Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38446

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, 779

Length: 1299
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25


Found at i:896 original size:3 final size:3

Alignment explanation


    Indices: 888--935  Score: 69
    Period size: 3  Copynumber: 16.0  Consensus size: 3

        878 CGCAGCAACT

                            *   *   *                                      
        888 GCA GCA GCA GCA ACA ACA CCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
          1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA

        936 AAGGCAAAAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   42  1.00

ACGTcount: A:0.38, C:0.35, G:0.27, T:0.00


Consensus pattern (3 bp):   
GCA

Found at i:899 original size:15 final size:15

Alignment explanation


    Indices: 879--935  Score: 69
    Period size: 15  Copynumber: 3.8  Consensus size: 15

        869 AGCAACAAAC

                    *      
        879 GCAGCAACTGCAGCA
          1 GCAGCAACAGCAGCA

                     *  *  
        894 GCAGCAACAACACCA
          1 GCAGCAACAGCAGCA

                  *        
        909 GCAGCAGCAGCAGCA
          1 GCAGCAACAGCAGCA

                  *     
        924 GCAGCAGCAGCA
          1 GCAGCAACAGCA

        936 AAGGCAAAAA


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   36  1.00

ACGTcount: A:0.37, C:0.35, G:0.26, T:0.02


Consensus pattern (15 bp):   
GCAGCAACAGCAGCA

Found at i:903 original size:27 final size:27

Alignment explanation


    Indices: 868--926  Score: 84
    Period size: 27  Copynumber: 2.2  Consensus size: 27

        858 ACCATCTCCT

                                *       
        868 CAGCAACAA-ACGCAGCAACTGCAGCAG
          1 CAGCAACAACAC-CAGCAACAGCAGCAG

                             *         
        895 CAGCAACAACACCAGCAGCAGCAGCAG
          1 CAGCAACAACACCAGCAACAGCAGCAG

                 
        922 CAGCA
          1 CAGCA

        927 GCAGCAGCAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   27  0.93
  28    2  0.07

ACGTcount: A:0.41, C:0.36, G:0.22, T:0.02


Consensus pattern (27 bp):   
CAGCAACAACACCAGCAACAGCAGCAG

Done.