Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009538.1 Corchorus olitorius cultivar O-4 contig09570, 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: 20539
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:6260 original size:45 final size:45
Alignment explanation
Indices: 6196--6291 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
6186 CAAAGGAAGG
6196 GGAGCAGCATCACCATTGCTTTTCTCCTCAAGTAGTTCAGCAGGA
1 GGAGCAGCATCACCATTGCTTTTCTCCTCAAGTAGTTCAGCAGGA
6241 GGAGCAGCATCACCATTGCTTTTCTCCTCAAGTAGTTCAGCAGGA
1 GGAGCAGCATCACCATTGCTTTTCTCCTCAAGTAGTTCAGCAGGA
*
6286 GCAGCA
1 GGAGCA
6292 TTAGATGCCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (45 bp):
GGAGCAGCATCACCATTGCTTTTCTCCTCAAGTAGTTCAGCAGGA
Found at i:7042 original size:2 final size:2
Alignment explanation
Indices: 7035--7079 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
7025 ATGAAGAAAA
7035 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7077 AG A
1 AG A
7080 CTTGCCTGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11232 original size:75 final size:75
Alignment explanation
Indices: 11142--11294 Score: 297
Period size: 75 Copynumber: 2.0 Consensus size: 75
11132 GGTTTTGTAC
11142 ATGATGATCCATTATTTCAATTCATTCTCCTTCTTCAGTTTGCTGTTCCACCTGCAATGAATATA
1 ATGATGATCCATTATTTCAATTCATTCTCCTTCTTCAGTTTGCTGTTCCACCTGCAATGAATATA
11207 GGTATCATAG
66 GGTATCATAG
*
11217 ATGATGTTCCATTATTTCAATTCATTCTCCTTCTTCAGTTTGCTGTTCCACCTGCAATGAATATA
1 ATGATGATCCATTATTTCAATTCATTCTCCTTCTTCAGTTTGCTGTTCCACCTGCAATGAATATA
11282 GGTATCATAG
66 GGTATCATAG
11292 ATG
1 ATG
11295 TTAAAATCAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (75 bp):
ATGATGATCCATTATTTCAATTCATTCTCCTTCTTCAGTTTGCTGTTCCACCTGCAATGAATATA
GGTATCATAG
Found at i:13189 original size:2 final size:2
Alignment explanation
Indices: 13182--13239 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
13172 TATTGAAAAT
13182 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13224 AG AG AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG A
13240 CCTTGACAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18029 original size:12 final size:12
Alignment explanation
Indices: 18012--18036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18002 TCCCACGAAC
18012 TTAGAGTCCCTT
1 TTAGAGTCCCTT
18024 TTAGAGTCCCTT
1 TTAGAGTCCCTT
18036 T
1 T
18037 GCAAATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAGAGTCCCTT
Found at i:20144 original size:2 final size:2
Alignment explanation
Indices: 20137--20188 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
20127 CATTAAGCTC
* *
20137 AT AT AT AT GGT AT AT GT AT A- 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 AT AT AT AT
*
20179 AT AT AC AT AT
1 AT AT AT AT AT
20189 TTAGACATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Done.