Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015931.1 Corchorus capsularis cultivar CVL-1 contig15952, 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: 41735
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3621 original size:32 final size:34
Alignment explanation
Indices: 3580--3648 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 34
3570 ATATATATAT
*
3580 ATATATATAATAATGATAT-TGCCC-AAATTGAA
1 ATATATATAATAATGATATCTCCCCAAAATTGAA
*
3612 ATATATATAATAATGATTTCTCCCCAAAATTGAA
1 ATATATATAATAATGATATCTCCCCAAAATTGAA
3646 ATA
1 ATA
3649 CTCATTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 18 0.55
33 4 0.12
34 11 0.33
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (34 bp):
ATATATATAATAATGATATCTCCCCAAAATTGAA
Found at i:3758 original size:20 final size:20
Alignment explanation
Indices: 3705--3762 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
3695 GGGAGGGGTA
* *
3705 GTAGATATATATATATATTAT
1 GTAGATATAT-TATATAATAC
* *
3726 ATA-ATA-ATGATATAATAC
1 GTAGATATATTATATAATAC
3744 GTAGATATATTATATAATA
1 GTAGATATATTATATAATA
3763 ATAACAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 9 0.31
19 5 0.17
20 13 0.45
21 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (20 bp):
GTAGATATATTATATAATAC
Found at i:3851 original size:82 final size:82
Alignment explanation
Indices: 3693--3854 Score: 199
Period size: 84 Copynumber: 2.0 Consensus size: 82
3683 AAAACAATGG
* *
3693 CAGGGAGGGGTAGTAGATATATATATATATTATATAATAATGATATAATACGTAGATATATTATA
1 CAGGGAGGGGTAGTAGATATATATATATATGATATAATAATGATATAATAC-TAGATATAATATA
3758 TAATAATAACAACAATAA
65 TAATAATAACAACAATAA
* *
3776 CAGGGAGGGGATAGTAGATATCTATA-ATAATGATAATAAT-ATG-TAT-ATA-TATATATAATA
1 CAGGGAGGGG-TAGTAGATATATATATAT-ATGAT-ATAATAATGATATAATACTAGATATAAT-
3836 ATAATAATAATAACAACAA
62 AT-ATAATAATAACAACAA
3855 CATACGAATC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
80 8 0.11
81 2 0.03
82 19 0.27
83 15 0.21
84 21 0.30
85 5 0.07
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.31
Consensus pattern (82 bp):
CAGGGAGGGGTAGTAGATATATATATATATGATATAATAATGATATAATACTAGATATAATATAT
AATAATAACAACAATAA
Found at i:4912 original size:13 final size:13
Alignment explanation
Indices: 4894--4919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4884 TTTTTCCTTC
4894 TTCAGTCCATTTT
1 TTCAGTCCATTTT
4907 TTCAGTCCATTTT
1 TTCAGTCCATTTT
4920 CGTTGGGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (13 bp):
TTCAGTCCATTTT
Found at i:14644 original size:106 final size:106
Alignment explanation
Indices: 14459--14674 Score: 297
Period size: 106 Copynumber: 2.0 Consensus size: 106
14449 TAAATACAAT
* * * *
14459 ATATAAGCATTAAATGAAAAGTCATCTTTGCCCATAGTTATCTCAATTCAAGATTATTTGACATT
1 ATATAAGCATGAAATGAAAAGTCATCTTTGCCCATAATTATCTCAATCCAAGATTATTTGACATG
*
14524 AAGTTAATAGGGATAAAATAGTAATTCTCTAAACAAAATGG
66 AAATTAATAGGGATAAAATAGTAATTCTCTAAACAAAATGG
* * * * * * *
14565 ATATAAGCGTGAAGTGAAAAGTCTTCTTTGTCCATAATTATTTCGATCCATGATTATTTGACATG
1 ATATAAGCATGAAATGAAAAGTCATCTTTGCCCATAATTATCTCAATCCAAGATTATTTGACATG
* * *
14630 AAATTAATAGGGATAAAATGGTAATTCTCTAGACAAATTGG
