Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401193.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4343.0, 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: 1700
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 411 characters in sequence are not A, C, G, or T
Found at i:570 original size:171 final size:169
Alignment explanation
Indices: 16--891 Score: 604
Period size: 171 Copynumber: 5.1 Consensus size: 169
6 TTCTTGGCAA
* * * *
16 TGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCTATTATAATCTATTTTAATGAAAAAA
1 TGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAAT
* *
81 GTAAAAAAATTGAACTTAAAATTAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCCT
66 GT-AAAAAATTCAACTT-AAATCAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCCT
* * *
146 TTTAAAACAATAGGAGACAATAAATGGACTTTTCTTTGCAT
129 TTTAAAAGAATAGGAGACTATAAATGGACTTTTCTTTCCAT
********** * *
187 TGAATGCCTTTTTCTTCATGTTTCTCAAGGTNNNNNNNNNNTTATAGTCTGTTTTAATCAAAAAT
1 TGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAAT
* * * * * * **
252 ATAAAAAGATACAACTTAATATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGGT
66 GTAAAAA-ATTCAACTTAA-ATCAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCCT
** *
317 TTCGAAAGAATGGGAGACTATAAATGGACTTTTCTTTCC-T
129 TTTAAAAGAATAGGAGACTATAAATGGACTTTTCTTTCCAT
* * ** * *
357 CTGAATGCTTTTTTCTTCATCTTTCTCAAGACAGATATTCAATTACAATCTGTTTTAATGAAAAA
1 -TGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAA
* *
422 TGTAAAAAACTTCAACTTCAAATCAATTCTAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGTC
65 TGTAAAAAA-TTCAACTT-AAATCAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCC
* * * *
487 TTTTAAAAGAATAAGAAACTATAAATGGATTTTTCGTTCCAT
128 TTTTAAAAGAATAGGAGACTATAAATGGACTTTTCTTTCCAT
********** * * * **
529 TNNNNNNNNNNTTCTTTATGTTTCTCAAGGTAGACATTCAATTATAATATGTTTAAACCAAAAAT
1 TGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAAT
* * * * * * ** * * * **
594 CTACAATGAATTCAAATTAAAATCAATTTTGAGATTGTAAAACTATTTAAAGAGAGTAATAAGGA
66 GTA-AA-AAATTCAACTT-AAATCAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCC
* * * * * * * *
659 TTTTAAAGGAATGGGAGACTATGAATTGACTTTCCTTGCTAA
128 TTTTAAAAGAATAGGAGACTATAAATGGACTTTTCTTTCCAT
* * * * * * * * *
701 TGAA-GGCTTTTGTCTTCACGTTTCCCAAGCTAGGCATTCAATTACATTCTTTTTTAATCAAAAN
1 TGAATGCCTTTT-TCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAA-
********* * * * * * * * *
765 NNNNNNNNNATTTAACTTAAAATGAATTATGAGATTATAAAACGATTTAAAGCGAGTAATAAGGC
64 ATGTAAAAAATTCAACTT-AAATCAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCC
** * * ** *
830 TTTGGAAGGAATGGGAGACTATAAACAGACTTTTCTTACCAT
128 TTTTAAAAGAATAGGAGACTATAAATGGACTTTTCTTTCCAT
872 TGAATGCCTTTTTCTTCATG
1 TGAATGCCTTTTTCTTCATG
892 NNNNNNNNNN
Statistics
Matches: 536, Mismatches: 158, Indels: 22
0.75 0.22 0.03
Matches are distributed among these distances:
170 9 0.02
171 400 0.75
172 125 0.23
173 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.35
Consensus pattern (169 bp):
TGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAAT
GTAAAAAATTCAACTTAAATCAATTATAAGCTTAAAAAACCATTTAAAGCGAGTAGTAAGCCTTT
TAAAAGAATAGGAGACTATAAATGGACTTTTCTTTCCAT
Done.