Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010877.1 Corchorus capsularis cultivar CVL-1 contig10898, 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: 70826
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:259 original size:6 final size:6
Alignment explanation
Indices: 241--272 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
231 AAGAAGGTAA
241 TTTCTT ATTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT T
273 CGTAAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:2630 original size:21 final size:21
Alignment explanation
Indices: 2606--2645 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2596 TGAATCCCAT
2606 CCTCCAACTCCTCTTCTTCAA
1 CCTCCAACTCCTCTTCTTCAA
**
2627 CCTCCTCCTCCTCTTCTTC
1 CCTCCAACTCCTCTTCTTC
2646 CTCTTCCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.53, G:0.00, T:0.38
Consensus pattern (21 bp):
CCTCCAACTCCTCTTCTTCAA
Found at i:2633 original size:3 final size:3
Alignment explanation
Indices: 2627--2676 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
2617 TCTTCTTCAA
* * * *
2627 CCT CCT CCT CCT CTT CTT CCT CTT CCT CCT CCT CCT CCT CCT CTT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
2675 CC
1 CC
2677 AAATCACCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (3 bp):
CCT
Found at i:2653 original size:21 final size:21
Alignment explanation
Indices: 2613--2676 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
2603 CATCCTCCAA
** *
2613 CTCCTCTTCTTCAACCTCCTC
1 CTCCTCTTCTTCCTCTTCCTC
2634 CTCCTCTTCTTCCTCTTCCTC
1 CTCCTCTTCTTCCTCTTCCTC
* *
2655 CTCCTCCTCCTCCTCTTCCTC
1 CTCCTCTTCTTCCTCTTCCTC
2676 C
1 C
2677 AAATCACCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.56, G:0.00, T:0.41
Consensus pattern (21 bp):
CTCCTCTTCTTCCTCTTCCTC
Found at i:12514 original size:72 final size:72
Alignment explanation
Indices: 12426--12570 Score: 211
Period size: 72 Copynumber: 2.0 Consensus size: 72
12416 GACAGGAACC
* * *
12426 GTTGAAACGTTTGGTTTTTGCA-AAGGAGGAAAATGGGTCTTTTGAATAACAGGCAATTTCACTT
1 GTTGAAACGTTGGGTTTTTGCACAAGG-GGAAAATGGGTCTTTAGAATAACAGGCAAATTCACTT
*
12490 CTTTCACT
65 CTTTAACT
* * *
12498 GTTGAAAGGTTGGGTTTTTGCACAAGGGGGAAATGGGTCTTTAGAATAACAGGCAAATTCTCTTC
1 GTTGAAACGTTGGGTTTTTGCACAAGGGGAAAATGGGTCTTTAGAATAACAGGCAAATTCACTTC
12563 TTTAACT
66 TTTAACT
12570 G
1 G
12571 CATACATGAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 61 0.94
73 4 0.06
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (72 bp):
GTTGAAACGTTGGGTTTTTGCACAAGGGGAAAATGGGTCTTTAGAATAACAGGCAAATTCACTTC
TTTAACT
Found at i:25435 original size:168 final size:168
Alignment explanation
Indices: 25157--25631 Score: 878
Period size: 168 Copynumber: 2.8 Consensus size: 168
25147 CACAAAATCA
*
25157 TCTTCATCAAATGCATAAGGATCCTGACTATCCTCTAAAAGCTGCCATTTGCCAGCTTTTGGACC
1 TCTTCATCAAATGCATAAGGATCCCGACTATCCTCTAAAAGCTGCCATTTGCCAGCTTTTGGACC
*
25222 ATCAGGTTTTACACTAAGAGACCCTAACCGATTGCTTGTTACAGGTATTCCATCATATGAACTTC
66 ATCAGGTTTTTCACTAAGAGACCCTAACCGATTGCTTGTTACAGGTATTCCATCATATGAACTTC
*
25287 CTATTTTCCATTTGCCAGCTTTAGGATCCTGACTATCC
131 CTAATTTCCATTTGCCAGCTTTAGGATCCTGACTATCC
* *
25325 TCTTCATCAAATGCATAAGGATCCCGACTATCCTCTATAAGCTGCAATTTGCCAGCTTTTGGACC
1 TCTTCATCAAATGCATAAGGATCCCGACTATCCTCTAAAAGCTGCCATTTGCCAGCTTTTGGACC
* *
25390 ATCAGGTTTTTCACTAAGAGACCGTAACCGATTGCTTCTTACAGGTATTCCATCATATGAACTTC
66 ATCAGGTTTTTCACTAAGAGACCCTAACCGATTGCTTGTTACAGGTATTCCATCATATGAACTTC
25455 CTAATTTCCATTTGCCAGCTTTAGGATCCTGACTATCC
131 CTAATTTCCATTTGCCAGCTTTAGGATCCTGACTATCC
*
25493 TCTTCATCAAATGCATAAGGATCCCGACTATCCTCTAAAAGCTGCCATTTGCCAACTTTTGGACC
1 TCTTCATCAAATGCATAAGGATCCCGACTATCCTCTAAAAGCTGCCATTTGCCAGCTTTTGGACC
25558 ATCAGGTTTTTCACTAAGAGACCCTAACCGATTGCTTGTTACAGGTATTCCATCATATGAACTTC
66 ATCAGGTTTTTCACTAAGAGACCCTAACCGATTGCTTGTTACAGGTATTCCATCATATGAACTTC
25623 CTAATTTCC
131 CTAATTTCC
25632 CACTACATGA
Statistics
Matches: 295, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 295 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (168 bp):
TCTTCATCAAATGCATAAGGATCCCGACTATCCTCTAAAAGCTGCCATTTGCCAGCTTTTGGACC
ATCAGGTTTTTCACTAAGAGACCCTAACCGATTGCTTGTTACAGGTATTCCATCATATGAACTTC
CTAATTTCCATTTGCCAGCTTTAGGATCCTGACTATCC
Found at i:29748 original size:11 final size:11
Alignment explanation
Indices: 29705--29742 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29695 TTCCTATATA
*
29705 AAATAAATTAT
1 AAATTAATTAT
29716 CAAA-TAATTAT
1 -AAATTAATTAT
29727 AAATTAATTAT
1 AAATTAATTAT
29738 AAATT
1 AAATT
29743 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:30435 original size:9 final size:10
