Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013090.1 Corchorus olitorius cultivar O-4 contig13123, 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: 22218
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:1236 original size:21 final size:21
Alignment explanation
Indices: 1212--1254 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202 CTTCTTTATA
*
1212 CTACTCGAACCCTTCCAATTT
1 CTACCCGAACCCTTCCAATTT
1233 CTACCCGAACCCTTCCAATTT
1 CTACCCGAACCCTTCCAATTT
1254 C
1 C
1255 AAACCCGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.42, G:0.05, T:0.30
Consensus pattern (21 bp):
CTACCCGAACCCTTCCAATTT
Found at i:3377 original size:25 final size:25
Alignment explanation
Indices: 3347--3394 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3337 ATGCAATGTC
3347 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
3372 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
3395 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:13054 original size:26 final size:26
Alignment explanation
Indices: 13018--13069 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
13008 TAGCATAAGG
* *
13018 TATTTCCATAGGATGTTGCCACAGGA
1 TATTTCCATAGGATCTTACCACAGGA
*
13044 TATTTCCATAGGGTCTTACCACAGGA
1 TATTTCCATAGGATCTTACCACAGGA
13070 ACGGTCACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (26 bp):
TATTTCCATAGGATCTTACCACAGGA
Found at i:13166 original size:18 final size:19
Alignment explanation
Indices: 13143--13179 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
13133 TACCCATGTC
13143 AGAAAAAAAAT-AATAAAT
1 AGAAAAAAAATGAATAAAT
*
13161 AGAAAATAAATGAATAAAT
1 AGAAAAAAAATGAATAAAT
13180 TATTTTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AGAAAAAAAATGAATAAAT
Found at i:14654 original size:21 final size:21
Alignment explanation
Indices: 14619--14660 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14609 TATGTGTGTG
*
14619 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
14641 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
14661 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:18055 original size:14 final size:14
Alignment explanation
Indices: 18033--18069 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
18023 TGCATGCAAA
18033 CAAACAAAAAAATG
1 CAAACAAAAAAATG
18047 CAAA-AAAAAAATG
1 CAAACAAAAAAATG
18060 CAAACAAAAA
1 CAAACAAAAA
18070 TGCATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.76, C:0.14, G:0.05, T:0.05
Consensus pattern (14 bp):
CAAACAAAAAAATG
Found at i:18056 original size:13 final size:13
Alignment explanation
Indices: 18033--18073 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
18023 TGCATGCAAA
18033 CAAACAAAAAAATG
1 CAAA-AAAAAAATG
18047 CAAAAAAAAAATG
1 CAAAAAAAAAATG
*
18060 C-AAACAAAAATG
1 CAAAAAAAAAATG
18072 CA
1 CA
18074 TTTTTTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 10 0.40
14 4 0.16
ACGTcount: A:0.71, C:0.15, G:0.07, T:0.07
Consensus pattern (13 bp):
CAAAAAAAAAATG
Done.