Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02062.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: 2111
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30


Found at i:264 original size:27 final size:27

Alignment explanation


    Indices: 245--377  Score: 158
    Period size: 27  Copynumber: 4.9  Consensus size: 27

        235 CAACGGCAGT

                         *       *     
        245 CAAGGATGGTAACGTGCCAATTCCAGG
          1 CAAGGATGGTAACATGCCAATGCCAGG

              *                        
        272 CATGGATGGTAACATGCCAATGCCAGG
          1 CAAGGATGGTAACATGCCAATGCCAGG

                        *              
        299 CAAGGATGGTAATATGCCAATGCCAGG
          1 CAAGGATGGTAACATGCCAATGCCAGG

              *  *      **             
        326 CATGGCTGGTAATTTGCCAATGCCAGG
          1 CAAGGATGGTAACATGCCAATGCCAGG

              *  *      **           
        353 CATGGCTGGTAATTTGCCAATGCCA
          1 CAAGGATGGTAACATGCCAATGCCA

        378 ATGCCAGGCA


Statistics
Matches: 98,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   98  1.00

ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22


Consensus pattern (27 bp):   
CAAGGATGGTAACATGCCAATGCCAGG

Found at i:303 original size:54 final size:54

Alignment explanation


    Indices: 245--377  Score: 185
    Period size: 54  Copynumber: 2.5  Consensus size: 54

        235 CAACGGCAGT

                        **       *                                
        245 CAAGGATGGTAACGTGCCAATTCCAGGCATGGATGGTAACATGCCAATGCCAGG
          1 CAAGGATGGTAATATGCCAATGCCAGGCATGGATGGTAACATGCCAATGCCAGG

                                            *      **             
        299 CAAGGATGGTAATATGCCAATGCCAGGCATGGCTGGTAATTTGCCAATGCCAGG
          1 CAAGGATGGTAATATGCCAATGCCAGGCATGGATGGTAACATGCCAATGCCAGG

              *  *       *           
        353 CATGGCTGGTAATTTGCCAATGCCA
          1 CAAGGATGGTAATATGCCAATGCCA

        378 ATGCCAGGCA


Statistics
Matches: 70,  Mismatches: 9, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  54   70  1.00

ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22


Consensus pattern (54 bp):   
CAAGGATGGTAATATGCCAATGCCAGGCATGGATGGTAACATGCCAATGCCAGG

Found at i:322 original size:33 final size:32

Alignment explanation


    Indices: 259--403  Score: 131
    Period size: 27  Copynumber: 5.0  Consensus size: 32

        249 GATGGTAACG

                   *                        
        259 TGCCAATTCCAGGCATGGATGGTAA-----CA
          1 TGCCAATGCCAGGCATGGATGGTAATTTGCCA

                           *                
        286 TGCCAATGCCAGGCAAGGATGGTAA--T---A
          1 TGCCAATGCCAGGCATGGATGGTAATTTGCCA

                              *             
        313 TGCCAATGCCAGGCATGGCTGGTAA-TT----
          1 TGCCAATGCCAGGCATGGATGGTAATTTGCCA

                              *              
        340 TGCCAATGCCAGGCATGGCTGGTAATTTGCCAA
          1 TGCCAATGCCAGGCATGGATGGTAATTTGCC-A

                                     *     
        373 TGCCAATGCCAGGCATGGATGGTAAATTGCC
          1 TGCCAATGCCAGGCATGGATGGTAATTTGCC

        404 TGGCATGAAA


Statistics
Matches: 104,  Mismatches: 6, Indels: 10
        0.87            0.05        0.08

Matches are distributed among these distances:
  27   72  0.69
  28    3  0.03
  33   29  0.28

ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23


Consensus pattern (32 bp):   
TGCCAATGCCAGGCATGGATGGTAATTTGCCA

Found at i:337 original size:81 final size:81

Alignment explanation


    Indices: 223--377  Score: 202
    Period size: 81  Copynumber: 1.9  Consensus size: 81

        213 GTGCCAGTTA

                             *   *                     *                     
        223 ATGGTAATATACCAACGGCAGTCAAGGATGGTAACGTGCCAATTCCAGGCATGGATGGTAACATG
          1 ATGGTAATATACCAACGCCAGGCAAGGATGGTAACGTGCCAATGCCAGGCATGGATGGTAACATG

                            
        288 CCAATGCCAGGCAAGG
         66 CCAATGCCAGGCAAGG

                      *    *        *  *      **                  *      **  
        304 ATGGTAATATGCCAATGCCAGGCATGGCTGGTAATTTGCCAATGCCAGGCATGGCTGGTAATTTG
          1 ATGGTAATATACCAACGCCAGGCAAGGATGGTAACGTGCCAATGCCAGGCATGGATGGTAACATG

                     
        369 CCAATGCCA
         66 CCAATGCCA

        378 ATGCCAGGCA


Statistics
Matches: 62,  Mismatches: 12, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  81   62  1.00

ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22


Consensus pattern (81 bp):   
ATGGTAATATACCAACGCCAGGCAAGGATGGTAACGTGCCAATGCCAGGCATGGATGGTAACATG
CCAATGCCAGGCAAGG

Done.