Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00312.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: 3234
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26


Found at i:948 original size:27 final size:27

Alignment explanation


    Indices: 907--1258  Score: 623
    Period size: 27  Copynumber: 13.0  Consensus size: 27

        897 AAATCAGAAG

                     **                
        907 AGAAATCTAAAGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                       
        934 AGAAATCTACTGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                       
        961 AGAAATCTACTGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                           *           
        988 AGAAATCTACTGCTATTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                       
       1015 AGAAATCTACTGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                           *           
       1042 AGAAATCTACTGCTATTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                       
       1069 AGAAATCTACTGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                     * 
       1096 AGAAATCTACTGCTACTGAGTCGAGAA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                       
       1123 AGAAATCTACTGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                       
       1150 AGAAATCTACTGCTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                 *                *    
       1177 AGAAACCTACTGCTACTGAGTCAAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                                  *    
       1204 AGAAATCTACTGCTACTGAGTCAAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

                        *              
       1231 AGAAATCTACTGGTACTGAGTCGAGCA
          1 AGAAATCTACTGCTACTGAGTCGAGCA

             
       1258 A
          1 A

       1259 TAATTTGACC


Statistics
Matches: 312,  Mismatches: 13, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27  312  1.00

ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22


Consensus pattern (27 bp):   
AGAAATCTACTGCTACTGAGTCGAGCA

Found at i:2656 original size:33 final size:33

Alignment explanation


    Indices: 2596--2658  Score: 99
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       2586 GTACTGCTAG

                                  *          
       2596 ATCACCTGCTAAATTACCCAAAGCCACTCCTAA
          1 ATCACCTGCTAAATTACCCAAACCCACTCCTAA

                              **          
       2629 ATCACCTGCTAAATTACCGGAACCCACTCC
          1 ATCACCTGCTAAATTACCCAAACCCACTCC

       2659 CACACCTGGT


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   27  1.00

ACGTcount: A:0.33, C:0.38, G:0.08, T:0.21


Consensus pattern (33 bp):   
ATCACCTGCTAAATTACCCAAACCCACTCCTAA
Done.