Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2817

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, 505

Length: 843
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29


Found at i:72 original size:46 final size:46

Alignment explanation


    Indices: 4--843  Score: 1146
    Period size: 46  Copynumber: 18.3  Consensus size: 46

          1 TAG

                                         *       **       
          4 CAGATCTTGTCTTCCTGTATTTGGCAGCGAAAGGGATTAAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *       *      **                      
         50 AAGATCTTCTCTTCCTTTATTTGTTAGCGG-AGGAGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGG-GATCGAAGATAT

                             *                    *      *
         96 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *         *                           
        142 GAGATCTTATCTTCCTGTCTTTGGCAGCGGAAGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                             *                    *      *
        188 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *         *                           
        234 GAGATCTTATCTTCCTGTCTTTGGCAGCGGAAGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                             *                    *      *
        280 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *         *                           
        326 GAGATCTTATCTTCCTGTCTTTGGCAGCGGAAGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                             *                    *      *
        372 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *         *                           
        418 GAGATCTTATCTTCCTGTCTTTGGCAGCGGAAGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                             *                    *      *
        464 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *         *                           
        510 GAGATCTTATCTTCCTGTCTTTGGCAGCGGAAGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                             *                    *      *
        556 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

            *       *         *                           
        602 GAGATCTTATCTTCCTGTCTTTGGCAGCGGAAGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                                       *   *             *
        648 CAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGGGATCGAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                                           *              
        694 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAT
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

                        *                          *      *
        740 CAGATCTTGTCTCCCTGTATTTGGCAGCGG-AGGAGATCAAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGG-GATCGAAGATAT

                  *          *                            *
        786 CAGATCCTGTCTTCCTGAATTTGGCAAG-GGAAGGGATCGAAGATAG
          1 CAGATCTTGTCTTCCTGTATTTGGC-AGCGGAAGGGATCGAAGATAT

                        
        832 CAGATCTTGTCT
          1 CAGATCTTGTCT


Statistics
Matches: 690,  Mismatches: 99, Indels: 10
        0.86            0.12        0.01

Matches are distributed among these distances:
  45    5  0.01
  46  677  0.98
  47    8  0.01

ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29


Consensus pattern (46 bp):   
CAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGGGATCGAAGATAT

Found at i:171 original size:92 final size:92

Alignment explanation


    Indices: 4--843  Score: 1398
    Period size: 92  Copynumber: 9.1  Consensus size: 92

          1 TAG

                             *           *       *       **       *       * *
          4 CAGATCTTGTCTTCCTGTATTTGGCAGCGAAAGGGATTAAAGATATAAGATCTTCTCTTCCTTTA
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                **                      
         69 TTTGTTAGCGG-AGGAGATCGAAGATAT
         66 TTTGGCAGCGGAAGG-GATCGAAGATAT

                                                                             
         96 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                                       
        161 TTTGGCAGCGGAAGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                                                                             
        188 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                                       
        253 TTTGGCAGCGGAAGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                                                                             
        280 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                                       
        345 TTTGGCAGCGGAAGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                                                                             
        372 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                                       
        437 TTTGGCAGCGGAAGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                                                                             
        464 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                                       
        529 TTTGGCAGCGGAAGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                                                                             
        556 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                                       
        621 TTTGGCAGCGGAAGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                             *         *   *      *       *       *         *
        648 CAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTA
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC

                        *              
        713 TTTGGCAGCGGAGGGGATCGAAGATAT
         66 TTTGGCAGCGGAAGGGATCGAAGATAT

                        *    *                             *     * *        *
        740 CAGATCTTGTCTCCCTGTATTTGGCAGCGG-AGGAGATCAAAGATAGCAGATCCTGTCTTCCTGA
          1 CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGG-GATCAAAGATAGGAGATCTTATCTTCCTGT

            *                           *
        804 ATTTGGCAAG-GGAAGGGATCGAAGATAG
         65 CTTTGGC-AGCGGAAGGGATCGAAGATAT

                        
        832 CAGATCTTGTCT
          1 CAGATCTTGTCT


Statistics
Matches: 719,  Mismatches: 26, Indels: 6
        0.96            0.03        0.01

Matches are distributed among these distances:
  91    2  0.00
  92  712  0.99
  93    5  0.01

ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29


Consensus pattern (92 bp):   
CAGATCTTGTCTTCCTGAATTTGGCAGCGGAAGGGATCAAAGATAGGAGATCTTATCTTCCTGTC
TTTGGCAGCGGAAGGGATCGAAGATAT

Done.