Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1758

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: 20089
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31


Found at i:9940 original size:27 final size:27

Alignment explanation


    Indices: 9910--10113  Score: 257
    Period size: 27  Copynumber: 7.6  Consensus size: 27

       9900 ATATTGAGTC

                    *       *   *    * 
       9910 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
       9937 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                     * 
       9964 CGCACACTTAGTGCTACATAGTCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                          **   *     * 
       9991 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
      10018 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
      10045 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                       
      10072 CGCACACTTAGTGCTACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
      10099 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

      10114 GTACAATTTA


Statistics
Matches: 156,  Mismatches: 19, Indels: 4
        0.87            0.11        0.02

Matches are distributed among these distances:
  27  155  0.99
  28    1  0.01

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:17825 original size:27 final size:27

Alignment explanation


    Indices: 17795--17999  Score: 259
    Period size: 27  Copynumber: 7.6  Consensus size: 27

      17785 ATATTGAGTC

                    *       *   *    * 
      17795 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
      17822 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
      17849 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
      17877 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
      17904 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
      17931 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                       
      17958 CGCACACTTAGTGCTACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
      17985 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

      18000 GTACAATTTA


Statistics
Matches: 157,  Mismatches: 18, Indels: 6
        0.87            0.10        0.03

Matches are distributed among these distances:
  27  133  0.85
  28   24  0.15

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Done.