Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398004.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_131.0, 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: 1670
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.32
Warning! 237 characters in sequence are not A, C, G, or T
Found at i:350 original size:172 final size:166
Alignment explanation
Indices: 1--593 Score: 433
Period size: 172 Copynumber: 3.5 Consensus size: 166
* * *
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGATTTTTCTTGCCAATAA
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATGACTTTTCTTGCCAATAA
* * * *
66 ATACCTTTTTCTTCATGTTTTTTGAGGTAGGCATTCAATTATAATCTGTTTTAACCAAAAATGTT
66 ATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA
*****
131 CAAAGAATTAAAATTTNNNNNNNNNNTGAGATTATAAAACT
131 CAAAGAATTAAAATTT-----AAATCTGAGATTATAAAACT
* *
172 ATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATTACTATAAATAGACTTTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAAT-GACTTTTCTTGCCAATA
* * * * *
237 AATTCTTTTTTCTTTATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACTAAAAATAT
65 AATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATAT
* *********** *
302 ACAAAGAATTCAAATTTAAATCNNNNNNNNNNNNNNNNAACC
130 ACAAAGAATTAAAATTTAAATC-----TGAGATTATAAAACT
* * *
344 ATTTAAAGTGAGTAATAAGGCTTTT-AAAGAAATGGGTGACTATAAATGGA-GTTCCTTGCCAAT
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAAG-AATGGATGACTATAAAT-GACTTTTCTTGCCAAT
* * * * * * * *
407 GAATGA-CTTTTTATTCAAGTATCTTGAGCTAGACAATCAATTATAATCTATTTTAACTAAANNN
64 AAAT-ACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAA---
******* *
471 NNNNNNNAAATTGAACTTAAAA-TTAAATTTGAGATTATAAAACT
125 AATATACAAA--GAA-TTAAAATTTAAATCTGAGATTATAAAACT
* * * *
515 ATTTAAAGTGAGTAGT-AGAGCTTTTGAAGGAATAGG-TGACAATAAATGGACTTTTCTTGCTAA
1 ATTTAAAGTGAGTAATAAG-GCTTTTGAAAGAAT-GGATGACTATAAAT-GACTTTTCTTGCCAA
*
578 TGAATACCTTTTTCTT
63 TAAATACCTTTTTCTT
594 TAGGTGCCCC
Statistics
Matches: 328, Mismatches: 75, Indels: 37
0.75 0.17 0.08
Matches are distributed among these distances:
170 2 0.01
171 150 0.46
172 159 0.48
174 3 0.01
176 9 0.03
177 5 0.02
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.36
Consensus pattern (166 bp):
ATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATGACTTTTCTTGCCAATAA
ATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA
CAAAGAATTAAAATTTAAATCTGAGATTATAAAACT
Done.