Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397965.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1271.0, 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: 4315
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.25
Warning! 1449 characters in sequence are not A, C, G, or T
Found at i:479 original size:171 final size:170
Alignment explanation
Indices: 18--744 Score: 530
Period size: 171 Copynumber: 4.2 Consensus size: 170
8 AAATATAGGT
* * * * * * *
18 TTTTTTAAATTTTTTGTTAAAAAAGATTATAATTGAATTTCTACCTTAACAAATGT-GAAGAAGA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGGAA-AAAA
* * * * * * ** *
82 AGGCAATCATTGGCAAG-AAATGTCTATTTATAATCACTCATTCCTTTAAAAATCTTATTACTCA
65 AGGCATTCATTAGCAAGAAAAT-TC-ATTTATAGTAACCCATTCCTTCAAAAGCCTTATTACTCG
* ********** * *
146 CTTTAAATGGTTTTATANNNNNNNNNNTGATTTTAAGTTGAAT
128 CTTTAAATTGTTTTATAATCTCAAAATTAATTTTAAGTTGAAA
* * ** * *
189 TTTTTTACATTTTTAGTTTAAACAGATTATAATTGAATGTCTACCTCTGGAAACG-AGAAGAAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGGAA-AAAA
* * ********** * * *
253 AGGCATTTATT-GACAAGCAAAGTNNNNNNNNNNTCACCCATACCTTCAGAAGCCTTATTACTCG
65 AGGCATTCATTAG-CAAG-AAAATTCATTTATAGTAACCCATTCCTTCAAAAGCCTTATTACTCG
* * *
317 CTTTAAATTATTTTATAAACTCAAAATTCATTTTAAGTTGAAA
128 CTTTAAATTGTTTTATAATCTCAAAATTAATTTTAAGTTGAAA
* * * * **********
360 TTTTTTACATTTTTGGTTAAAACATATTATTATTGAATGTTTACCTTAAGAANNNNNNNNNNAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGGAAAAAAA
* * * *
425 GGCATTCATTGGTAAGAAATATAT-ATTTATAGTAACCCATTCTTTCAAAAGCCTTGTTACTCGC
66 GGCATTCATTAGCAAGAAA-AT-TCATTTATAGTAACCCATTCCTTCAAAAGCCTTATTACTCGC
* * *
489 TTTAAATGGTTTTATAATTTCATAATTAATTTTAAGTT-AAA
129 TTTAAATTGTTTTATAATCTCAAAATTAATTTTAAGTTGAAA
** * *
530 GTTTTTTACATTTTTGGCAAAAACAGACTACAATTGAATGTCTACCTCAAGAAATGTGGAAAAAA
1 -TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGGAAAAAA
* * * * *
595 AGGCATTGATTAGCAAGAAAATTCCATTTATAGTGACCCATTCCTTCAAAAGCATTATTCCTCAC
65 AGGCATTCATTAGCAAGAAAATT-CATTTATAGTAACCCATTCCTTCAAAAGCCTTATTACTCGC
* * *
660 TTTAAATTGTTTTATAATCTCAAAATTGATCTTAAGTTGAAT
129 TTTAAATTGTTTTATAATCTCAAAATTAATTTTAAGTTGAAA
*
702 TTTTTGTACAGTTTTGGTTAAAACAGATTATAATTGAATGTCT
1 TTTTT-TACATTTTTGGTTAAAACAGATTATAATTGAATGTCT
745 NNNNNNNNNN
Statistics
Matches: 420, Mismatches: 123, Indels: 25
0.74 0.22 0.04
Matches are distributed among these distances:
169 1 0.00
170 9 0.02
171 372 0.89
172 35 0.08
173 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.38
Consensus pattern (170 bp):
TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGGAAAAAAA
GGCATTCATTAGCAAGAAAATTCATTTATAGTAACCCATTCCTTCAAAAGCCTTATTACTCGCTT
TAAATTGTTTTATAATCTCAAAATTAATTTTAAGTTGAAA
Done.