Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000919.1 Corchorus olitorius cultivar O-4 contig00919, 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: 2154
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:1181 original size:164 final size:164
Alignment explanation
Indices: 911--1237 Score: 507
Period size: 164 Copynumber: 2.0 Consensus size: 164
901 AAGATCACAT
*
911 GTCACTCTCCTTGAAGCAAAATTAAAATTTATTAAGTCATTCTCTTCAAAGCTTGCTTGGATGAA
1 GTCACTCTCCTTGAAGCAAAATTAAAATTTATTAAGTCATTCTCTTCAAAGCTTACTTGGATGAA
**
976 GTGAAGATGAAACTCCAATCAGAGTTAGTAGTTGCTTAAATAGCATGCA-ATATTATTGTAATAA
66 GTGAAGATGAAACTCCAATCAGAGTTAGTAGTTGCTTAAATAGCA-AAATATATTATTGTAATAA
1040 ACGAATACTTTGACTCCATAAACATA-TTTTTTTG
130 ACGAATACTTTGACTCCATAAACATACTTTTTTTG
* *
1074 GTCACTCTCTTTGAAGCAAAATTAAAATTTATTTATAGTCATTCTCTTC-AGGCTTACTTGGATG
1 GTCACTCTCCTTGAAGCAAAATTAAAATTTA-TTA-AGTCATTCTCTTCAAAGCTTACTTGGATG
* *
1138 AATTGAAGATGAAACTCCAATCAGAGTTAGTGGTTGCTTAAATAGCAAAATATATTATTGTAATA
64 AAGTGAAGATGAAACTCCAATCAGAGTTAGTAGTTGCTTAAATAGCAAAATATATTATTGTAATA
* * * *
1203 GACTAATACTTTGACTCGATGAACATACTTTTTTT
129 AACGAATACTTTGACTCCATAAACATACTTTTTTT
1238 TTACTCTATA
Statistics
Matches: 149, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
163 31 0.21
164 98 0.66
165 20 0.13
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (164 bp):
GTCACTCTCCTTGAAGCAAAATTAAAATTTATTAAGTCATTCTCTTCAAAGCTTACTTGGATGAA
GTGAAGATGAAACTCCAATCAGAGTTAGTAGTTGCTTAAATAGCAAAATATATTATTGTAATAAA
CGAATACTTTGACTCCATAAACATACTTTTTTTG
Done.