Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011230.1 Corchorus capsularis cultivar CVL-1 contig11251, 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: 19376
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Found at i:3850 original size:35 final size:35
Alignment explanation
Indices: 3811--3929 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 35
3801 CAAGCAAGTT
3811 CAAAGACTTAATTTCACAAGAATTAAGTAAACTAG
1 CAAAGACTTAATTTCACAAGAATTAAGTAAACTAG
* * *
3846 CAAAGA-TATAATCTCACAAGAATTAAGAAAAATTAG
1 CAAAGACT-TAATTTCACAAGAATTAAG-TAAACTAG
* *
3882 CAAAAACTTAATTTCACAAGAATTAAGTAAAGTCAG
1 CAAAGACTTAATTTCACAAGAATTAAGTAAACT-AG
*
3918 CAAAGATTTAAT
1 CAAAGACTTAAT
3930 CCATAGATGA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.01
35 28 0.39
36 41 0.58
37 1 0.01
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (35 bp):
CAAAGACTTAATTTCACAAGAATTAAGTAAACTAG
Found at i:4052 original size:11 final size:11
Alignment explanation
Indices: 3988--4132 Score: 89
Period size: 11 Copynumber: 13.1 Consensus size: 11
3978 TTAGGCAAAA
*
3988 GAAATTAGACT
1 GAAATAAGACT
3999 GAAACT-AGACT
1 GAAA-TAAGACT
**
4010 GAAACCAGACT
1 GAAATAAGACT
* * *
4021 GAAAGAATATT
1 GAAATAAGACT
*
4032 GAAATTAGACT
1 GAAATAAGACT
*
4043 GATATAAGACT
1 GAAATAAGACT
4054 -AATATTAA-ACT
1 GAA-A-TAAGACT
*
4065 GAAAAGAAGACT
1 G-AAATAAGACT
*
4077 GAAATTAGACT
1 GAAATAAGACT
* *
4088 GAAAGAGGACT
1 GAAATAAGACT
*
4099 GAAATAAGACC
1 GAAATAAGACT
* *
4110 GAAAGAGGACT
1 GAAATAAGACT
*
4121 GAAAGAAGACT
1 GAAATAAGACT
4132 G
1 G
4133 GCTTAATTTC
Statistics
Matches: 102, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
10 1 0.01
11 90 0.88
12 9 0.09
13 2 0.02
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (11 bp):
GAAATAAGACT
Found at i:4053 original size:44 final size:45
Alignment explanation
Indices: 3988--4091 Score: 115
Period size: 44 Copynumber: 2.3 Consensus size: 45
3978 TTAGGCAAAA
* * *
3988 GAAATTAGACTGAAACTAGACTGAA-ACCAGACTG-AAAGAATATT
1 GAAATTAGACTGAAACTAGACT-AATACCAAACTGAAAAGAAGACT
* **
4032 GAAATTAGACTGATA-TAAGACTAATATTAAACTGAAAAGAAGACT
1 GAAATTAGACTGAAACT-AGACTAATACCAAACTGAAAAGAAGACT
4077 GAAATTAGACTGAAA
1 GAAATTAGACTGAAA
4092 GAGGACTGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 3 0.06
44 25 0.50
45 22 0.44
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (45 bp):
GAAATTAGACTGAAACTAGACTAATACCAAACTGAAAAGAAGACT
Found at i:4168 original size:36 final size:36
Alignment explanation
Indices: 4126--4361 Score: 316
Period size: 36 Copynumber: 6.6 Consensus size: 36
4116 GGACTGAAAG
4126 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * *
4162 TAGACTGGC-TAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
4197 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * *
4233 TAGACTGGCTTAGTTTCAAGGAAACTACGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * *
4269 AAGACTGGTTTAATTTCAAGGAAATTAGGTAAGGGA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
4305 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
4340 GACACAGGCTTAATTTC-AGGAA
1 AAGACTGGCTTAATTTCAAGGAA
4362 GGGTAATTAA
Statistics
Matches: 173, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
34 5 0.03
35 46 0.27
36 122 0.71
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
Found at i:4412 original size:32 final size:33
Alignment explanation
Indices: 4363--4464 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 33
4353 TTTCAGGAAG
*
4363 GGTAATTAAGTAG--AATAAAGAACTTAATTCAA
1 GGTAATTAAG-AGCCAATAAAGAACTTAATTAAA
4395 GGTAATTAA-AGCCAATAAAGAACTTAATTTAAA
1 GGTAATTAAGAGCCAATAAAGAACTTAA-TTAAA
* *
4428 GGTAGTTAAGTGCAGTCAATAAAGAACTTAATCTAAA
1 GGTAATTAA--G-AGCCAATAAAGAACTTAAT-TAAA
4465 ACGAGATTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
30 2 0.03
32 23 0.39
33 12 0.20
36 1 0.02
37 21 0.36
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (33 bp):
GGTAATTAAGAGCCAATAAAGAACTTAATTAAA
Found at i:4449 original size:37 final size:33
Alignment explanation
Indices: 4376--4464 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 33
4366 AATTAAGTAG
*
4376 AATAAAGAACTTAA-TTCAAGGTAATTAAAGCC
1 AATAAAGAACTTAATTTAAAGGTAATTAAAGCC
* *
4408 AATAAAGAACTTAATTTAAAGGTAGTTAAGTGCAGTC
1 AATAAAGAACTTAATTTAAAGGTAATTAA----AGCC
*
4445 AATAAAGAACTTAATCTAAA
1 AATAAAGAACTTAATTTAAA
4465 ACGAGATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 14 0.29
33 12 0.25
37 22 0.46
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (33 bp):
AATAAAGAACTTAATTTAAAGGTAATTAAAGCC
Found at i:16557 original size:26 final size:26
Alignment explanation
Indices: 16528--16579 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
16518 TTCAAGAAAT
16528 TGCCAAGGGGCATTTTCGTCAT-TTTA
1 TGCC-AGGGGCATTTTCGTCATCTTTA
*
16554 TGCCCGGGGCATTTTCGTCATCTTTA
1 TGCCAGGGGCATTTTCGTCATCTTTA
16580 AACTAGACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TGCCAGGGGCATTTTCGTCATCTTTA
Done.