Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g03098.F1

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: 5144
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28


Found at i:2814 original size:27 final size:26

Alignment explanation


    Indices: 2775--2909  Score: 91
    Period size: 27  Copynumber: 5.2  Consensus size: 26

       2765 TCAATTTGAA

                    *        *  *      
       2775 CAGCAGCGGCAGTTGGAACTACAACGG
          1 CAGCAGC-ACAGTTGGAGCTTCAACGG

                                        
       2802 CAGCAGCATCAGTTGGAGCTTCAGA-GG
          1 CAGCAGCA-CAGTTGGAGCTTCA-ACGG

                                  *   
       2829 CAGCAG--CAGTTGGAGCTTCAGCGG
          1 CAGCAGCACAGTTGGAGCTTCAACGG

                            *     * * 
       2853 CAGCAG--CAGTTGGAACTTCAGCAG
          1 CAGCAGCACAGTTGGAGCTTCAACGG

              *  *  *        *     *   
       2877 CATCAACGGCAGTTGGAACTTCAGCGG
          1 CAGCAGC-ACAGTTGGAGCTTCAACGG

                  
       2904 CAGCAG
          1 CAGCAG

       2910 GAGCTTCGTC


Statistics
Matches: 91,  Mismatches: 11, Indels: 12
        0.80            0.10        0.11

Matches are distributed among these distances:
  24   42  0.46
  27   48  0.53
  28    1  0.01

ACGTcount: A:0.27, C:0.25, G:0.33, T:0.16


Consensus pattern (26 bp):   
CAGCAGCACAGTTGGAGCTTCAACGG

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

Alignment explanation


    Indices: 2777--2909  Score: 117
    Period size: 24  Copynumber: 5.3  Consensus size: 24

       2767 AATTTGAACA

                 *            *      
       2777 GCAGCGGCAGTTGGAACTACA-ACG
          1 GCAGCAGCAGTTGGAACTTCAGA-G

                              *        
       2801 GCAGCAGCATCAGTTGGAGCTTCAGAG
          1 GCAGCAG---CAGTTGGAACTTCAGAG

                           *      * 
       2828 GCAGCAGCAGTTGGAGCTTCAGCG
          1 GCAGCAGCAGTTGGAACTTCAGAG

                                     
       2852 GCAGCAGCAGTTGGAACTTCAGCA-
          1 GCAGCAGCAGTTGGAACTTCAG-AG

               *                     * 
       2876 GCATCAACGGCAGTTGGAACTTCAGCG
          1 GCAGC-A--GCAGTTGGAACTTCAGAG

                   
       2903 GCAGCAG
          1 GCAGCAG

       2910 GAGCTTCGTC


Statistics
Matches: 91,  Mismatches: 9, Indels: 18
        0.77            0.08        0.15

Matches are distributed among these distances:
  24   48  0.53
  25    1  0.01
  26    1  0.01
  27   40  0.44
  28    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.33, T:0.16


Consensus pattern (24 bp):   
GCAGCAGCAGTTGGAACTTCAGAG

Found at i:2854 original size:51 final size:48

Alignment explanation


    Indices: 2775--2909  Score: 146
    Period size: 51  Copynumber: 2.7  Consensus size: 48

       2765 TCAATTTGAA

                   *            *  *                    *      
       2775 CAGCAGCGGCAGTTGGAACTACAACGGCAGCAGCATCAGTTGGAGCTTCAG
          1 CAGCAGCAGCAGTTGGAACTTCAGCGGCAGCAG---CAGTTGGAACTTCAG

                              *                              
       2826 -AGGCAGCAGCAGTTGGAGCTTCAGCGGCAGCAGCAGTTGGAACTTCAG
          1 CA-GCAGCAGCAGTTGGAACTTCAGCGGCAGCAGCAGTTGGAACTTCAG

                 *                              
       2874 CAGCATCAACGGCAGTTGGAACTTCAGCGGCAGCAG
          1 CAGCAGC-A--GCAGTTGGAACTTCAGCGGCAGCAG

       2910 GAGCTTCGTC


Statistics
Matches: 72,  Mismatches: 7, Indels: 10
        0.81            0.08        0.11

Matches are distributed among these distances:
  48   18  0.25
  49    2  0.03
  50    1  0.01
  51   51  0.71

ACGTcount: A:0.27, C:0.25, G:0.33, T:0.16


Consensus pattern (48 bp):   
CAGCAGCAGCAGTTGGAACTTCAGCGGCAGCAGCAGTTGGAACTTCAG
Done.