Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04295

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, 867

Length: 1446
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22


Found at i:1126 original size:36 final size:36

Alignment explanation


    Indices: 1070--1305  Score: 280
    Period size: 36  Copynumber: 6.9  Consensus size: 36

       1060 CCTTCTTCTT

                *   *                           
       1070 GTCCGAGTAAGCCTCGAATTCGCAGCCCCAGCCCCA
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

             *                                  
       1106 GCCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

               *     *                  *     * 
       1142 GTCTAAGTCGGCCTCGAATTCGCAGCCCGAGCCCAA
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

               *                  *     *     * 
       1178 GTCTAAGTCAGCCTCGAATTCGTAGCCCGAGCCCAA
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

               *                                
       1214 GTCTAAGTCAGCCTCGAATT--C-G---CAGCCCCA
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

                                                
       1244 GTCCAAGTCAGCCTCGAATT--C-G---CAGCCCCA
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

                                            
       1274 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGC
          1 GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGC

       1306 TCATGCCGCC


Statistics
Matches: 180,  Mismatches: 14, Indels: 12
        0.87            0.07        0.06

Matches are distributed among these distances:
  30   55  0.31
  32    1  0.01
  33    2  0.01
  36  122  0.68

ACGTcount: A:0.23, C:0.39, G:0.22, T:0.16


Consensus pattern (36 bp):   
GTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCCCA

Done.