Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020312.1 Corchorus olitorius cultivar O-4 contig20345, 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: 4888
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Found at i:223 original size:47 final size:47
Alignment explanation
Indices: 164--258 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
154 TGGATGGATT
164 CTCTGGGTACAATCAGATCAAAATGGCGCCCGAAGATATGGAGAAGA
1 CTCTGGGTACAATCAGATCAAAATGGCGCCCGAAGATATGGAGAAGA
211 CTCTGGGTACAATCAGATCAAAATGGCGCCCGAAGATATGGAGAAGA
1 CTCTGGGTACAATCAGATCAAAATGGCGCCCGAAGATATGGAGAAGA
258 C
1 C
259 CGCCTTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (47 bp):
CTCTGGGTACAATCAGATCAAAATGGCGCCCGAAGATATGGAGAAGA
Found at i:4163 original size:26 final size:27
Alignment explanation
Indices: 4107--4175 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
4097 AAAATTCACT
* *
4107 AGGGGCATTGTGGTCATTTTCACCTCG
1 AGGGGCATTTTGGTCATTTTCACCTCC
*
4134 A-GGGCATTTTGGTCATTTTCTGCC-CC
1 AGGGGCATTTTGGTCATTTTC-ACCTCC
*
4160 AGGGGCATTTCGGTCA
1 AGGGGCATTTTGGTCA
4176 AAATTATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 20 0.56
27 16 0.44
ACGTcount: A:0.14, C:0.23, G:0.29, T:0.33
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACCTCC
Done.