Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401739.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4854.0, 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, 604
Length: 1007
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.31
Warning! 241 characters in sequence are not A, C, G, or T
Found at i:694 original size:171 final size:170
Alignment explanation
Indices: 410--726 Score: 433
Period size: 171 Copynumber: 1.9 Consensus size: 170
400 NNACTCGCTT
410 TAAATAGTTTATAATCTAATAATTAATTTTAAGTTAAAATTTTTTATATTTTTCATTAAAACAAA
1 TAAATAGTTTATAATCTAATAATTAATTTTAAGTTAAAATTTTTTATATTTTTCATTAAAACAAA
* * *
475 CTATAATTGAACGTCTGCCTTGACATACATGAAAAAAAAATCATTCATT-GATAAGAAAAGTCCA
66 CTATAATTGAACGTCTGCCTTGACATAAATGAAAAAAAAAGCATTCATTAG-CAAGAAAAGTCCA
539 TTTATAGCCTCCCATTCATTTAATAACCTTTTTACTCATTC
130 TTTATAGCCTCCCATTCATTTAATAACCTTTTTACTCATTC
* * **
580 TAAATAGTTTTATAATTTCATAATTAATTTTAAG-TGCAATTTTTTAATATTTTTCATTAAAACA
1 TAAATAG-TTTATAATCTAATAATTAATTTTAAGTTAAAATTTTTT-ATATTTTTCATTAAAACA
* * * * * *
644 AACTATAATTGAATGTCTGGCTTGAGA-AAAGTGAAGAATAAAGCATTCATTAGCAAGAAAAGTT
64 AACTATAATTGAACGTCTGCCTTGACATAAA-TGAAAAAAAAAGCATTCATTAGCAAGAAAAGTC
** *
708 TTTTTATAGCCTCTCATTC
128 CATTTATAGCCTCCCATTC
727 CNNNNNNNNN
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
170 18 0.14
171 108 0.85
172 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (170 bp):
TAAATAGTTTATAATCTAATAATTAATTTTAAGTTAAAATTTTTTATATTTTTCATTAAAACAAA
CTATAATTGAACGTCTGCCTTGACATAAATGAAAAAAAAAGCATTCATTAGCAAGAAAAGTCCAT
TTATAGCCTCCCATTCATTTAATAACCTTTTTACTCATTC
Found at i:763 original size:171 final size:169
Alignment explanation
Indices: 406--814 Score: 423
Period size: 171 Copynumber: 2.4 Consensus size: 169
396 NNNNNNACTC
* *
406 GCTTTAAATAG-TTTATAATCTAATAATTAATTTTAAGTTAAAATTTTTTATATTTTTCATTAAA
1 GCTTTAAATAGTTTTATAATATAATAATTAATTTTAAGTT-GAATTTTTTATATTTTTCATTAAA
* * *
470 ACAAACTATAATTGAACGTCTGCCTTGACATACATGAAAAAAAAATCATTCATTGATAAGAAAAG
65 ACAAACTATAATTGAACGTCTGCCTTGACATAAATGAAAAAAAAAGCATTCATTGACAAGAAAAG
*
535 TCCATTTATAGCCTCCCATTCATTTAATAACCTTTTTACT
130 TCCATTTATAGCCTCCCATTCATTTAATAACCTTATTACT
* *
575 -CATTCTAAATAGTTTTATAATTTCATAATTAATTTTAAG-TGCAATTTTTTAATATTTTTCATT
1 GC-TT-TAAATAGTTTTATAATATAATAATTAATTTTAAGTTG-AATTTTTT-ATATTTTTCATT
* * * * *
638 AAAACAAACTATAATTGAATGTCTGGCTTGAGA-AAAGTGAAGAATAAAGCATTCATT-AGCAAG
62 AAAACAAACTATAATTGAACGTCTGCCTTGACATAAA-TGAAAAAAAAAGCATTCATTGA-CAAG
*** * ***********
701 AAAAGTTTTTTTATAGCCTCTCATTCCNNNNNNNNNNTTATTACTT
125 AAAAGTCCATTTATAGCCTCCCATTCATTTAATAACCTTATTAC-T
* * *
747 GCTTTAAATGGTTTTATAATATAATAATTCATTTTAAGTTGAATTTTTTTATATTTTTTATTAAA
1 GCTTTAAATAGTTTTATAATATAATAATTAATTTTAAGTTGAA-TTTTTTATATTTTTCATTAAA
812 ACA
65 ACA
815 GATAATAATT
Statistics
Matches: 197, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
168 1 0.01
169 2 0.01
170 19 0.10
171 163 0.83
172 11 0.06
173 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.42
Consensus pattern (169 bp):
GCTTTAAATAGTTTTATAATATAATAATTAATTTTAAGTTGAATTTTTTATATTTTTCATTAAAA
CAAACTATAATTGAACGTCTGCCTTGACATAAATGAAAAAAAAAGCATTCATTGACAAGAAAAGT
CCATTTATAGCCTCCCATTCATTTAATAACCTTATTACT
Done.