Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011514.1 Corchorus olitorius cultivar O-4 contig11547, 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: 3005
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Found at i:46 original size:33 final size:33
Alignment explanation
Indices: 4--100 Score: 110
Period size: 33 Copynumber: 2.9 Consensus size: 33
1 TGA
*
4 GTGTTGTTTGTGATGACACTAAA-TCTGTTTTAG
1 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTTAG
37 GTGTTGTTTGTGATGAAACAAATTCTGTTTT-G
1 GTGTTGTTTGTGATGAAACAAATTCTGTTTTAG
* **
69 GATGCTAATTGTGATGTAAACAAA-TCTGTTTT
1 G-TGTTGTTTGTGATG-AAACAAATTCTGTTTT
101 GGTTGATCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.09
33 45 0.79
34 7 0.12
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (33 bp):
GTGTTGTTTGTGATGAAACAAATTCTGTTTTAG
Found at i:1951 original size:21 final size:21
Alignment explanation
Indices: 1925--2037 Score: 149
Period size: 21 Copynumber: 5.4 Consensus size: 21
1915 TGCTAGAAGT
1925 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
1946 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* * *
1967 TCATTGGAGCAGGTTACAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
1988 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
2009 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
2030 TCATTGGA
1 TCATTGGA
2038 AATGCCTAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 1 0.01
21 82 0.99
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.