Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35316

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, 743

Length: 1239
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22


Found at i:401 original size:42 final size:42

Alignment explanation


    Indices: 335--439  Score: 111
    Period size: 42  Copynumber: 2.4  Consensus size: 42

        325 TCATTGCCTT

                 *        *                     **    
        335 CTTCTTCAGCCAAGCCAGTGGCAACTACTGCCTCTGTTCCAA
          1 CTTCTCCAGCCAAGACAGTGGCAACTACTGCCTCTGCACCAA

                        *      *      *   *           
        377 CTTCTCCAGCCAGGACAGTTGCAACTGCTGTCTCTGCACCAA
          1 CTTCTCCAGCCAAGACAGTGGCAACTACTGCCTCTGCACCAA

                                 
        419 CTTCTTCTCCAGCCAAGACAG
          1 ---CTTCTCCAGCCAAGACAG

        440 CCCCAACTAC


Statistics
Matches: 51,  Mismatches: 9, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  42   34  0.67
  45   17  0.33

ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25


Consensus pattern (42 bp):   
CTTCTCCAGCCAAGACAGTGGCAACTACTGCCTCTGCACCAA
Done.