705 TG
66 TG
* ** * *
15707 CTGATTACTCTTTACCACTT-TTCTTTACTGATTACTCTTTTCTTTACTCTTCATTATTTTACTT
1 TTCTTTACTCTTTACCA-TTCTTCTTTACTGATTACTCTTTACTTTACTCTTCATTATTTTACCT
*
15771 TTT
65 TTG
15774 TTCTTTACT
1 TTCTTTACT
15783 GATTACTCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 62 0.97
68 2 0.03
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (67 bp):
TTCTTTACTCTTTACCATTCTTCTTTACTGATTACTCTTTACTTTACTCTTCATTATTTTACCTT
TG
Found at i:15977 original size:42 final size:42
Alignment explanation
Indices: 15839--16129 Score: 250
Period size: 42 Copynumber: 6.8 Consensus size: 42
15829 TAATTACTCT
* * * * * *
15839 TTACTGATTATTCTTTTACTTTTTTACTGATTGCCTTTTTCCTTT
1 TTACTGATTACTATTTTAC--TCTTACTGATTACC-TTTTACTTC
* * *
15884 TTGCTGATTAC-CTTTTACTTCTTACTGATTAACTTTTTAC-TC
1 TTACTGATTACTATTTTAC-TCTTACTGATT-ACCTTTTACTTC
*
15926 TTTACTGATTACCT-TTTTACTCTTACTGATTATCTTTTACTTC
1 -TTACTGATTA-CTATTTTACTCTTACTGATTACCTTTTACTTC
* *
15969 TTACTGATTGCTATTTTACTCTTACTGATTA-CTATTTACTTT
1 TTACTGATTACTATTTTACTCTTACTGATTACCT-TTTACTTC
* * * * *
16011 TTGCCGATTACTAATTTACTCTTACTAATTACCTTTTACTTT
1 TTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTC
* ** *
16053 TTACTGACTACTATTTTACTCTTGTTGACTACCTTCTTACTT-
1 TTACTGATTACTATTTTACTCTTACTGATTACCTT-TTACTTC
16095 TCTACTGATTACTATTTTACTCTTTTACTGATTAC
1 T-TACTGATTACTATTTTACTC--TTACTGATTAC
16130 TATTTCTGCT
Statistics
Matches: 205, Mismatches: 29, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
41 4 0.02
42 104 0.51
43 65 0.32
44 15 0.07
45 17 0.08
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (42 bp):
TTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTTC
Found at i:16156 original size:27 final size:23
Alignment explanation
Indices: 15832--16134 Score: 213
Period size: 21 Copynumber: 14.0 Consensus size: 23
15822 TTTTTACTAA
* *
15832 TTACTC-TTTACTGATTATTCTT
1 TTACTCTTTTACTGATTACTATT
* *
15854 TTACTTTTTTACTGATTGCCT-TT
1 TTACTCTTTTACTGATT-ACTATT
* * *
15877 TTCCT-TTTTGCTGATTAC-CTT
1 TTACTCTTTTACTGATTACTATT
*
15898 TTACT-TCTTACTGATTAACT-TT
1 TTACTCTTTTACTGATT-ACTATT
15920 TTACTC-TTTACTGATTACCT-TT
1 TTACTCTTTTACTGATTA-CTATT
*
15942 TTACTC--TTACTGATTA-TCTT
1 TTACTCTTTTACTGATTACTATT
* *
15962 TTACT-TCTTACTGATTGCTATT
1 TTACTCTTTTACTGATTACTATT
15984 TTACTC--TTACTGATTACTA-T
1 TTACTCTTTTACTGATTACTATT
* * *
16004 TTACT-TTTTGCCGATTACTAAT
1 TTACTCTTTTACTGATTACTATT
* *
16026 TTACTC--TTACTAATTAC-CTT
1 TTACTCTTTTACTGATTACTATT
*
16046 TTACT-TTTTACTGACTACTATT
1 TTACTCTTTTACTGATTACTATT
* * *
16068 TTACTCTTGT--TGACTACCT-TC
1 TTACTCTTTTACTGATTA-CTATT
*
16089 TTACT-TTCTACTGATTACTATT
1 TTACTCTTTTACTGATTACTATT
16111 TTACTCTTTTACTGATTACTATT
1 TTACTCTTTTACTGATTACTATT
16134 T
1 T
16135 CTGCTCCTTT
Statistics
Matches: 227, Mismatches: 29, Indels: 49
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.00
20 22 0.10
21 90 0.40
22 77 0.34
23 36 0.16
24 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (23 bp):
TTACTCTTTTACTGATTACTATT
Found at i:16167 original size:26 final size:27
Alignment explanation
Indices: 16117--16169 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
16107 TATTTTACTC
* * *
16117 TTTTACTGATTACTATTTCTGCTCCTT
1 TTTTACTGATTACCATTGCTACTCCTT
16144 TTTTACTGATTACCATTGC-ACTCCTT
1 TTTTACTGATTACCATTGCTACTCCTT
16170 GAATTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.17, C:0.25, G:0.08, T:0.51
Consensus pattern (27 bp):
TTTTACTGATTACCATTGCTACTCCTT
Found at i:25602 original size:13 final size:14
Alignment explanation
Indices: 25584--25612 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25574 ATAATCGGAC
25584 TTTGCATCCAT-CA
1 TTTGCATCCATGCA
25597 TTTGCATCCATGCA
1 TTTGCATCCATGCA
25611 TT
1 TT
25613 AAGTAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTGCATCCATGCA
Found at i:37761 original size:33 final size:33
Alignment explanation
Indices: 37714--37820 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
37704 CACCAAGCGA
*
37714 TGGCCGGTTG-TGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGG-TGATGGCCGGACATCTCCGA-GTCGCG
** *
37747 TGGTTGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
* * * * * *
37780 TGGCCGGTGTTGGCCGGTCTTCTCCAAATCGCA
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
37813 TGGCCGGT
1 TGGCCGGT
37821 TACTCGCACC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
32 2 0.03
33 57 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.38, T:0.25
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
Done.