Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6273.1

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, 1000

Length: 12688
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26


Found at i:255 original size:95 final size:95

Alignment explanation


    Indices: 91--279  Score: 360
    Period size: 95  Copynumber: 2.0  Consensus size: 95

         81 AAAGCTTCAA

                                                                             
         91 AGTATGGTTTCATTAAACTATAAGGTGATCTTGGTTTCGATGGTTTAGAGTATCGTGTCCTAACA
          1 AGTATGGTTTCATTAAACTATAAGGTGATCTTGGTTTCGATGGTTTAGAGTATCGTGTCCTAACA

                                          
        156 TGCTGGATGTGATATTCATTCGGAACAAGT
         66 TGCTGGATGTGATATTCATTCGGAACAAGT

                                                                            *
        186 AGTATGGTTTCATTAAACTATAAGGTGATCTTGGTTTCGATGGTTTAGAGTATCGTGTCCTAACG
          1 AGTATGGTTTCATTAAACTATAAGGTGATCTTGGTTTCGATGGTTTAGAGTATCGTGTCCTAACA

                             *           
        251 TGCTGGATGTGATATTCCTTCGGAACAAG
         66 TGCTGGATGTGATATTCATTCGGAACAAG

        280 AGAATCTTAT


Statistics
Matches: 92,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  95   92  1.00

ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37


Consensus pattern (95 bp):   
AGTATGGTTTCATTAAACTATAAGGTGATCTTGGTTTCGATGGTTTAGAGTATCGTGTCCTAACA
TGCTGGATGTGATATTCATTCGGAACAAGT

Found at i:11933 original size:87 final size:87

Alignment explanation


    Indices: 11625--12570  Score: 1662
    Period size: 87  Copynumber: 10.9  Consensus size: 87

      11615 ATATTGGTAG

                                                                            *
      11625 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAA
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                          *      * 
      11690 ATCTTGTCTTCATGTATTGGCGT
         66 ATCTTGTC-TCATGAATTGGCAT

                                                                            *
      11713 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAA
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                          *      * 
      11778 ATCTTGTCTTCATGTATTGGCGT
         66 ATCTTGTC-TCATGAATTGGCAT

                                                                             
      11801 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                         *        
      11866 ATCTTGTCTCATGTATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                  *                                                          
      11888 GAAGTGAATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                                  
      11953 ATCTTGTCTCATGAATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                                                                             
      11975 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                                  
      12040 ATCTTGTCTCATGAATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                                                                             
      12062 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                                  
      12127 ATCTTGTCTCATGAATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                                                                             
      12149 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                                  
      12214 ATCTTGTCTCATGAATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                                                                             
      12236 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                                  
      12301 ATCTTGTCTCATGAATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                                                                             
      12323 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                                  
      12388 ATCTTGTCTCATGAATTGGCAT
         66 ATCTTGTCTCATGAATTGGCAT

                                                                             
      12410 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
          1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG

                          *   *  * 
      12475 ATCTTGTCTTCATGTATTAGCGT
         66 ATCTTGTC-TCATGAATTGGCAT

                 *        *   *     * *      *        *       *          *   
      12498 GAAGTAGATCGAAGGTAGTAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCA
          1 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCA

                      
      12561 GATCTTGTCT
         65 GATCTTGTCT

      12571 TCCCATATTG


Statistics
Matches: 839,  Mismatches: 17, Indels: 6
        0.97            0.02        0.01

Matches are distributed among these distances:
  86    1  0.00
  87  618  0.74
  88  198  0.24
  89   22  0.03

ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28


Consensus pattern (87 bp):   
GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
ATCTTGTCTCATGAATTGGCAT

Found at i:12678 original size:44 final size:44

Alignment explanation


    Indices: 11553--12688  Score: 499
    Period size: 44  Copynumber: 26.0  Consensus size: 44

      11543 AAGTCATTAA

                    * *     * *      * *            *   
      11553 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAGGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT

                 *                     *     *          
      11597 AGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      11641 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                *   * *     * *      ***     *          
      11685 AGCAAATCTTGTCTTCATGTATTGGCGTGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      11729 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                *   * *     * *      ***     *          
      11773 AGCAAATCTTGTCTTCATGTATTGGCGTGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      11817 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     * *      * *                 
      11861 AGCAGATCTTGTC-TCATGTATTGGCATGAAGT-GAATCGAAGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAG-ATCGAAGAT

                    * *      *         **               *
      11904 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     *         * *     *          
      11948 AGCAGATCTTGTC-TCATGA-ATTGGCATGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCT-ATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      11991 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     *         * *     *          
      12035 AGCAGATCTTGTC-TCATGA-ATTGGCATGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCT-ATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      12078 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     *         * *     *          
      12122 AGCAGATCTTGTC-TCATGA-ATTGGCATGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCT-ATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      12165 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     *         * *     *          
      12209 AGCAGATCTTGTC-TCATGA-ATTGGCATGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCT-ATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      12252 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     *         * *     *          
      12296 AGCAGATCTTGTC-TCATGA-ATTGGCATGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCT-ATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      12339 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     *         * *     *          
      12383 AGCAGATCTTGTC-TCATGA-ATTGGCATGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCT-ATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **               *
      12426 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     * *                         * 
      12470 AGCAGATCTTGTCTTCATGTATTAGCGT--GAAGTAGATCGAAGGT
          1 AGCAGATCCTATCTTCCTATATT-G-GTAAGAAGTAGATCGAAGAT

              *                        *     *          
      12514 AGTAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT

                    * *      *         **           *   *
      12558 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAA
          1 AGCAGATCCTATCTTCCTATATTGGT-AAGAAGTAGATCGAAGAT

                    * *     * *      ***                
      12602 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT

                 *                  *        *    *    
      12646 AGCAGGTCCTATCTTCCTATATTGATAAGAAGTGGATCCAAGA
          1 AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGA


Statistics
Matches: 859,  Mismatches: 186, Indels: 94
        0.75            0.16        0.08

Matches are distributed among these distances:
  42   93  0.11
  43  230  0.27
  44  362  0.42
  45  171  0.20
  46    1  0.00
  47    2  0.00

ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29


Consensus pattern (44 bp):   
AGCAGATCCTATCTTCCTATATTGGTAAGAAGTAGATCGAAGAT
Done.