Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05722

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, 675

Length: 1125
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.23


Found at i:936 original size:6 final size:6

Alignment explanation


    Indices: 925--1043  Score: 69
    Period size: 6  Copynumber: 19.8  Consensus size: 6

        915 AGAGATAGGA

                                    *  *      *   *  *          *   
        925 GATGAT GATGAT GATG-T GGACGAG GATGAG GACGAG GATGAT GAGGAT
          1 GATGAT GATGAT GATGAT -GATGAT GATGAT GATGAT GATGAT GATGAT

              *      *      *  *   *         *      *      *      *
        973 GAAGAT GAAGAT GAGGAC GAGGAT GATGAG GATGAA GATGAA GATGAC
          1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT

                 *          *         
       1021 GATGAC GATGAT GAGGAT GATGA
          1 GATGAT GATGAT GATGAT GATGA

       1044 AGGAAGTAAG


Statistics
Matches: 93,  Mismatches: 18, Indels: 4
        0.81            0.16        0.03

Matches are distributed among these distances:
   5    1  0.01
   6   92  0.99

ACGTcount: A:0.36, C:0.04, G:0.41, T:0.18


Consensus pattern (6 bp):   
GATGAT

Found at i:986 original size:33 final size:33

Alignment explanation


    Indices: 949--1040  Score: 157
    Period size: 33  Copynumber: 2.8  Consensus size: 33

        939 TGTGGACGAG

                                             
        949 GATGAGGACGAGGATGATGAGGATGAAGATGAA
          1 GATGAGGACGAGGATGATGAGGATGAAGATGAA

                                             
        982 GATGAGGACGAGGATGATGAGGATGAAGATGAA
          1 GATGAGGACGAGGATGATGAGGATGAAGATGAA

                 *  *  *              
       1015 GATGACGATGACGATGATGAGGATGA
          1 GATGAGGACGAGGATGATGAGGATGA

       1041 TGAAGGAAGT


Statistics
Matches: 56,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   56  1.00

ACGTcount: A:0.38, C:0.04, G:0.41, T:0.16


Consensus pattern (33 bp):   
GATGAGGACGAGGATGATGAGGATGAAGATGAA

Done.