Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29265

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, 1000

Length: 4104
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27


Found at i:143 original size:21 final size:21

Alignment explanation


    Indices: 118--157  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        108 CGGCACAGGT

                                 
        118 GGAGGGGAAGGGGGAGGAGGA
          1 GGAGGGGAAGGGGGAGGAGGA

                   *   *       
        139 GGAGGGGGAGGTGGAGGAG
          1 GGAGGGGAAGGGGGAGGAG

        158 CTGGAGGAGG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.25, C:0.00, G:0.72, T:0.03


Consensus pattern (21 bp):   
GGAGGGGAAGGGGGAGGAGGA

Found at i:144 original size:15 final size:15

Alignment explanation


    Indices: 126--167  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

        116 GTGGAGGGGA

                           
        126 AGGGGGAGGAGGAGG
          1 AGGGGGAGGAGGAGG

                     *     
        141 AGGGGGAGGTGGAGG
          1 AGGGGGAGGAGGAGG

              **        
        156 AGCTGGAGGAGG
          1 AGGGGGAGGAGG

        168 GGGAAGTATG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.24, C:0.02, G:0.69, T:0.05


Consensus pattern (15 bp):   
AGGGGGAGGAGGAGG

Found at i:163 original size:21 final size:21

Alignment explanation


    Indices: 117--164  Score: 60
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        107 GCGGCACAGG

                                *
        117 TGGAGGGGAAGGGGGAGGAGG
          1 TGGAGGGGAAGGGGGAGGAGC

            *       *   *        
        138 AGGAGGGGGAGGTGGAGGAGC
          1 TGGAGGGGAAGGGGGAGGAGC

                  
        159 TGGAGG
          1 TGGAGG

        165 AGGGGGAAGT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.23, C:0.02, G:0.69, T:0.06


Consensus pattern (21 bp):   
TGGAGGGGAAGGGGGAGGAGC
Done.