Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015890.1 Corchorus capsularis cultivar CVL-1 contig15911, 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: 27855
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:725 original size:18 final size:19
Alignment explanation
Indices: 679--730 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
669 TTTCACATCT
679 AATAAGGTTACTAAAAAAAC
1 AATAAGGTTA-TAAAAAAAC
*
699 TATAGAGGTTATAAAAAAA-
1 AATA-AGGTTATAAAAAAAC
718 AATAAGGTTATAA
1 AATAAGGTTATAA
731 CTTTAACGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 9 0.31
19 3 0.10
20 11 0.38
21 6 0.21
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (19 bp):
AATAAGGTTATAAAAAAAC
Found at i:3314 original size:161 final size:162
Alignment explanation
Indices: 3025--3316 Score: 498
Period size: 161 Copynumber: 1.8 Consensus size: 162
3015 TTAATAAGGC
*
3025 TTGAAAGAGGTTTTAAATCAAAGGAACACTAAAATTTTAAAAATAAAAAATAGTTTTTTTTAAAC
1 TTGAAAGAGGTTTTAAATCAAAGGAACACTAAAATTTTAAAAATAAAAAATAGTTTTTTTAAAAC
* *
3090 GGTTGAAAGAGGTTTAAAAATAAAAAACACTAAATTTTAAAATTAAAAAAGGCATTTTAGATATT
66 GGTTGAAAGAGGTATAAAAATAAAAAACACTAAATTTTAAAATTAAAAAAGACATTTTAGATATT
3155 TCAAATTAAGGTTTTTAAAGTTTAGAATTATA
131 TCAAATTAAGGTTTTTAAAGTTTAGAATTATA
* * *
3187 TTGAAAGAGGTTTTAAATGAAAGGAACACTAAGATTTTAAAAATAAAAAATAG-TTTTTTAAAAT
1 TTGAAAGAGGTTTTAAATCAAAGGAACACTAAAATTTTAAAAATAAAAAATAGTTTTTTTAAAAC
*
3251 GGTTGAAAGAGGTATAAAAAT-AAAAACACTTAAATTTTAAAATTAAAAAATACATTTTAGATAT
66 GGTTGAAAGAGGTATAAAAATAAAAAACAC-TAAATTTTAAAATTAAAAAAGACATTTTAGATAT
3315 TT
130 TT
3317 AGATCTATGT
Statistics
Matches: 122, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
160 8 0.07
161 63 0.52
162 51 0.42
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.34
Consensus pattern (162 bp):
TTGAAAGAGGTTTTAAATCAAAGGAACACTAAAATTTTAAAAATAAAAAATAGTTTTTTTAAAAC
GGTTGAAAGAGGTATAAAAATAAAAAACACTAAATTTTAAAATTAAAAAAGACATTTTAGATATT
TCAAATTAAGGTTTTTAAAGTTTAGAATTATA
Found at i:7197 original size:15 final size:15
Alignment explanation
Indices: 7158--7199 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
7148 TTCCTTCATT
7158 TTAATCATAAACTAA
1 TTAATCATAAACTAA
7173 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
7184 TTAATCATAAACTAA
1 TTAATCATAAACTAA
7199 T
1 T
7200 AAACTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
11 9 0.39
13 4 0.17
15 10 0.43
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:8112 original size:2 final size:2
Alignment explanation
Indices: 8105--8133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8095 CCAAAAGATA
8105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8134 GTTGTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11101 original size:6 final size:6
Alignment explanation
Indices: 11090--11122 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
11080 TTTTTTTTTC
11090 TTTCTT TTTCTT TTTCTTT TTTCTT TTT-TT TTT
1 TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTT
11123 TTTGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTCTT
Found at i:11113 original size:23 final size:21
Alignment explanation
Indices: 11083--11125 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
11073 TGCAGGATTT
11083 TTTTTTCTTTCTTTTTCTTTTTC
1 TTTTTTCTTT-TTTTT-TTTTTC
11106 TTTTTTCTTTTTTTTTTTTT
1 TTTTTTCTTTTTTTTTTTTT
11126 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 10 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTTTTTTC
Found at i:11123 original size:19 final size:18
Alignment explanation
Indices: 11080--11125 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
11070 TAATGCAGGA
11080 TTTTTTTTTCTTTCTTTT
1 TTTTTTTTTCTTTCTTTT
11098 TCTTTTTCTTT-TTTCTTTT
1 T-TTTTT-TTTCTTTCTTTT
11117 TTTTTTTTT
1 TTTTTTTTT
11126 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.12
18 6 0.23
19 14 0.54
20 3 0.12
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTCTTTCTTTT
