Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397440.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_561.0, 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: 17962
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.21

Warning! 5575 characters in sequence are not A, C, G, or T


Found at i:13924 original size:12 final size:12

Alignment explanation


    Indices: 13907--13937  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      13897 TTTTCCCTGA

                    *   
      13907 CCAAACACTATC
          1 CCAAACACAATC

                        
      13919 CCAAACACAATC
          1 CCAAACACAATC

                   
      13931 CCAAACA
          1 CCAAACA

      13938 TCTACCTCAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.48, C:0.42, G:0.00, T:0.10


Consensus pattern (12 bp):   
CCAAACACAATC

Found at i:15009 original size:14 final size:16

Alignment explanation


    Indices: 14985--15018  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

      14975 ATGATGAATT

                            
      14985 AGCAGCAAAGAGA-AA
          1 AGCAGCAAAGAGACAA

                            
      15000 AGCA-CAAAGAGACAA
          1 AGCAGCAAAGAGACAA

                
      15015 AGCA
          1 AGCA

      15019 ACCTCACCGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    8  0.44
  15   10  0.56

ACGTcount: A:0.59, C:0.18, G:0.24, T:0.00


Consensus pattern (16 bp):   
AGCAGCAAAGAGACAA

Found at i:15086 original size:37 final size:38

Alignment explanation


    Indices: 15039--15140  Score: 134
    Period size: 37  Copynumber: 2.7  Consensus size: 38

      15029 AAGCACCGAC

                 *     *                          
      15039 AAAAGCAAAGGTGGACAAAGCGGCCTCAAAAA-TAACA
          1 AAAAGTAAAGGCGGACAAAGCGGCCTCAAAAAGTAACA

                        *        *                
      15076 AAAAGTAAAGGCAGACAAAGCAGCCTCAAAAAGTAACA
          1 AAAAGTAAAGGCGGACAAAGCGGCCTCAAAAAGTAACA

               *     *          *      
      15114 AAAGGTAAAAGCGGACAAAGTGGCCTC
          1 AAAAGTAAAGGCGGACAAAGCGGCCTC

      15141 CTTCACCGAA


Statistics
Matches: 55,  Mismatches: 9, Indels: 1
        0.85            0.14        0.02

Matches are distributed among these distances:
  37   28  0.51
  38   27  0.49

ACGTcount: A:0.50, C:0.19, G:0.23, T:0.09


Consensus pattern (38 bp):   
AAAAGTAAAGGCGGACAAAGCGGCCTCAAAAAGTAACA

Found at i:15140 original size:38 final size:37

Alignment explanation


    Indices: 15051--15140  Score: 126
    Period size: 38  Copynumber: 2.4  Consensus size: 37

      15041 AAGCAAAGGT

                                              *  
      15051 GGACAAAGCGGCCTCAAAAATAACAAAAAGTAAAGGC
          1 GGACAAAGCGGCCTCAAAAATAACAAAAAGTAAAAGC

            *        *                   *        
      15088 AGACAAAGCAGCCTCAAAAAGTAACAAAAGGTAAAAGC
          1 GGACAAAGCGGCCTCAAAAA-TAACAAAAAGTAAAAGC

                    *      
      15126 GGACAAAGTGGCCTC
          1 GGACAAAGCGGCCTC

      15141 CTTCACCGAA


Statistics
Matches: 45,  Mismatches: 7, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  37   18  0.40
  38   27  0.60

ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09


Consensus pattern (37 bp):   
GGACAAAGCGGCCTCAAAAATAACAAAAAGTAAAAGC

Found at i:15906 original size:13 final size:13

Alignment explanation


    Indices: 15888--15912  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      15878 ATAAAGAGAG

                         
      15888 GACACTTAAGTAT
          1 GACACTTAAGTAT

                        
      15901 GACACTTAAGTA
          1 GACACTTAAGTA

      15913 AATTGTTAGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28


Consensus pattern (13 bp):   
GACACTTAAGTAT
Done.