Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022323.1 Corchorus olitorius cultivar O-4 contig22356, 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: 7855
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Found at i:4443 original size:31 final size:31
Alignment explanation
Indices: 4405--4465 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
4395 TTGTTGCTCG
* * *
4405 CTTGTTTGATATCCTGAACCCGTTGTTTCTA
1 CTTGTTTGACATCCTAAACCCGCTGTTTCTA
4436 CTTGTTTGACATCCTAAACCCGCTGTTTCT
1 CTTGTTTGACATCCTAAACCCGCTGTTTCT
4466 GTTTTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.15, T:0.43
Consensus pattern (31 bp):
CTTGTTTGACATCCTAAACCCGCTGTTTCTA
Found at i:6932 original size:21 final size:21
Alignment explanation
Indices: 6902--7035 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
6892 TGCTAGAAGT
6902 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
6923 TCAATGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
6944 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
6965 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
6986 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
7007 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
7028 TCATTGGA
1 TCATTGGA
7036 ATTGCCTAAG
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 2 0.02
21 104 0.98
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.