Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398596.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1887.0, 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, 770
Length: 1284
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:506 original size:176 final size:161
Alignment explanation
Indices: 318--644 Score: 304
Period size: 172 Copynumber: 1.9 Consensus size: 161
308 TGGATGACTG
318 TAAATAGAC-TTTTCTTGCCAATGAATGCCTTGCCTTTTTCTTCATGTTTCC-TAAGGTAAACAT
1 TAAATAGACTTTTTC-TGCCAATGAATG-C-T---TTTTTCTTCATG-TTCCTTAAGGTAAACAT
* * * *
381 TCAATTATTG-CTTGTTTTAATCGAA-AACGT-AAAGAAATTCAAATTAAAATCAATTATTAGAT
59 TCAATTATAGTCTT-TTTTAA-CCAATAACGTAAAACAAATT-AAATTAAAATCAATTATGAGAT
*
443 TATAAATTAATTTAAAGCGAGTAATAAGGCTTNNNNNNNNNNGAGTAACTA
121 TATAAAGTAATTTAAAGCGAGTAATAAGGCTT----------GAGTAACTA
* * * * * *
494 TAAATGGACTTTTTCTGTCAATGAATGCTTTTTTCTTTATGTTCCTTGAGGTAGATATTCAATTA
1 TAAATAGACTTTTTCTGCCAATGAATGCTTTTTTCTTCATGTTCCTTAAGGTAAACATTCAATTA
* * *
559 TAGTCTTTTTTAACCAATAATGTAAAAACAAATTGACTTAAAATCAATTATGAGATTATAAAGTA
66 TAGTCTTTTTTAACCAATAACGT-AAAACAAATTAAATTAAAATCAATTATGAGATTATAAAGTA
624 ATTTAAAGCGAGTAATAAGGC
130 ATTTAAAGCGAGTAATAAGGC
645 ATTTGAAGAA
Statistics
Matches: 131, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
170 7 0.05
171 39 0.30
172 51 0.39
173 8 0.06
174 1 0.01
175 1 0.01
176 19 0.15
177 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.37
Consensus pattern (161 bp):
TAAATAGACTTTTTCTGCCAATGAATGCTTTTTTCTTCATGTTCCTTAAGGTAAACATTCAATTA
TAGTCTTTTTTAACCAATAACGTAAAACAAATTAAATTAAAATCAATTATGAGATTATAAAGTAA
TTTAAAGCGAGTAATAAGGCTTGAGTAACTA
Found at i:1157 original size:171 final size:170
Alignment explanation
Indices: 1--1284 Score: 872
Period size: 171 Copynumber: 7.5 Consensus size: 170
* * * * *
1 ATGCCTTTTTCTTCAAGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATC-AAAATGTA
1 ATGCTTTTTTCTTCATGTTT-TTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATA
* * * * * *
65 AAAATATTCAACTTAAAATCAATTATGAGATTGTAAAACAATTTAAAGCTAGTAATAACGCTTTT
65 AAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTT
********** *
130 GAAGGAATGAGTGACTATNNNNNNNNNNTTCTTGCCAATAA
130 GAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGA
* * * * * ** *
171 ATACCTTTTTCATAATGTTTTTTGAGGCAGACATTTTATTATAGTCTGTTTTAACCAAAACTATA
1 ATGCTTTTTTCTTCATG-TTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATA
** * * * * ** * * *
236 AAACCACTGAACTTAAAATCAATTATAGGTTTATAAAACCATTTAAAGTGAGTAGTAAGACTTTT
65 AAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTT
* * *
301 GAACGAATG-GATGACTGTAAATAGACTTTTCTTGCCAATGA
130 GAAGGAATGAG-TGACTATAAATGGACTTTTCTTGCCAATGA
* * * * * *
342 ATGCCTTGCCTTTTTCTTCATGTTTCCTAAGGTAAACATTCAATTATTG-CTTGTTTTAATCGAA
1 ATG-C-T---TTTTTCTTCATGTTT-TTGAGGTAGACATTCAATTATAGTC-TGTTTTAACCAAA
** * * * *
406 AACGTAAAGAAATTCAAATTAAAATCAATTATTAGATTATAAATTAATTTAAAGCGAGTAATAAG
59 AATATAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAG
********** * *
471 GCTTNNNNNNNNNNGAGTAACTATAAATGGACTTTT-TCTGTCAATGA
124 GCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCT-TGCCAATGA
* * * * * *
518 ATGCTTTTTTCTTTATGTTCCTTGAGGTAGATATTCAATTATAGTCTTTTTTAACCAATAATGTA
1 ATGCTTTTTTCTTCATGTT-TTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT-
* * * *
583 AAAACAAATT-GACTTAAAATCAATTATGAGATTATAAAGTAATTTAAAGCGAGTAATAAGGCAT
64 AAAA-AAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTT
* * *
647 TTGAAGAAATGGGTGACTATCAATGGACTTTTCTT-CTCAATGA
128 TTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGC-CAATGA
* * * * * *
690 ATGAC--TTTTCTACATGTTTATCGAGGCAAACATTCAATTATAGTCTGTTTTAACTAAAACTGG
1 ATG-CTTTTTTCTTCATGTTT-TTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT--
* * * ********** *
753 A-AAAAAAATTCAACTTAAAATCAGTTTTGAGATTATAAANNNNNNNNNNGTGAGTAATAAGGCT
62 ATAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCT
*
817 TTTGAAGGAATGGGTGA-TCAT-AATGGACTTTTCTT-CCACATGA
127 TTTGAAGGAATGAGTGACT-ATAAATGGACTTTTCTTGCCA-ATGA
* * * * * *
860 ATGCATTTTTCTTCATATTTCTTGAGGTAAACATTCAATTATAATCTATTTTAACTAAAAATATA
1 ATGCTTTTTTCTTCATGTTT-TTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATA
* * * * * *
925 AAAAAAGTCAACTCAGAACCAATTATAAGATTGTAAAATAATTTAAAGCAAGTAATAAGGCTTTT
65 AAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTT
* * *
990 GAAGGAATGAGT-AGTCATAAATGAACTTTTCTTGCCAATAA
130 GAAGGAATGAGTGACT-ATAAATGGACTTTTCTTGCCAATGA
* * *
1031 ATAG-TTTTTTCATCATGTTTTTCAAGGTAGACATTCTATTATAGTCTGTTTTAACCAAAAATAT
1 AT-GCTTTTTTCTTCATGTTTTT-GAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT
* * * * * *
1095 AAAAAAACTCAACGTAAAATCAATTATAAGTTTATAAAATCATTTAAGGCGAGAAATAAGGCTTT
64 AAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
* ********** * *
1160 TCAAGGAANNNNNNNNNNTAAATGGACTTTTCTTGCTAATAA
129 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGA
* * ** ** * *
1202 ACGGC-TTTTTCTTTATGTTTCCCGAAACT-GACATTCAATTATAGTCTTTTTTAACCAAAAATG
1 A-TGCTTTTTTCTTCATGTTT-TTG-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATA
*
1265 TAAAACAATTCAACTTAAAA
63 TAAAAAAATTCAACTTAAAA
Statistics
Matches: 856, Mismatches: 220, Indels: 75
0.74 0.19 0.07
Matches are distributed among these distances:
169 5 0.01
170 135 0.16
171 496 0.58
172 89 0.10
173 7 0.01
174 1 0.00
175 6 0.01
176 116 0.14
177 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
ATGCTTTTTTCTTCATGTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAA
AAAAATTCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGA
Done.