Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_27239

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: 1989
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25


Found at i:163 original size:3 final size:3

Alignment explanation


    Indices: 155--201  Score: 51
    Period size: 3  Copynumber: 16.0  Consensus size: 3

        145 AGCGACCCCA

                                *     *                   *  *             
        155 ACC ACC ACC ACC ACC TCC ACG A-C ACC ACC ACC ACT ATC ACC ACC ACC
          1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC

        202 TCTGACAACA


Statistics
Matches: 35,  Mismatches: 8, Indels: 2
        0.78            0.18        0.04

Matches are distributed among these distances:
   2    1  0.03
   3   34  0.97

ACGTcount: A:0.32, C:0.60, G:0.02, T:0.06


Consensus pattern (3 bp):   
ACC

Found at i:182 original size:14 final size:15

Alignment explanation


    Indices: 163--201  Score: 53
    Period size: 14  Copynumber: 2.7  Consensus size: 15

        153 CAACCACCAC

                   *       
        163 CACCACCTCCACGA-
          1 CACCACCACCACGAT

                        *  
        177 CACCACCACCACTAT
          1 CACCACCACCACGAT

                      
        192 CACCACCACC
          1 CACCACCACC

        202 TCTGACAACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  14   12  0.55
  15   10  0.45

ACGTcount: A:0.31, C:0.59, G:0.03, T:0.08


Consensus pattern (15 bp):   
CACCACCACCACGAT
Done.