Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016042.1 Corchorus olitorius cultivar O-4 contig16075, 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: 7183
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:263 original size:21 final size:21
Alignment explanation
Indices: 237--349 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
227 TGCTAGAAGT
237 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
258 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
279 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
300 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
321 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
342 TCATTGGA
1 TCATTGGA
350 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:6658 original size:21 final size:21
Alignment explanation
Indices: 6632--6673 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6622 TAAGGAAGAA
6632 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
6653 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
6674 CCTAAGATGC
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:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Done.