Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006882.1 Corchorus capsularis cultivar CVL-1 contig06903, 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: 85019
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2196 original size:44 final size:45
Alignment explanation
Indices: 2126--2213 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
2116 TAGTTGAAAT
* *
2126 AGTTATACATTCTCTCTAAATTTTAAGATCCTAG-GTTTATGCTTCA
1 AGTTATACA-TCTCCCTAAATCTTAAGATCCT-GTGTTTATGCTTCA
2172 AGTTATACA-CTCCCTAAATCTTAAGATCCTGTGTTTATGCTT
1 AGTTATACATCTCCCTAAATCTTAAGATCCTGTGTTTATGCTT
2214 TAAAATGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 29 0.74
46 9 0.23
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.42
Consensus pattern (45 bp):
AGTTATACATCTCCCTAAATCTTAAGATCCTGTGTTTATGCTTCA
Found at i:2579 original size:25 final size:26
Alignment explanation
Indices: 2522--2571 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2512 TGAAAAGTTT
*
2522 AAAAGGGTAATTAATATGATGCAAAAA
1 AAAAGGGTAATTAATA-GAGGCAAAAA
2549 AAAAGGGTAATTAATA-AGGCAAA
1 AAAAGGGTAATTAATAGAGGCAAA
2572 TAATAAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
27 16 0.73
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (26 bp):
AAAAGGGTAATTAATAGAGGCAAAAA
Found at i:7085 original size:2 final size:2
Alignment explanation
Indices: 7078--7220 Score: 124
Period size: 2 Copynumber: 71.5 Consensus size: 2
7068 GAACACCTTT
* * ** * * *
7078 AC AC AC AC AG AG AC AC AC AC AC AC AC TG AC AC AC AC GC GC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
** * * * *
7120 AC AC AC AC AC AC AC AC AC AC AC TG AC AC AC AC GC GC GC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
** * * *
7162 AC AC AC AC AC AC AC AC AC AC AC TG AC AC AC AC GC GC GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
7204 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
7221 AAGTAAAATG
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 121 1.00
ACGTcount: A:0.41, C:0.46, G:0.10, T:0.02
Consensus pattern (2 bp):
AC
Found at i:7123 original size:40 final size:40
Alignment explanation
Indices: 7079--7220 Score: 234
Period size: 40 Copynumber: 3.5 Consensus size: 40
7069 AACACCTTTA
* *
7079 CACACACAGAGACACACACACACACTGACACACACGCGCG
1 CACACACACACACACACACACACACTGACACACACGCGCG
7119 --CACACACACACACACACACACACTGACACACACGCGCGCG
1 CACACACACACACACACACACACACTGACACACA--CGCGCG
7159 CACACACACACACACACACACACACTGACACACACGCGCG
1 CACACACACACACACACACACACACTGACACACACGCGCG
7199 CACACACACACACACACACACA
1 CACACACACACACACACACACA
7221 AAGTAAAATG
Statistics
Matches: 96, Mismatches: 2, Indels: 8
0.91 0.02 0.08
Matches are distributed among these distances:
38 30 0.31
40 34 0.35
42 32 0.33
ACGTcount: A:0.41, C:0.46, G:0.11, T:0.02
Consensus pattern (40 bp):
CACACACACACACACACACACACACTGACACACACGCGCG
Found at i:7132 original size:38 final size:38
Alignment explanation
Indices: 7081--7220 Score: 226
Period size: 38 Copynumber: 3.6 Consensus size: 38
7071 CACCTTTACA
* *
7081 CACACAGAGACACACACACACACTGACACACACGCGCG
1 CACACACACACACACACACACACTGACACACACGCGCG
7119 CACACACACACACACACACACACTGACACACACGCGCGCG
1 CACACACACACACACACACACACTGACACACA--CGCGCG
7159 CACACACACACACACACACACACACTGACACACACGCGCG
1 --CACACACACACACACACACACACTGACACACACGCGCG
7199 CACACACACACACACACACACA
1 CACACACACACACACACACACA
7221 AAGTAAAATG
Statistics
Matches: 96, Mismatches: 2, Indels: 8
0.91 0.02 0.08
Matches are distributed among these distances:
38 52 0.54
40 12 0.12
42 32 0.33
ACGTcount: A:0.41, C:0.46, G:0.11, T:0.02
Consensus pattern (38 bp):
CACACACACACACACACACACACTGACACACACGCGCG
Found at i:7137 original size:42 final size:42
Alignment explanation
Indices: 7078--7220 Score: 231
Period size: 42 Copynumber: 3.5 Consensus size: 42
7068 GAACACCTTT
* *
7078 ACACACACAGAGACACACACACACACTGACACACACGCGCG-
1 ACACACACACACACACACACACACACTGACACACACGCGCGC
7119 ---CACACACACACACACACACACACTGACACACACGCGCGC
1 ACACACACACACACACACACACACACTGACACACACGCGCGC
*
7158 GCACACACACACACACACACACACACTGACACACACGCGCGC
1 ACACACACACACACACACACACACACTGACACACACGCGCGC
7200 ACACACACACACACACACACA
1 ACACACACACACACACACACA
7221 AAGTAAAATG
Statistics
Matches: 95, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
38 36 0.38
42 59 0.62
ACGTcount: A:0.41, C:0.46, G:0.10, T:0.02
Consensus pattern (42 bp):
ACACACACACACACACACACACACACTGACACACACGCGCGC
Found at i:18174 original size:16 final size:17
Alignment explanation
