Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3928

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, 375

Length: 625
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31


Found at i:68 original size:46 final size:46

Alignment explanation


    Indices: 8--625  Score: 745
    Period size: 46  Copynumber: 13.4  Consensus size: 46

          1 GATAGTT

                                               **       **
          8 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATTTAAGATAGTT
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                  *                   *       *           
         54 GATCTTCTCTTCCTGTATTTGGCAGCAGAGGGGAACGAAGATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

            *  *        *            *             *      
        100 AATTTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGAAAATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                   *                              *       
        146 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAGGATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                           *  *        * *          *   *  
        192 GATCTTGTCTTCCTGAATATGGCAGCGAAAGGGAGT-GAATATATCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGA-TCGAAGATAGCA

            *           *            *             *      
        238 AATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGAAAATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                   *                              *       
        284 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAGGATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                           *  *        * *          *   *  
        330 GATCTTGTCTTCCTGAATATGGCAGCGAAAGGGAGT-GAATATATCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGA-TCGAAGATAGCA

            *           *            *             *      
        376 AATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGAAAATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                   *                                      
        422 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                                  *   *  **            *  
        468 GATCTTGTCTTCCTGTATTTGGTAGCAGAATGGATCGAAGATATCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                           *           * *     *   *   *  
        514 GATCTTGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAATATATCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

            *                       *          *          
        560 AATCTTGTCTTCCTGTATTTGGCATCGGAGGGGATTGAAGATAGCA
          1 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

                                
        606 GATCTTGTCTTCCTGTATTT
          1 GATCTTGTCTTCCTGTATTT


Statistics
Matches: 480,  Mismatches: 88, Indels: 8
        0.83            0.15        0.01

Matches are distributed among these distances:
  45    2  0.00
  46  476  0.99
  47    2  0.00

ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31


Consensus pattern (46 bp):   
GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA

Found at i:621 original size:138 final size:138

Alignment explanation


    Indices: 8--625  Score: 882
    Period size: 138  Copynumber: 4.5  Consensus size: 138

          1 GATAGTT

                   *                           **       **      *            
          8 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATTTAAGATAGTTGATCTTCTCTTCCTGTATT
          1 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT

                       *    **       *     *                                 
         73 TGGCAGC-AGAGGGGAACGAAGATAGCAAATTTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCG
         66 TGGCAGCGA-AAGGGAGTGAAGATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCG

                     
        137 AAAATAGCA
        130 AAAATAGCA

                                                  *                      *  *
        146 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAGGATAGCAGATCTTGTCTTCCTGAATA
          1 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT

                                *                                            
        211 TGGCAGCGAAAGGGAGTGAATATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGA
         66 TGGCAGCGAAAGGGAGTGAAGATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGA

                    
        276 AAATAGCA
        131 AAATAGCA

                                                  *                      *  *
        284 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAGGATAGCAGATCTTGTCTTCCTGAATA
          1 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT

                                *                                            
        349 TGGCAGCGAAAGGGAGTGAATATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGA
         66 TGGCAGCGAAAGGGAGTGAAGATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGA

                    
        414 AAATAGCA
        131 AAATAGCA

                                                                             
        422 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT
          1 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT

               *        *                *           *  *         * * *     *
        487 TGGTAGC-AGAATGGA-TCGAAGATATCAGATCTTGTCTTCCTGAATTTGGCAGCGAAAGGGATT
         66 TGGCAGCGA-AAGGGAGT-GAAGATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATC

               *   *  
        550 GAATATATCA
        129 GAAAATAGCA

            *      *                *          *                             
        560 AATCTTGTCTTCCTGTATTTGGCATCGGAGGGGATTGAAGATAGCAGATCTTGTCTTCCTGTATT
          1 GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT

             
        625 T
         66 T


Statistics
Matches: 443,  Mismatches: 34, Indels: 6
        0.92            0.07        0.01

Matches are distributed among these distances:
 137    2  0.00
 138  440  0.99
 139    1  0.00

ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31


Consensus pattern (138 bp):   
GATCTTGGCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATT
TGGCAGCGAAAGGGAGTGAAGATATCAAATCTTGTCTTCTTGTATTTGGCAGGGGAGGGGATCGA
AAATAGCA
Done.