Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401149.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4302.0, 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, 650
Length: 1084
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:340 original size:171 final size:170
Alignment explanation
Indices: 5--1080 Score: 780
Period size: 171 Copynumber: 6.3 Consensus size: 170
1 ACTA
* * * * * **
5 AAAATCAATTATGAGATTATAAGAACATTTAAAGTGAGTAATAAGTCTTTCGAAGGCATGGGTGA
1 AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTAAAGGCATGGGTGA
* * * * * * *
70 CTATAAATAGACTTTTCTTGTCAATGGATACCTTTTTCTTCAAGTTT-CTCAAGGTAGACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCT-GAGGCAGACATTCA
********** ** *
134 ATTANNNNNNNNNNTAATAAAAAATATAAAAAAATTTAACCT
130 ATTATTATCTGTTTTAACCAAAAATGT-AAAAAATTTAACCT
* * * * * * *
176 AAAATCAATTATCAGATTATAAAAATATTTAAAGTGAGCAATAAGGCTTTTAAAGGCATGCGCGA
1 AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTAAAGGCATGGGTGA
********** * * *
241 CTATAAATGGACTTTTCTTGCCNNNNNNNNNNTTTTTCTTCATGTTTCTTGAGGCAAATATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAA
* * * **
306 TTATTATCTTTTTTAACCAAAAACGTAGAAAAATTCAATTT
131 TTATTATCTGTTTTAACCAAAAATGTA-AAAAATTTAACCT
* * * * * * *
347 TAACTCAATTATAAGATTATAAAAACATTTAAAGTGAGTAATAAGGTTTTTGAAGGCATGGGTGC
1 AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTAAAGGCATGGGTGA
* * * * *
412 CTATAAATGGACTTTTCTTACTAATGTATATCTTTTTCTTCACGTTTCCT-AGGGTAGACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTGA-GGCAGACATTCA
* * *
476 GTTATTATCTGTTTTATCCAAAAATGTAAAAAAATTTAGCCT
130 ATTATTATCTGTTTTAACCAAAAATGT-AAAAAATTTAACCT
* * * *
518 AAAATCCATTATGAGATTATAAAAATATTTAAAGCGAGTAAAAAGGCTTTTGAAAGTG--TAGGT
1 AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTT-AAAG-GCATGGGT
* *
581 GACTATAAATGGACTTTTCTTTCCAATGAATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTT
64 GACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTC
* * ** * *
646 AATTATAATATGTTTTAATTAAAAATATAAAAGAATTTAACTT
129 AATTATTATCTGTTTTAACCAAAAATGTAAAA-AATTTAACCT
* * *
689 AAAATCAATTATAAGTTTATAAAAACATTTAAAGCGAGTAAAAAGGATTTTAAAGGCATGGGTGG
1 AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTAAAGGCATGGGTGA
* * * * * *
754 CTATAAATGGGCTTTTTTTGCCAATGGATATCTTTTTCTTCATATTT-CTAGAGGTAGACATTTA
66 CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCT-GAGGCAGACATTCA
* * ** * *
818 ATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAA-CT
130 ATTATTATCTGTTTTAACCAAAAATGT-AAAAAATTTAACCT
* * * * * ***********
859 AAAAATCTATTATAAGATTAGAAAAATATTTAAAGCAAGTAATAAGGCTTTT-GNNNNNNNNNNG
1 -AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTAAAGGCATGGGTG
* * * * * ********** *
923 ACTATAAATGGACTTCTCTTACCATTGGATATCTTTTTCTTCACGTTTCCNNNNNNNNNNATGCA
65 ACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCA
** * **
988 ATTATTATCTGTTTTAACCAAAAACATAAAAAAATCTAATTT
130 ATTATTATCTGTTTTAACCAAAAATGT-AAAAAATTTAACCT
* * * *
1030 TAAATCAATTATGAGATTATAAAAGCATTTAAAGCGAGTAATAAGGCTTTT
1 AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTT
1081 GAAG
Statistics
Matches: 714, Mismatches: 176, Indels: 31
0.78 0.19 0.03
Matches are distributed among these distances:
169 1 0.00
170 133 0.19
171 569 0.80
172 10 0.01
173 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTAAAGGCATGGGTGA
CTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAA
TTATTATCTGTTTTAACCAAAAATGTAAAAAATTTAACCT
