Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_11919

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, 851

Length: 1419
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25


Found at i:127 original size:15 final size:15

Alignment explanation


    Indices: 109--160  Score: 59
    Period size: 15  Copynumber: 3.5  Consensus size: 15

         99 AGACGAAGAG

                          *
        109 GAGGAAGTGGAAGTT
          1 GAGGAAGTGGAAGTA

                   *  *  * 
        124 GAGGAAGAGGTAGAA
          1 GAGGAAGTGGAAGTA

                           
        139 GAGGAAGTGGAAGTA
          1 GAGGAAGTGGAAGTA

              *    
        154 GAAGAAG
          1 GAGGAAG

        161 AAGAGGACGA


Statistics
Matches: 29,  Mismatches: 8, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  15   29  1.00

ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12


Consensus pattern (15 bp):   
GAGGAAGTGGAAGTA

Found at i:162 original size:24 final size:25

Alignment explanation


    Indices: 98--167  Score: 70
    Period size: 30  Copynumber: 2.6  Consensus size: 25

         88 TATGAAGCAA

                *     *              
         98 TAGACGAAGAGGAGGAAGTGGAAGT
          1 TAGAAGAAGAAGAGGAAGTGGAAGT

                                          
        123 TGAGGAAGAGGTAGAAGAGGAAGTGGAAG-
          1 T-A-GAAGA---AGAAGAGGAAGTGGAAGT

                            
        152 TAGAAGAAGAAGAGGA
          1 TAGAAGAAGAAGAGGA

        168 CGAGGATGCT


Statistics
Matches: 38,  Mismatches: 2, Indels: 11
        0.75            0.04        0.22

Matches are distributed among these distances:
  24    9  0.24
  25    1  0.03
  26    1  0.03
  27    9  0.24
  28    1  0.03
  29    1  0.03
  30   16  0.42

ACGTcount: A:0.44, C:0.01, G:0.44, T:0.10


Consensus pattern (25 bp):   
TAGAAGAAGAAGAGGAAGTGGAAGT
Done.