Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2816

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, 506

Length: 844
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26


Found at i:105 original size:46 final size:46

Alignment explanation


    Indices: 1--839  Score: 1224
    Period size: 46  Copynumber: 18.3  Consensus size: 46

                           *   *      *      *        *   
          1 TGCCAAATACAGGAAGACAAGATCTGATATCTTTGATC-CCTCCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                 *         * * **                    *     
         46 TGCCATATACAGGAAGATAAAATCTGCTATCTTCGATC-CCCTCTGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTC-GC

                   *       *   *     *  *     *      *  * 
         92 TGCCAAAAACAGGAAGACAAGATCTACTGTCTTCAATC-CCCTCAC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

             *             *   *     *            *   * * 
        137 TACCAAATACAGGAAGACAAGATCTACTATCTTCGATCCCCTCCAC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                     *     *   *   *  *              *     
        183 T-CCAAATATAGGAAGACAAGATTTGATATCTTCGATC-CCCTCTGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTC-GC

                                                          
        228 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        274 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        320 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        366 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        412 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        458 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        504 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        550 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        596 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        642 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                                                          
        688 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                           *   *                  *   *   
        734 TGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

                       *   *   *    *      *         *     
        780 T-CCAAATACATGAAGACAAGATCCGCTATCGTCGATC-CCCTCTGC
          1 TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTC-GC

                           
        825 TGCCAAATACAGGAA
          1 TGCCAAATACAGGAA

        840 GACAA


Statistics
Matches: 743,  Mismatches: 44, Indels: 13
        0.93            0.05        0.02

Matches are distributed among these distances:
  44    6  0.01
  45  141  0.19
  46  592  0.80
  47    4  0.01

ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26


Consensus pattern (46 bp):   
TGCCAAATACAGGAAAACATGATCTGCTATCTTCGATCTCCTTCGC

Done.