Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2888

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, 498

Length: 830
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26


Found at i:325 original size:132 final size:132

Alignment explanation


    Indices: 84--757  Score: 1012
    Period size: 132  Copynumber: 5.1  Consensus size: 132

         74 ATTGACAGTA

                        *                   *                           *    
         84 GAGCAGATCGAAAACGGAGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCATCAAG
          1 GAGCAGATCGAAGACGGAGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAG

             *                *          *    **                             
        149 CATTGTCTCCCTGAGCAGTAGTGGAGAAGATTGATGATTGTAGATCTTATCTCCCTAAGCAGTAG
         66 CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAG

              
        214 TG
        131 TG

                          *  *                             *                 
        216 GAGCAGATCGAAGAAGGCGAATCTTATCTTTCTAAGATAGTGGGAAGTAGATTTAAGCCACCAAG
          1 GAGCAGATCGAAGACGGAGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAG

               **           *           **  *      *                         
        281 CCTCATCTCCCTGAGCTGCAGTGGAGAAAATTAAAAATTATAGATCTTATCTCCCTAAGCAGTAG
         66 CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAG

              
        346 TG
        131 TG

                              *                                              
        348 GAGCAGATCGAAGACGGAAAATCTTATCTTT-TCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
          1 GAGCAGATCGAAGACGGAGAATCTTATCTTTCT-AAGATAGTGGGAAGCAGATTTAAGCCACCAA

                         *                        *    *                     
        412 GCCTTGTCTCCCTAAGCAGCAGTGGAGAAGGTTGAAAACTGTAAATCTTATCTCCCTAAGCAGTA
         65 GCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTA

               
        477 GTG
        130 GTG

                              *                                              
        480 GAGCAGATCGAAGACGGAAAATCTTATCTTT-TCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
          1 GAGCAGATCGAAGACGGAGAATCTTATCTTTCT-AAGATAGTGGGAAGCAGATTTAAGCCACCAA

                                                  *    *                     
        544 GCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAACTGTAAATCTTATCTCCCTAAGCAGTA
         65 GCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTA

               
        609 GTG
        130 GTG

                             *              *                *               
        612 GAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCATATTTAAGCCACCAAG
          1 GAGCAGATCGAAGACGGAGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAG

                        *        *             *                          *  
        677 CCTTGTCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATT-TCAGATCTTATCTCCCTAAGCAATA
         66 CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAATTGT-AGATCTTATCTCCCTAAGCAGTA

               
        741 GTG
        130 GTG

                          
        744 GAGCAGATCGAAGA
          1 GAGCAGATCGAAGA

        758 TGACAGATTT


Statistics
Matches: 498,  Mismatches: 41, Indels: 6
        0.91            0.08        0.01

Matches are distributed among these distances:
 131    2  0.00
 132  496  1.00

ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25


Consensus pattern (132 bp):   
GAGCAGATCGAAGACGGAGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAG
CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAG
TG

Found at i:372 original size:44 final size:44

Alignment explanation


    Indices: 154--757  Score: 231
    Period size: 44  Copynumber: 13.7  Consensus size: 44

        144 TCAAGCATTG

                   *             *       *  ** * *      
        154 TCTCCCTGAGCAGTAGTGGAGAAGATTGATGATTGTAGATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                                      *     *   *       
        198 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAGGCGAATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

               **                  *     *   * **   **  * 
        242 TCTTTCTAAG-A-TAGTGGGAAGTAGATTTAAGCCACCAAGCCTCA
          1 TCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAAATCTTA

                   *   * *       * *   *  * **** *      
        286 TCTCCCTGAGCTGCAGTGGAGAAAATTAAAAATTATAGATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                                      *        *        
        330 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                **                        *   * **   **   *
        374 TCT-TTTCAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAGCCTTG
          1 TCTCCCT-AAGCAGTAGT-GG-AGCAGATTGAAGACGGCAAATCTTA

                         *       *  *     *  * *        
        418 TCTCCCTAAGCAGCAGTGGAGAAGGTTGAAAACTGTAAATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                                      *        *        
        462 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                **                        *   * **   **   *
        506 TCT-TTTCAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAGCCTTG
          1 TCTCCCT-AAGCAGTAGT-GG-AGCAGATTGAAGACGGCAAATCTTA

                   *     *       *  *     *  * *        
        550 TCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAACTGTAAATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                                      *         *       
        594 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                *                     *   *   * **   **   *
        638 TCTTTCC-AAG-A-TAGTGGGAAGCATATTTAAGCCACCAAGCCTTG
          1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAAATCTTA

                   *     *  *    *  *       ***  *      
        682 TCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATTTCAGATCTTA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

                        *             *     
        726 TCTCCCTAAGCAATAGTGGAGCAGATCGAAGA
          1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA

        758 TGACAGATTT


Statistics
Matches: 384,  Mismatches: 154, Indels: 44
        0.66            0.26        0.08

Matches are distributed among these distances:
  42   16  0.04
  43   17  0.04
  44  324  0.84
  45   16  0.04
  46   11  0.03

ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25


Consensus pattern (44 bp):   
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAAATCTTA

Done.