Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397686.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2196.0, 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, 685
Length: 1142
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.35
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:914 original size:333 final size:330
Alignment explanation
Indices: 250--848 Score: 716
Period size: 333 Copynumber: 1.8 Consensus size: 330
240 NTAAAATTAT
* * * ** * *
250 TTAAAAAGTTATAAATTCGCTTAAAGTGCGTAACAAGGCTTTTGAAGGCAATAGTGACTATAAAT
1 TTAAAAAGTTAGAAATCCGCTTAAAGTGAGTAACAAGGCTTTAAAAGCCAAGAGTGACTATAAAT
* * * **
315 GGACTTTTCTTCTCAATGGGTGGCTTTCATTTCATGTTTCCTAATGCAAACATCAAATTATGATC
66 GGACTTTACTTCTCAAAGGATGGCTTTCAACTCATGTTTCCTAATGC-AACATCAAATTATGATC
* * * *
380 TATTTTACTAAAATAAGAAAATTAAATTCAATTCATAAATCATTTAAAATGTAATATCTCTTAAA
130 TATTTAACTAAAATAAGAAAA-TAAATTCAATTCATAAATCATTTAAAATGTAAAATCACATAAA
* * * **
445 CTGAGTAACAAGGCTTTCGAAGGCATGTGACAACTTAACTGACTTTTCTTTCAATGATGGCTTTT
194 ATGAGTAACAAGACTTTCGAAGGCATGTGACAAC-TAAATGACTTTTCTTTCAATGACAGCTTTT
* * *
510 GTTTCATGTTTCCGATACAAACATTAAATTATGATATGTTTGAAACAAAAATATGAAAAATTAAT
258 GCTTCATGTTTCCGATACAAACATTAAATTATGATATGTTTAAAAAAAAAATATGAAAAATTAAT
575 AAAGTGAA
323 AAAGTGAA
583 TTAAAAAGTTAGAAATCCGCTTAAAGTGAGTAACAAGGCTTTAAAAGCCAAGAGTGACTATAAAT
1 TTAAAAAGTTAGAAATCCGCTTAAAGTGAGTAACAAGGCTTTAAAAGCCAAGAGTGACTATAAAT
* *
648 GGACTTTACTTGTCAAAGGATGGCTTTCACACT-ATG-TTCTTAATGC-A-ATCAAATTATGATC
66 GGACTTTACTTCTCAAAGGATGGCTTTCA-ACTCATGTTTCCTAATGCAACATCAAATTATGATC
* * *
709 TGCTTTAACTAAAA-ATG-TAA-AAATTCAATTCA-AAATCATTTAAAAATGTATAAATCACATA
130 T-ATTTAACTAAAATAAGAAAATAAATTCAATTCATAAATCATTT-AAAATGTA-AAATCACATA
* * * * *
770 AAATGGGTAAC-AGACTTTTGAAGGTATAGTGACTAC-AAATGGACTTTTCTTGT-TATGGACAG
192 AAATGAGTAACAAGACTTTCGAAGGCAT-GTGACAACTAAAT-GACTTTTCTT-TCAAT-GACAG
832 CTTTTGCTTCATGTTTC
253 CTTTTGCTTCATGTTTC
849 TTGATGTAGA
Statistics
Matches: 226, Mismatches: 32, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
325 12 0.05
326 45 0.20
327 43 0.19
328 2 0.01
329 17 0.08
330 11 0.05
332 9 0.04
333 86 0.38
334 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (330 bp):
TTAAAAAGTTAGAAATCCGCTTAAAGTGAGTAACAAGGCTTTAAAAGCCAAGAGTGACTATAAAT
GGACTTTACTTCTCAAAGGATGGCTTTCAACTCATGTTTCCTAATGCAACATCAAATTATGATCT
ATTTAACTAAAATAAGAAAATAAATTCAATTCATAAATCATTTAAAATGTAAAATCACATAAAAT
GAGTAACAAGACTTTCGAAGGCATGTGACAACTAAATGACTTTTCTTTCAATGACAGCTTTTGCT
TCATGTTTCCGATACAAACATTAAATTATGATATGTTTAAAAAAAAAATATGAAAAATTAATAAA
GTGAA
Done.