Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01870.F5

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: 2613
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31


Found at i:1814 original size:55 final size:54

Alignment explanation


    Indices: 1714--1960  Score: 231
    Period size: 55  Copynumber: 4.6  Consensus size: 54

       1704 TTAATGGTAC

                         *     *    *                *           *  
       1714 CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTT-TCTAAGGCAAGGAAAT
          1 CATGTAAGACCATGTCAAGACATGGC-ATTGGTAA-GTTCTATAAGGCAAGGATAT

                                          *                       * 
       1769 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGG-TCT
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT-CTATAAGGC-AAGGATAT

                       *  *    *            *                    *
       1824 CATGTAAGACCGTGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATAC
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT

                                       *            *            *
       1877 CATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT-T-CAA---AAGGATAC
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT

              *           *    *       *       
       1926 CACGTAAGACCATGACAAGTCATGGCAATGGTAAG
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAG

       1961 GTACCCGCAT


Statistics
Matches: 164,  Mismatches: 23, Indels: 16
        0.81            0.11        0.08

Matches are distributed among these distances:
  49   40  0.24
  52    6  0.04
  53   43  0.26
  54    8  0.05
  55   63  0.38
  56    4  0.02

ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22


Consensus pattern (54 bp):   
CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT

Found at i:1912 original size:108 final size:110

Alignment explanation


    Indices: 1714--1913  Score: 291
    Period size: 108  Copynumber: 1.8  Consensus size: 110

       1704 TTAATGGTAC

                                                                  *          
       1714 CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
          1 CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC

                             *                           
       1779 CATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCT
         66 CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCT

                       *             *        *                   *          
       1824 CATGTAAGACCGTGC-CAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
          1 CATGTAAGACCAT-CTCAAGGCATGACAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG

                                  *      
       1885 ACCATGTCAAGACATGGCAATGGTAAGTT
         64 ACCATGTCAAGACATGGCAATGATAAGTT

       1914 TCAAAAGGAT


Statistics
Matches: 81,  Mismatches: 7, Indels: 6
        0.86            0.07        0.06

Matches are distributed among these distances:
 107    3  0.04
 108   48  0.59
 109    7  0.09
 110   22  0.27
 111    1  0.01

ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23


Consensus pattern (110 bp):   
CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCT
Done.