Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400404.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3601.0, 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, 846
Length: 1411
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.27
Warning! 378 characters in sequence are not A, C, G, or T
Found at i:505 original size:170 final size:170
Alignment explanation
Indices: 1--954 Score: 702
Period size: 170 Copynumber: 5.6 Consensus size: 170
* * * * *
1 GAAGGCATGGGTTACTATAAATTGACTTTTCTTGCCAATGGATATCTTTTTCTTAACGTTTCTCA
1 GAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCG
* * ** * * ***
66 AGGAAGACATTGAATTATAATCAATTTTAATAAAAA-ATATAAAAAATTCAAATTAAAATCANNN
66 AGGCAGACATTCAATTATAATCTGTTTTAATAAAAATATA-AAAAAATTCAACTTAAAATTAATT
******* * ** * *
130 NNNNNNNTATAAAATTATTTAAAGCGAGTAATAAAGCTTTT
130 ATAAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTC
* * * * * * *
171 GAAAGCGTGGGTGACTATAAATAGACTTTTCTTGCCAATGGATATCTTTTTGTTCAAGTTTCTTG
1 GAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCG
** * * * * * * *
236 AGGCAGATGTTCAATTATAATATGTTTTTATAAATATTCTAAAAGAATTTAACTT-AAATCCAAT
66 AGGCAGACATTCAATTATAATCTGTTTTAATAAA-AATATAAAAAAATTCAACTTAAAAT-TAAT
* * * * * * *
300 TATAAGGTCATACAATCATTTAAAGCAAGTAATAAGACTTTC
129 TATAAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTC
* * * * *
342 GAAGGTATGTGTTACCATAAATGGACTTTTCTTGCCAATGGATATCTTTTT-TTCACATTTCTCG
1 GAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCG
* * *
406 AGGTAGACATTCAATTAGAATCTGTTTTAATTAAAAATGTAAAAAAATTCAACTTAAAATTAATT
66 AGGCAGACATTCAATTATAATCTGTTTTAA-TAAAAATATAAAAAAATTCAACTTAAAATTAATT
* * *
471 ATGAGATTACAAAAGCATTTAAAGCTAGTAATAAGGCTTTC
130 ATAAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTC
** **********
512 GAAGGCAT-AGGTGACTATAAATGGACTTTTCTTATCANNNNNNNNNNTTTTCTTCACGTTTC-C
1 GAAGGCATGA-GTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTC
* * * *
575 TGAAGCAGATAATT-AATTATAATCTGTTTTAATAAGAAATATAAAAAAATTTCTACTTAAAACT
65 -GAGGCAGA-CATTCAATTATAATCTGTTTTAATAA-AAATATAAAAAAA-TTCAACTTAAAATT
* * ********** *
639 AATTATGAGATTAAAAAAGCTTTTAAANNNNNNNNNNAGGCTTTT
126 AATTATAAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTC
* * **
684 GAAGGTATGAGTGACTATAAATGGACTTTTCTTTCCAATGGATATCTTTTTCTTCTTGTTTC-CT
1 GAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTC-
* * ********** ** * *
748 GAAGCAGATAATT-AANNNNNNNNNNTTTTAATAAAAAATATAAAAAAGGTCTACTTAAAACTAA
65 GAGGCAGA-CATTCAATTATAATCTGTTTTAAT-AAAAATATAAAAAAATTCAACTTAAAATTAA
* *
812 TTATAAGATTAAAAAAGTATTTAAAGCGAGCAATAAGGCTTTC
128 TTATAAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTC
* * *
855 GAAGGCATGAGTTACGATAAATGGACTTTTCTTGCCTATGGATATC-TTTTCTTCACGTTTCTCG
1 GAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCG
*
919 AGGCAAACATTCAATTATAATCTGTTTTAATAAAAA
66 AGGCAGACATTCAATTATAATCTGTTTTAATAAAAA
955 NNNNNNNNNN
Statistics
Matches: 603, Mismatches: 166, Indels: 31
0.75 0.21 0.04
Matches are distributed among these distances:
169 8 0.01
170 239 0.40
171 223 0.37
172 130 0.22
173 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
GAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCG
AGGCAGACATTCAATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAACTTAAAATTAATTA
TAAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTC
Done.