Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006488.1 Corchorus olitorius cultivar O-4 contig06513, 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, 915
Length: 1526
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:143 original size:14 final size:12
Alignment explanation
Indices: 110--148 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
100 GGAATTATTG
110 ATTTATTATTAA
1 ATTTATTATTAA
*
122 ACTTATTATTAGTA
1 ATTTATTATTA--A
136 ATTTATTATTAA
1 ATTTATTATTAA
148 A
1 A
149 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (12 bp):
ATTTATTATTAA
Found at i:564 original size:45 final size:45
Alignment explanation
Indices: 513--600 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
503 CCTAAATTTA
* *
513 ACTCCTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCT
1 ACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAATATTCT
* *
558 ACTCCTCCATCTCTATATAATTCATCAAAATAAAATTAATATT
1 ACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAATATT
601 AATTGTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (45 bp):
ACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAATATTCT
Done.