66 AAATTAATAGGGATAAAATAGTAATTCTCTAAACAAAATGG
14671 ATAT
1 ATAT
14675 TGTGACGGAA
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (106 bp):
ATATAAGCATGAAATGAAAAGTCATCTTTGCCCATAATTATCTCAATCCAAGATTATTTGACATG
AAATTAATAGGGATAAAATAGTAATTCTCTAAACAAAATGG
Found at i:17207 original size:69 final size:68
Alignment explanation
Indices: 17086--17278 Score: 230
Period size: 70 Copynumber: 2.8 Consensus size: 68
17076 ATATAGTGGA
* * * *
17086 AAGAGA-TGGAAGAATTATCACTGAAAAGAGAATAGATTTGATTTTGATGGAAAAAAATGAGTAG
1 AAGAGACT-GAAGAATTATCAATAAAAAGAGAAGAGATTTGATTTTGAGGGAAAAAAATGAGTAG
17150 CAGC
65 CAGC
* *
17154 AAGAGACTGAAGAATTATTAGATTAAAAAGAGAA-AGATTTGATTTTGAGGGAAACAAATTGAGT
1 AAGAGACTGAAGAATTATCA-A-TAAAAAGAGAAGAGATTTGATTTTGAGGGAAA-AAAATGAGT
*
17218 AGCGGC
63 AGCAGC
* * * *
17224 AAGAGATTGAAGAATTATCAATAAAAACATAAGAGATTGGA-TTTGAGGGAAAAAA
1 AAGAGACTGAAGAATTATCAATAAAAAGAGAAGAGATTTGATTTTGAGGGAAAAAA
17279 TTTGAGTAAC
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
67 3 0.03
68 37 0.34
69 28 0.26
70 41 0.38
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.23
Consensus pattern (68 bp):
AAGAGACTGAAGAATTATCAATAAAAAGAGAAGAGATTTGATTTTGAGGGAAAAAAATGAGTAGC
AGC
Found at i:17286 original size:68 final size:67
Alignment explanation
Indices: 17086--17286 Score: 242
Period size: 68 Copynumber: 2.9 Consensus size: 67
17076 ATATAGTGGA
* * * * *
17086 AAGAGATGGAAGAATTATCACTGAAAAGAGAATAGATTTGATTTTGATGGAAAAAAATGAGTAGC
1 AAGAGATTGAAGAATTATCAATAAAAAGAGAA-AGATTTGATTTTGAGGGAAAAAATTGAGTAGC
17151 AGC
65 AGC
* *
17154 AAGAGACTGAAGAATTATTAGATTAAAAAGAGAAAGATTTGATTTTGAGGGAAACAAATTGAGTA
1 AAGAGATTGAAGAATTATCA-A-TAAAAAGAGAAAGATTTGATTTTGAGGGAAA-AAATTGAGTA
*
17219 GCGGC
63 GCAGC
* * *
17224 AAGAGATTGAAGAATTATCAATAAAAACATAAGAGATTGGA-TTTGAGGGAAAAAATTTGAGTA
1 AAGAGATTGAAGAATTATCAATAAAAAGAGAA-AGATTTGATTTTGAGGGAAAAAA-TTGAGTA
17287 ACGACATGGA
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
67 3 0.03
68 44 0.38
69 27 0.23
70 41 0.36
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (67 bp):
AAGAGATTGAAGAATTATCAATAAAAAGAGAAAGATTTGATTTTGAGGGAAAAAATTGAGTAGCA
GC
Found at i:18565 original size:9 final size:10
Alignment explanation
Indices: 18541--18570 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
18531 ATATGTAGAC
18541 ATTATTTTTT
1 ATTATTTTTT
18551 ATTATTTTTT
1 ATTATTTTTT
18561 A-TATTTTTT
1 ATTATTTTTT
18570 A
1 A
18571 CTGTGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:20123 original size:10 final size:10
Alignment explanation
Indices: 20108--20133 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20098 AATTTAATAT
20108 GGATATTTAC
1 GGATATTTAC
20118 GGATATTTAC
1 GGATATTTAC
20128 GGATAT
1 GGATAT
20134 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:20640 original size:28 final size:28
Alignment explanation
Indices: 20608--20664 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20598 ACGAAGTTAA
20608 TTGATTTTTTAAAGAACACTTTCAAACC
1 TTGATTTTTTAAAGAACACTTTCAAACC
20636 TTGATTTTTTAAAGAACACTTTCAAACC
1 TTGATTTTTTAAAGAACACTTTCAAACC
20664 T
1 T
20665 AACAACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (28 bp):
