Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_02276

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, 714

Length: 1191
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21


Found at i:814 original size:183 final size:182

Alignment explanation


    Indices: 502--1026  Score: 759
    Period size: 183  Copynumber: 2.9  Consensus size: 182

        492 GGTCTTAAGC

                       *                        *               *            
        502 CATGAACTAGGCCAAACCACTGCAACTACAACCCCCGGCATCTACAAGGAGCGCATACCAACC-A
          1 CATGAACTAGGTCAAACCACTGCAACTACAACCCCCAGCATC-ACAAGGAGCACATACCAACCAA

                                                *                    *       
        566 CCAACAGCACTTCCCAAGATATAGCAAGATACAAGATG-AAGAGGCCTAGACTGAGTTCGAGTTT
         65 CC-ACAGCACTTCCCAAGATATAGCAAGATACAAGAAGAAAG-GGCCTAGACTGAGTACGAGTTT

                                 *                                 
        630 AGAATTGACTCTGAAACCAACCACAACTGAGTATCATTTGGCAGATGTCCTGAAA
        128 AGAATTGACTCTGAAACCAACTACAACTGAGTATCATTTGGCAGATGTCCTGAAA

                         *          *   *                                    
        685 CATGAACTAGGTCGAACCACTGCAGCTAGAACCCCCAGCATCACCAAGGAGCACATACCAACCAA
          1 CATGAACTAGGTCAAACCACTGCAACTACAACCCCCAGCATCA-CAAGGAGCACATACCAACCAA

              *                                              *       *       
        750 CCGCAGCACTTCCCAAGATATAGCAAGATACAAGAAGAAAGGGCCTAGATTGAGTACAAGTTTAG
         65 CCACAGCACTTCCCAAGATATAGCAAGATACAAGAAGAAAGGGCCTAGACTGAGTACGAGTTTAG

                      *            *         *                  *
        815 AATTGACTCTAAAACCAACTACAGCTGAGTATCTTTTGGCAGATGTCCTGAAC
        130 AATTGACTCTGAAACCAACTACAACTGAGTATCATTTGGCAGATGTCCTGAAA

                     **     *                                    *           
        868 CATGAACTAAATCAAATCACTGCAACTACAACCCCCAGCATCAACAAGGAGCATATACCAACCAA
          1 CATGAACTAGGTCAAACCACTGCAACTACAACCCCCAGCATC-ACAAGGAGCACATACCAACCAA

                                        *                         * *        
        933 CCACAGCACTTCCCAAGATATAGCAAGACACAAGACA-AAAGGGCCTAGACTGAATCCGAGTTTA
         65 CCACAGCACTTCCCAAGATATAGCAAGATACAAGA-AGAAAGGGCCTAGACTGAGTACGAGTTTA

                              *           
        997 GAATTGACTCTGAAACCAGCTACAACTGAG
        129 GAATTGACTCTGAAACCAACTACAACTGAG

       1027 GGTATGACAG


Statistics
Matches: 305,  Mismatches: 32, Indels: 10
        0.88            0.09        0.03

Matches are distributed among these distances:
 182    1  0.00
 183  296  0.97
 184    8  0.03

ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18


Consensus pattern (182 bp):   
CATGAACTAGGTCAAACCACTGCAACTACAACCCCCAGCATCACAAGGAGCACATACCAACCAAC
CACAGCACTTCCCAAGATATAGCAAGATACAAGAAGAAAGGGCCTAGACTGAGTACGAGTTTAGA
ATTGACTCTGAAACCAACTACAACTGAGTATCATTTGGCAGATGTCCTGAAA
Done.