Alignment explanation
Indices: 30419--30443 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30409 AAGAGACCTT
30419 CTTTTTTTAG
1 CTTTTTTTAG
30429 CTTTTTTTAG
1 CTTTTTTTAG
30439 CTTTT
1 CTTTT
30444 GTAATTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.72
Consensus pattern (10 bp):
CTTTTTTTAG
Found at i:35784 original size:18 final size:19
Alignment explanation
Indices: 35736--35789 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
35726 AGCTTGCAAT
35736 TTGATATGTTTTCTGTCTAAG
1 TTGAT-TGTTTT-TGTCTAAG
* *
35757 ATGGTTGTTTTTGTCTAA-
1 TTGATTGTTTTTGTCTAAG
*
35775 TTGATTGTTTGTGTC
1 TTGATTGTTTTTGTC
35790 AACAGGTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.43
19 7 0.25
20 6 0.21
21 3 0.11
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (19 bp):
TTGATTGTTTTTGTCTAAG
Found at i:36742 original size:38 final size:38
Alignment explanation
Indices: 36700--36810 Score: 222
Period size: 38 Copynumber: 2.9 Consensus size: 38
36690 AGTACACTTA
36700 TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTGAGT
1 TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTGAGT
36738 TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTGAGT
1 TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTGAGT
36776 TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTG
1 TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTG
36811 TTTCCATTAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (38 bp):
TTATTTCTTCTTTGTTTCAGTTGAGTTAAAACTTGAGT
Found at i:37907 original size:2 final size:2
Alignment explanation
Indices: 37900--37925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37890 TATTATTTGA
37900 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
37926 TTTTGTGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:50151 original size:24 final size:24
Alignment explanation
Indices: 50100--50154 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
50090 ATATGATACT
* *
50100 TAAAACAGCATTTAATGTTTTTTA
1 TAAAACAGCATTTAAAGTTCTTTA
*
50124 TAAAACAGCATTTAGAAG-TCTTTC
1 TAAAACAGCATTTA-AAGTTCTTTA
50148 TAAAACA
1 TAAAACA
50155 CACAAATCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (24 bp):
TAAAACAGCATTTAAAGTTCTTTA
Found at i:53437 original size:6 final size:6
Alignment explanation
Indices: 53428--53457 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
53418 AGTTGAACTT
*
53428 GAACGG GAACGG GACCGG GAACGG GAACGG
1 GAACGG GAACGG GAACGG GAACGG GAACGG
53458 CGGGTGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.50, T:0.00
Consensus pattern (6 bp):
GAACGG
Found at i:53981 original size:5 final size:6
Alignment explanation
Indices: 53963--54008 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
53953 GGTTGGCGAC
53963 GGCGGG GGCGGG GGCGGG GGCGGG GGC-GG GGC-GG GGCGGG GGCGGG
1 GGCGGG GGCGGG GGCGGG GGCGGG GGCGGG GGCGGG GGCGGG GGCGGG
54009 TGCCAGTGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.00, C:0.17, G:0.83, T:0.00
Consensus pattern (6 bp):
GGCGGG
Found at i:60237 original size:21 final size:22
Alignment explanation
Indices: 60213--60257 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
60203 AGAATGCTCC
60213 TTTCTCATCTTTCTT-TTTCTT
1 TTTCTCATCTTTCTTCTTTCTT
** *
60234 TTTCTTTTCTTTTTTCTTTCTT
1 TTTCTCATCTTTCTTCTTTCTT
60256 TT
1 TT
60258 CTTTGAAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTCATCTTTCTTCTTTCTT
Found at i:60239 original size:12 final size:12
Alignment explanation
Indices: 60222--60261 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
60212 CTTTCTCATC
60222 TTTCTTTTTCTT
1 TTTCTTTTTCTT
60234 TTTC-TTTTCTT
1 TTTCTTTTTCTT
*
60245 TTT-TCTTTC-T
1 TTTCTTTTTCTT
60255 TTTCTTT
1 TTTCTTT
60262 GAAGGCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 4 0.17
11 16 0.67
12 4 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:60246 original size:16 final size:17
Alignment explanation
Indices: 60222--60261 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
60212 CTTTCTCATC
60222 TTTCTTTTTCTT-TTTCT
1 TTTCTTTTT-TTCTTTCT
60239 TTTC-TTTTTTCTTTCT
1 TTTCTTTTTTTCTTTCT
60255 TTTCTTT
1 TTTCTTT
60262 GAAGGCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTTTCTTTCT
Found at i:63106 original size:12 final size:12
Alignment explanation
Indices: 63091--63116 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
63081 TAAGTGGAAA
63091 ATATCTATCTAT
1 ATATCTATCTAT
63103 ATATCTATCTAT
1 ATATCTATCTAT
63115 AT
1 AT
63117 TGTAATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATCTATCTAT
Done.