Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398599.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_189.0, 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: 2847
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.30
Warning! 493 characters in sequence are not A, C, G, or T
Found at i:2110 original size:181 final size:180
Alignment explanation
Indices: 1779--2124 Score: 451
Period size: 180 Copynumber: 1.9 Consensus size: 180
1769 AAGGCATGGG
* * * ** *
1779 TGACTATAAATGGACTTCTCTTGTCAATGATTCATGTTCTTTTCATGTTTCTTGAGGCAAACACT
1 TGACTATAAATGAACTTCTCTTGCCAATGAATCATGTTCGCTTCATATTTCTTGAGGCAAACACT
* *
1844 CAATTATAATATATTTTAACAAAAATGTAAAACAATTCAACTTCAAATAAATTATGAGATTGTAA
66 CAATTATAATATATTTTAACAAAAATGTAAAACAATTCAACTTAAAATAAATTATAAGATTGTAA
********** *
1909 AACCNNNNNNNNNNAGTAATAAGGCTTTGGAAGGCTTCGAAAGGTATAGA
131 AACCATTTCAAGCAAGTAATAAGGCTTTCGAAGGCTTCGAAAGGTATAGA
* * *
1959 TGACTCTAAATGAACTTCTCTTGCCAATGAATCATGTTCGCTTCATATTTTTTGAGGTAAACACT
1 TGACTATAAATGAACTTCTCTTGCCAATGAATCATGTTCGCTTCATATTTCTTGAGGCAAACACT
* *
2024 CTATTATAAT-TGATTTTAACTAAAAATGTAAAACAATTCAACTTAAAATCAATTATAAGATTGT
66 CAATTATAATAT-ATTTTAAC-AAAAATGTAAAACAATTCAACTTAAAATAAATTATAAGATTGT
2088 AAAACCATTTCAAGCAAGTAATAAGGCTTTCGAAGGC
129 AAAACCATTTCAAGCAAGTAATAAGGCTTTCGAAGGC
2125 ANNNNNNNNN
Statistics
Matches: 140, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
179 1 0.01
180 73 0.52
181 66 0.47
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.33
Consensus pattern (180 bp):
TGACTATAAATGAACTTCTCTTGCCAATGAATCATGTTCGCTTCATATTTCTTGAGGCAAACACT
CAATTATAATATATTTTAACAAAAATGTAAAACAATTCAACTTAAAATAAATTATAAGATTGTAA
AACCATTTCAAGCAAGTAATAAGGCTTTCGAAGGCTTCGAAAGGTATAGA
Done.