Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07513

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: 2202
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22


Found at i:296 original size:33 final size:33

Alignment explanation


    Indices: 259--398  Score: 147
    Period size: 33  Copynumber: 4.2  Consensus size: 33

        249 GGAGAAGATA

                                             
        259 GAGAAGGAGAAGAAGAAGAAGGAAGAGGAGGAG
          1 GAGAAGGAGAAGAAGAAGAAGGAAGAGGAGGAG

                                      *         
        292 GAGAAGGAGAAGAAGAAGAAAGAGGAGGAGGAGGAG
          1 GAGAAGGAGAAGAAGAAG--A-AGGAAGAGGAGGAG

                     *  *  *    *  *         
        328 GAGAAGGAGGAGGAGGAGAAAGAGGAGGAGGAG
          1 GAGAAGGAGAAGAAGAAGAAGGAAGAGGAGGAG

             *            *  *                
        361 GGGAAGGAGAAGGAGGAGGAAGGAA-AGGAGGAG
          1 GAGAAGGAGAA-GAAGAAGAAGGAAGAGGAGGAG

            *    
        394 AAGAA
          1 GAGAA

        399 AGAGGAGGAA


Statistics
Matches: 88,  Mismatches: 15, Indels: 8
        0.79            0.14        0.07

Matches are distributed among these distances:
  33   51  0.58
  34    8  0.09
  35    1  0.01
  36   28  0.32

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (33 bp):   
GAGAAGGAGAAGAAGAAGAAGGAAGAGGAGGAG

Found at i:319 original size:3 final size:3

Alignment explanation


    Indices: 278--422  Score: 96
    Period size: 3  Copynumber: 48.3  Consensus size: 3

        268 AAGAAGAAGA

                 *                *       *   *   *   *  *                 
        278 AGG AAG AGG AGG AGG AGA AGG AGA AGA AGA AGA AAG AGG AGG AGG AGG
          1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG

                  *                   *  *                             *
        326 AGG AGA AGG AGG AGG AGG AGA AAG AGG AGG AGG AGG -GG AAGG AGA
          1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG -AGG AGG

                               *           *   *  *           **        
        371 AGG AGG AGG AAGG A-A AGG AGG AGA AGA AAG AGG AGG AAA AGG AGG
          1 AGG AGG AGG -AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG

              *      
        416 AGA AGG A
          1 AGG AGG A

        423 AAAGGAGGGA


Statistics
Matches: 110,  Mismatches: 28, Indels: 8
        0.75            0.19        0.05

Matches are distributed among these distances:
   2    3  0.03
   3  102  0.93
   4    5  0.05

ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00


Consensus pattern (3 bp):   
AGG

Found at i:376 original size:36 final size:36

Alignment explanation


    Indices: 283--393  Score: 124
    Period size: 36  Copynumber: 3.2  Consensus size: 36

        273 GAAGAAGGAA

                      *                *        
        283 GAGGAGGAGGAGAAGGAGAA-GA--AGAAGAAAGAG
          1 GAGGAGGAGGGGAAGGAGAAGGAGGAGGAGAAAGAG

                            *  *                 
        316 GAGGAGGAGGAGG-AGAAGGAGGAGGAGGAGAAAGAG
          1 GAGGAGGAGG-GGAAGGAGAAGGAGGAGGAGAAAGAG

                                           *     
        352 GAGGAGGAGGGGAAGGAGAAGGAGGAGGAAGGAA-AG
          1 GAGGAGGAGGGGAAGGAGAAGGAGGAGG-AGAAAGAG

                  
        388 GAGGAG
          1 GAGGAG

        394 AAGAAAGAGG


Statistics
Matches: 65,  Mismatches: 7, Indels: 9
        0.80            0.09        0.11

Matches are distributed among these distances:
  33   15  0.23
  34    3  0.05
  35    2  0.03
  36   41  0.63
  37    4  0.06

ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00


Consensus pattern (36 bp):   
GAGGAGGAGGGGAAGGAGAAGGAGGAGGAGAAAGAG

Found at i:428 original size:24 final size:26

Alignment explanation


    Indices: 263--430  Score: 101
    Period size: 24  Copynumber: 6.8  Consensus size: 26

        253 AAGATAGAGA

                    *          *  **   
        263 AGGAGAAGAAGAAGAAGGAAGAGGAGG
          1 AGGAGAAGGAGAAG-AGGAGGAAAAGG

                           *  *        
        290 AGGAGAAGGAGAAGAAGAAGAAAGAGG
          1 AGGAGAAGGAGAAGAGGAGGAAA-AGG

                 *     *               
        317 AGGAGGAGGAGGAGAAGGAGG---AGG
          1 AGGAGAAGGAGAAG-AGGAGGAAAAGG

                        *         **  
        341 AGGAGAA--AGAGGAGGAGG-AGGGG
          1 AGGAGAAGGAGAAGAGGAGGAAAAGG

                                        
        364 AAGGAGAAGGAG--GAGGAAGG-AAAGG
          1 -AGGAGAAGGAGAAGAGG-AGGAAAAGG

                                      
        389 AGGAGAA-GA-AAGAGGAGGAAAAGG
          1 AGGAGAAGGAGAAGAGGAGGAAAAGG

                                
        413 AGGAGAAGGA-AA-AGGAGG
          1 AGGAGAAGGAGAAGAGGAGG

        431 GAGTTGAAGA


Statistics
Matches: 115,  Mismatches: 14, Indels: 27
        0.74            0.09        0.17

Matches are distributed among these distances:
  21    6  0.05
  22    3  0.03
  23    7  0.06
  24   49  0.43
  25   10  0.09
  26    8  0.07
  27   28  0.24
  28    4  0.03

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (26 bp):   
AGGAGAAGGAGAAGAGGAGGAAAAGG
Done.