Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401720.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4834.0, 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: 1727
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.25
Warning! 479 characters in sequence are not A, C, G, or T
Found at i:1567 original size:171 final size:171
Alignment explanation
Indices: 1390--1727 Score: 399
Period size: 171 Copynumber: 2.0 Consensus size: 171
1380 NNNNNNTAAA
* * * * *
1390 ATCAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAAGCTTTTGACGGGATGGGTGACTA
1 ATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAAGCTTTTAAAGGAATGGGAGACTA
* * **
1455 TAAATGGACATTTCTTGCT-AATGAATGGCTTTCTCTACATGTTTCTCAAGGTAAACATTCAATT
66 TAAATGGACATTTCTT-CTCAATGAATGACTTTCTATACATGTTTCTCAAGACAAACATTCAATT
* * * *
1519 ATAGTCTGTTTTGATGAAAAATGTAAAAAATTTCAACTTAAT
130 ATAGTCTATTTTAATGAAAAATATAAAAAAATTCAACTTAAT
********** *
1561 ATCAATTATGAGATTATAAAACCATTTAANNNNNNNNNNAACGCTTTTAAAGGAATGGGAGACTA
1 ATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAAGCTTTTAAAGGAATGGGAGACTA
* * * **
1626 TAAATGGACTTTTCTTCTCAATGAATGATTTTTTATACATGTTTCTTGAGACAAACATTCAATTA
66 TAAATGGACATTTCTTCTCAATGAATGACTTTCTATACATGTTTCTCAAGACAAACATTCAATTA
1691 TAGTCTATTTTAATGAAAAATATAAAAAAATTCAACT
131 TAGTCTATTTTAATGAAAAATATAAAAAAATTCAACT
Statistics
Matches: 137, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
170 2 0.01
171 135 0.99
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
ATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAAGCTTTTAAAGGAATGGGAGACTA
TAAATGGACATTTCTTCTCAATGAATGACTTTCTATACATGTTTCTCAAGACAAACATTCAATTA
TAGTCTATTTTAATGAAAAATATAAAAAAATTCAACTTAAT
Done.