Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398601.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1891.0, 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, 936
Length: 1560
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.27
Warning! 360 characters in sequence are not A, C, G, or T
Found at i:364 original size:172 final size:172
Alignment explanation
Indices: 1--686 Score: 747
Period size: 171 Copynumber: 4.0 Consensus size: 172
* * * *
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACT-TTTCATAAG
1 GGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCA-TGTTTCTTAAG
* * * * * * * * *
65 GTAGACGTTCAGTTACAGTCTGTTTGAACTAAAAATG-AAAAATAATTTAACTTAAAATCAATTA
65 GTAGACATTCAATTATAATATGTTTGAACCAAAAATGTAAAAAAAATTAAACCTAAAATCAATTA
** *
129 TGAGATTATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTGAA
130 TGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
* * **
172 GGAATGGGTA-ACTGTAAATGGACTTTTCTTGCCAATGAATGTATTTTTCTTCATGTTTCTCGAG
1 GGAATGGG-AGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAG
* * * * *
236 CTGGACATTTAATTATAATATGTTTGAACCAATAATGTAAAAAAAATTGAACCTAAAATCAATT-
65 GTAGACATTCAATTATAATATGTTTGAACCAAAAATGTAAAAAAAATTAAACCTAAAATCAATTA
* * * *
300 TGGAGATTATTAAATCATTTAAAGCGAGTAATAAGGGTTTTGAA
130 T-GAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
** * * * * * *
344 GGAATAAGAGACTATAAATGGACTTGTCTTACTAATAAATGCATGTTTCTTTATGTTTCTTAAGG
1 GGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAGG
* * * * ** * * *
409 TAGACATTCAATTATAGTCTATTTTAATGAAAAATGT-AACAAAATTCAACTTAAAATCAATTAT
66 TAGACATTCAATTATAATATGTTTGAACCAAAAATGTAAAAAAAATTAAACCTAAAATCAATTAT
*
473 GAGATTATAAAACCATTTAAAGCAAGTAATAAGGTTTTTGAA
131 GAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
* * * * * *
515 TGAATGGGCGACTATAAATGGACTTTTCTT-CTCAATGAATGCCTTTTTCTTAACGTTTCTTGAG
1 GGAATGGGAGACTATAAATGGACTTTTCTTGC-CAATGAATGCATTTTTCTTCATGTTTCTTAAG
* * * * *
579 GTAAACATTCAATTATAATATGTTTTAACCAATAATGTAAAAAAAA-TAAACCTAAAATTAATTT
65 GTAGACATTCAATTATAATATGTTTGAACCAAAAATGTAAAAAAAATTAAACCTAAAATCAATTA
* *
643 TGAGATTATAAAACCATTTAAAGCAAGTAATAAGCCCTTTGAA
130 TGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
686 G
1 G
687 AAATANNNNN
Statistics
Matches: 424, Mismatches: 83, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
170 2 0.00
171 277 0.65
172 145 0.34
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (172 bp):
GGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAGG
TAGACATTCAATTATAATATGTTTGAACCAAAAATGTAAAAAAAATTAAACCTAAAATCAATTAT
GAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
Done.