Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011179.1 Corchorus capsularis cultivar CVL-1 contig11200, 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: 9505
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Found at i:1630 original size:15 final size:16
Alignment explanation
Indices: 1610--1645 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1600 CTCAAATGTC
1610 GGGTC-ATTTGGGTTT
1 GGGTCAATTTGGGTTT
*
1625 GGGTCAATTTTGGTTT
1 GGGTCAATTTGGGTTT
1641 GGGTC
1 GGGTC
1646 TTTTTCAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.08, C:0.08, G:0.39, T:0.44
Consensus pattern (16 bp):
GGGTCAATTTGGGTTT
Found at i:4383 original size:25 final size:25
Alignment explanation
Indices: 4355--4405 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4345 GAGTTATAGC
4355 TCAGATGCATTCCAGAAGAATCCAG
1 TCAGATGCATTCCAGAAGAATCCAG
4380 TCAGATGCATTCCAGAAGAATCCAG
1 TCAGATGCATTCCAGAAGAATCCAG
4405 T
1 T
4406 ACAGCAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (25 bp):
TCAGATGCATTCCAGAAGAATCCAG
Found at i:6369 original size:41 final size:41
Alignment explanation
Indices: 6293--6426 Score: 202
Period size: 41 Copynumber: 3.3 Consensus size: 41
6283 TAATTTGGAT
6293 AGTCAAACATAGTTAAAG-T-TAATCCAGGGCGATTAAGAA
1 AGTCAAACATAGTTAAAGTTGTAATCCAGGGCGATTAAGAA
6332 AGTCAAACATAGTTAAAGTTGTAATCCAGGGCGATTAAGAA
1 AGTCAAACATAGTTAAAGTTGTAATCCAGGGCGATTAAGAA
* * * *
6373 AGTCAAACATAGTTGAAGTTGAAATCCATGGTGATTAAGAAA
1 AGTCAAACATAGTTAAAGTTGTAATCCAGGGCGATTAAG-AA
6415 AG-CAAACATAGT
1 AGTCAAACATAGT
6427 CCTAATTCAG
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
39 18 0.20
40 1 0.01
41 65 0.74
42 4 0.05
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (41 bp):
AGTCAAACATAGTTAAAGTTGTAATCCAGGGCGATTAAGAA
Found at i:6596 original size:22 final size:22
Alignment explanation
Indices: 6570--6663 Score: 109
Period size: 22 Copynumber: 4.3 Consensus size: 22
6560 AGGCAAAGTT
*
6570 AGACTGAAATTAGACTGATAGA
1 AGACTGAAATTAGACTGAAAGA
**
6592 AGACTGAAATTAGACTGATATTA
1 AGACTGAAATTAGACTGA-AAGA
*
6615 A-ACTGAAATCAGACTGAAAGA
1 AGACTGAAATTAGACTGAAAGA
* **
6636 ATACTGAAAGAAGACTGAAAGA
1 AGACTGAAATTAGACTGAAAGA
6658 AGACTG
1 AGACTG
6664 GCTTAGTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
21 3 0.05
22 56 0.92
23 2 0.03
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (22 bp):
AGACTGAAATTAGACTGAAAGA
Found at i:6629 original size:33 final size:33
Alignment explanation
Indices: 6568--6663 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 33
6558 TTAGGCAAAG
* *
6568 TTAGACTGAAATTAGACTGATAGAAGACTGAAA
1 TTAGACTGAAATTAAACTGAAAGAAGACTGAAA
* **
6601 TTAGACTGATATTAAACTGAAATCAGACTGAAA
1 TTAGACTGAAATTAAACTGAAAGAAGACTGAAA
** * *
6634 GAATACTGAAA-GAAGACTGAAAGAAGACTG
1 TTAGACTGAAATTAA-ACTGAAAGAAGACTG
6664 GCTTAGTTTC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 2 0.04
33 48 0.96
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (33 bp):
TTAGACTGAAATTAAACTGAAAGAAGACTGAAA
Found at i:6641 original size:11 final size:11
Alignment explanation
Indices: 6570--6663 Score: 82
Period size: 11 Copynumber: 8.5 Consensus size: 11
6560 AGGCAAAGTT
**
6570 AGACTGAAATT
1 AGACTGAAAGA
*
6581 AGACTGATAGA
1 AGACTGAAAGA
**
6592 AGACTGAAATT
1 AGACTGAAAGA
**
6603 AGACTGATATTA
1 AGACTGA-AAGA
**
6615 A-ACTGAAATC
1 AGACTGAAAGA
6625 AGACTGAAAGA
1 AGACTGAAAGA
*
6636 ATACTGAAAGA
1 AGACTGAAAGA
6647 AGACTGAAAGA
1 AGACTGAAAGA
6658 AGACTG
1 AGACTG
6664 GCTTAGTTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
