Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_27358

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: 3162
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29


Found at i:1229 original size:216 final size:216

Alignment explanation


    Indices: 920--2005  Score: 1350
    Period size: 216  Copynumber: 5.0  Consensus size: 216

        910 ATGGTATCAG

                  *     *        *        *      *       *        *     *    
        920 AGATGGATTTAGCTCCTGATATAGAAAAGGTTTCTCCCCCACTGGGAGCTTCTGATATTGGAAGT
          1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT

                            **              **   ***                         
        985 GAAATTACAACTGAATCGGCTCCTTCAGAGTCTGGTTTGGAAAGTGAAGTTCCCCACAGTGTTAA
         66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA

                     *                          *        **                  
       1050 GTTGGAAGAAGAAGAAAACGCTGGTGCTGAGGAAAATGGTGAGGGGTTTGGTAAAATTGAGTGTA
        131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA

                         *       
       1115 CTATTTTGAATACAGAGTCTA
        196 CTATTTTGAATACGGAGTCTA

                           *                * * *      *    *                
       1136 AGATGGCTTTAGTTCTTGATACAGAAAAGGCTGCGCTTCCACTTGAAGTTTCTGCTATTGAAAGT
          1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT

                                                                             
       1201 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
         66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA

                        *     *                                         *   *
       1266 GTTGGAAGAGGATGAAAATGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAATGTT
        131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA

                         *       
       1331 CTATTTTGAATACAGAGTCTA
        196 CTATTTTGAATACGGAGTCTA

                                                               *             
       1352 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTTTGCTATTGAAAGT
          1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT

                *        *                               *          *      * 
       1417 GAAACTACAACTGCATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCAGAGTGTTCA
         66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA

                   *          **              *                           *  
       1482 GTTGGAAAAGGAAGAAAATACTGGTGCTGAGGAAGAAGGTGAGGGAATTGGTAAAATTGAGTTTA
        131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA

             *                   
       1547 CAATTTTGAATACGGAGTCTA
        196 CTATTTTGAATACGGAGTCTA

                *         *                                        *         
       1568 AGATAGCTTTAGTTACTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCCATTGAAAGT
          1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT

                            *        *       *               *      *        
       1633 GAAATTACAACTGAATCAGCTCCTTTAGAGTCCGGTTCCAAAAGTGAAGATCCCCAGAGTGTTAA
         66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA

                            *  *  *                   **           *         
       1698 GTTGGAAGAGGAAGAAGACACTAGTGCTGAGGAAAAAGGTGAAAGAATTGGTAAATTTGAGTGTA
        131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA

               *  *     *        
       1763 CTACTTCGAATATGGAGTCTA
        196 CTATTTTGAATACGGAGTCTA

                                **                   *        *      *  *    
       1784 AGATGGCTTTAGTTCCTGATTTAGAAAAGGCTTCTCCTCCATTGGAAGCTCCTGCTAGTGGAAGT
          1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT

                *  *             *   *       *           *      * *          
       1849 GAAACTAGAACTGAATTAGCTTCTTTAGAG-CTTAGTTCCAAAAGCGAAGTTTCTCACAGTGTTA
         66 GAAATTACAACTGAATTAGCTCCTTCAGAGTC-CAGTTCCAAAAGTGAAGTTCCCCACAGTGTTA

                    *            *        * *      *      *                **
       1913 A-TCTGGAGGAGGAAGAAAATAG-TGGTGCCGGGGAAAATGGTGAGAGAATTGGTAAAATTGAAA
        130 AGT-TGGAAGAGGAAGAAAA-CGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGT

               *  *        *   *    
       1976 GTATTACTTTGAATATGGAATCTA
        193 GTACTATTTTGAATACGGAGTCTA

                  
       2000 AGATGG
          1 AGATGG

       2006 ACTTAGCAGT


Statistics
Matches: 757,  Mismatches: 110, Indels: 6
        0.87            0.13        0.01

Matches are distributed among these distances:
 215    2  0.00
 216  755  1.00

ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28


Consensus pattern (216 bp):   
AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA
CTATTTTGAATACGGAGTCTA

Done.