Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398296.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_16.0, 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: 8184
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.22

Warning! 3360 characters in sequence are not A, C, G, or T


Found at i:1721 original size:173 final size:161

Alignment explanation


    Indices: 1562--1874  Score: 434
    Period size: 173  Copynumber: 1.9  Consensus size: 161

       1552 NNNNNNNNNN

                                                                  *          
       1562 TGAGGCTTCTGAAGGAAT-GAGTGACTATAAATAGACTTTTGTTACCAATGAATGC-TTTTTCC-
          1 TGAGGCTTCTGAAGGAATAG-GTGACTATAAATAGACTTTTGTTACCAATGAATACTTTTTTCCT

                                                                             
       1624 CTCATGTTTCTCAACATAGACATTCAATTATGATCTGTTTTAACAAAAAAAAGTAACAAAAATTG
         65 CTCA--TTTCTCAACATAGACATTCAATTATGATCTGTTTT-A-AAAAAAAAGTAACAAAAATTG

                      *                                   
       1689 AACTTAAAATTAATTANNNNNNNNNNAAACTATTTAAAGCGAGTAC
        126 AACTTAAAATCAATTA----------AAACTATTTAAAGCGAGTAC

                    *                                                        
       1735 TGAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTGTTACCAATGAATACTTTTTTCCTC
          1 TGAGGCTTCTGAAGGAATAGGTGACTATAAATAGACTTTTGTTACCAATGAATACTTTTTTCCTC

                       *                                                     
       1800 TCATTTCTCAATATAGACATTCAATTATGATCTGTTTTAAAAAAAAAGTAACAAAAATTGAACTT
         66 TCATTTCTCAACATAGACATTCAATTATGATCTGTTTTAAAAAAAAAGTAACAAAAATTGAACTT

                      
       1865 AAAATCAATT
        131 AAAATCAATT

       1875 TTGAGATTAT


Statistics
Matches: 133,  Mismatches: 4, Indels: 8
        0.92            0.03        0.06

Matches are distributed among these distances:
 171   35  0.26
 172    1  0.01
 173   85  0.64
 174    8  0.06
 175    4  0.03

ACGTcount: A:0.38, C:0.13, G:0.12, T:0.34


Consensus pattern (161 bp):   
TGAGGCTTCTGAAGGAATAGGTGACTATAAATAGACTTTTGTTACCAATGAATACTTTTTTCCTC
TCATTTCTCAACATAGACATTCAATTATGATCTGTTTTAAAAAAAAAGTAACAAAAATTGAACTT
AAAATCAATTAAAACTATTTAAAGCGAGTAC

Found at i:4450 original size:12 final size:12

Alignment explanation


    Indices: 4419--4450  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       4409 TAACCTCAAG

                   *    
       4419 AAAAGCAAAGAA
          1 AAAAGCATAGAA

                        
       4431 AAAAGCATAGAA
          1 AAAAGCATAGAA

                    
       4443 AAAAGCAT
          1 AAAAGCAT

       4451 CCATTAGCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.69, C:0.09, G:0.16, T:0.06


Consensus pattern (12 bp):   
AAAAGCATAGAA
Done.