Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399679.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2925.0, 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, 823
Length: 1373
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.29
Warning! 316 characters in sequence are not A, C, G, or T
Found at i:782 original size:169 final size:169
Alignment explanation
Indices: 14--968 Score: 732
Period size: 169 Copynumber: 5.6 Consensus size: 169
4 GCTTTTTGTG
* * * *
14 CATGTTTCTTAAGGCAAGCATTCAATTATAGTCTGTTTTAATAAAAACTAAG-AAAAAA-TTTAA
1 CATGTTTCTCAAGGCAAGCATTCAATTATAGTCTATTTTAACAAAAA-T--GTAAAAAAGTTCAA
* ********** * *
77 CTTAAAATTAATTATGAGATTATAANNNNNNNNNNAGTGAGTAATAAGGCTTTTGAAA-GATTGG
63 CTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTT-AAAGGAATGG
* * * *
141 GTGACTGTAAATGGATTTTTTTCTTAATGAATG-GTTTTTTTA
127 GTGACTATAAATGGACTTTTTTCTCAATGAATGAATTTTTTTA
* * * * * **********
183 TACGTTTCTCGAGGCAAGCATTCGATTATAGTCT-TTTTAACCATAAANNNNNNNNNNTTCAACT
1 CATGTTTCTCAAGGCAAGCATTCAATTATAGTCTATTTTAA-CAAAAATGTAAAAAAGTTCAACT
* * *
247 TAAAATCAATTATTAGATTATAAAATAATTTAAAGCGATTCATAAGGCTTTTAAAGGAATGGGTG
65 TAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTG
* * **
312 ACTATAAATGAACTTTTTTCTCAATGAGTAGCTTTTTTTTTA
130 ACTATAAATGGACTTTTTTCTCAATGAAT-G-AATTTTTTTA
* *
354 -ATGTTTCTCTAGGTCAA-CATTCAATTATTGTCTATTTTAACTAAAAATGTAAAAAAAAGTTCA
1 CATGTTTCTCAAGG-CAAGCATTCAATTATAGTCTATTTTAAC-AAAAATGT--AAAAAAGTTCA
* ********** *
417 ACTTAAAATCAATTATGAGATTACAAAATAATTTANNNNNNNNNNTAAGGCTTTTGAAGGAATGG
62 ACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGG
*
482 GTGACTATAAAT-GACTTTTTTTTCTCAATGAAT-AGATTTTTTTG
127 GTGACTATAAATGGAC--TTTTTTCTCAATGAATGA-ATTTTTTTA
** * ** * * * * *
526 CACATTTCTCAAGAC-AGCATTCCGTTACAGTCTGTTCTAACAAAAAATGTAAAAAAATTCATCT
1 CATGTTTCTCAAGGCAAGCATTCAATTATAGTCTATTTTAAC-AAAAATGTAAAAAAGTTCAACT
* * * * *
590 TAAAATCAATTATGAGTTTATAAAACAATTTAAAGTGAGTAATAAGGCTTATAAAGAAATGGGTG
65 TAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTG
655 ACTATAAATGGACTTTTTTCTCAATGAATGAATTTTTTTA
130 ACTATAAATGGACTTTTTTCTCAATGAATGAATTTTTTTA
* * * *
695 CATGTTTTTAAAGGCAAGCATTCAATTATAGTCTATTTTAAGC-ATAATGTAAAAAAGTTTAACT
1 CATGTTTCTCAAGGCAAGCATTCAATTATAGTCTATTTTAA-CAAAAATGTAAAAAAGTTCAACT
* * **********
759 CAAAATCAATTTTGAGATTATAAAATAATTTAAAGCGAGTAATNNNNNNNNNNAAGGAATGGGTG
65 TAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTG
***
824 ACTATAAATGGACTTTTCTTGC-CAATGAATGCCCTTTTTT-
130 ACTATAAATGGACTTTT-TT-CTCAATGAATGAATTTTTTTA
** ** * * * * *
864 CATGTTTCTTGAGATAAACATTCAATTATTGCCTATTTTAACCAAAAATGTAAAACA-TTTAACT
1 CATGTTTCTCAAGGCAAGCATTCAATTATAGTCTATTTTAA-CAAAAATGTAAAAAAGTTCAACT
928 TAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTA
65 TAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTA
969 NNNNNNNNNN
Statistics
Matches: 615, Mismatches: 147, Indels: 48
0.76 0.18 0.06
Matches are distributed among these distances:
167 3 0.00
168 81 0.13
169 231 0.38
170 145 0.24
171 27 0.04
172 36 0.06
173 77 0.13
174 15 0.02
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (169 bp):
CATGTTTCTCAAGGCAAGCATTCAATTATAGTCTATTTTAACAAAAATGTAAAAAAGTTCAACTT
AAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGA
CTATAAATGGACTTTTTTCTCAATGAATGAATTTTTTTA
Done.