Found at i:11124 original size:13 final size:13
Alignment explanation
Indices: 11080--11124 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11070 TAATGCAGGA
*
11080 TTTTTTT-TTCTT
1 TTTTTTTCTTTTT
*
11092 TCTTTTTCTTTTT
1 TTTTTTTCTTTTT
*
11105 CTTTTTTCTTTTT
1 TTTTTTTCTTTTT
11118 TTTTTTT
1 TTTTTTT
11125 TGAATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:11132 original size:23 final size:23
Alignment explanation
Indices: 11083--11134 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
11073 TGCAGGATTT
*
11083 TTTTTTCTTTCTTTTTCTTTTTC
1 TTTTTTCTTTCTTTTTCTTTTTA
11106 TTTTTTCTTT-TTTTT-TTTTTGAA
1 TTTTTTCTTTCTTTTTCTTTTT--A
11129 TTTTTT
1 TTTTTT
11135 TATTGAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 16 0.62
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.85
Consensus pattern (23 bp):
TTTTTTCTTTCTTTTTCTTTTTA
Found at i:16211 original size:29 final size:30
Alignment explanation
Indices: 16179--16236 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
16169 TAAGCTAACT
* *
16179 CTCCA-TTCTCAAGTATTTTTGTCATTGTG
1 CTCCATTTCTAAAGTATTGTTGTCATTGTG
*
16208 CTCCATTTTTAAAGTATTGTTGTCATTGT
1 CTCCATTTCTAAAGTATTGTTGTCATTGT
16237 TCTACTACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (30 bp):
CTCCATTTCTAAAGTATTGTTGTCATTGTG
Found at i:20561 original size:20 final size:21
Alignment explanation
Indices: 20526--20566 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
20516 TCATTTTTAG
20526 TATTTTGGTATATATTAGAACA
1 TATTTTGG-ATATATTAGAACA
20548 TATTTTGG-TATATTAGAAC
1 TATTTTGGATATATTAGAAC
20567 TAAATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (21 bp):
TATTTTGGATATATTAGAACA
Found at i:23114 original size:20 final size:20
Alignment explanation
Indices: 23077--23114 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23067 TTTTATGTTT
*
23077 TATATATATTATTATATTAC
1 TATATATATCATTATATTAC
23097 TATATATTATCATT-TATT
1 TATATA-TATCATTATATT
23115 TATGATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATATATCATTATATTAC
Found at i:25178 original size:44 final size:44
Alignment explanation
Indices: 25100--25242 Score: 109
Period size: 44 Copynumber: 3.3 Consensus size: 44
25090 TCACAGATAG
* * *
25100 ATTATCAAAA-ATCTTAGGGAAGTTTATTAAAATTTCATAGTTA
1 ATTATCAAAATTTCTTAGGGAAGTTTATCAAAATTTCATAGGTA
* * * * *
25143 GGTTATCAAAGTTTCTTATGG-AGTTTATCACAATTTTATAGGTA
1 -ATTATCAAAATTTCTTAGGGAAGTTTATCAAAATTTCATAGGTA
* *
25187 ATTATCAAAATTTCAT-GGTG--G-TTATCAAAATTTAATAGGGTA
1 ATTATCAAAATTTCTTAGG-GAAGTTTATCAAAATTTCATA-GGTA
* *
25229 GTTATCTAAATTTC
1 ATTATCAAAATTTC
25243 GTAAAAATAT
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
41 14 0.17
42 18 0.22
43 14 0.17
44 27 0.34
45 7 0.09
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (44 bp):
ATTATCAAAATTTCTTAGGGAAGTTTATCAAAATTTCATAGGTA
Found at i:25239 original size:22 final size:21
Alignment explanation
Indices: 25123--25241 Score: 80
Period size: 22 Copynumber: 5.6 Consensus size: 21
25113 TTAGGGAAGT
* * *
25123 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTAATAGGTA-G
* **
25145 TTATCAAAGTTTCTTATGG-AG
1 TTATCAAAATTTAATA-GGTAG
* * *
25166 TTTATCACAATTTTATAGGTAA
1 -TTATCAAAATTTAATAGGTAG
* *
25188 TTATCAAAATTTCAT-GGTGG
1 TTATCAAAATTTAATAGGTAG
25208 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTAATA-GGTAG
*
25230 TTATCTAAATTT
1 TTATCAAAATTT
25242 CGTAAAAATA
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
20 17 0.22
21 16 0.21
22 42 0.55
23 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (21 bp):
TTATCAAAATTTAATAGGTAG
Found at i:27353 original size:19 final size:19
Alignment explanation
Indices: 27315--27353 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27305 AAACTACTGT
* *
27315 TATATATTGTAACTGTCAC
1 TATATATTGTAACCGCCAC
27334 TATATATTGTAACCGCCAC
1 TATATATTGTAACCGCCAC
27353 T
1 T
27354 TTGCTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (19 bp):
TATATATTGTAACCGCCAC
Done.