Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2269

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, 606

Length: 1010
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25


Found at i:53 original size:34 final size:33

Alignment explanation


    Indices: 1--71  Score: 97
    Period size: 34  Copynumber: 2.1  Consensus size: 33

                                    *  *     
          1 AAAAAAATGTATAAGTATATATATTTACAATAT
          1 AAAAAAATGTATAAGTATATATATATAAAATAT

                          *        *          
         34 AAAAGAAATGTATATGTATATATCTATAAAATAT
          1 AAAA-AAATGTATAAGTATATATATATAAAATAT

                
         68 AAAA
          1 AAAA

         72 TATATAAAAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  33    4  0.12
  34   29  0.88

ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34


Consensus pattern (33 bp):   
AAAAAAATGTATAAGTATATATATATAAAATAT

Found at i:186 original size:24 final size:24

Alignment explanation


    Indices: 154--202  Score: 64
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        144 AAGTTTATGG

                     *               
        154 ATATATATATGTATTAC-ATAAAAA
          1 ATATATATAGGTA-TACTATAAAAA

                *                   
        178 ATATGTATAGGTATACTATAAAAA
          1 ATATATATAGGTATACTATAAAAA

             
        202 A
          1 A

        203 GATGCGTGTG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  23    3  0.14
  24   19  0.86

ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35


Consensus pattern (24 bp):   
ATATATATAGGTATACTATAAAAA
Done.