Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002676.1 Hibiscus syriacus cultivar Beakdansim tig00005524_pilon, 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: 209796
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:206632 original size:29 final size:26
Alignment explanation
Indices: 206590--206663 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 26
206580 AGAAGTAAAT
*
206590 AAAAATAAGAGAATAAAAACTTTGACAAC
1 AAAAATAAGAGAATGAAAACTTT---AAC
206619 AAAAATAAGAGAATGAAAAC-TTAAC
1 AAAAATAAGAGAATGAAAACTTTAAC
206644 -AAAATAAGAGAATGAAAACT
1 AAAAATAAGAGAATGAAAACT
206664 GACGAGTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 19 0.44
25 3 0.07
28 2 0.05
29 19 0.44
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (26 bp):
AAAAATAAGAGAATGAAAACTTTAAC
Found at i:206650 original size:24 final size:26
Alignment explanation
Indices: 206585--206663 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 26
206575 AGCAAAGAAG
* *
206585 TAAATAAAAATAAGAGAATAAAAACTT
1 TAAACAAAAATAAGAGAATGAAAAC-T
206612 TGACAACAAAAATAAGAGAATGAAAACT
1 T-A-AACAAAAATAAGAGAATGAAAACT
206640 T-AAC-AAAATAAGAGAATGAAAACT
1 TAAACAAAAATAAGAGAATGAAAACT
206664 GACGAGTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
24 20 0.42
25 3 0.06
27 1 0.02
28 3 0.06
29 21 0.44
ACGTcount: A:0.63, C:0.08, G:0.11, T:0.18
Consensus pattern (26 bp):
TAAACAAAAATAAGAGAATGAAAACT
Done.