Indices: 18153--18188 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
18143 GCAAATGGAT
18153 AAAATGGGCACTA-AAA
1 AAAATGGGCACTAGAAA
18169 AAAATGGGCACTAGAAA
1 AAAATGGGCACTAGAAA
18186 AAA
1 AAA
18189 GTCCATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.58, C:0.11, G:0.19, T:0.11
Consensus pattern (17 bp):
AAAATGGGCACTAGAAA
Found at i:25017 original size:26 final size:27
Alignment explanation
Indices: 24987--25037 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
24977 AAGATTATAA
* *
24987 TTTTACC-TATTCTAAATTATCATTCT
1 TTTTACCGAATTCTAAATTACCATTCT
25013 TTTTACCGAATTCTAAATTACCATT
1 TTTTACCGAATTCTAAATTACCATT
25038 TATTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTACCGAATTCTAAATTACCATTCT
Found at i:34220 original size:29 final size:30
Alignment explanation
Indices: 34142--34221 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
34132 CTTCCCATCC
* * * *
34142 ATTT-GGGTGCATATCATCCATACATTATA
1 ATTTAGGGTGCAAATTATCCATAAATTAAA
*
34171 ATTTAGGATGCAAAATT-TCCA-AAATTAAA
1 ATTTAGGGTGC-AAATTATCCATAAATTAAA
34200 ATTTAGGGTGCAAATTATCCAT
1 ATTTAGGGTGCAAATTATCCAT
34222 TCATTAATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 5 0.12
29 24 0.59
30 9 0.22
31 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (30 bp):
ATTTAGGGTGCAAATTATCCATAAATTAAA
Found at i:46833 original size:16 final size:16
Alignment explanation
Indices: 46794--46836 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
46784 GGATTTTGTT
**
46794 GGTTTCGGGTTATCTC
1 GGTTTCGGGTTAAATC
*
46810 -GATTCGGGTTAAATC
1 GGTTTCGGGTTAAATC
46825 GGTTTCGGGTTA
1 GGTTTCGGGTTA
46837 TAGTACTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.40
Consensus pattern (16 bp):
GGTTTCGGGTTAAATC
Found at i:47333 original size:2 final size:2
Alignment explanation
Indices: 47326--47358 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
47316 GTCATGTATG
47326 AT AT 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 AT AT A
47359 AAAGTACGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47571 original size:82 final size:86
Alignment explanation
Indices: 47478--47648 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 86
47468 TCTATTTTTA
47478 TTTAATTAAATCTAAT-TCTTTATAACTATTTTATTTTTACCA-TTTTACTATTTTAATTAAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
47541 ACTTA-A-ATATATTAGAATT
66 ACTTAGATATATATTAGAATT
* *
47560 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACATA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
*
47625 ACTTAGATATATATTATAATT
66 ACTTAGATATATATTAGAATT
47646 TTT
1 TTT
47649 TAAATATATT
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
82 16 0.20
83 26 0.32
84 24 0.29
85 1 0.01
86 15 0.18
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.53
Consensus pattern (86 bp):
TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
ACTTAGATATATATTAGAATT
Found at i:48846 original size:13 final size:13
Alignment explanation
Indices: 48828--48870 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
48818 GTCTCATAAT
*
48828 CAAAGTCATAAAC
1 CAAAGTAATAAAC
48841 CAAAGTAATAAAC
1 CAAAGTAATAAAC
48854 CAGAA-TAATAAAC
1 CA-AAGTAATAAAC
48867 CAAA
1 CAAA
48871 ACAGTCAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 2 0.07
13 24 0.86
14 2 0.07
ACGTcount: A:0.60, C:0.19, G:0.07, T:0.14
Consensus pattern (13 bp):
CAAAGTAATAAAC
Found at i:50373 original size:12 final size:13
Alignment explanation
Indices: 50344--50374 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50334 CTTGGTTTGC
*
50344 AAAAAGTGCTTTT
1 AAAAAGTACTTTT
50357 AAAAAGTACTTTT
1 AAAAAGTACTTTT
50370 AAAAA
1 AAAAA
50375 TAGTTGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (13 bp):
AAAAAGTACTTTT
Found at i:53610 original size:15 final size:15
Alignment explanation
Indices: 53590--53622 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
53580 AAATTATATA
53590 TATATATATATATT-T
1 TATATATAT-TATTAT
53605 TATATATATTATTAT
1 TATATATATTATTAT
53620 TAT
1 TAT
53623 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATATATTATTAT
Found at i:59635 original size:39 final size:39
Alignment explanation
Indices: 59568--59643 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
59558 ATTTAATTAA
59568 ATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAAAAT
1 ATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAAAAAT
* *
59607 ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAA
