Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400386.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3586.0, 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, 1000
Length: 2244
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.31
Warning! 398 characters in sequence are not A, C, G, or T
Found at i:692 original size:170 final size:168
Alignment explanation
Indices: 516--1072 Score: 614
Period size: 170 Copynumber: 3.3 Consensus size: 168
506 NNNAGGTATG
* * * * *
516 GGTGACTATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTCATCAACGCAGACA
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTCATCGAGGCAGACA
** * *
581 TTCAATTATTATTTATTTTAAAGAAAAATGAAAAAAAATTGACTTAAAATCTATTTTGAGGTTAT
66 TTCAATTATTATTTATTTTAACCAAAAATGAAAAAAAATTGACTTAAAATCAATTATGAGGTTAT
*
646 AAAAATATTTAAAGCGAGTAAAACACCTTTTGAAGGCAT
131 AAAAATATTTAAAGCAAGTAAAA-ACCTTTTGAAGGCAT
********** * * * *
685 AGGTGACTATAAATAGACTNNNNNNNNNNATGAATATCTTTTTCTTCCCGTTTATTGAGGCCGAC
1 -GGTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTCATCGAGGCAGAC
* * * ** * *
750 ATTCAATTATTATCTATTTTAACTAAAATTCTAAAAAAATTCAACTTAAAATCCATTATGAGGTT
65 ATTCAATTATTATTTATTTTAACCAAAAATGAAAAAAAATT-GACTTAAAATCAATTATGAGGTT
*
815 ATAAAAATATTTAAAGCAAGTAAAAAGCCTTTTGAAGGCCT
129 ATAAAAATATTTAAAGCAAGTAAAAA-CCTTTTGAAGGCAT
* * * * * * * *
856 GGGTGATTATAAATGGACTTTTTTTGTCACTGGATATCTTTTTTTTCACGTTTC-TCGAGGTAGA
1 -GGTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCACG-TTCATCGAGGCAGA
* * *
920 CATTCAATT-TTAATTATTTTAACCAAAAATGTAAAAAAAATTGACTTAAAATCAATTATAAGTT
64 CATTCAATTATTATTTATTTTAACCAAAAATG-AAAAAAAATTGACTTAAAATCAATTATGAGGT
* *
984 TATAAAAATATTTAAAGAAAGTAAAAACTCTTTTAAAGGCAT
128 TATAAAAATATTTAAAGCAAGTAAAAAC-CTTTTGAAGGCAT
1026 GAGTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTC
1 G-GTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTC
1073 NNNNNNNNNN
Statistics
Matches: 310, Mismatches: 71, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
169 2 0.01
170 191 0.62
171 115 0.37
172 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.37
Consensus pattern (168 bp):
GGTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTCATCGAGGCAGACA
TTCAATTATTATTTATTTTAACCAAAAATGAAAAAAAATTGACTTAAAATCAATTATGAGGTTAT
AAAAATATTTAAAGCAAGTAAAAACCTTTTGAAGGCAT
Found at i:869 original size:171 final size:168
Alignment explanation
Indices: 331--1072 Score: 594
Period size: 170 Copynumber: 4.4 Consensus size: 168
321 NNNNNTAAGA
* * * * * *
331 CTTTCGAAGGCATGGGTGGCTATAAATAGACTTTTCTT-TCTAATGAATGTCTTTTTTTTCACGT
1 CTTTTGAAGGCATGGGTGACTATAAATAGACTTTTTTTGTC-ACTGAATATCTTTTTCTTCACGT
* * * * * * * * *
395 TTCTCGA-GCTAAACTTTCAATTATAATCTGTTTTAA-TAAAAGATATAAAACAATTTAACTTAA
65 TTATCGAGGC-AGACATTCAATTATTAT-TATTTTAACCAAAA-ATGTAAAA-AAATTGACTTAA
* * *** * ***
458 AATCAAATATGAGATTATAAAGCCATTTAAAGCGAGTAATANNN
126 AATCAATTATGAGGTTATAAAAATATTTAAAGCAAGTAA-AAAC
******* * * * * * * *
502 NNNNNNNAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTT
1 CTTTTGAAGGCATGGGTGACTATAAATAGACTTTTTTTGTCACTGAATATCTTTTTCTTCACGTT
* * * ** *
567 CATCAACGCAGACATTCAATTATTATTTATTTTAAAGAAAAATGAAAAAAAATTGACTTAAAATC
66 TATCGAGGCAGACATTCAATTATTA-TTATTTTAACCAAAAATGTAAAAAAATTGACTTAAAATC
* * *
632 TATTTTGAGGTTATAAAAATATTTAAAGCGAGTAAAACAC
130 AATTATGAGGTTATAAAAATATTTAAAGCAAGTAAAA-AC
* ********* *
672 CTTTTGAAGGCATAGGTGACTATAAATAGACTNNNNNNNNNNA-TGAATATCTTTTTCTTCCCGT
1 CTTTTGAAGGCATGGGTGACTATAAATAGACT-TTTTTTGTCACTGAATATCTTTTTCTTCACGT
* * * * * *
736 TTATTGAGGCCGACATTCAATTATTATCTATTTTAACTAAAATTCTAAAAAAATTCAACTTAAAA
65 TTATCGAGGCAGACATTCAATTATTAT-TATTTTAACCAAAAATGTAAAAAAATT-GACTTAAAA
*
801 TCCATTATGAGGTTATAAAAATATTTAAAGCAAGTAAAAAGC
128 TCAATTATGAGGTTATAAAAATATTTAAAGCAAGTAAAAA-C
* * * * *
843 CTTTTGAAGGCCTGGGTGATTATAAATGGACTTTTTTTGTCACTGGATATCTTTTTTTTCACGTT
1 CTTTTGAAGGCATGGGTGACTATAAATAGACTTTTTTTGTCACTGAATATCTTTTTCTTCACGTT
* *
908 TCTCGAGGTAGACATTCAATT-TTAATTATTTTAACCAAAAATGTAAAAAAAATTGACTTAAAAT
66 TATCGAGGCAGACATTCAATTATT-ATTATTTTAACCAAAAATGT-AAAAAAATTGACTTAAAAT
* * *
972 CAATTATAAGTTTATAAAAATATTTAAAGAAAGTAAAAAC
129 CAATTATGAGGTTATAAAAATATTTAAAGCAAGTAAAAAC
* * * * *
1012 TCTTTTAAAGGCATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTTCTTC
1 -CTTTTGAAGGCATGGGTGACTATAAATAGACTTTTTTTGTCACTGAATATCTTTTTCTTC
1073 NNNNNNNNNN
Statistics
Matches: 447, Mismatches: 111, Indels: 27
0.76 0.19 0.05
Matches are distributed among these distances:
169 3 0.01
170 238 0.53
171 198 0.44
172 8 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.36
Consensus pattern (168 bp):
CTTTTGAAGGCATGGGTGACTATAAATAGACTTTTTTTGTCACTGAATATCTTTTTCTTCACGTT
TATCGAGGCAGACATTCAATTATTATTATTTTAACCAAAAATGTAAAAAAATTGACTTAAAATCA
ATTATGAGGTTATAAAAATATTTAAAGCAAGTAAAAAC
Done.