Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012954.1 Corchorus olitorius cultivar O-4 contig12987, 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: 18826
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Found at i:1399 original size:27 final size:24
Alignment explanation
Indices: 1353--1417 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
1343 GTGAAAAGGA
*
1353 AGGAGGAGATGGAAAGGAAGAAAG
1 AGGAGGAGAGGGAAAGGAAGAAAG
1377 AGGAGGAGAGGGAAAGGAAG-AAG
1 AGGAGGAGAGGGAAAGGAAGAAAG
* *
1400 AAGATGGAGAAGGAAAGG
1 AGGA-GGAGAGGGAAAGG
1418 TTGGAGAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 6 0.16
24 31 0.84
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.03
Consensus pattern (24 bp):
AGGAGGAGAGGGAAAGGAAGAAAG
Found at i:2614 original size:24 final size:24
Alignment explanation
Indices: 2587--2632 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2577 AAGTAATATT
2587 AGGGGAGTACATAATATGGCCATC
1 AGGGGAGTACATAATATGGCCATC
2611 AGGGGAGTACATAATATGGCCA
1 AGGGGAGTACATAATATGGCCA
2633 CTATTAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (24 bp):
AGGGGAGTACATAATATGGCCATC
Found at i:4845 original size:21 final size:21
Alignment explanation
Indices: 4821--4888 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
4811 AATTCTCTAT
4821 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
4842 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
4863 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
4884 AAATT
1 AAATT
4889 CCGATCCTTA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:4867 original size:42 final size:42
Alignment explanation
Indices: 4808--4887 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
4798 GCTAAGTCTT
4808 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
* *
4850 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAAT
1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAAT
4888 TCCGATCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
Found at i:5095 original size:108 final size:108
Alignment explanation
Indices: 4906--5123 Score: 418
Period size: 108 Copynumber: 2.0 Consensus size: 108
4896 TTAGCTATCT
4906 TATCTAAAAACTTTGTTCTAACTTAAAAGAAAATATTTTTTATTTTGTAGAATAATTAAGTAGAA
1 TATCTAAAAACTTTGTTCTAACTTAAAAGAAAATATTTTTTATTTTGTAGAATAATTAAGTAGAA
*
4971 ATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGAA
66 ATAAGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGAA
5014 TATCTAAAAACTTTGTTCTAACTTAAAAGAAAATATTTTTTATTTTGTAGAATAATTAAGTAGAA
1 TATCTAAAAACTTTGTTCTAACTTAAAAGAAAATATTTTTTATTTTGTAGAATAATTAAGTAGAA
*
5079 ATAAGGGGATATGATTTATTATAACATTTATTGTGTGAAAGAA
66 ATAAGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGAA
5122 TA
1 TA
5124 ATTAAGTAGA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (108 bp):
TATCTAAAAACTTTGTTCTAACTTAAAAGAAAATATTTTTTATTTTGTAGAATAATTAAGTAGAA
ATAAGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGAA
Found at i:5143 original size:56 final size:56
Alignment explanation
Indices: 5062--5175 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
5052 TTTATTTTGT
5062 AGAATAATTAAGTAGAAATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
** *
5118 AGAATAATTAAGTAGAGTTAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
5174 AG
1 AG
5176 GAAATAGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
Found at i:10857 original size:7 final size:7
Alignment explanation
Indices: 10842--10887 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
10832 CTGTTTTAGA
*
10842 CAAACAC
1 CAAAAAC
10849 CAAAAAC
1 CAAAAAC
10856 C-AAAAC
1 CAAAAAC
10862 C-AAAAC
1 CAAAAAC
10868 C-AAAAC
1 CAAAAAC
10874 CAAAAAC
1 CAAAAAC
10881 CAAAAAC
1 CAAAAAC
10888 GAATGGCATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
6 18 0.49
7 19 0.51
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAC
Found at i:10862 original size:6 final size:6
Alignment explanation
Indices: 10851--10885 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
10841 ACAAACACCA
10851 AAAACC AAAACC AAAACC AAAACC AAAAACC AAAA
1 AAAACC AAAACC AAAACC AAAACC -AAAACC AAAA
10886 ACGAATGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:10868 original size:12 final size:13
Alignment explanation
Indices: 10842--10885 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
10832 CTGTTTTAGA
10842 CAAACACCAAAAAC
1 CAAA-ACCAAAAAC
10856 CAAAACC-AAAAC
1 CAAAACCAAAAAC
10868 CAAAACCAAAAAC
1 CAAAACCAAAAAC
10881 CAAAA
1 CAAAA
10886 ACGAATGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.41
13 13 0.45
14 4 0.14
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAACCAAAAAC
Found at i:18489 original size:31 final size:31
Alignment explanation
Indices: 18431--18491 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
18421 CTTGAGGTCA
*
18431 AAACCCGAACCCGTACGACCCTAAACCCAGC
1 AAACCCGAACCCGAACGACCCTAAACCCAGC
* *
18462 AAACCCGAGACCCGAATGA-CCTGAACCCAG
1 AAACCCGA-ACCCGAACGACCCTAAACCCAG
18492 ATGAGCCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.36, C:0.41, G:0.16, T:0.07
Consensus pattern (31 bp):
AAACCCGAACCCGAACGACCCTAAACCCAGC
Found at i:18511 original size:16 final size:15
Alignment explanation
Indices: 18471--18513 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
18461 CAAACCCGAG
*
18471 ACCCGAATGACCTGA
1 ACCCGAATGACCGGA
18486 ACCC-AGATGAGCCGGA
1 ACCCGA-ATGA-CCGGA
18502 ACCCGAATGACC
1 ACCCGAATGACC
18514 CACGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 12 0.50
17 1 0.04
ACGTcount: A:0.33, C:0.35, G:0.23, T:0.09
Consensus pattern (15 bp):
ACCCGAATGACCGGA
Done.