Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_32626

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, 581

Length: 969
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27


Found at i:740 original size:12 final size:12

Alignment explanation


    Indices: 723--766  Score: 61
    Period size: 12  Copynumber: 3.7  Consensus size: 12

        713 AGGACGACAC

                  *     
        723 GGCTCAGGCTCA
          1 GGCTCAAGCTCA

                     *  
        735 GGCTCAAGCGCA
          1 GGCTCAAGCTCA

                        
        747 GGCTCAAGCTCA
          1 GGCTCAAGCTCA

            *       
        759 AGCTCAAG
          1 GGCTCAAG

        767 AGCATGCTGT


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   28  1.00

ACGTcount: A:0.25, C:0.32, G:0.30, T:0.14


Consensus pattern (12 bp):   
GGCTCAAGCTCA

Found at i:750 original size:18 final size:18

Alignment explanation


    Indices: 727--761  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        717 CGACACGGCT

                    *         
        727 CAGGCTCAGGCTCAAGCG
          1 CAGGCTCAAGCTCAAGCG

                             
        745 CAGGCTCAAGCTCAAGC
          1 CAGGCTCAAGCTCAAGC

        762 TCAAGAGCAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11


Consensus pattern (18 bp):   
CAGGCTCAAGCTCAAGCG

Found at i:765 original size:6 final size:6

Alignment explanation


    Indices: 724--766  Score: 50
    Period size: 6  Copynumber: 7.2  Consensus size: 6

        714 GGACGACACG

                 *      *          *  *                       
        724 GCTCAG GCTCAG GCTCAA GCGCAG GCTCAA GCTCAA GCTCAA G
          1 GCTCAA GCTCAA GCTCAA GCTCAA GCTCAA GCTCAA GCTCAA G

        767 AGCATGCTGT


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   32  1.00

ACGTcount: A:0.26, C:0.33, G:0.28, T:0.14


Consensus pattern (6 bp):   
GCTCAA
Done.