Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018023.1 Corchorus olitorius cultivar O-4 contig18056, 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: 13083
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4217 original size:32 final size:32
Alignment explanation
Indices: 4162--4259 Score: 90
Period size: 32 Copynumber: 3.1 Consensus size: 32
4152 TCAGGTCAGG
** *
4162 TTAAATTTGGGCCAGGTTGATTCGGGTTCGGA
1 TTAAATTTGGATCAGGTTAATTCGGGTTCGGA
* *
4194 TTAAATTTGGATCAAGTTAATTCGAGTTCAGG-
1 TTAAATTTGGATCAGGTTAATTCGGGTTC-GGA
* ** * *
4226 TCAGTTTTGGATTAGGTTAATTTGGGTTCGGA
1 TTAAATTTGGATCAGGTTAATTCGGGTTCGGA
4258 TT
1 TT
4260 CGAACTAGGT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
31 2 0.04
32 47 0.92
33 2 0.04
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.40
Consensus pattern (32 bp):
TTAAATTTGGATCAGGTTAATTCGGGTTCGGA
Found at i:10383 original size:15 final size:15
Alignment explanation
Indices: 10360--10394 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
10350 GGGGAATAAT
*
10360 CAATCCAAAAACAAA
1 CAATTCAAAAACAAA
10375 CAATTCAAAAACAAA
1 CAATTCAAAAACAAA
10390 CAATT
1 CAATT
10395 TTCTATCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (15 bp):
CAATTCAAAAACAAA
Done.