Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014771.1 Corchorus capsularis cultivar CVL-1 contig14792, 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: 57025
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:366 original size:2 final size:2
Alignment explanation
Indices: 318--347 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
308 TTGTAATCAG
318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
348 CAAAGCAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6564 original size:11 final size:11
Alignment explanation
Indices: 6550--6592 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
6540 AATTAAGTTA
6550 AAAATTTATTT
1 AAAATTTATTT
*
6561 AAAATTTATTGCA
1 AAAATTTATT--T
6574 AAAATTTATTT
1 AAAATTTATTT
6585 AAAATTTA
1 AAAATTTA
6593 ATTATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
AAAATTTATTT
Found at i:9229 original size:24 final size:22
Alignment explanation
Indices: 9181--9222 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9171 GGAAAATCTC
* *
9181 AAATCAGGAAAGAGAGAAAAAA
1 AAATCTGGAAAAAGAGAAAAAA
9203 AAATCTGGAAAAAGAGAAAA
1 AAATCTGGAAAAAGAGAAAA
9223 GTGAAAAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.21, T:0.07
Consensus pattern (22 bp):
AAATCTGGAAAAAGAGAAAAAA
Found at i:12133 original size:2 final size:2
Alignment explanation
Indices: 12128--12164 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
12118 ATAATATGTA
12128 AT AT AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
12165 CATAAATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15825 original size:6 final size:6
Alignment explanation
Indices: 15794--15823 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
15784 GGAAGGCAGG
15794 GCCAAA GCCAAA GCCAAA GCCAAA GGCCAA
1 GCCAAA GCCAAA GCCAAA GCCAAA -GCCAA
15824 GGGCTCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.47, C:0.33, G:0.20, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:21994 original size:17 final size:17
Alignment explanation
Indices: 21972--22008 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21962 GTTATCCAGC
21972 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
*
21989 ACCTCATGCTACCTGGT
1 ACCTCATGCTACCTAGT
22006 ACC
1 ACC
22009 ATGAGGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:34580 original size:2 final size:2
Alignment explanation
Indices: 34573--34606 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34563 TTTTGGGTCA
34573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34607 CTTCTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53153 original size:17 final size:18
Alignment explanation
Indices: 53131--53165 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53121 AATACAGAGA
53131 GGAGACTG-GAGAGAAAT
1 GGAGACTGAGAGAGAAAT
53148 GGAGACTGAGAGAGAAAT
1 GGAGACTGAGAGAGAAAT
53166 CAGAAGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.06, G:0.40, T:0.11
Consensus pattern (18 bp):
GGAGACTGAGAGAGAAAT
Found at i:53574 original size:25 final size:26
Alignment explanation
Indices: 53525--53574 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
53515 TTATATATTT
*
53525 ATATACAACTTAAAATTTTTGAATTA
1 ATATACAACTTAAAATTTTTAAATTA
*
53551 ATATATAACTT-AAATTTTTAAATT
1 ATATACAACTTAAAATTTTTAAATT
53575 CTTTAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATACAACTTAAAATTTTTAAATTA
Done.