Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29628

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, 761

Length: 1269
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27


Found at i:169 original size:12 final size:12

Alignment explanation


    Indices: 154--218  Score: 67
    Period size: 12  Copynumber: 5.4  Consensus size: 12

        144 AATTGGAGGT

                        
        154 GGTGGTGGAATA
          1 GGTGGTGGAATA

                 *  *  *
        166 GGTGGAGGTATT
          1 GGTGGTGGAATA

                        
        178 GGTGGTGGAATA
          1 GGTGGTGGAATA

                 *  *   
        190 GGTGGAGGTATA
          1 GGTGGTGGAATA

              *        *
        202 GGAGGTGGAATT
          1 GGTGGTGGAATA

                 
        214 GGTGG
          1 GGTGG

        219 AGGCATAGGA


Statistics
Matches: 40,  Mismatches: 13, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  12   40  1.00

ACGTcount: A:0.22, C:0.00, G:0.52, T:0.26


Consensus pattern (12 bp):   
GGTGGTGGAATA

Found at i:194 original size:36 final size:36

Alignment explanation


    Indices: 154--227  Score: 85
    Period size: 36  Copynumber: 2.1  Consensus size: 36

        144 AATTGGAGGT

                 *        *     *        *      
        154 GGTGGTGGAATAGGTGGAGGTATTGGTGGTGGAATA
          1 GGTGGAGGAATAGGAGGAGGAATTGGTGGAGGAATA

                    *        *              *   
        190 GGTGGAGGTATAGGAGGTGGAATTGGTGGAGGCATA
          1 GGTGGAGGAATAGGAGGAGGAATTGGTGGAGGAATA

              
        226 GG
          1 GG

        228 AGTTGGAGGT


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.23, C:0.01, G:0.51, T:0.24


Consensus pattern (36 bp):   
GGTGGAGGAATAGGAGGAGGAATTGGTGGAGGAATA

Found at i:226 original size:24 final size:24

Alignment explanation


    Indices: 157--234  Score: 111
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        147 TGGAGGTGGT

                                *  *
        157 GGTGGAATAGGTGGAGGTATTGGT
          1 GGTGGAATAGGTGGAGGTATAGGA

                                    
        181 GGTGGAATAGGTGGAGGTATAGGA
          1 GGTGGAATAGGTGGAGGTATAGGA

                    *        *      
        205 GGTGGAATTGGTGGAGGCATAGGA
          1 GGTGGAATAGGTGGAGGTATAGGA

             *    
        229 GTTGGA
          1 GGTGGA

        235 GGTGGAGCTG


Statistics
Matches: 49,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   49  1.00

ACGTcount: A:0.24, C:0.01, G:0.50, T:0.24


Consensus pattern (24 bp):   
GGTGGAATAGGTGGAGGTATAGGA
Done.