Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_06588

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: 3939
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27


Found at i:3058 original size:150 final size:149

Alignment explanation


    Indices: 2787--3375  Score: 837
    Period size: 150  Copynumber: 3.9  Consensus size: 149

       2777 AGAAGAGAAA

                            **                      *                       *
       2787 GCACAGTGAAGAAAATGATGGAAGGAAAACTGATAAAAAGCGTGGAGGACA-GACTCCTAGAAGC
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGAT-AAAAGAGTGGAGGA-AGGACTCCTAGAAGT

                                               *                           * 
       2851 GAGACACAT-GATGGAATTCCTCACTCTTCTCCATTCAATGTGATGGGTAGTAGTAGATCCTCGG
         64 GAGACACATAG-TGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAG

                                  
       2915 TGGAAGGTGCCTCCTCCAAATT
        128 TGGAAGGTGCCTCCTCCAAATT

                                *                   *                        
       2937 GCACAGTGAAGAAAATCTTGTAAGGAAAACTGATATAAAGGGTGGAGGAAGGACTCCTAGAAGTG
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATA-AAAGAGTGGAGGAAGGACTCCTAGAAGTG

               **                          *                                 
       3002 AGATGCATAGTGGAATTCCTCACTCTTCTCCGTCCAATGTGATGGGTAGTAGTAGATCCTCAGTG
         65 AGACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTG

            *           *       
       3067 AAAGGTGCCTCCCCCAAATT
        130 GAAGGTGCCTCCTCCAAATT

                                                                             
       3087 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAAAATGAGTGGAGGAAGGACTCCTAGAAGTG
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAAAA-GAGTGGAGGAAGGACTCCTAGAAGTG

                   **          *           * *   *                           
       3152 AGACACACGGTGGAATTCCCCACTCTTCTCCGTACAACGTGATGGGTAGTAGTAGATCCTCAGTG
         65 AGACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTG

                       *        
       3217 GAAGGTGCCTCTTCCAAATT
        130 GAAGGTGCCTCCTCCAAATT

                **                         *                                 
       3237 GCACTCTGAAGAAAATCTTGGAAGGAAAACTAATAAGAAGAGT---GGAAGGACTCCTAGAAGTG
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAA-AAGAGTGGAGGAAGGACTCCTAGAAGTG

                 * *           *                               *             
       3299 AGACATACAGTGGAATTCCGCACTCTTCTCCATCCAATGTGATGGGTAGTATTAGATCCTCAGTG
         65 AGACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTG

               *        
       3364 GAATGTGCCTCC
        130 GAAGGTGCCTCC

       3376 AGATCGCCTA


Statistics
Matches: 398,  Mismatches: 36, Indels: 13
        0.89            0.08        0.03

Matches are distributed among these distances:
 147   87  0.22
 149    5  0.01
 150  303  0.76
 151    3  0.01

ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23


Consensus pattern (149 bp):   
GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAAAAGAGTGGAGGAAGGACTCCTAGAAGTGA
GACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTGG
AAGGTGCCTCCTCCAAATT

Done.