10 3 0.04
11 61 0.91
12 3 0.04
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (11 bp):
AGACTGAAAGA
Found at i:6698 original size:36 final size:36
Alignment explanation
Indices: 6657--7016 Score: 486
Period size: 36 Copynumber: 9.9 Consensus size: 36
6647 AGACTGAAAG
6657 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
**
6693 AAGACTGATTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
* * * * * *
6729 TAGACTGACTTAATTTCAAGGAAATTAAGTAAAGAG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
*
6765 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAC
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
6801 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
* * * * * *
6837 TAGACTGACTTAATTTCAAGGAAATTAAGTAAAAAAA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGT-AAAGAA
*
6874 AGAGAACTGGCTTAGTTTCAAGAAAACTAGGTAAAGAA
1 A-AG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
6912 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
* * *
6948 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
* * * *
6984 AAGACTAGCTTAATTTCAAGGAAATTAAGTAAA
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAA
7017 AAGACACATT
Statistics
Matches: 287, Mismatches: 34, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
36 250 0.87
37 7 0.02
38 8 0.03
39 22 0.08
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (36 bp):
AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
Found at i:7114 original size:32 final size:32
Alignment explanation
Indices: 7077--7181 Score: 131
Period size: 32 Copynumber: 3.2 Consensus size: 32
7067 CAGGAAAGGA
7077 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
*
7109 AATTAAGTGAAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-AA---AATAAAGA-ACTTAATTCAGGGT
* *
7145 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
7177 AATTA
1 AATTA
7182 TGTGAAGTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
32 31 0.49
33 3 0.05
35 2 0.03
36 27 0.43
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (32 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGGGT
Found at i:7127 original size:36 final size:35
Alignment explanation
Indices: 7087--7205 Score: 147
Period size: 36 Copynumber: 3.4 Consensus size: 35
7077 AATTAAGTAA
7087 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGT
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGT
*
7122 CAATAAA-AGGCTTAATTCAGGGTAATTAAGT--AG-
1 -AATAAAGA-ACTTAATTCAGGGTAATTAAGTGAAGT
* *
7155 AATAAAGAACTTAATTCAAGGTAATTATGTGAAGTT
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAG-T
*
7191 AATAAAGAGCTTAAT
1 AATAAAGAACTTAAT
7206 ATAGAAAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
32 25 0.35
33 1 0.01
34 4 0.06
35 1 0.01
36 41 0.57
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (35 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGT
Found at i:7159 original size:68 final size:68
Alignment explanation
Indices: 7077--7205 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 68
7067 CAGGAAAGGA
*
7077 AATTAAGTAAAATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTCAATAAA-AGGCTTAATTCA
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGA-GCTTAATTCA
7141 GGGT
65 GGGT
* * *
7145 AATTAAGTAGAATAAAGAACTTAATTCAAGGTAATTATGTGAAGTTAATAAAGAGCTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
7206 ATAGAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
68 55 0.98
69 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAATTCAG
GGT
Done.