Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011275.1 Corchorus olitorius cultivar O-4 contig11308, 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: 3127
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:340 original size:21 final size:21
Alignment explanation
Indices: 316--358 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
306 CTTGCTCTTG
316 TCAATGGA-CATAATGGCATCT
1 TCAATGGATCA-AATGGCATCT
337 TCAATGGATCAAATGGCATCT
1 TCAATGGATCAAATGGCATCT
358 T
1 T
359 TGGCATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
TCAATGGATCAAATGGCATCT
Found at i:2382 original size:21 final size:21
Alignment explanation
Indices: 2356--2447 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
2346 TGCTAGGAGA
2356 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
2377 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2398 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
2419 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2440 TCATTGGA
1 TCATTGGA
2448 ATTGCTTAAG
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 2 0.03
21 67 0.97
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.