Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399621.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2871.0, 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: 4187
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.25
Warning! 1413 characters in sequence are not A, C, G, or T
Found at i:1708 original size:169 final size:160
Alignment explanation
Indices: 1428--1755 Score: 311
Period size: 168 Copynumber: 2.0 Consensus size: 160
1418 CATTTAAACT
* * *
1428 GAGTAATAAGGCTTTTGAAAGCATGGGTGATTATAAATAGACTTCTCTTGCCATTGGATATCATT
1 GAGTAATAAGGCTTTCGAAAGCATGGGTGATTATAAATAGACTTCTCTTACCAATGGATATCATT
* * * * * * *
1493 TTTTTTACGTTTTTTAAGGCGGATATTCAATTTAATCCACTTTAATAAAAA-TATAAAA-AAGTT
66 TTCTTCACGTTTCTCAAGCCAGACATTCAATTTAATCCACTTTAATAAAAATTATAAAACAA-TT
*
1556 CAACTTAAAACCAATCATGAGATTAAAANNNNNNNNNNAGC
130 CAAATTAAAACCAATCATGAGATTAAAA----------AGC
* * * *
1597 GAGTACTAAGGCTTTCGAAGGCATGGGTGA-TATAAATGGACTTTTCTTACCAATGGATATCATT
1 GAGTAATAAGGCTTTCGAAAGCATGGGTGATTATAAATAGACTTCTCTTACCAATGGATATCATT
* *** *
1661 TTCTTCACGTTTCTCGAGCCAGACATTCAATTATAATCTGTTTTAATAAAAATTGTAAAACAATT
66 TTCTTCACGTTTCTCAAGCCAGACATTCAATT-TAATCCACTTTAATAAAAATTATAAAACAATT
* * *
1726 CAAATTAAAATCAATTATGAGGTTATAAAA
130 CAAATTAAAACCAATCATGAGATTA-AAAA
1756 TCATTTAAAC
Statistics
Matches: 132, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
161 1 0.01
168 54 0.41
169 43 0.33
170 29 0.22
171 5 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.34
Consensus pattern (160 bp):
GAGTAATAAGGCTTTCGAAAGCATGGGTGATTATAAATAGACTTCTCTTACCAATGGATATCATT
TTCTTCACGTTTCTCAAGCCAGACATTCAATTTAATCCACTTTAATAAAAATTATAAAACAATTC
AAATTAAAACCAATCATGAGATTAAAAAGC
Done.