Found at i:638 original size:342 final size:336
Alignment explanation
Indices: 6--1084 Score: 1012
Period size: 342 Copynumber: 3.2 Consensus size: 336
1 ACTAA
* * * *
6 AAATCAATTATGAGATTATAAGAACATTTAAAGTGAGTAATAA-GTCTTTCGAAGGCATGGGTGA
1 AAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAATAAGGT-TTTTGAAGGCATGGGTGA
* * * *
70 CTATAAATAGACTTTTCTTGTCAATGGATACCTTTTTCTTCAAGTTTCTCAAGGTAGACATTCAA
65 CTATAAATGGACTTTTCTTCT-AATGGATATCTTTTTCTTCAAGTTTCT-AGGGTAGACATTCAA
********* * *
135 TTANNNNNNNNNNTAATAAAAAATATAAAAAAATTTAACCTAAAATCAATTATCAGATTATAAAA
128 TTA-TAATCTATTTTATAAAAAATATAAAAAAATTT-ACCTAAAATCAATTATAAGATTATAAAA
* * * *
200 ATATTTAAAGTGAGCAATAAGGCTTTT-AAAGGCATGCGCGACTATAAATGGACTTTTCTTGCCN
191 ATATTTAAAGCGAGTAATAAGGCTTTTGAAAGGCA-G-GCGACTATAAATGGACTTTTCTTACCA
********* * * *
264 NNNNNNNNNTTTTTCTTCATGTTTCTTGAGGCAAATATTCAATTATTATCTTTTTTAACCAAAAA
254 ATGAATATCTTTTTCTTCATGTTTCCTGAGGCAAACATTCAATTATTATCTGTTTTAACCAAAAA
*
329 CGTAGAAAAATTCAATTTT
319 CATA-AAAAATTCAATTTT
* * *
348 AACTCAATTATAAGATTATAAAAACATTTAAAGTGAGTAATAAGGTTTTTGAAGGCATGGGTGCC
1 AAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAATAAGGTTTTTGAAGGCATGGGTGAC
* * *
413 TATAAATGGACTTTTCTTACTAATGTATATCTTTTTCTTCACGTTTCCTAGGGTAGACATTCAGT
66 TATAAATGGACTTTTCTT-CTAATGGATATCTTTTTCTTCAAGTTT-CTAGGGTAGACATTCAAT
* * * * * *
478 TATTATCTGTTTTATCCAAAAATGTAAAAAAATTTAGCCTAAAATCCATTATGAGATTATAAAAA
129 TATAATCTATTTTAT-AAAAAATATAAAAAAATTTA-CCTAAAATCAATTATAAGATTATAAAAA
* * * *
543 TATTTAAAGCGAGTAAAAAGGCTTTTGAAAGTGTAGGTGACTATAAATGGACTTTTCTTTCCAAT
192 TATTTAAAGCGAGTAATAAGGCTTTTGAAAG-GCAGGCGACTATAAATGGACTTTTCTTACCAAT
* * * * ** *
608 GAATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTTAATTATAATATGTTTTAATTAAAAATA
256 GAATATCTTTTTCTTCATGTTTCCTGAGGCAAACATTCAATTATTATCTGTTTTAACCAAAAACA
* * *
673 TAAAAGAATTTAACTTA
321 TAAAA-AATTCAATTTT
* * * * *
690 AAATCAATTATAAGTTTATAAAAACATTTAAAGCGAGTAAAAAGGATTTTAAAGGCATGGGTGGC
1 AAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAATAAGGTTTTTGAAGGCATGGGTGAC
* * * *
755 TATAAATGGGCTTTTTTTGCCAATGGATATCTTTTTCTTCATA-TTTCTAGAGGTAGACATTTAA
66 TATAAATGGACTTTTCTT-CTAATGGATATCTTTTTCTTCA-AGTTTCTAG-GGTAGACATTCAA
* * * *
819 TTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTAAAAATCTATTATAAGATTAGAAAA
128 TTATAATCTATTTT-ATAAAAAATATAAAAAAATTTACCT-AAAATCAATTATAAGATTATAAAA
* ********** * *
884 ATATTTAAAGCAAGTAATAAGGCTTTTGNNNNNNNNNNGACTATAAATGGACTTCTCTTACCATT
191 ATATTTAAAGCGAGTAATAAGGCTTTTGAAAGGCAGGCGACTATAAATGGACTTTTCTTACCAAT
* * ********** *
949 GGATATCTTTTTCTTCACGTTTCCNNNNNNNNNNATGCAATTATTATCTGTTTTAACCAAAAACA
256 GAATATCTTTTTCTTCATGTTTCCTGAGGCAAACATTCAATTATTATCTGTTTTAACCAAAAACA
*
1014 TAAAAAAATCTAATTTT
321 TAAAAAATTC-AATTTT
* * *
1031 AAATCAATTATGAGATTATAAAAGCATTTAAAGCGAGTAATAAGGCTTTTGAAG
1 AAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAATAAGGTTTTTGAAG
Statistics
Matches: 600, Mismatches: 124, Indels: 27
0.80 0.17 0.04
Matches are distributed among these distances:
340 3 0.00
341 140 0.23
342 443 0.74
343 12 0.02
344 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (336 bp):
AAATCAATTATAAGATTATAAAAACATTTAAAGCGAGTAATAAGGTTTTTGAAGGCATGGGTGAC
TATAAATGGACTTTTCTTCTAATGGATATCTTTTTCTTCAAGTTTCTAGGGTAGACATTCAATTA
TAATCTATTTTATAAAAAATATAAAAAAATTTACCTAAAATCAATTATAAGATTATAAAAATATT
TAAAGCGAGTAATAAGGCTTTTGAAAGGCAGGCGACTATAAATGGACTTTTCTTACCAATGAATA
TCTTTTTCTTCATGTTTCCTGAGGCAAACATTCAATTATTATCTGTTTTAACCAAAAACATAAAA
AATTCAATTTT
Done.