Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05072

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, 316

Length: 528
ACGTcount: A:0.15, C:0.18, G:0.40, T:0.27


Found at i:310 original size:27 final size:27

Alignment explanation


    Indices: 280--398  Score: 193
    Period size: 27  Copynumber: 4.4  Consensus size: 27

        270 TGGTGGTTTG

                                *   *  
        280 GGTGGACTTGGAGGAACCGGAGGATTC
          1 GGTGGACTTGGAGGAACCGGTGGAGTC

                                    *  
        307 GGTGGACTTGGAGGAACCGGTGGATTC
          1 GGTGGACTTGGAGGAACCGGTGGAGTC

                          *            
        334 GGTGGACTTGGAGGTACCGGTGGAGTC
          1 GGTGGACTTGGAGGAACCGGTGGAGTC

                                       
        361 GGTGGACTTGGAGGAACCGGTGGAGTC
          1 GGTGGACTTGGAGGAACCGGTGGAGTC

                  *    
        388 GGTGGATTTGG
          1 GGTGGACTTGG

        399 TGGTGCTGGT


Statistics
Matches: 87,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27   87  1.00

ACGTcount: A:0.18, C:0.13, G:0.47, T:0.22


Consensus pattern (27 bp):   
GGTGGACTTGGAGGAACCGGTGGAGTC

Found at i:411 original size:12 final size:12

Alignment explanation


    Indices: 396--439  Score: 54
    Period size: 12  Copynumber: 3.7  Consensus size: 12

        386 TCGGTGGATT

                        
        396 TGGTGGTGCTGG
          1 TGGTGGTGCTGG

                         
        408 TGGTGGTG-TAGG
          1 TGGTGGTGCT-GG

                  *     
        420 TGGTGGCGCTGG
          1 TGGTGGTGCTGG

              *     
        432 TGCTGGTG
          1 TGGTGGTG

        440 GTGGAGTAGG


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  11    1  0.04
  12   25  0.93
  13    1  0.04

ACGTcount: A:0.02, C:0.09, G:0.57, T:0.32


Consensus pattern (12 bp):   
TGGTGGTGCTGG
Done.