Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012545.1 Corchorus capsularis cultivar CVL-1 contig12566, 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: 16597
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:6271 original size:26 final size:26
Alignment explanation
Indices: 6240--6290 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
6230 TGGTAAACAA
6240 TCTTATCTCGAGACTCAAGTCCCGAT
1 TCTTATCTCGAGACTCAAGTCCCGAT
* *
6266 TCTTATCTCGAGATTCGAGTCCCGA
1 TCTTATCTCGAGACTCAAGTCCCGA
6291 CAAAGATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (26 bp):
TCTTATCTCGAGACTCAAGTCCCGAT
Found at i:12059 original size:13 final size:13
Alignment explanation
Indices: 12041--12084 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
12031 GGTTACGAAT
12041 ATACAGTATATGA
1 ATACAGTATATGA
*
12054 ATACAG-ATGA-GT
1 ATACAGTAT-ATGA
12066 ATACAGTATATGA
1 ATACAGTATATGA
12079 ATACAG
1 ATACAG
12085 ATGAGTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (13 bp):
ATACAGTATATGA
Found at i:12071 original size:12 final size:12
Alignment explanation
Indices: 12054--12096 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
12044 CAGTATATGA
12054 ATACAGATGAGT
1 ATACAGATGAGT
*
12066 ATACAGTAT-ATGA
1 ATACAG-ATGA-GT
12079 ATACAGATGAGT
1 ATACAGATGAGT
12091 ATACAG
1 ATACAG
12097 TACAACCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (12 bp):
ATACAGATGAGT
Found at i:12074 original size:25 final size:25
Alignment explanation
Indices: 12040--12098 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
12030 TGGTTACGAA
12040 TATACAGTATATGAATACAGATGAG
1 TATACAGTATATGAATACAGATGAG
12065 TATACAGTATATGAATACAGATGAG
1 TATACAGTATATGAATACAGATGAG
12090 TATACAGTA
1 TATACAGTA
12099 CAACCAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (25 bp):
TATACAGTATATGAATACAGATGAG
Found at i:12512 original size:12 final size:12
Alignment explanation
Indices: 12495--12520 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12485 ACCATAATCA
12495 GGTGCGCGACGT
1 GGTGCGCGACGT
12507 GGTGCGCGACGT
1 GGTGCGCGACGT
12519 GG
1 GG
12521 ATCGGATCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.54, T:0.15
Consensus pattern (12 bp):
GGTGCGCGACGT
Done.