Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03994

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, 463

Length: 773
ACGTcount: A:0.21, C:0.10, G:0.46, T:0.24


Found at i:285 original size:23 final size:24

Alignment explanation


    Indices: 240--302  Score: 67
    Period size: 23  Copynumber: 2.7  Consensus size: 24

        230 CTAGTGGTCT

                  *    *   *        
        240 TGGAGAAGGTGGAGGTGGAGGTGG
          1 TGGAGAGGGTGAAGGAGGAGGTGG

                              *     
        264 -GGAGAGGGTGAAGGAGGCGGTGG
          1 TGGAGAGGGTGAAGGAGGAGGTGG

                             
        287 TGGTAG-GGGTGAAGGA
          1 TGG-AGAGGGTGAAGGA

        303 TCAGGGTATG


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  23   19  0.58
  24   12  0.36
  25    2  0.06

ACGTcount: A:0.22, C:0.02, G:0.62, T:0.14


Consensus pattern (24 bp):   
TGGAGAGGGTGAAGGAGGAGGTGG

Found at i:346 original size:36 final size:36

Alignment explanation


    Indices: 306--379  Score: 130
    Period size: 36  Copynumber: 2.1  Consensus size: 36

        296 TGAAGGATCA

                             *                  
        306 GGGTATGGGTCAGGATCTAGATCGGGGTATGGGTCT
          1 GGGTATGGGTCAGGATCCAGATCGGGGTATGGGTCT

                              *                 
        342 GGGTATGGGTCAGGATCCGGATCGGGGTATGGGTCT
          1 GGGTATGGGTCAGGATCCAGATCGGGGTATGGGTCT

              
        378 GG
          1 GG

        380 TGGTGGCATA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.15, C:0.12, G:0.47, T:0.26


Consensus pattern (36 bp):   
GGGTATGGGTCAGGATCCAGATCGGGGTATGGGTCT

Found at i:483 original size:24 final size:24

Alignment explanation


    Indices: 456--505  Score: 82
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        446 CAGTGGAAAA

                             *      
        456 GGGTCTGGATCCAGATATGGAAGT
          1 GGGTCTGGATCCAGATACGGAAGT

                        *           
        480 GGGTCTGGATCCGGATACGGAAGT
          1 GGGTCTGGATCCAGATACGGAAGT

              
        504 GG
          1 GG

        506 AGTTGGTGGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.22, C:0.14, G:0.42, T:0.22


Consensus pattern (24 bp):   
GGGTCTGGATCCAGATACGGAAGT
Done.