Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00053.N1

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: 3369
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30


Found at i:1653 original size:39 final size:39

Alignment explanation


    Indices: 1599--1691  Score: 168
    Period size: 39  Copynumber: 2.4  Consensus size: 39

       1589 TGCATGGTAT

                  *                                
       1599 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGC
          1 TGGAAATATATCCGGACTTGAAGTCCGCAGGCTTTATGC

                                                  *
       1638 TGGAAATATATCCGGACTTGAAGTCCGCAGGCTTTATGG
          1 TGGAAATATATCCGGACTTGAAGTCCGCAGGCTTTATGC

                           
       1677 TGGAAATATATCCGG
          1 TGGAAATATATCCGG

       1692 GTAAGTCCCG


Statistics
Matches: 52,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  39   52  1.00

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Consensus pattern (39 bp):   
TGGAAATATATCCGGACTTGAAGTCCGCAGGCTTTATGC

Found at i:1749 original size:39 final size:39

Alignment explanation


    Indices: 1683--1926  Score: 375
    Period size: 39  Copynumber: 6.3  Consensus size: 39

       1673 ATGGTGGAAA

                                         *       * 
       1683 TATATCCGGG-TAAGTCCCGAAGGCATTCATGCTGGTGT
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

                              *    *               
       1721 TATATCCGGGCTAAGTCCTGAAGACATTCGTGCTGGTAT
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

                              **       *           
       1760 TATATCCGGGCTAAGTCCTAAAGGCATACGTGCTGGTAT
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

                                                 **
       1799 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGC
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

                                                 * 
       1838 TATAT-CGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

              *                                    
       1876 TACATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

                        
       1915 TATATCCGGGCT
          1 TATATCCGGGCT

       1927 TAAAGTCCTG


Statistics
Matches: 188,  Mismatches: 16, Indels: 3
        0.91            0.08        0.01

Matches are distributed among these distances:
  38   46  0.24
  39  142  0.76

ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28


Consensus pattern (39 bp):   
TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT

Found at i:1849 original size:116 final size:117

Alignment explanation


    Indices: 1683--1926  Score: 393
    Period size: 116  Copynumber: 2.1  Consensus size: 117

       1673 ATGGTGGAAA

                                                  *                  *       
       1683 TATATCCGGG-TAAGTCCCGAAGGCATTCATGCTGGTGTTATATCCGGGCTAAGTCCTGAAGACA
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCATGCTGGTGCTATATCCGGGCTAAGTCCCGAAGACA

                           *               *                    
       1747 TTCGTGCTGGTATTATATCCGGGCTAAGTCCTAAAGGCATACGTGCTGGTAT
         66 TTCGTGCTGGTATTACATCCGGGCTAAGTCCCAAAGGCATACGTGCTGGTAT

                                         *                                *  
       1799 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGCTATAT-CGGGCTAAGTCCCGAAGGCA
          1 TATATCCGGGCTAAGTCCCGAAGGCATTCATGCTGGTGCTATATCCGGGCTAAGTCCCGAAGACA

                       *                    *       *           
       1863 TTCGTGCTGGTGTTACATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTAT
         66 TTCGTGCTGGTATTACATCCGGGCTAAGTCCCAAAGGCATACGTGCTGGTAT

                        
       1915 TATATCCGGGCT
          1 TATATCCGGGCT

       1927 TAAAGTCCTG


Statistics
Matches: 118,  Mismatches: 9, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
 116   87  0.74
 117   31  0.26

ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28


Consensus pattern (117 bp):   
TATATCCGGGCTAAGTCCCGAAGGCATTCATGCTGGTGCTATATCCGGGCTAAGTCCCGAAGACA
TTCGTGCTGGTATTACATCCGGGCTAAGTCCCAAAGGCATACGTGCTGGTAT
Done.