Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402731.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5792.0, 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, 601
Length: 1002
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.36
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:549 original size:173 final size:160
Alignment explanation
Indices: 370--898 Score: 382
Period size: 170 Copynumber: 3.1 Consensus size: 160
360 NNNNNNNNNA
** *
370 GCTTTTCTTGCCAATGAATGGGTTTTTCTTTGTGCTTTTC-GAGACAAACATTCAATTATAATCT
1 GCTTTTCTTGCCAATGAATGGGTTTTTCTTCATG-TTTCCTGAGACAAACATTCAATTATAATC-
* * * *
434 GTGTTTTAACTAAAAATGTTAAAAAATTCAACTTAAAATCAATTTTAAGGCTATAAAACCT-TTT
64 -TGTTTTAACTAAAAAT-ATAAAAAATTCAACCTAAAATCAATTATAAGACTATAAAA-CTATTT
*
498 AAAGAGAGTAATAAGGCTTNNNNNNNNNNGGGTGACTATAAATGG
126 AAAGAGAGCAATAAGGCTT----------GGGTGACTATAAATGG
* * **
543 GCTTTTCTTTCCAATGAATGGGTTTTTCTTCATGTTTCCTTAGGTAAACATTCAATTATAATCTG
1 GCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCTGAGACAAACATTCAATTATAATCTG
* * *
608 TTTTAACTAAAAATATAAAAAATTTAACCTAAAATCAATTATGAGATTATAAAACTATTTAAAGA
66 TTTTAACTAAAAATATAAAAAATTCAACCTAAAATCAATTATAAGACTATAAAACTATTTAAAGA
*
673 GAGCAATAAGACATTTGAAGGCTTGTGTGACTATAAATGG
131 GAGC------A-A--T-AAGGCTTGGGTGACTATAAATGG
* * * * * * *
713 ACTTTTCTTGTCGATGAATGGCTTTTTCTTTAGGTTT-CTAATGGA-AAACATTCAATTATAATC
1 GCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCTGA--GACAAACATTCAATTATAATC
* ** * * * ** *
776 TGTTTTAAATAAAAATATAAAAACATTTGACTTAAAATCAATTTTGAGGTTATAAAATTATTTAA
64 TGTTTTAACTAAAAATATAAAAA-ATTCAACCTAAAATCAATTATAAGACTATAAAACTATTT--
* *
841 AAAGAGTAACAAGGCTTTTGAAGGCTTGGGTGAATATAAATGG
126 AAAGAG-AGCAA------T-AAGGCTTGGGTGACTATAAATGG
884 GCTTTTCTTGCCAAT
1 GCTTTTCTTGCCAAT
899 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 37, Indels: 46
0.78 0.10 0.12
Matches are distributed among these distances:
167 1 0.00
168 1 0.00
169 5 0.02
170 129 0.43
171 88 0.30
172 4 0.01
173 57 0.19
174 2 0.01
176 1 0.00
177 1 0.00
179 1 0.00
180 7 0.02
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.37
Consensus pattern (160 bp):
GCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCTGAGACAAACATTCAATTATAATCTG
TTTTAACTAAAAATATAAAAAATTCAACCTAAAATCAATTATAAGACTATAAAACTATTTAAAGA
GAGCAATAAGGCTTGGGTGACTATAAATGG
Found at i:709 original size:170 final size:171
Alignment explanation
Indices: 13--1002 Score: 880
Period size: 171 Copynumber: 5.8 Consensus size: 171
3 TAAAGGGTTC
* * * ** ** * *
13 GGTGATTATCAATGGGATTTTCTTGCCAATGAATGTATTTTTCTTTATGTTTTACATAGCAAACA
1 GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTCCCATGGAAAACA
**********
78 TTCAATTATAATCTGTTTTAACTAAAAATATANNNNNNNNNNACTTAAAATCAATTATGAGATTA
66 TTCAATTATAATCTGTTTTAACTAAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATTA
* * * *
143 GAAAACCATTGAAAGAGAGTAATAAGGCTTTTGAATGCTTG
131 TAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTG
* * * * * * * *
184 GATGACTATAAATGGGATTCTATTGCCAGTGAATGGCTTTTACTTTAGGTTTCCCATGGAAAATA
1 GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTCCCATGGAAAACA
* * * *
249 TTCAATTATAATCTGTTTTAAATAAAAATATAAAAACATTTAACTTCAAATCAATTTTGAGACTA
66 TTCAATTATAATCTGTTTTAACTAAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATTA
* *
314 TAAAA-TCAATTACAGAGAGTAATAAGGCTTTTGAAGGCTTG
131 TAAAACT-ATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTG
*********** * * * *
355 GGTGNNNNNNNNNNAGCTTTTCTTGCCAATGAATGGGTTTTTCTTTGTGCTTTTCGA--GACAAA
1 GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATG-TTTCCCATGGA-AAA
* * * *
418 CATTCAATTATAATCTGTGTTTTAACTAAAAATGTTAAAAA-ATTCAACTTAAAATCAATTTTAA
64 CATTCAATTATAATC--TGTTTTAACTAAAAAT-ATAAAAACATTTAACTTAAAATCAATTATGA
** **********
482 GGCTATAAAACCT-TTTAAAGAGAGTAATAAGGCTTNNNNNNNNNNG
126 GATTATAAAA-CTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTG
* * * * *
528 GGTGACTATAAATGGGCTTTTCTTTCCAATGAATGGGTTTTTCTTCATGTTT-CCTTAGGTAAAC
1 GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTCCCAT-GGAAAAC
*
592 ATTCAATTATAATCTGTTTTAACTAAAAATATAAAAA-ATTTAACCTAAAATCAATTATGAGATT
65 ATTCAATTATAATCTGTTTTAACTAAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATT
* * *
656 ATAAAACTATTTAAAGAGAGCAATAAGACATTTGAAGGCTTG
130 ATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTG
* * * * * **
698 TGTGACTATAAATGGACTTTTCTTGTCGATGAATGGCTTTTTCTTTAGGTTTCTAATGGAAAACA
1 GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTCCCATGGAAAACA
* * * *
763 TTCAATTATAATCTGTTTTAAATAAAAATATAAAAACATTTGACTTAAAATCAATTTTGAGGTTA
66 TTCAATTATAATCTGTTTTAACTAAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATTA
* * *
828 TAAAATTATTTAAAAAGAGTAACAAGGCTTTTGAAGGCTTG
131 TAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTG
* ********** * * *
869 GGTGAATATAAATGGGCTTTTCTTGCCAATNNNNNNNNNNTTCTTCAAGTTTCCCATGAAAAACA
1 GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTCCCATGGAAAACA
* *
934 TTCAATTATGATCTTTTTTAAAC-AAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATT
66 TTCAATTATAATCTGTTTT-AACTAAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATT
998 ATAAA
130 ATAAA
Statistics
Matches: 642, Mismatches: 162, Indels: 30
0.77 0.19 0.04
Matches are distributed among these distances:
169 2 0.00
170 141 0.22
171 363 0.57
172 10 0.02
173 118 0.18
174 7 0.01
175 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
GGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTCCCATGGAAAACA
TTCAATTATAATCTGTTTTAACTAAAAATATAAAAACATTTAACTTAAAATCAATTATGAGATTA
TAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTG
Done.