TTGATTTTTTAAAGAACACTTTCAAACC
Found at i:21778 original size:239 final size:238
Alignment explanation
Indices: 21350--21826 Score: 848
Period size: 239 Copynumber: 2.0 Consensus size: 238
21340 TTAATCATAA
* *
21350 TACATTAAATTATCAAATAGAAACAGGTCAATCACAATAACCTTTTAAATTAAAATGGTAAAAAA
1 TACACTAAACTATCAAATAGAAACAGGTCAATCACAATAACCTTTTAAATTAAAATGGTAAAAAA
* *
21415 AATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTGTTAGTAGAATAAAACTGTATA
66 AATAATTATAAAATATGGAATTTAATTAAATGAAAATAAAGTTGTTAGTAGAATAAAACTGTATA
21480 TTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTAT
131 TTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTAT
21545 AAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAG
196 AAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAG
* *
21588 TACACTAAACTATCAAATAGAAATAGGTCAATCACAATAATCTTTTAAATTAAAATGGTAAAAAT
1 TACACTAAACTATCAAATAGAAACAGGTCAATCACAATAACCTTTTAAATTAAAATGGT-AAAA-
*
21653 AAAATAATTATAAAATATGGAATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAAC-GTA
64 AAAATAATTATAAAATATGGAATTTAATTAAATGAAAATAAAGTTGTTAGTAGAATAAAACTGTA
*
21717 TATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTGAAAATAAAGAAATT
129 TATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATT
*
21782 GTAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAG
194 ATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAG
21827 AATCTACAAT
Statistics
Matches: 228, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
238 55 0.24
239 115 0.50
240 58 0.25
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.34
Consensus pattern (238 bp):
TACACTAAACTATCAAATAGAAACAGGTCAATCACAATAACCTTTTAAATTAAAATGGTAAAAAA
AATAATTATAAAATATGGAATTTAATTAAATGAAAATAAAGTTGTTAGTAGAATAAAACTGTATA
TTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTAT
AAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAG
Found at i:21819 original size:121 final size:121
Alignment explanation
Indices: 21400--21829 Score: 468
Period size: 121 Copynumber: 3.6 Consensus size: 121
21390 CCTTTTAAAT
* *
21400 TAAAATGGT-AAAA-AAAATAATTATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTGTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAATATTAGAATTTAATTAAATAAAAATAGAGTTTTTA
21462 GTAGAATAAAACTGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAG
66 GTAGAATAAAAC-GTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAG
*
21519 TAAAATGGTAAAAATAAAGA-AATTATAAAGATATTAG-ATTTAATTGAATAAAAATAGAGTTTT
1 TAAAATGGTAAAAATAAA-ATAATTATAAA-ATATTAGAATTTAATTAAATAAAAATAGAGTTTT
* * * *
21582 TAGTAGTACACT-AAAC-TATCAAATAGAAA---TAGGTCA-ATCACAATAATCTT-TT---AAA
64 TAGTAG-A-A-TAAAACGTAT--ATTAAAAATTTTA-AT-ATATC-CAAT--TTTTATTGAAAAA
21637 T--
119 TAG
* * *
21638 TAAAATGGTAAAAATAAAATAATTATAAAATA-TGGAATTTAATTAAATGAAAATAAAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAATATTAGAATTTAATTAAATAAAAATAGAGTTTTTA
21702 GTAGAATAAAACGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAG
66 GTAGAATAAAACGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAG
* * *
21758 TAAAATGGTGAAAATAAAGA-AATTGTAAAGATATTAG-ATTTAATTGAATAAAAATAGAGTTTT
