Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_34094

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: 2160
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27


Found at i:600 original size:168 final size:166

Alignment explanation


    Indices: 316--815  Score: 653
    Period size: 168  Copynumber: 3.0  Consensus size: 166

        306 ATCAGAGATT

                                            *                            **  
        316 GAATATCCATGCAAGAGCCATATTGAAGATCAGAAGAGTGATGATCAAATGTGTCTAAAACTTGT
          1 GAATATCCATGCAAGAGCCATATTGAAGATC-CAAGAGTGATGATCAAATGTGTCTAAAACCCGT

                      *                                 *       * *          
        381 CAAGGAAGAACCTAAAGATGATGTTTGTGATAAACCCTTGTATGGGACTCCTTCTTGCAAGGAAA
         65 CAAGGAAGAAGCTAAAGATGATGTTTGTGATAAA-CCTTGTATGAGACTCCTCCATGCAAGGAAA

               *              *     *              
        446 CTAAGAGGAAGAAATCACGACCACTATGTTCTAACA-CA
        129 CTAGGAGGAAGAAATCACAACCACAATGTTCTAA-AGCA

                   *          *                             *                
        484 GAATATCTATGCAAGAGCTATATTGAAGATCCTAAGAGTGATGATCAATTGTGTCTAAAACCCGT
          1 GAATATCCATGCAAGAGCCATATTGAAGATCC-AAGAGTGATGATCAAATGTGTCTAAAACCCGT

                                *     *                                      
        549 CAAGGAAGAAGCTAAAGATGGTGTTTATGATGAAACCTTGTATGAGACTCCTCCATGCAA-GAAA
         65 CAAGGAAGAAGCTAAAGATGATGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAAA

                       *         *               **
        613 GCTAGGAGGAATAAATCACAATCACAATGTTCTAAAGTT
        129 -CTAGGAGGAAGAAATCACAACCACAATGTTCTAAAGCA

                            *              *         *      *  *             
        652 GAATATCCATGCAAGAACCATATTGAAGATAACAAGAGTGAAGATCAAGTGAGTCTAAAACCCGT
          1 GAATATCCATGCAAGAGCCATATTGAAGAT-CCAAGAGTGATGATCAAATGTGTCTAAAACCCGT

               *                                                             
        717 CAAAGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTGTATGAGACTCCTCCATGCAAGGAAA
         65 CAAGGAAGAAGCTAAAGATGATGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAAA

                  *       * *   *             
        782 CTAGGAAGAAGAAACCGCAATCACAATGTTCTAA
        129 CTAGGAGGAAGAAATCACAACCACAATGTTCTAA

        816 GCCTCGAAAG


Statistics
Matches: 292,  Mismatches: 34, Indels: 12
        0.86            0.10        0.04

Matches are distributed among these distances:
 167    5  0.02
 168  279  0.96
 169    8  0.03

ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24


Consensus pattern (166 bp):   
GAATATCCATGCAAGAGCCATATTGAAGATCCAAGAGTGATGATCAAATGTGTCTAAAACCCGTC
AAGGAAGAAGCTAAAGATGATGTTTGTGATAAACCTTGTATGAGACTCCTCCATGCAAGGAAACT
AGGAGGAAGAAATCACAACCACAATGTTCTAAAGCA

Found at i:2107 original size:159 final size:159

Alignment explanation


    Indices: 1827--2133  Score: 384
    Period size: 159  Copynumber: 1.9  Consensus size: 159

       1817 ATGATGTGAA

                                                *                            
       1827 AGCCAGTCAAGTTGCATCCAAAAATTGCTCGGTACCTAAAATTGAAGCTGATGATGAATTTGGCA
          1 AGCCAGTCAAGTTGCATCCAAAAATTGCTCGGTACCGAAAATTGAAGCTGATGATGAATTTGGCA

             *   *    *         *              *    *    *                   
       1892 ATTGTTATGCTGGAAATCCTGGCCCTGCTGCCCAACCCACTACCATAGGACTTCAAGATA-ATGA
         66 AGTGTCATGCCGGAAATCCTAGCCCTGCTGCCCAAACCACCACCACAGGACTTCAAGA-AGATGA

                     *  *                 
       1956 AGAGGAAGTTAATCCTACTGATGATGCTAT
        130 AGAGGAAGTCAAACCTACTGATGATGCTAT

                              *   *   *  *   *      *      *         *       
       1986 AGCCAGTCAAGTTGCATCTAAAGATTTCTTGGTGCCGAAAGTTGAAGTTGATGATGATTTTGGCA
          1 AGCCAGTCAAGTTGCATCCAAAAATTGCTCGGTACCGAAAATTGAAGCTGATGATGAATTTGGCA

                             **                 *                        *   
       2051 AGTGTCATGCCGGAAATTTTAGCCCTGCTGCCCAAATCACCACCACAGGA-TATCAAGAAGCTGA
         66 AGTGTCATGCCGGAAATCCTAGCCCTGCTGCCCAAACCACCACCACAGGACT-TCAAGAAGATGA

                               
       2115 AGAGGAAGTCAAACCTACT
        130 AGAGGAAGTCAAACCTACT

       2134 ATATCTACAA


Statistics
Matches: 124,  Mismatches: 22, Indels: 4
        0.83            0.15        0.03

Matches are distributed among these distances:
 158    2  0.02
 159  122  0.98

ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26


Consensus pattern (159 bp):   
AGCCAGTCAAGTTGCATCCAAAAATTGCTCGGTACCGAAAATTGAAGCTGATGATGAATTTGGCA
AGTGTCATGCCGGAAATCCTAGCCCTGCTGCCCAAACCACCACCACAGGACTTCAAGAAGATGAA
GAGGAAGTCAAACCTACTGATGATGCTAT
Done.