Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_02939

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: 3056
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28


Found at i:2228 original size:90 final size:90

Alignment explanation


    Indices: 2075--2347  Score: 465
    Period size: 90  Copynumber: 3.0  Consensus size: 90

       2065 TTTAGGGATA

                                                 *           *               
       2075 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATGTCAAAGGAGATGAATGTGAAGTCTACA
          1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA

                         **       *  
       2140 TCATTCAGCAAGGAAAATAGCAACC
         66 TCATTCAGCAAGGGGAATAGCAGCC

                                                            *                
       2165 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGACAAATGTGAAGTCTACA
          1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA

                *                    
       2230 TCATCCAGCAAGGGGAATAGCAGCC
         66 TCATTCAGCAAGGGGAATAGCAGCC

                                                *                            
       2255 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGAACTCAAAGGAGATAAATGTGAAGTCTACA
          1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA

                      *              
       2320 TCATTCAGCAGGGGGAATAGCAGCC
         66 TCATTCAGCAAGGGGAATAGCAGCC

               
       2345 AAA
          1 AAA

       2348 GACCTGGAGA


Statistics
Matches: 172,  Mismatches: 11, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  90  172  1.00

ACGTcount: A:0.40, C:0.19, G:0.25, T:0.15


Consensus pattern (90 bp):   
AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
TCATTCAGCAAGGGGAATAGCAGCC
Done.