Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402446.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5524.0, 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, 892
Length: 1488
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:516 original size:171 final size:170
Alignment explanation
Indices: 96--1488 Score: 635
Period size: 173 Copynumber: 8.1 Consensus size: 170
86 NNNNNNNNNN
* ** * * ** *
96 TCAATTTTGAGATTATAAAATCAATTAAAGC-AGGCAATAAGGCTTTTGAAGGAATGGGTGACTA
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGA-GTAATAAGGCTTTTGAAGGAATAAGAGACTA
* * * * **
160 TAAATGGATTTTTCTTGCAAAGGAATGCCTTTTCTTCA-AGTTTCTCACTGTAGACATTCAATTA
65 TAAATGAACTTTTCTTGC-AATGAATGCTTTTTCTTCATA-TTTCTCAAGGTAGACATTCAATTA
* * * *** * * *
224 TTGTCTGTTTTAA-CCTAAA-ATGCAAAAACATTCAACTGAAAA
128 TAGTCCGTTTAAATAAAAAATATGCAAAAA-TTTGAACTTAAAA
* ********** * *
266 TTAATTATGAGATTATAAANNNNNNNNNNGCGAGTAATAAGGCTTTTGAAGAAATACGAGACTAT
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
* * * * * *
331 AAATGGAGTTTTCTTGCCAATAAATGCTTTTTGTTCATGTTTCTCAAAGTAGACATTCAATTATA
66 AAATGAACTTTTCTTG-CAATGAATGCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATA
* *
396 GTCCGTTTTAATAAAAAATTTGCAAACAA-TTGAACTTAAAA
130 GTCCGTTTAAATAAAAAATATGCAAA-AATTTGAACTTAAAA
********** *
437 TCAATTATGAGATTATAANNNNNNNNNNAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGCCTAT
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
* * * *
502 AAATAAACTTTTCTTAGCAATGAATGCTTTTTTTCTTCACATTTCTTAAGGTAGACATTGAATTA
66 AAATGAACTTTTCTT-GCAATGAATGC--TTTTTCTTCATATTTCTCAAGGTAGACATTCAATTA
* * *
567 CAGTCTGTTTAAATCAAAAATATGCAAAAATTTGAACTTAAAA
128 TAGTCCGTTTAAATAAAAAATATGCAAAAATTTGAACTTAAAA
* * *
610 TCATTTATGAGATTATAAAGCCATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATTAGAGACTAT
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
* *
675 AAATGAACTTTTCCTAGCAATGAATGCTTTTTCTTTATATTTCTCAAGGTAGACATTCAATTATC
66 AAATGAACTTTT-CTTGCAATGAATGCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTAT-
* * * *** *
740 A-TCGGTTTGAACTAAAAATGTAAAAAAAAATTTGAACATAAAA
129 AGTCCGTTT-AAATAAAAA-ATATGCAAAAATTTGAACTTAAAA
********** * * * * * * *
783 TCAATNNNNNNNNNNTAAAACTATTTAAAGTGGGTAATAAGGCTTTTGAAGAAATGAGAGACTAC
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
* * * * ** * * *
848 AAATGGACTTTTTTTACCAATAAACACTTTTTTCTTCATATTTTTCAAGGTAAACATTGAATTAT
66 AAATGAACTTTTCTT-GCAATGAATGC-TTTTTCTTCATATTTCTCAAGGTAGACATTCAATTAT
* * * * ** *
913 AGTCTGTTTTAACT-AAAACTGTAAAAAAAAATTGAACTTAAAA
129 AGTCCG-TTTAAATAAAAAATAT-GCAAAAATTTGAACTTAAAA
********** * * * *
956 TCAATTATGAGATTATAANNNNNNNNNNAGTGAGTAATAAGGCTTTTAAAAGAATGAGAGACTAT
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
* * * * ** *
1021 ATATGAA-TTTTCTTGCCAAGGAATCCTTCTTTCTTTACGTTTCTCTAA-GTAAACATTCAATTA
66 AAATGAACTTTTCTTG-CAATGAATGCTT-TTTCTTCATATTTCTC-AAGGTAGACATTCAATTA
* * * ** *
1084 TAGTCTGTTTTAAA-CAAAAATGTAAAAAGAAATTGAA-TATAAAA
128 TAGTCCG-TTTAAATAAAAAATATGCAAA-AATTTGAACT-TAAAA
* * * * * * ** *
1128 TCAATTTTAAGATAATAGAA-CTATTTAAAG-GTGGTAATAAGGCTTTTGAAAGAATGGGTGACT
1 TCAATTATGAGATTATA-AAGCCATTTAAAGCG-AGTAATAAGGCTTTTGAAGGAATAAGAGACT
********* * *
1191 ATAAAATG-ACTTTNNNNNNNNNNGAATGCCTTTTTCTTCA-AGTGTT-TCAACGTAAACATTCA
64 AT-AAATGAACTTT-TCTTGCAATGAATG-CTTTTTCTTCATA-T-TTCTCAAGGTAGACATTCA
* * * * * * * *
1253 ATTATAATCTGTTTTATTCAAAAATGT-AAAAAGAGTTGAACTTAAAA
124 ATTATAGTCCGTTTAAATAAAAAATATGCAAAA-ATTTGAACTTAAAA
* * * * * * * *******
1300 TTAATTTTGAGAGTATAAAACCATTTAAAGTGAGTAATAAGGCTTCTGAAGGAATGAGNNNNNNN
1 TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
*** * * * * *
1365 NNNTGGACTTTTCTTGCCAATGAATGCCTTTTCTTCATGTTTCTCAAGATAGACTTTCAATTATA
66 AAATGAACTTTTCTTG-CAATGAATGCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATA
** * ** * * * *
1430 GTCTTTTTTAACGAAAAATAT-AAAAAAATTCAACTTCAAA
130 GTCCGTTTAAATAAAAAATATGCAAAAATTTGAACTTAAAA
1470 TCAATTATGAGATTATAAA
1 TCAATTATGAGATTATAAA
Statistics
Matches: 942, Mismatches: 238, Indels: 86
0.74 0.19 0.07
Matches are distributed among these distances:
170 138 0.15
171 196 0.21
172 211 0.22
173 347 0.37
174 47 0.05
175 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Consensus pattern (170 bp):
TCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
AAATGAACTTTTCTTGCAATGAATGCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAG
TCCGTTTAAATAAAAAATATGCAAAAATTTGAACTTAAAA
Done.