Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2850

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, 501

Length: 836
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36


Found at i:40 original size:27 final size:26

Alignment explanation


    Indices: 1--390  Score: 354
    Period size: 27  Copynumber: 14.5  Consensus size: 26

                          *            
          1 CTATGGGGGTATTTTAGTCATTTTACC
          1 CTAT-GGGGTATTTCAGTCATTTTACC

                                       
         28 CTATGGGGTTATTTCAGTCATTTTACC
          1 CTATGGGG-TATTTCAGTCATTTTACC

                           *            
         55 CTATGGGGGTATTTCGGTTC-TTTTACC
          1 CTAT-GGGGTATTTCAG-TCATTTTACC

                           *           *
         82 CTATGAGGGTATTT-TGATCATTTTACT
          1 CTATG-GGGTATTTCAG-TCATTTTACC

                  *               *    
        109 CTATTGAGGTATTTCAGTCATTCTACC
          1 CTA-TGGGGTATTTCAGTCATTTTACC

                                   *    
        136 CTATTGGGGTATTTC-GATCATTCTACC
          1 CTA-TGGGGTATTTCAG-TCATTTTACC

             *           *            
        163 CCATGGGGTATTTTAGTCATTTTACC
          1 CTATGGGGTATTTCAGTCATTTTACC

                      *   **  *        
        189 CTATGAGGGTTTTTTGGTAATTTTACC
          1 CTATG-GGGTATTTCAGTCATTTTACC

                          *      *    
        216 CTATGGGGTATTTCGGTCATTCTACC
          1 CTATGGGGTATTTCAGTCATTTTACC

            *              *  *        
        242 TTATAGGGGTATTTCGGTTATTTTACC
          1 CTAT-GGGGTATTTCAGTCATTTTACC

            *     *       **  *        
        269 TTATTGAGGTATTTTGGTTATTTTACC
          1 CTA-TGGGGTATTTCAGTCATTTTACC

            *                          
        296 TTATTGGGGTATTTCAGTCATTTTACC
          1 CTA-TGGGGTATTTCAGTCATTTTACC

                          *   *        
        323 CTATGGGGGTATTTTAGTTATTTTACC
          1 CTAT-GGGGTATTTCAGTCATTTTACC

               *          *  *      * 
        350 CTACGGGGTATTTCGGTTATTTTATC
          1 CTATGGGGTATTTCAGTCATTTTACC

                           
        376 CTATGGCGGTATTTC
          1 CTATGG-GGTATTTC

        391 GGTCGCCTCG


Statistics
Matches: 311,  Mismatches: 38, Indels: 28
        0.82            0.10        0.07

Matches are distributed among these distances:
  26   77  0.25
  27  224  0.72
  28   10  0.03

ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45


Consensus pattern (26 bp):   
CTATGGGGTATTTCAGTCATTTTACC

Found at i:83 original size:54 final size:53

Alignment explanation


    Indices: 1--390  Score: 390
    Period size: 54  Copynumber: 7.3  Consensus size: 53

                          *                           *           
          1 CTATGGGGGTATTTTAGTCATTTTACCCTATGGGGTTATTTCAGTCATTTTACC
          1 CTATGGGGGTATTTCAGTCATTTTACCCTATGGGG-TATTTCGGTCATTTTACC

                           *                          * *         *
         55 CTATGGGGGTATTTCGGTTC-TTTTACCCTATGAGGGTATTTTGATCATTTTACT
          1 CTATGGGGGTATTTCAG-TCATTTTACCCTATG-GGGTATTTCGGTCATTTTACC

                * *               *                    *     *    
        109 CTATTGAGGTATTTCAGTCATTCTACCCTATTGGGGTATTTCGATCATTCTACC
          1 CTATGGGGGTATTTCAGTCATTTTACCCTA-TGGGGTATTTCGGTCATTTTACC

             *            *                      *   *   *        
        163 CCAT-GGGGTATTTTAGTCATTTTACCCTATGAGGGTTTTTTGGTAATTTTACC
          1 CTATGGGGGTATTTCAGTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACC

                           *      *    *                 *        
        216 CTAT-GGGGTATTTCGGTCATTCTACCTTATAGGGGTATTTCGGTTATTTTACC
          1 CTATGGGGGTATTTCAGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC

            *   * *       **  *        *              *           
        269 TTATTGAGGTATTTTGGTTATTTTACCTTATTGGGGTATTTCAGTCATTTTACC
          1 CTATGGGGGTATTTCAGTCATTTTACCCTA-TGGGGTATTTCGGTCATTTTACC

                          *   *           *             *      * 
        323 CTATGGGGGTATTTTAGTTATTTTACCCTACGGGGTATTTCGGTTATTTTATC
          1 CTATGGGGGTATTTCAGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACC

                  *        
        376 CTATGGCGGTATTTC
          1 CTATGGGGGTATTTC

        391 GGTCGCCTCG


Statistics
Matches: 280,  Mismatches: 48, Indels: 17
        0.81            0.14        0.05

Matches are distributed among these distances:
  52    2  0.01
  53  118  0.42
  54  152  0.54
  55    8  0.03

ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45


Consensus pattern (53 bp):   
CTATGGGGGTATTTCAGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACC
Done.