Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002359.1 Corchorus olitorius cultivar O-4 contig02359, 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: 3791
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:151 original size:44 final size:44
Alignment explanation
Indices: 88--172 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
78 TAATTTTTTA
88 ATCTTACTACTATATAAAATCATGAACTCAAAAATTCTAATCTT
1 ATCTTACTACTATATAAAATCATGAACTCAAAAATTCTAATCTT
*
132 ATCTTACTATTATATAAAATCATGAACTCAAAAATTCTAAT
1 ATCTTACTACTATATAAAATCATGAACTCAAAAATTCTAAT
173 TGGGAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.36
Consensus pattern (44 bp):
ATCTTACTACTATATAAAATCATGAACTCAAAAATTCTAATCTT
Found at i:1225 original size:43 final size:43
Alignment explanation
Indices: 1178--1273 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 43
1168 GAGGTTACTT
1178 AAATTATAAAAGATGGGTACCAAAATTTCAAATGAGGATATCA
1 AAATTATAAAAGATGGGTACCAAAATTTCAAATGAGGATATCA
* * * * * * * * **
1221 AAATTACAAAGGGTTGTTATCAAAGTTTCAATTGAGTTTATCA
1 AAATTATAAAAGATGGGTACCAAAATTTCAAATGAGGATATCA
1264 AAATTATAAA
1 AAATTATAAA
1274 GAGCTTTTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (43 bp):
AAATTATAAAAGATGGGTACCAAAATTTCAAATGAGGATATCA
Done.