Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_7295

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: 3440
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27


Found at i:841 original size:41 final size:39

Alignment explanation


    Indices: 708--1033  Score: 183
    Period size: 41  Copynumber: 8.3  Consensus size: 39

        698 CGTGAAACTA

                                   *      *   *      
        708 GGTGTGCGGAGCC-C-GGCACC-CCGGCAAACTAAGCCCTT
          1 GGTGTGCGGAGCCTCGGGCACCATCGGC-ACCTAGGCCC-T

                *                *            *   * * 
        746 GGTATTGCAGGAGCCTCGGGCGCCAT-GGCACCTCGGTGCTT
          1 GGT-GTGC-GGAGCCTCGGGCACCATCGGCACCTAGG-CCCT

              *                                       
        787 CGATGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCT
          1 -GGTGTGC-GGAGCCTCGGGCACCATCGGC-ACCTAGGCCCT

                                             *       
        829 GGTCGTGCGGAGCCTCGGGCACCATCGGCA-CTCGTG--CT
          1 GGT-GTGCGGAGCCTCGGGCACCATCGGCACCTAG-GCCCT

            *   *              *  **    *         * 
        867 TGTGGGCGGGAGCCTC-GGAACTGTCGGAACCT-GGCCTT
          1 GGTGTGC-GGAGCCTCGGGCACCATCGGCACCTAGGCCCT

                                             *  **  
        905 GGTGTGCGGAGCCTCGGAGCACCATCGGCACCTTGGTGCT
          1 GGTGTGCGGAGCCTCGG-GCACCATCGGCACCTAGGCCCT

                  *    *     *         *             
        945 GGATGTCCGGAACCTCGCGC-CCATCGACACCTAGGCCCTT
          1 GG-TGTGCGGAGCCTCGGGCACCATCGGCACCTAGGCCC-T

                        *                 *       * 
        985 GGTCGTGCGGAGGCTCGGGCACCATCGG-AAC-A-GCCTT
          1 GGT-GTGCGGAGCCTCGGGCACCATCGGCACCTAGGCCCT

                        
       1022 GGTGTGCGGAGC
          1 GGTGTGCGGAGC

       1034 TGTGACATCG


Statistics
Matches: 218,  Mismatches: 48, Indels: 46
        0.70            0.15        0.15

Matches are distributed among these distances:
  36    9  0.04
  37   25  0.11
  38   27  0.12
  39   33  0.15
  40   32  0.15
  41   66  0.30
  42   20  0.09
  43    6  0.03

ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18


Consensus pattern (39 bp):   
GGTGTGCGGAGCCTCGGGCACCATCGGCACCTAGGCCCT

Found at i:920 original size:75 final size:82

Alignment explanation


    Indices: 755--1012  Score: 261
    Period size: 78  Copynumber: 3.2  Consensus size: 82

        745 TGGTATTGCA

                        *                         *              *           
        755 GGAGCCTCGGGCGCCAT-GGCACCTCGGTGCTTCGATGTGCGGGAGCCTCGGGCACCATCGGCAA
          1 GGAGCCTCGGGCACCATCGGCA-CTCGGTGCTTCGATGGGCGGGAGCCTCGGGAACCATCGGCAA

                              
        819 CCTAGGCCCTGGTCGTGC
         65 CCTAGGCCCTGGTCGTGC

                                                                   **        
        837 GGAGCCTCGGGCACCATCGGCACTC-GTGCTT-G-TGGGCGGGAGCCTC-GGAACTGTCGG-AAC
          1 GGAGCCTCGGGCACCATCGGCACTCGGTGCTTCGATGGGCGGGAGCCTCGGGAACCATCGGCAAC

                   *         
        897 CT-GGCCTTGGT-GTGC
         66 CTAGGCCCTGGTCGTGC

                                      *       *     * *   *     *  *      *  
        912 GGAGCCTCGGAGCACCATCGGCACCTTGGTGC-TGGAT-GTCCGGAACCTCGCG-CCCATCGAC-
          1 GGAGCCTCGG-GCACCATCGGCA-CTCGGTGCTTCGATGGGCGGGAGCCTCGGGAACCATCGGCA

                                
        973 ACCTAGGCCCTTGGTCGTGC
         64 ACCTAGGCCC-TGGTCGTGC

                *               
        993 GGAGGCTCGGGCACCATCGG
          1 GGAGCCTCGGGCACCATCGG

       1013 AACAGCCTTG


Statistics
Matches: 148,  Mismatches: 17, Indels: 24
        0.78            0.09        0.13

Matches are distributed among these distances:
  75   14  0.09
  76   20  0.14
  77    8  0.05
  78   30  0.20
  79   19  0.13
  80   15  0.10
  81   19  0.13
  82   19  0.13
  83    4  0.03

ACGTcount: A:0.13, C:0.33, G:0.36, T:0.18


Consensus pattern (82 bp):   
GGAGCCTCGGGCACCATCGGCACTCGGTGCTTCGATGGGCGGGAGCCTCGGGAACCATCGGCAAC
CTAGGCCCTGGTCGTGC
Done.