Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397545.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_562.0, 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: 8609
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.22

Warning! 2261 characters in sequence are not A, C, G, or T


Found at i:3031 original size:2 final size:2

Alignment explanation


    Indices: 3024--3050  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       3014 TTTGAGAAAA

                                                    
       3024 AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG A

       3051 AAGTGAGTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:3145 original size:25 final size:25

Alignment explanation


    Indices: 3093--3152  Score: 77
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       3083 AAGGGTAAAT

                             *    *  
       3093 AAGAAAAAAGAAAAAAATGAACGGA
          1 AAGAAAAAAGAAAAAAACGAACAGA

                                    * 
       3118 AAGAAAAAA-AAAAAAACGAAACATA
          1 AAGAAAAAAGAAAAAAACG-AACAGA

                      
       3143 AAGAAAAAAG
          1 AAGAAAAAAG

       3153 GGAAGATGCA


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  24    8  0.27
  25   22  0.73

ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03


Consensus pattern (25 bp):   
AAGAAAAAAGAAAAAAACGAACAGA

Found at i:3916 original size:25 final size:28

Alignment explanation


    Indices: 3864--3932  Score: 74
    Period size: 27  Copynumber: 2.5  Consensus size: 28

       3854 TAAAAGAGGT

                    *                    
       3864 TAAAAATAGTGAAATTATTGAAAGT-AAA
          1 TAAAAATAAT-AAATTATTGAAAGTAAAA

                                         
       3892 T-AAAATAATAAATT-TTGAACA-TAAAA
          1 TAAAAATAATAAATTATTGAA-AGTAAAA

                           
       3918 TAAAAATTAATAAAT
          1 TAAAAA-TAATAAAT

       3933 ATTTTACTCA


Statistics
Matches: 36,  Mismatches: 1, Indels: 8
        0.80            0.02        0.18

Matches are distributed among these distances:
  25    6  0.17
  26   10  0.28
  27   11  0.31
  28    9  0.25

ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30


Consensus pattern (28 bp):   
TAAAAATAATAAATTATTGAAAGTAAAA
Done.