Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g02322.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, 216

Length: 360
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.15


Found at i:257 original size:3 final size:3

Alignment explanation


    Indices: 251--340  Score: 69
    Period size: 3  Copynumber: 29.7  Consensus size: 3

        241 AAAAAAAAAG

                                       *                    *             
        251 AGA AGA AGA A-A AGGA AGA AGG AGA AGA AGGA AGA AGG AGA AGA AGGA
          1 AGA AGA AGA AGA A-GA AGA AGA AGA AGA A-GA AGA AGA AGA AGA A-GA

              *         *                      *               *       
        298 AGG AGA AGA TGA A-A AGAA AGA AG- AGC AGA AGA AGA AGG AGA AG
          1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AG

        341 GAGTCGGCAG


Statistics
Matches: 69,  Mismatches: 11, Indels: 14
        0.73            0.12        0.15

Matches are distributed among these distances:
   2    6  0.09
   3   52  0.75
   4   11  0.16

ACGTcount: A:0.59, C:0.01, G:0.39, T:0.01


Consensus pattern (3 bp):   
AGA

Found at i:269 original size:12 final size:13

Alignment explanation


    Indices: 246--321  Score: 61
    Period size: 13  Copynumber: 6.1  Consensus size: 13

        236 GAAGAAAAAA

                         
        246 AAAAGAGAAGAAG
          1 AAAAGAGAAGAAG

                          
        259 AAAAG-GAAGAAGG
          1 AAAAGAGAAGAA-G

             *      *    
        272 AGAAGA-AGGAAG
          1 AAAAGAGAAGAAG

               *         
        284 -AAGGAGAAGAAG
          1 AAAAGAGAAGAAG

            *  *       * 
        296 GAAGGAGAAGATG
          1 AAAAGAGAAGAAG

                         
        309 AAAAGA-AAGAAG
          1 AAAAGAGAAGAAG

             
        321 A
          1 A

        322 GCAGAAGAAG


Statistics
Matches: 50,  Mismatches: 9, Indels: 9
        0.74            0.13        0.13

Matches are distributed among these distances:
  11    3  0.06
  12   18  0.36
  13   29  0.58

ACGTcount: A:0.62, C:0.00, G:0.37, T:0.01


Consensus pattern (13 bp):   
AAAAGAGAAGAAG

Found at i:280 original size:16 final size:16

Alignment explanation


    Indices: 251--340  Score: 89
    Period size: 16  Copynumber: 5.7  Consensus size: 16

        241 AAAAAAAAAG

                 *          
        251 AGAAGAAGAA-AAGGA
          1 AGAAGGAGAAGAAGGA

                            
        266 AGAAGGAGAAGAAGGA
          1 AGAAGGAGAAGAAGGA

                            
        282 AGAAGGAGAAGAAGGA
          1 AGAAGGAGAAGAAGGA

                  *          * 
        298 AGGAGAAGATGAA-AAGAA
          1 A-GA-AGGA-GAAGAAGGA

                    *       
        316 AGAA-GAGCAGAA-GA
          1 AGAAGGAGAAGAAGGA

                       
        330 AGAAGGAGAAG
          1 AGAAGGAGAAG

        341 GAGTCGGCAG


Statistics
Matches: 63,  Mismatches: 6, Indels: 12
        0.78            0.07        0.15

Matches are distributed among these distances:
  14    7  0.11
  15   18  0.29
  16   23  0.37
  17    4  0.06
  18    8  0.13
  19    3  0.05

ACGTcount: A:0.59, C:0.01, G:0.39, T:0.01


Consensus pattern (16 bp):   
AGAAGGAGAAGAAGGA
Done.