1 TAAAATGGTAAAAATAAA-ATAATTATAAA-ATATTAGAATTTAATTAAATAAAAATAGAGTTTT
21821 TAGTAGAAT
64 TAGTAGAAT
21830 CTACAATAGT
Statistics
Matches: 258, Mismatches: 21, Indels: 62
0.76 0.06 0.18
Matches are distributed among these distances:
114 3 0.01
115 9 0.03
116 10 0.04
117 10 0.04
118 39 0.15
119 36 0.14
120 29 0.11
121 54 0.21
122 44 0.17
123 7 0.03
124 13 0.05
125 4 0.02
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (121 bp):
TAAAATGGTAAAAATAAAATAATTATAAAATATTAGAATTTAATTAAATAAAAATAGAGTTTTTA
GTAGAATAAAACGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAG
Found at i:27668 original size:19 final size:20
Alignment explanation
Indices: 27621--27679 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
27611 ATGCTTATGG
27621 AATTAATTAATAATTAATATAAT
1 AATTAATTAATAA-TAA-A-AAT
27644 AATTAATTAATAATAAAAA-
1 AATTAATTAATAATAAAAAT
* *
27663 AGTTAA-AAATAATAAAA
1 AATTAATTAATAATAAAA
27680 TTATTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 10 0.29
19 5 0.15
20 2 0.06
21 1 0.03
22 3 0.09
23 13 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AATTAATTAATAATAAAAAT
Found at i:33934 original size:12 final size:12
Alignment explanation
Indices: 33902--33940 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
33892 ATGGAATTAA
33902 ATATCCGTCG--
1 ATATCCGTCGAT
33912 ATA-CC-TCGAT
1 ATATCCGTCGAT
33922 ATATCCGTCGAT
1 ATATCCGTCGAT
33934 ATATCCG
1 ATATCCG
33941 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:34073 original size:10 final size:10
Alignment explanation
Indices: 34051--34089 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
34041 AAATCTCGAT
*
34051 ATATCCGTAA
1 ATATCCATAA
34061 ATATCCATAA
1 ATATCCATAA
*
34071 ATATCCGTAA
1 ATATCCATAA
34081 ATATCCATA
1 ATATCCATA
34090 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:34074 original size:20 final size:20
Alignment explanation
Indices: 34051--34089 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34041 AAATCTCGAT
34051 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
34071 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
34090 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:35130 original size:25 final size:25
Alignment explanation
Indices: 35102--35169 Score: 136
Period size: 25 Copynumber: 2.7 Consensus size: 25
35092 CATCGATACC
35102 TCGATATATCCGTCGATATATCCGT
1 TCGATATATCCGTCGATATATCCGT
35127 TCGATATATCCGTCGATATATCCGT
1 TCGATATATCCGTCGATATATCCGT
35152 TCGATATATCCGTCGATA
1 TCGATATATCCGTCGATA
35170 CCTGTATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (25 bp):
TCGATATATCCGTCGATATATCCGT
Found at i:35132 original size:13 final size:12
Alignment explanation
Indices: 35102--35169 Score: 118
Period size: 12 Copynumber: 5.5 Consensus size: 12
35092 CATCGATACC
35102 TCGATATATCCG
1 TCGATATATCCG
35114 TCGATATATCCG
1 TCGATATATCCG
35126 TTCGATATATCCG
1 -TCGATATATCCG
35139 TCGATATATCCG
1 TCGATATATCCG
35151 TTCGATATATCCG
1 -TCGATATATCCG
35164 TCGATA
1 TCGATA
35170 CCTGTATTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
12 30 0.56
13 24 0.44
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Done.