Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012115.1 Corchorus capsularis cultivar CVL-1 contig12136, 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: 24742
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1947 original size:21 final size:20
Alignment explanation
Indices: 1923--1965 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1913 TAGATTTAGA
*
1923 TTTAATCTACTTTGCTTTCTT
1 TTTAATCTA-ATTGCTTTCTT
* *
1944 TTTAGTTTAATTGCTTTCTT
1 TTTAATCTAATTGCTTTCTT
1964 TT
1 TT
1966 CAATTGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTAATCTAATTGCTTTCTT
Found at i:3362 original size:38 final size:38
Alignment explanation
Indices: 3314--3392 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
3304 CAGCAAATGT
3314 AAATAATCCAAATATCCCAAACATACTT-CAAATGATCC
1 AAATAATCCAAATATCCCAAA-ATACTTACAAATGATCC
* * * *
3352 AAATATTCCAAATTTCCCTAAATACTTAGCAAATTATCC
1 AAATAATCCAAATATCCCAAAATACTTA-CAAATGATCC
3391 AA
1 AA
3393 CCAAATACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 6 0.17
38 18 0.51
39 11 0.31
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.28
Consensus pattern (38 bp):
AAATAATCCAAATATCCCAAAATACTTACAAATGATCC
Found at i:4683 original size:15 final size:15
Alignment explanation
Indices: 4649--4693 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
4639 ACGACAGGGG
*
4649 CTTCTCAGCAGCAGC
1 CTTCTCAGCAGAAGC
* *
4664 TTTCTGAGCAGAAGC
1 CTTCTCAGCAGAAGC
*
4679 CTTCTCAGCTGAAGC
1 CTTCTCAGCAGAAGC
4694 TGAACTACTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (15 bp):
CTTCTCAGCAGAAGC
Found at i:6129 original size:20 final size:21
Alignment explanation
Indices: 6104--6146 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6094 TGAAGGGAAT
6104 CTTGT-CATAAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
* *
6124 CTTGTCCTTGAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
6145 CT
1 CT
6147 GATGAAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATG
Found at i:6525 original size:3 final size:3
Alignment explanation
Indices: 6517--6543 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6507 TTCACTATTC
6517 ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA
6544 TACACCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:9866 original size:2 final size:2
Alignment explanation
Indices: 9859--9885 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9849 ACTCAATGTG
9859 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9886 GTATTGCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20867 original size:15 final size:15
Alignment explanation
Indices: 20849--20931 Score: 66
Period size: 15 Copynumber: 5.5 Consensus size: 15
20839 ATAGGTAATG
20849 AAATTATAATATTAT
1 AAATTATAATATTAT
*
20864 AAA-TATTATATT-T
1 AAATTATAATATTAT
*
20877 AGGAATTATAAATATTAG
1 A--AATTAT-AATATTAT
20895 AAA--ATAATATTAT
1 AAATTATAATATTAT
* *
20908 AAATTATAATGTAAT
1 AAATTATAATATTAT
20923 GAAATTATA
1 -AAATTATA
20932 TCTAGGAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 12 0.22
14 10 0.19
15 13 0.24
16 13 0.24
17 5 0.09
18 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
AAATTATAATATTAT
Found at i:20926 original size:29 final size:30
Alignment explanation
Indices: 20896--20952 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
20886 AAATATTAGA
*
20896 AAATAATAT-TATAAATTATA-ATGTAATG
1 AAATAATATCTAGAAATTATATATGTAATG
* *
20924 AAATTATATCTAGGAATTATATATGTAAT
1 AAATAATATCTAGAAATTATATATGTAAT
20953 TATATTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 9 0.38
30 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (30 bp):
AAATAATATCTAGAAATTATATATGTAATG
Found at i:20943 original size:13 final size:13
Alignment explanation
Indices: 20925--20969 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
20915 AATGTAATGA
*
20925 AATTATATCTAGG
1 AATTATATATAGG
*
20938 AATTATATAT-GT
1 AATTATATATAGG
*
20950 AATTATATTTAGG
1 AATTATATATAGG
20963 AATTATA
1 AATTATA
20970 AAATCAGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (13 bp):
AATTATATATAGG
Found at i:21294 original size:15 final size:16
Alignment explanation
Indices: 21262--21295 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21252 AAAGAAGAAT
*
21262 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
21278 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
21293 TAA
1 TAA
21296 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:21338 original size:36 final size:36
Alignment explanation
Indices: 21297--21374 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
21287 ATTAACTAAG
21297 AAAGCAATCAAGAAAATTAAAGAA-AACAATTAATCA
1 AAAGCAATCAAGAAAATT-AAGAATAACAATTAATCA
* * * ** *
21333 AAAGCAGTGAATATTATTGAGAATAACAATTAATCA
1 AAAGCAATCAAGAAAATTAAGAATAACAATTAATCA
21369 AAAGCA
1 AAAGCA
21375 GGAGCAATCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.21
Consensus pattern (36 bp):
AAAGCAATCAAGAAAATTAAGAATAACAATTAATCA
Done.