Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_32480

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, 682

Length: 1137
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23


Found at i:1042 original size:3 final size:3

Alignment explanation


    Indices: 1036--1082  Score: 58
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       1026 CAAGCAACAA

                                          *   *   *       *               
       1036 CAG CAG CAG CAG CAG CAG CAG CAA CAA CAA CAG CAA CAG CAG CAG CA
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA

       1083 ACAACAATCA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:1083 original size:12 final size:12

Alignment explanation


    Indices: 1028--1085  Score: 80
    Period size: 12  Copynumber: 4.8  Consensus size: 12

       1018 TTTGCTTCCA

                *       
       1028 AGCAACAACAGC
          1 AGCAGCAACAGC

                   *    
       1040 AGCAGCAGCAGC
          1 AGCAGCAACAGC

                      * 
       1052 AGCAGCAACAAC
          1 AGCAGCAACAGC

             *          
       1064 AACAGCAACAGC
          1 AGCAGCAACAGC

                      
       1076 AGCAGCAACA
          1 AGCAGCAACA

       1086 ACAATCAGCT


Statistics
Matches: 39,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  12   39  1.00

ACGTcount: A:0.47, C:0.33, G:0.21, T:0.00


Consensus pattern (12 bp):   
AGCAGCAACAGC
Done.