Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38512

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: 3696
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26


Found at i:2929 original size:69 final size:68

Alignment explanation


    Indices: 2834--3281  Score: 518
    Period size: 69  Copynumber: 6.5  Consensus size: 68

       2824 GGGAAAGGTC

                                        *        *    * *        *           
       2834 CATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAGGGGAAGAGC
          1 CATT-TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC

                
       2899 TCAT
         65 TCAT

                     **  *              *     *                  *        *  
       2903 CAGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGGGAAGGGC
          1 CA-TTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC

                
       2968 TCAT
         65 TCAT

              *                            *             *      *           *
       2972 CTCTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTAAGGGGAAGAGT
          1 C-ATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC

              * 
       3037 TCGT
         65 TCAT

             *                                             *    *     **  * *
       3041 CCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGGGT
          1 CATT-TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC

                
       3106 TCAT
         65 TCAT

                *    *                                     *              * *
       3110 CCATATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGGGAAGGGT
          1 -CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC

              * 
       3175 TCGT
         65 TCAT

              * *            *                                               
       3179 CCGTATTTGCAGATTCTATTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
          1 -CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC

                
       3244 TCAT
         65 TCAT

                                        *     
       3248 CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
          1 C-ATTTTTGCAGATTCTGTTCCAAGCACTCCTGC

       3282 TTATCATTAT


Statistics
Matches: 328,  Mismatches: 46, Indels: 10
        0.85            0.12        0.03

Matches are distributed among these distances:
  68    4  0.01
  69  320  0.98
  70    4  0.01

ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30


Consensus pattern (68 bp):   
CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCT
CAT

Found at i:3191 original size:207 final size:207

Alignment explanation


    Indices: 2831--3281  Score: 593
    Period size: 207  Copynumber: 2.2  Consensus size: 207

       2821 CCAGGGAAAG

                                                         * *        *        
       2831 GTCCATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAGGGGAAG
          1 GTCC-TTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAG

                       *     *                       *                  *    
       2896 AGCTCATCAGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGG
         65 AGCTCATCAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG

                           *            *                           *      * 
       2961 GAAGGGCTCATCTCTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTA
        130 GAAGGGCTCATCTCTATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCA

                      *  
       3026 AGGGGAAGAGTTC
        195 AGGGGAAGAGCTC

                                          *        *         *    *     **  *
       3039 GTCCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGG
          1 GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAGA

             *                  *              *                  *          
       3104 GTTCATCCA-TATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGG
         66 GCTCAT-CAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG

                  *  *                                 *                     
       3168 GAAGGGTTCGTC-CGTATTTGCAGATTCTATTCCAAGCACTCCTGCCTATGCAGATAACATGTTC
        130 GAAGGGCTCATCTC-TATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTC

                          
       3232 AAGGGGAAGAGCTC
        194 AAGGGGAAGAGCTC

            *      *                             
       3246 AT-CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
          1 GTCCT-TGTTTGCAGATTCTGTTCCAAGCACCCCTGC

       3282 TTATCATTAT


Statistics
Matches: 211,  Mismatches: 29, Indels: 7
        0.85            0.12        0.03

Matches are distributed among these distances:
 206    3  0.01
 207  202  0.96
 208    6  0.03

ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30


Consensus pattern (207 bp):   
GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAGA
GCTCATCAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGG
AAGGGCTCATCTCTATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCAA
GGGGAAGAGCTC
Done.