Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g03098.F2

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: 5195
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28


Found at i:2838 original size:24 final size:24

Alignment explanation


    Indices: 2804--2960  Score: 138
    Period size: 24  Copynumber: 6.3  Consensus size: 24

       2794 TACAACGGCA

                  *                 
       2804 GCAGCATCAGTTGGAGCTTCAGAG
          1 GCAGCAGCAGTTGGAGCTTCAGAG

                             *    * 
       2828 GCAGCAGCAGTTGGAGCATCAGCG
          1 GCAGCAGCAGTTGGAGCTTCAGAG

                                     
       2852 GCAGCAGCAGTTGGAGCTTCAGCA-
          1 GCAGCAGCAGTTGGAGCTTCAG-AG

               *       *             * 
       2876 GCATCAACGTCTGTTGGAGCTTCAGCG
          1 GCAGC-A-G-CAGTTGGAGCTTCAGAG

                           *         
       2903 GCAGCAGCAGTTGGAACTTCAGCA-
          1 GCAGCAGCAGTTGGAGCTTCAG-AG

               *              *      * 
       2927 GCATCAACGGCAGTTGGAACTTCAGCG
          1 GCAGC-A--GCAGTTGGAGCTTCAGAG

                   
       2954 GCAGCAG
          1 GCAGCAG

       2961 GAGCTTCGTC


Statistics
Matches: 108,  Mismatches: 15, Indels: 20
        0.76            0.10        0.14

Matches are distributed among these distances:
  24   64  0.59
  25    3  0.03
  26    3  0.03
  27   38  0.35

ACGTcount: A:0.25, C:0.25, G:0.32, T:0.18


Consensus pattern (24 bp):   
GCAGCAGCAGTTGGAGCTTCAGAG

Found at i:2854 original size:51 final size:49

Alignment explanation


    Indices: 2775--2960  Score: 157
    Period size: 51  Copynumber: 3.7  Consensus size: 49

       2765 TCAATTTGAA

                   *         *     *                           
       2775 CAGCAGCGGCAGTTGGAACTACAACGGCAGCAGCATCAGTTGGAGCTTCAG
          1 CAGCAGCAGCAGTTGGAGCT-CAGCGGCAGCAGCA-CAGTTGGAGCTTCAG

                                                               
       2826 -AGGCAGCAGCAGTTGGAGCATCAGCGGCAGCAG--CAGTTGGAGCTTCAG
          1 CA-GCAGCAGCAGTTGGAGC-TCAGCGGCAGCAGCACAGTTGGAGCTTCAG

                 *       *                                *      
       2874 CAGCATCAACGTCTGTTGGAGCTTCAGCGGCAGCAG--CAGTTGGAACTTCAG
          1 CAGCAGC-A-G-CAGTTGGAGC-TCAGCGGCAGCAGCACAGTTGGAGCTTCAG

                 *              *               
       2925 CAGCATCAACGGCAGTTGGAACTTCAGCGGCAGCAG
          1 CAGCAGC-A--GCAGTTGGAGC-TCAGCGGCAGCAG

       2961 GAGCTTCGTC


Statistics
Matches: 118,  Mismatches: 10, Indels: 14
        0.83            0.07        0.10

Matches are distributed among these distances:
  48   19  0.16
  49    2  0.02
  50    2  0.02
  51   93  0.79
  52    2  0.02

ACGTcount: A:0.26, C:0.25, G:0.32, T:0.17


Consensus pattern (49 bp):   
CAGCAGCAGCAGTTGGAGCTCAGCGGCAGCAGCACAGTTGGAGCTTCAG

Found at i:2858 original size:27 final size:27

Alignment explanation


    Indices: 2775--2960  Score: 149
    Period size: 27  Copynumber: 7.2  Consensus size: 27

       2765 TCAATTTGAA

                   *         *  *  * * 
       2775 CAGCAGCGGCAGTTGGAACTACAACGG
          1 CAGCAGCAGCAGTTGGAGCTTCAGCAG

                    *                  
       2802 CAGCAGCATCAGTTGGAGCTTCAG-AG
          1 CAGCAGCAGCAGTTGGAGCTTCAGCAG

                               *       
       2828 --GCAGCAGCAGTTGGAGCATCAGC-G
          1 CAGCAGCAGCAGTTGGAGCTTCAGCAG

                                       
       2852 --GCAGCAGCAGTTGGAGCTTCAGCAG
          1 CAGCAGCAGCAGTTGGAGCTTCAGCAG

              *  *     *                
       2877 CATCAAC-GTCTGTTGGAGCTTCAGC-G
          1 CAGCAGCAG-CAGTTGGAGCTTCAGCAG

                             *         
       2903 --GCAGCAGCAGTTGGAACTTCAGCAG
          1 CAGCAGCAGCAGTTGGAGCTTCAGCAG

              *  * *         *       * 
       2928 CATCAACGGCAGTTGGAACTTCAGCGG
          1 CAGCAGCAGCAGTTGGAGCTTCAGCAG

                  
       2955 CAGCAG
          1 CAGCAG

       2961 GAGCTTCGTC


Statistics
Matches: 128,  Mismatches: 22, Indels: 18
        0.76            0.13        0.11

Matches are distributed among these distances:
  24   60  0.47
  25    3  0.02
  26    3  0.02
  27   62  0.48

ACGTcount: A:0.26, C:0.25, G:0.32, T:0.17


Consensus pattern (27 bp):   
CAGCAGCAGCAGTTGGAGCTTCAGCAG
Done.