Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01563.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: 4161
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29


Found at i:3043 original size:9 final size:9

Alignment explanation


    Indices: 3023--3097  Score: 53
    Period size: 9  Copynumber: 8.3  Consensus size: 9

       3013 GGCATTGTTT

                   * 
       3023 ATGATGAAG
          1 ATGATGATG

                *    
       3032 ATGAAGATG
          1 ATGATGATG

               **    
       3041 ATGGGGATG
          1 ATGATGATG

               *     
       3050 ATGGTGATG
          1 ATGATGATG

            *        
       3059 GTGATGATG
          1 ATGATGATG

                    * 
       3068 ATGATGGAAG
          1 ATGAT-GATG

                     
       3078 -TGATGATG
          1 ATGATGATG

            *     *  
       3086 GTGATGGTG
          1 ATGATGATG

               
       3095 ATG
          1 ATG

       3098 CATGCAACAC


Statistics
Matches: 52,  Mismatches: 12, Indels: 4
        0.76            0.18        0.06

Matches are distributed among these distances:
   8    3  0.06
   9   46  0.88
  10    3  0.06

ACGTcount: A:0.29, C:0.00, G:0.43, T:0.28


Consensus pattern (9 bp):   
ATGATGATG

Found at i:3049 original size:15 final size:15

Alignment explanation


    Indices: 3031--3097  Score: 62
    Period size: 15  Copynumber: 4.3  Consensus size: 15

       3021 TTATGATGAA

                 *         
       3031 GATGAAGATGATGGG
          1 GATGATGATGATGGG

                   *      *
       3046 GATGATGGTGATGGT
          1 GATGATGATGATGGG

                             
       3061 GATGATGATGATGGAAG
          1 GATGATGATGATGG--G

                    *      *
       3078 TGATGATGGTGATGGT
          1 -GATGATGATGATGGG

                
       3094 GATG
          1 GATG

       3098 CATGCAACAC


Statistics
Matches: 42,  Mismatches: 7, Indels: 6
        0.76            0.13        0.11

Matches are distributed among these distances:
  15   29  0.69
  18   13  0.31

ACGTcount: A:0.27, C:0.00, G:0.45, T:0.28


Consensus pattern (15 bp):   
GATGATGATGATGGG
Done.