Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020676.1 Corchorus olitorius cultivar O-4 contig20709, 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: 10490
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:7596 original size:43 final size:43
Alignment explanation
Indices: 7535--7619 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
7525 TTGCCTCACA
7535 AAACCATTTTGGACTGGATGCTTTTGGCATATAAATAAATGAG
1 AAACCATTTTGGACTGGATGCTTTTGGCATATAAATAAATGAG
7578 AAACCATTTTGGACTGGATGCTTTTGGCATATAAATAAATGA
1 AAACCATTTTGGACTGGATGCTTTTGGCATATAAATAAATGA
7620 TCATTTTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (43 bp):
AAACCATTTTGGACTGGATGCTTTTGGCATATAAATAAATGAG
Found at i:7869 original size:26 final size:26
Alignment explanation
Indices: 7840--7893 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
7830 CCATTAAAAC
7840 CAATGGATACAATGCAACAATACCTA
1 CAATGGATACAATGCAACAATACCTA
7866 CAATGGATACAATGCAACAATACCTA
1 CAATGGATACAATGCAACAATACCTA
7892 CA
1 CA
7894 GCAGCAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (26 bp):
CAATGGATACAATGCAACAATACCTA
Found at i:9433 original size:21 final size:21
Alignment explanation
Indices: 9409--9450 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9399 ACAATAAGTA
9409 ATAAAATTATATATATAGCAT
1 ATAAAATTATATATATAGCAT
9430 ATAAAATTATATATATAGCAT
1 ATAAAATTATATATATAGCAT
9451 GGCTATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATAAAATTATATATATAGCAT
Found at i:9803 original size:19 final size:20
Alignment explanation
Indices: 9765--9803 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9755 CATGAAATCT
9765 AAACCCTAACCATGACATGAC
1 AAACCCTAA-CATGACATGAC
*
9786 AAACCCTAA-ATGAGATGA
1 AAACCCTAACATGACATGA
9804 AACATTGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (20 bp):
AAACCCTAACATGACATGAC
Found at i:9875 original size:40 final size:42
Alignment explanation
Indices: 9831--9915 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
9821 CATGAAAGCC
*
9831 AAACCCT-AACAAACA-ATATAAACCCTAAGTGAGAT-AAAAG
1 AAACCCTCAAAAAACACAT-TAAACCCTAAGTGAGATGAAAAG
*
9871 AAACCCTCAAAAAACACATTAAACCCTAGGTGAGATGAAAAG
1 AAACCCTCAAAAAACACATTAAACCCTAAGTGAGATGAAAAG
9913 AAA
1 AAA
9916 AAAATGAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 7 0.17
41 23 0.57
42 10 0.25
ACGTcount: A:0.54, C:0.20, G:0.12, T:0.14
Consensus pattern (42 bp):
AAACCCTCAAAAAACACATTAAACCCTAAGTGAGATGAAAAG
Found at i:10170 original size:5 final size:5
Alignment explanation
Indices: 10148--10187 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
10138 TTGTTTGTTT
10148 ATATA TATATA TATATA ATATA ATATA ATATA ATATA ATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATA
10188 ACGCGAGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Done.