Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_01309

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, 201

Length: 336
ACGTcount: A:0.48, C:0.10, G:0.29, T:0.13


Found at i:330 original size:12 final size:12

Alignment explanation


    Indices: 211--333  Score: 140
    Period size: 12  Copynumber: 10.2  Consensus size: 12

        201 AGGACCTGCT

                    *   
        211 AAAGAAGAGAAG
          1 AAAGAAGAAAAG

              *         
        223 AAGGAAGAAAA-
          1 AAAGAAGAAAAG

                         
        234 AAAGGAAGAAAAG
          1 AAA-GAAGAAAAG

                 *      
        247 AAAGAGGAAAAG
          1 AAAGAAGAAAAG

                 *  *   
        259 AAAGAGGAGAAG
          1 AAAGAAGAAAAG

                    *   
        271 AAAGAAGAGAAG
          1 AAAGAAGAAAAG

              *     *   
        283 AAGGAAGAGAAG
          1 AAAGAAGAAAAG

                 *      
        295 AAAGAGGAAAAG
          1 AAAGAAGAAAAG

                        
        307 AAAGAAGAAAAG
          1 AAAGAAGAAAAG

              *         
        319 AAGGAAGAAAAG
          1 AAAGAAGAAAAG

               
        331 AAA
          1 AAA

        334 TAA


Statistics
Matches: 96,  Mismatches: 13, Indels: 4
        0.85            0.12        0.04

Matches are distributed among these distances:
  11    2  0.02
  12   91  0.95
  13    3  0.03

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (12 bp):   
AAAGAAGAAAAG

Found at i:332 original size:48 final size:48

Alignment explanation


    Indices: 211--332  Score: 190
    Period size: 48  Copynumber: 2.5  Consensus size: 48

        201 AGGACCTGCT

                                   *                        
        211 AAAGAAGAGAAGAAGGAAGAAAAAAAGGAAGAAAAGAAAGAGGAAAAG
          1 AAAGAAGAGAAGAAGGAAGAAAAGAAGGAAGAAAAGAAAGAGGAAAAG

                 *        *     *           *               
        259 AAAGAGGAGAAGAAAGAAGAGAAGAAGGAAGAGAAGAAAGAGGAAAAG
          1 AAAGAAGAGAAGAAGGAAGAAAAGAAGGAAGAAAAGAAAGAGGAAAAG

                    *                 
        307 AAAGAAGAAAAGAAGGAAGAAAAGAA
          1 AAAGAAGAGAAGAAGGAAGAAAAGAA

        333 ATAA


Statistics
Matches: 65,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  48   65  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (48 bp):   
AAAGAAGAGAAGAAGGAAGAAAAGAAGGAAGAAAAGAAAGAGGAAAAG
Done.