Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398310.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1611.0, 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: 10916
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.20
Warning! 4843 characters in sequence are not A, C, G, or T
Found at i:2288 original size:171 final size:161
Alignment explanation
Indices: 1982--2301 Score: 293
Period size: 171 Copynumber: 1.9 Consensus size: 161
1972 CTAGCAAGAA
* *
1982 AGTCTATTTATAGTCACCCATTCCTTTAAAAGCCTTATTAATCCCTTTAAATGGTTTTATAATCT
1 AGTCTATTTATAGTCACCCATTCCTTAAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCT
* ********** * * *
2047 CATAATTGATTNNNNNNNNNNTTTTTAAATATTTTTTATTAAAACAGACTATAATTAATTGTCCA
66 CATAATAGATTTTAAGTTGCATTTTTAAATATTTTTGATTAAAACAGACTACAATCAATTGTCCA
2112 CCTCGAGAAACATGAAGAAAAAAGTACTCAT
131 CCTCGAGAAACATGAAGAAAAAAGTACTCAT
** * *
2143 NNNNNNNNNNAGTCTATTTATAGTTGCCCATTCCTTAAAAAGCGTTATTAATCACTTTCAATGGT
1 ----------AGTCTATTTATAGTCACCCATTCCTTAAAAAGCCTTATTAATCACTTTAAATGGT
* * *
2208 TTTATAATCTCATAATAGATTTTAAGTTGCATTTTTTAATATTTTTGGTTAAATCAGACTACAAC
56 TTTATAATCTCATAATAGATTTTAAGTTGCATTTTTAAATATTTTTGATTAAAACAGACTACAA-
* *
2273 TCAATCT-T-TACCTCGAGAAACGTGAAGAA
120 TCAAT-TGTCCACCTCGAGAAACATGAAGAA
2302 GAACGCATTC
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
171 116 0.95
172 5 0.04
173 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.37
Consensus pattern (161 bp):
AGTCTATTTATAGTCACCCATTCCTTAAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCT
CATAATAGATTTTAAGTTGCATTTTTAAATATTTTTGATTAAAACAGACTACAATCAATTGTCCA
CCTCGAGAAACATGAAGAAAAAAGTACTCAT
Done.