Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03070

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, 774

Length: 1290
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27


Found at i:794 original size:363 final size:363

Alignment explanation


    Indices: 82--1112  Score: 1255
    Period size: 363  Copynumber: 2.8  Consensus size: 363

         72 CAGAACCTAC

                    *        *      *  *                               *     
         82 ACAGTGGGAGACTCCACCGGTTGGAGAATCCCTACTAATAATAACGATGATTTTTATGATGATTG
          1 ACAGTGGGTGACTCCACTGGTTGGCGAGTCCCTACTAATAAT---GATGATTTTTATGAGGATTG

                  *      * *   *              *       *  *     * **  *  *    
        147 GGCTGACAATAAAGATTTCCTTGTTGGGGATGTTCTAGTGTTCAACTTTACTAATGGGCAACATA
         63 GGCTGATAATAAACACTTCGTTGTTGGGGATGTTTTAGTGTTTAATTTTACGACCGGACAGCATA

                       *          *                                 *       *
        212 ATGTTGTC-GAAGTGACCGAAGCTGGTTACGATG-CTTGCAACGCTGCAAAT-CCTGTATCTACG
        128 ATGTTG-CAGAGGTGACCGAAGATGGTTACGATGAC-TGCAACGCTGCAAATGCC-ATATCTACT

            *   *   *                 *       *   *  *            *     **   
        274 GTGAGCACTGGACCGGCGAGGATTACGCTTAACAGGACAGGGGAGT-ACTACTTTATTTGTGGTA
        190 TTGACCACCGGACCGGCGAGGATTACCCTTAACAAGACCGGTGA-TCACTACTTCATTTGCAGTA

                *     *     *        *     *  *  *           *               
        338 TCCCTGGTCACTGTTCTGCCGGCCAGAAGCTAAACGTGGAAGTACGAAATGGTAACACCACCGGC
        254 TCCCCGGTCATTGTTCCGCCGGCCAAAAGCTCAAGGTCGAAGTACGAAACGGTAACACCACCGGC

              *                                 *        
        403 GGTGTTACTCCGTCGACGCCTATAACTCCAACCACCTCCACTTAT
        319 GGCGTTACTCCGTCGACGCCTATAACTCCAACCACCACCACTTAT

              *                                                  *           
        448 ACGGTGGGTGACTCCACTGGTTGGCGAGTCCCTACTAATAATGATGATTTTTACGAGGATTGGGC
          1 ACAGTGGGTGACTCCACTGGTTGGCGAGTCCCTACTAATAATGATGATTTTTATGAGGATTGGGC

                              *  ** *        *                               
        513 TGATAATAAACACTTCGTCGTCAGAGATGTTTTGGTGTTTAATTTTACGACCGGACAGCATAATG
         66 TGATAATAAACACTTCGTTGTTGGGGATGTTTTAGTGTTTAATTTTACGACCGGACAGCATAATG

             *           *       *                *    *                     
        578 TCGCAGAGGTGACGGAAGATGCTTACGATGACTGCAACACTGCGAATGCCATATCTACTTTGACC
        131 TTGCAGAGGTGACCGAAGATGGTTACGATGACTGCAACGCTGCAAATGCCATATCTACTTTGACC

                 *                                   *               *       
        643 ACCGGTCCGGCGAGGATTACCCTTAACAAGACCGGTGATCATTACTTCATTTGCAGTGTCCCCGG
        196 ACCGGACCGGCGAGGATTACCCTTAACAAGACCGGTGATCACTACTTCATTTGCAGTATCCCCGG

                                          *     *    *               *      *
        708 TCATTGTTCCGCCGGCCAAAAGCTCAAGGTTGAAGTTCGAACCGGTAACACCACCGGTGGCGTTG
        261 TCATTGTTCCGCCGGCCAAAAGCTCAAGGTCGAAGTACGAAACGGTAACACCACCGGCGGCGTTA

                    *  *  *         *           * 
        773 CTCCGTCGCCGTCTGTAACTCCAAGCACCACCACTTTT
        326 CTCCGTCGACGCCTATAACTCCAACCACCACCACTTAT

                          *           *        * *                           
        811 ACAGTGGGTGACTCTACTGGTTGGCGTGTCCCTACCACTAATGATGATTTTTATGAGGATTGGGC
          1 ACAGTGGGTGACTCCACTGGTTGGCGAGTCCCTACTAATAATGATGATTTTTATGAGGATTGGGC

                                                                             
        876 TGATAATAAACACTTCGTTGTTGGGGATGTTTTAGTGTTTAATTTTACGACCGGACAGCATAATG
         66 TGATAATAAACACTTCGTTGTTGGGGATGTTTTAGTGTTTAATTTTACGACCGGACAGCATAATG

                         *           *  *                                    
        941 TTGCAGAGGTGACTGAAGATGGTTATGACGACTGCAACGCTGCAAATGCCATATCTACTTTGACC
        131 TTGCAGAGGTGACCGAAGATGGTTACGATGACTGCAACGCTGCAAATGCCATATCTACTTTGACC

                       *                            *                        
       1006 ACCGGACCGGCAATGG-TTACCCTTAAC-AGCACCGGTGACCACTACTTCATTTGCAGTATCCCC
        196 ACCGGACCGGCGA-GGATTACCCTTAACAAG-ACCGGTGATCACTACTTCATTTGCAGTATCCCC

                                                  *     
       1069 GGTCATTGTTCCGCCGGCCAAAAGCTCAAGGTCGAAGTCCGAAA
        259 GGTCATTGTTCCGCCGGCCAAAAGCTCAAGGTCGAAGTACGAAA

       1113 TGGCAACCGC


Statistics
Matches: 568,  Mismatches: 91, Indels: 15
        0.84            0.14        0.02

Matches are distributed among these distances:
 362    4  0.01
 363  522  0.92
 364    5  0.01
 366   37  0.07

ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27


Consensus pattern (363 bp):   
ACAGTGGGTGACTCCACTGGTTGGCGAGTCCCTACTAATAATGATGATTTTTATGAGGATTGGGC
TGATAATAAACACTTCGTTGTTGGGGATGTTTTAGTGTTTAATTTTACGACCGGACAGCATAATG
TTGCAGAGGTGACCGAAGATGGTTACGATGACTGCAACGCTGCAAATGCCATATCTACTTTGACC
ACCGGACCGGCGAGGATTACCCTTAACAAGACCGGTGATCACTACTTCATTTGCAGTATCCCCGG
TCATTGTTCCGCCGGCCAAAAGCTCAAGGTCGAAGTACGAAACGGTAACACCACCGGCGGCGTTA
CTCCGTCGACGCCTATAACTCCAACCACCACCACTTAT
Done.