Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401339.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4476.0, 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: 3038
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.25
Warning! 865 characters in sequence are not A, C, G, or T
Found at i:327 original size:171 final size:171
Alignment explanation
Indices: 1--328 Score: 413
Period size: 171 Copynumber: 1.9 Consensus size: 171
* * * *
1 TTTTGAAAGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATGGCTTTTCCTCCATGTTT
1 TTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTCCTCAATGTTT
* * * * *
66 CCCATGGTGGACATTCAATTATAGCATATTTTAACTAGAACTGTAGAAAAATTCAACTTAAAATC
66 CCCAAGGTCGACATTCAATTATAACATATTTTAACTAAAACTATAGAAAAATTCAACTTAAAATC
* **********
131 AATTATAANNNNNNNNNNCCATTTAAAACGAGTAATAAGGC
131 AAATATAAGATTATAAAACCATTTAAAACGAGTAATAAGGC
* * *
172 TTTTGGAAGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATTACTTTTTCTCAATGTTT
1 TTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTCCTCAATGTTT
* *
237 CCTAAGGTCGACATTCAATTATAACCTATTTTAACTAAAACTATAGAAAAATTCAACTTAAAATC
66 CCCAAGGTCGACATTCAATTATAACATATTTTAACTAAAACTATAGAAAAATTCAACTTAAAATC
* *
302 AAATATGAGATTATAAAATCATTTAAA
131 AAATATAAGATTATAAAACCATTTAAA
329 GTGAGTANNN
Statistics
Matches: 130, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
171 130 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.35
Consensus pattern (171 bp):
TTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTCCTCAATGTTT
CCCAAGGTCGACATTCAATTATAACATATTTTAACTAAAACTATAGAAAAATTCAACTTAAAATC
AAATATAAGATTATAAAACCATTTAAAACGAGTAATAAGGC
Found at i:1990 original size:171 final size:172
Alignment explanation
Indices: 1689--2288 Score: 617
Period size: 172 Copynumber: 3.5 Consensus size: 172
1679 NNNNNNNNNN
* * * * *
1689 AAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATTGGTGACTATAAATGAACTTTTCTTC
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACCATAAATGGACTTTTCTTC
* *
1754 TCAATGAATGGCTTTTTCTCCATGTTTCCCAAGGCAGGCATACAATTATAACCTATTTGAACTAA
66 TCAATGAATGGCTTTTTCTCCATGTTTCCCAAGGCAGGCATTCTATTATAACCTATTTGAACTAA
* * *
1819 AAATATAGAA-AAATTCAACTTAAAATCAATTATGAGATTAT
131 AAATATAAAACAAATTAAACTTAAAAACAATTATGAGATTAT
********** *
1860 AAAACCNNNNNNNNNNAGTAATAAGGCTTTTGGAAGAATGGGTGACCATAAATGGACTTTTCTTC
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACCATAAATGGACTTTTCTTC
* *********** *
1925 TCAATAAATGGCTTTTTCTCCATGTTTCCCAAGGCAGGCATTCTNNNNNNNNNNGTTTTAACTAA
66 TCAATGAATGGCTTTTTCTCCATGTTTCCCAAGGCAGGCATTCTATTATAACCTATTTGAACTAA
* *
1990 AAATGTAAAACAAATTAAACTTAAAAACAATTTTGAGATTAT
131 AAATATAAAACAAATTAAACTTAAAAACAATTATGAGATTAT
* *
2032 CAAACCATTTAAAGCGAGTAATAAGGGTTTTGAAAGAATGGGTGACCATAAATGGACTTTTCTTC
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACCATAAATGGACTTTTCTTC
* * * *******
2097 TCAACGAATGGCTTTTTTTCCATGTTTCCCAAGGCAGGCATTCTATTATAACCTGTTTNNNNNNN
66 TCAATGAATGGCTTTTTCTCCATGTTTCCCAAGGCAGGCATTCTATTATAACCTATTTGAACTAA
*** * * *
2162 NNNTGTAAAACAAATTAAACTTAAAACCAATTTTGAGATTAT
131 AAATATAAAACAAATTAAACTTAAAAACAATTATGAGATTAT
* * * * * *
2204 CAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTT
1 -AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACCATAAATGGACTTTTCTT
* * *
2269 CCCAACGAATGCCTTTTTCT
65 CTCAATGAATGGCTTTTTCT
2289 TCATAGTTCT
Statistics
Matches: 344, Mismatches: 83, Indels: 2
0.80 0.19 0.00
Matches are distributed among these distances:
171 108 0.31
172 163 0.47
173 73 0.21
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.32
Consensus pattern (172 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACCATAAATGGACTTTTCTTC
TCAATGAATGGCTTTTTCTCCATGTTTCCCAAGGCAGGCATTCTATTATAACCTATTTGAACTAA
AAATATAAAACAAATTAAACTTAAAAACAATTATGAGATTAT
Done.