Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403324.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_996.0, 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, 816
Length: 1360
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.30
Warning! 196 characters in sequence are not A, C, G, or T
Found at i:454 original size:170 final size:170
Alignment explanation
Indices: 1--908 Score: 901
Period size: 170 Copynumber: 5.4 Consensus size: 170
* * * * *
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAATCCATTTAAAATGAGCAATGAGGCTTTT-A
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGA
* ** * ** * *
65 AAAGCATAGGTGACTATAAATGGACTTTT-TTAGTAAATGAATATCTTTTTTTTTTCACATCTCC
66 AGA-CATAGGTGACTATAAATGGACTTTTCTT-GCCAATGAATATC---TTTTCTTCATGTTTCT
* * * * *
129 CAAGGCAGACATTCAACTGTAATCTGTTTTAAC----AA--AAAA
126 CGAGGTAGACATTCAATTATAATCGGTTTTAACAAAAAATGAAAA
* * ** *
168 AAAATTGAACTTAAAGTCAATAATGAGATTATAAAACCT-TTTAGGGAGAGTAATAAGGCTTTTG
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAAA-CTATTTAAAGTGAGTAATAAGGCTTTTG
* * * *
232 AAG-CATAAGTGACTATAAATGGACTTTTCTTGGCAATAAATATCTTTTCTTCATGTTTCTCGAT
65 AAGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTCTTCATGTTTCTCGAG
* * * * **
296 GTAAACATTTAATAATAATCGGTTTGAACCGAAAATGAAAA
130 GTAGACATTCAATTATAATCGGTTTTAACAAAAAATGAAAA
* * * * *
337 AAAATTTAGCTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGCAATAAGTCTTTGGA
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGA
** * *
402 AGGTATAGGTGACTATAAATGGGCTTTTCTTACCAATGAATAT-TTGTTCTTCATGTTTCTCGAG
66 AGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTT-TTCTTCATGTTTCTCGAG
* * * * *
466 GTAGGCACTCAATTATGATCTGTTTTAATAAAAAAT-ATAAA
130 GTAGACATTCAATTATAATCGGTTTTAACAAAAAATGA-AAA
* * * * * *
507 AAAATACAACTTCAACTTAATTATGAGGTTATCAAACTATTTAAAGTGAGTAATAAGGCTTTTGA
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGA
* *
572 AGACATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTGTTCTTCATGTTTCCCGAG
66 AGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTT-TTCTTCATGTTTCTCGAG
* ** ** * *
637 CTTCACATTCAATT-TCAATCTATTTTAACAAAAAAAGTAAA
130 GTAGACATTCAATTAT-AATCGGTTTTAACAAAAAATGAAAA
* * * * * **
678 ACAATTCCACTTCTAA-TCAATTATGAGATTATAAATCAATTTAAAGCAAGTAATAAGGCTTTTG
1 AAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTG
*
742 AAGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTCTCTTCATGTTTCTTGA
65 AAGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTT-TCTTCATGTTTCTCGA
* * * ** **
807 GGTTGACATTTAATTACAATCGACTTTAACCCAAAATGAAAA
129 GGTAGACATTCAATTATAATCGGTTTTAACAAAAAATGAAAA
*
849 AAAATT-AACTTAAAGTCAATTATAAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTT
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTT
909 NNNNNNNNNN
Statistics
Matches: 605, Mismatches: 116, Indels: 37
0.80 0.15 0.05
Matches are distributed among these distances:
163 34 0.06
166 34 0.06
167 55 0.09
168 5 0.01
169 64 0.11
170 217 0.36
171 194 0.32
172 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (170 bp):
AAAATTCAACTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGA
AGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTCTTCATGTTTCTCGAGG
TAGACATTCAATTATAATCGGTTTTAACAAAAAATGAAAA
Found at i:722 original size:341 final size:339
Alignment explanation
Indices: 1--908 Score: 833
Period size: 341 Copynumber: 2.7 Consensus size: 339
* * * *** * *
1 AAAATTCAACTTAAAGTCAATTATGAGATTATAAATCCATTTAAAATGAGCAATGAGGCTTT-TA
1 AAAATTCAGCTTAAAGTCAATTATGAGATTATAAAACAATTTAAAGCAAGCAATAAGGCTTTGGA
* ** * * ** * *
65 AAAGCATAGGTGACTATAAATGGACTTTT-TTAGTAAATGAATATCTTTTTTTTTTCACATCTCC
66 AGA-CATAGGTGACTATAAATGGACTTTTCTTA-CCAATGAATATC--TTTCTCTTCATGTTTCT
* * * * ** * * * *
129 CAAGGCAGACATTCAACTGTAATCTG-TTTTAAC---AAA--AAAAAAATTGAACTTAAAGTCAA
127 CGAGGTAGACACTCAATTACAATC-GACTTTAACAAAAAATGAAAAAAAATCAACTTAAACTCAA
* * ** *
188 TAATGAGATTATAAAACCT-TTTAGGGAGAGTAATAAGGCTTTTGAAGCATAAGTGACTATAAAT
191 TTATAAGATTATAAAA-CTATTTAAAGTGAGTAATAAGGCTTTTGAAGCATAAGTGACTATAAAT
* * *
252 GGACTTTTCTTGGCAATAAATATCTTTTCTTCATGTTTCTCGATGTAAACATTTAATAATAATCG
255 GGACTTTTCTTGCCAATAAATATCTTTTCTTCATGTTTCCCGATGTAAACATTCAATAATAATCG
* ** *
317 GTTTGAACCGAAAATGAAAA
320 ATTTGAACAAAAAAAGAAAA
* * ** *
337 AAAATTTAGCTTAAAGTCAATTATGAGATTATAAAACTATTTAAAGTGAGCAATAAGTCTTTGGA
1 AAAATTCAGCTTAAAGTCAATTATGAGATTATAAAACAATTTAAAGCAAGCAATAAGGCTTTGGA
** *
402 AGGTATAGGTGACTATAAATGGGCTTTTCTTACCAATGAATAT-TTGT-TCTTCATGTTTCTCGA
66 AGACATAGGTGACTATAAATGGACTTTTCTTACCAATGAATATCTT-TCTCTTCATGTTTCTCGA
* ** * * * *
465 GGTAGGCACTCAATTATGATCTG-TTTTAATAAAAAAT-ATAAAAAAATACAACTTCAACTTAAT
130 GGTAGACACTCAATTACAATC-GACTTTAACAAAAAATGA-AAAAAAAT-CAACTTAAACTCAAT
* * * **
528 TATGAGGTTATCAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGACATGGGTGACTATAAATG
192 TATAAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAG-CATAAGTGACTATAAATG
* ** *
593 GACTTTTCTTGCCAATGAATATCTTGTTCTTCATGTTTCCCGA-GCTTCACATTCAAT-TTCAAT
256 GACTTTTCTTGCCAATAAATATCTT-TTCTTCATGTTTCCCGATG-TAAACATTCAATAAT-AAT
* * *
656 CTATTTTAACAAAAAAAGTAAA
318 CGATTTGAACAAAAAAAGAAAA
* * * * *
678 ACAATTCCA-CTTCTAA-TCAATTATGAGATTATAAATCAATTTAAAGCAAGTAATAAGGCTTTT
1 AAAATT-CAGCTT-AAAGTCAATTATGAGATTATAAAACAATTTAAAGCAAGCAATAAGGCTTTG
* *
741 GAAGACATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTCTCTTCATGTTTCTTG
64 GAAGACATAGGTGACTATAAATGGACTTTTCTTACCAATGAATATCTTTCTCTTCATGTTTCTCG
* * * ** * *
806 AGGTTGACATTTAATTACAATCGACTTTAACCCAAAATGAAAAAAAATTAACTTAAAGTCAATTA
129 AGGTAGACACTCAATTACAATCGACTTTAACAAAAAATGAAAAAAAATCAACTTAAACTCAATTA
871 TAAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTT
194 TAAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTT
909 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 86, Indels: 35
0.79 0.15 0.06
Matches are distributed among these distances:
333 35 0.08
334 1 0.00
336 90 0.19
337 6 0.01
338 9 0.02
339 48 0.10
340 41 0.09
341 182 0.39
342 53 0.11
343 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (339 bp):
AAAATTCAGCTTAAAGTCAATTATGAGATTATAAAACAATTTAAAGCAAGCAATAAGGCTTTGGA
AGACATAGGTGACTATAAATGGACTTTTCTTACCAATGAATATCTTTCTCTTCATGTTTCTCGAG
GTAGACACTCAATTACAATCGACTTTAACAAAAAATGAAAAAAAATCAACTTAAACTCAATTATA
AGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGCATAAGTGACTATAAATGGACTT
TTCTTGCCAATAAATATCTTTTCTTCATGTTTCCCGATGTAAACATTCAATAATAATCGATTTGA
ACAAAAAAAGAAAA
Done.