Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01870.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: 5423
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33


Found at i:3673 original size:55 final size:54

Alignment explanation


    Indices: 3573--3819  Score: 231
    Period size: 55  Copynumber: 4.6  Consensus size: 54

       3563 TTAATGGTAC

                         *     *    *                *           *  
       3573 CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTT-TCTAAGGCAAGGAAAT
          1 CATGTAAGACCATGTCAAGACATGGC-ATTGGTAA-GTTCTATAAGGCAAGGATAT

                                          *                       * 
       3628 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGG-TCT
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT-CTATAAGGC-AAGGATAT

                       *  *    *            *                    *
       3683 CATGTAAGACCGTGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATAC
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT

                                       *            *            *
       3736 CATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT-T-CAA---AAGGATAC
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT

              *           *    *       *       
       3785 CACGTAAGACCATGACAAGTCATGGCAATGGTAAG
          1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAG

       3820 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:3771 original size:108 final size:110

Alignment explanation


    Indices: 3573--3772  Score: 291
    Period size: 108  Copynumber: 1.8  Consensus size: 110

       3563 TTAATGGTAC

                                                                  *          
       3573 CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
          1 CATGTAAGACCATCTCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC

                             *                           
       3638 CATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCT
         66 CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCT

                       *             *        *                   *          
       3683 CATGTAAGACCGTGC-CAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
          1 CATGTAAGACCAT-CTCAAGGCATGACAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG

                                  *      
       3744 ACCATGTCAAGACATGGCAATGGTAAGTT
         64 ACCATGTCAAGACATGGCAATGATAAGTT

       3773 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.