Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401420.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4547.0, 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: 2745
ACGTcount: A:0.16, C:0.06, G:0.07, T:0.17
Warning! 1508 characters in sequence are not A, C, G, or T
Found at i:2508 original size:170 final size:171
Alignment explanation
Indices: 2041--2743 Score: 477
Period size: 171 Copynumber: 4.1 Consensus size: 171
2031 NNTTCTTGTC
* * * * * * *
2041 AATGAATGCTTGTTTCTTCACGTTTCCT-GAGGTAGACATTCAATTACAGTCTGTTTTACTAAAA
1 AATGAATGCTTGTTTCTTCAC-ATTCCTCGAGATAGACATTTAATTATAGTATGTTTGAATAAAA
* ********** *
2105 AATGTAAAAAAATTCAACTTAAAATNNNNNNNNNNATTATAAAACTATTTAAAGCGAGTAAGAAG
65 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAG
* *
2170 CATTTTGAAGGAATAGGTGACTCTAAATGGACTTTTCCTGAT
130 CCTTTTGAAAGAATAGGTGACTCTAAATGGACTTTTCCTGAT
* * * * *
2212 AATGAATGCTTGTTTCTTCACGTTTCTTGAGGTAGATATTTAATTATAGTATGTTTGAATAAAAA
1 AATGAATGCTTGTTTCTTCACATTCCTCGAGATAGACATTTAATTATAGTATGTTTGAATAAAAA
**********
2277 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATNNNNNNNNNNAAAGCGAGTAATAAGC
66 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGC
* * *
2342 CTTTTGAAATAATGGGTGACTCTAAATTGACTTTTCCT-AT
131 CTTTTGAAAGAATAGGTGACTCTAAATGGACTTTTCCTGAT
********
2382 CAATGAATGCTTG-TTCTTCACATTCCTCGAGATAGACATTTAATTATAGTATGTTTNNNNNNNN
1 -AATGAATGCTTGTTTCTTCACATTCCTCGAGATAGACATTTAATTATAGTATGTTTGAATAAAA
** * * * * *
2446 NNTGTAAATAAATTCAACTTAAAATCGATTATGAGATTATAAAACTATTTAAAACAAGTAATAAG
65 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAG
********** *
2511 CCTTTT-AAAGGAATAGGTGACTNNNNNNNNNNTTTTCTTG-T
130 CCTTTTGAAA-GAATAGGTGACTCTAAATGGACTTTTCCTGAT
* * * * * * *
2552 CAATGAATGCTTGTTTTTTCACGATT-CTCAAGGTAGACATTCAATTAGAGTATGTTTTAATCAA
1 -AATGAATGCTTGTTTCTTCAC-ATTCCTCGAGATAGACATTTAATTATAGTATGTTTGAATAAA
* * ********** * *
2616 AAATGTAAAAACATTCAACTTNNNNNNNNNNATGAGATTATAAAACTATTTAAAACTAGTAATAA
64 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAA
* * * *
2681 GCTTTTTGAAGGAAT-GGATGACTCTAAATGGA-TTTTTCTTAT
129 GCCTTTTGAAAGAATAGG-TGACTCTAAATGGACTTTTCCTGAT
2723 CAATGAATGCTTGTTTCTTCA
1 -AATGAATGCTTGTTTCTTCA
2744 TG
Statistics
Matches: 402, Mismatches: 121, Indels: 18
0.74 0.22 0.03
Matches are distributed among these distances:
169 3 0.01
170 135 0.34
171 259 0.64
172 5 0.01
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
AATGAATGCTTGTTTCTTCACATTCCTCGAGATAGACATTTAATTATAGTATGTTTGAATAAAAA
ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGC
CTTTTGAAAGAATAGGTGACTCTAAATGGACTTTTCCTGAT
Done.