Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402113.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5207.0, 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: 1864
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33


Found at i:96 original size:57 final size:57

Alignment explanation


    Indices: 6--116  Score: 177
    Period size: 57  Copynumber: 1.9  Consensus size: 57

          1 CAGTA

                                   *                                 
          6 TATAAACCCCCTCCAGTTCCGGTCTACAAGAAACCACTTCCACCCCCAGTTCCAATC
          1 TATAAACCCCCTCCAGTTCCGGTATACAAGAAACCACTTCCACCCCCAGTTCCAATC

                                      * *            *  *         
         63 TATAAACCCCCTCCAGTTCCGGTATATACGAAACCACTTCCTCCTCCAGTTCCA
          1 TATAAACCCCCTCCAGTTCCGGTATACAAGAAACCACTTCCACCCCCAGTTCCA

        117 GTTTATAAGA


Statistics
Matches: 49,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  57   49  1.00

ACGTcount: A:0.27, C:0.41, G:0.09, T:0.23


Consensus pattern (57 bp):   
TATAAACCCCCTCCAGTTCCGGTATACAAGAAACCACTTCCACCCCCAGTTCCAATC

Found at i:111 original size:33 final size:33

Alignment explanation


    Indices: 72--139  Score: 100
    Period size: 33  Copynumber: 2.1  Consensus size: 33

         62 CTATAAACCC

                       *       *             
         72 CCTCCAGTTCCGGTATATACGAAACCACTTCCT
          1 CCTCCAGTTCCAGTATATAAGAAACCACTTCCT

                          *        *         
        105 CCTCCAGTTCCAGTTTATAAGAAGCCACTTCCT
          1 CCTCCAGTTCCAGTATATAAGAAACCACTTCCT

              
        138 CC
          1 CC

        140 ACTTCCAAAC


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.24, C:0.37, G:0.12, T:0.28


Consensus pattern (33 bp):   
CCTCCAGTTCCAGTATATAAGAAACCACTTCCT

Found at i:124 original size:57 final size:57

Alignment explanation


    Indices: 1--124  Score: 176
    Period size: 57  Copynumber: 2.2  Consensus size: 57

                                        *                            
          1 CAGTATATAAACCCCCTCCAGTTCCGGTCTACAAGAAACCACTTCCACCCCCAGTTC
          1 CAGTATATAAACCCCCTCCAGTTCCGGTATACAAGAAACCACTTCCACCCCCAGTTC

              * *                          * *            *  *       
         58 CAATCTATAAACCCCCTCCAGTTCCGGTATATACGAAACCACTTCCTCCTCCAGTTC
          1 CAGTATATAAACCCCCTCCAGTTCCGGTATACAAGAAACCACTTCCACCCCCAGTTC

                *     
        115 CAGTTTATAA
          1 CAGTATATAA

        125 GAAGCCACTT


Statistics
Matches: 58,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  57   58  1.00

ACGTcount: A:0.28, C:0.37, G:0.10, T:0.25


Consensus pattern (57 bp):   
CAGTATATAAACCCCCTCCAGTTCCGGTATACAAGAAACCACTTCCACCCCCAGTTC

Found at i:1017 original size:22 final size:21

Alignment explanation


    Indices: 987--1028  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        977 TGAATTTTAA

                         *        
        987 TATTATTTTATTACAAAATTAT
          1 TATTATTTTA-TAAAAAATTAT

                *               
       1009 TATTTTTTTATAAAAAATTA
          1 TATTATTTTATAAAAAATTA

       1029 ACTTAAAAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21    9  0.50
  22    9  0.50

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55


Consensus pattern (21 bp):   
TATTATTTTATAAAAAATTAT
Done.