1 ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAA
59644 TAAAATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 32 0.94
ACGTcount: A:0.54, C:0.01, G:0.12, T:0.33
Consensus pattern (39 bp):
ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAAAT
Found at i:59703 original size:109 final size:111
Alignment explanation
Indices: 59493--59714 Score: 412
Period size: 109 Copynumber: 2.0 Consensus size: 111
59483 AGATTTAATT
59493 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTAT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTA-TATAAAGATATTAT
59558 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
65 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
*
59605 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAG-T-TATAAATATATTATA
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
59668 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
59714 A
1 A
59715 CTTAAACAAT
Statistics
Matches: 109, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
109 61 0.56
111 1 0.01
112 47 0.43
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.36
Consensus pattern (111 bp):
ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
Found at i:60644 original size:11 final size:11
Alignment explanation
Indices: 60630--60667 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
60620 ATTCATAACA
60630 AATTTATAATT
1 AATTTATAATT
60641 AATTTATAATT
1 AATTTATAATT
60652 -ATTTGATAATT
1 AATTT-ATAATT
*
60663 TATTT
1 AATTT
60668 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:62117 original size:31 final size:31
Alignment explanation
Indices: 62079--62235 Score: 134
Period size: 31 Copynumber: 5.4 Consensus size: 31
62069 TTTTGTGCAC
* * **
62079 GTGGCATGCCATGTGCCATTTTTTGAAACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* *
62110 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* *
62141 GTGGCCTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
62172 GTGGCA---C----G--ACTTTTTGGTACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* ** *
62194 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
*
62225 GTGGCGTGCCA
1 GTGGCATGCCA
62236 CGTCGGACAC
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
22 19 0.18
24 1 0.01
25 1 0.01
28 1 0.01
29 1 0.01
31 81 0.78
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCATGTGTCACTTTTTGGTACAT
Found at i:62211 original size:53 final size:53
Alignment explanation
Indices: 62127--62229 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
62117 GCCACGTGTC
** *
62127 ACTTTTTGGTACACGTGGCCTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCCTGACACATGTCACTTTTTGGTACACGTGGCACG
* * *
62180 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCCTGACACATGTCACTTTTTGGTACACGTGGC
62230 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCCTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:74342 original size:49 final size:49
Alignment explanation
Indices: 74289--74492 Score: 255
Period size: 49 Copynumber: 4.2 Consensus size: 49
74279 TAAAAAAGCG
* * * * *
74289 AGTAAACATTAACGCCTTCCGTCCGGGAAGGGCGTTTTTGGAAAAAGCA
1 AGTAAAAATTAATGCCTTCCGTCCGGGAAGGGCGCTTTGGGAAATAGCA
** *
74338 AGTAAAAATTTGTGCCTTCCGGCCGGGAAGGGCGCTTTGGGAAATAGCA
1 AGTAAAAATTAATGCCTTCCGTCCGGGAAGGGCGCTTTGGGAAATAGCA
* * ** *
74387 AGTAAAAATAAATGGCTTCCGTCTAGGAAGGGCGCTTTGGGAAATTGCA
1 AGTAAAAATTAATGCCTTCCGTCCGGGAAGGGCGCTTTGGGAAATAGCA
* * * *
74436 AGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCA
1 AGTAAAAATTAATGCCTTCCGTCCGGGAAGGGCGCTTTGGGAAATAGCA
74485 AGTAAAAA
1 AGTAAAAA
74493 CTGAAAATTG
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 135 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (49 bp):
AGTAAAAATTAATGCCTTCCGTCCGGGAAGGGCGCTTTGGGAAATAGCA
Found at i:75283 original size:81 final size:81
Alignment explanation
Indices: 75192--75355 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
75182 CACTAAATTA
75192 CTACCCCAGGGACCTAATTGAACTAAAATTGGGGACCAAATTGAAAGAAAAACAGAAAACATACT
1 CTACCCCAGGGACCTAATTGAACTAAAATTGGGGACCAAATTGAAAGAAAAACAGAAAACATACT
75257 TGAAATTGGAGACTTT
66 TGAAATTGGAGACTTT
*
75273 CTACCTCAGGGACCTAATTGAACTAAAATTGGGGACCAAATTGAAAGAAAAACAGAAAACATACT
1 CTACCCCAGGGACCTAATTGAACTAAAATTGGGGACCAAATTGAAAGAAAAACAGAAAACATACT
75338 TGAAATTGGAGACTTT
66 TGAAATTGGAGACTTT
75354 CT
1 CT
75356 TCAACCTTAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (81 bp):
CTACCCCAGGGACCTAATTGAACTAAAATTGGGGACCAAATTGAAAGAAAAACAGAAAACATACT
TGAAATTGGAGACTTT
Done.