Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21475

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, 981

Length: 1635
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29


Found at i:147 original size:3 final size:3

Alignment explanation


    Indices: 139--176  Score: 58
    Period size: 3  Copynumber: 12.7  Consensus size: 3

        129 CCAGCACTTT

                                          *   *               
        139 CAA CAA CAA CAA CAA CAA CAA CAC CAG CAA CAA CAA CA
          1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA

        177 GCATCAGCAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.61, C:0.37, G:0.03, T:0.00


Consensus pattern (3 bp):   
CAA

Found at i:169 original size:18 final size:18

Alignment explanation


    Indices: 148--188  Score: 64
    Period size: 18  Copynumber: 2.3  Consensus size: 18

        138 TCAACAACAA

                              
        148 CAACAACAACAACACCAG
          1 CAACAACAACAACACCAG

                       *  *   
        166 CAACAACAACAGCATCAG
          1 CAACAACAACAACACCAG

                 
        184 CAACA
          1 CAACA

        189 GCTGTGGCTC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.54, C:0.37, G:0.07, T:0.02


Consensus pattern (18 bp):   
CAACAACAACAACACCAG

Found at i:178 original size:12 final size:12

Alignment explanation


    Indices: 142--190  Score: 62
    Period size: 12  Copynumber: 4.1  Consensus size: 12

        132 GCACTTTCAA

                       *
        142 CAACAACAACAA
          1 CAACAACAACAG

                    *   
        154 CAACAACACCAG
          1 CAACAACAACAG

                        
        166 CAACAACAACAG
          1 CAACAACAACAG

              *  *      
        178 CATCAGCAACAG
          1 CAACAACAACAG

             
        190 C
          1 C

        191 TGTGGCTCAG


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

Matches are distributed among these distances:
  12   32  1.00

ACGTcount: A:0.53, C:0.37, G:0.08, T:0.02


Consensus pattern (12 bp):   
CAACAACAACAG
Done.