Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.009G117400.2-JGI_221_v2.1

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: 4317
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29


Found at i:147 original size:84 final size:84

Alignment explanation


    Indices: 1--436  Score: 529
    Period size: 84  Copynumber: 5.2  Consensus size: 84

                   *                         *                               
          1 TGGAGATTGCTAAAGCACAGGAGAAGAGGAAGACTGCAGAAGAATTGAAGAAGAAGGCTGTTGAA
          1 TGGAGATGGCTAAAGCACAGGAGAAGAGGAAGATTGCAGAAGAATTGAAGAAGAAGGCTGTTGAA

                               
         66 GAAAGAAAATGTGCTGATT
         66 GAAAGAAAATGTGCTGATT

                   *                         *                       *       
         85 TGGAGATTGCTAAAGCACAGGAGAAGAGGAAGACTGCAGAAGAATTGAAGAAGAAGGTTGTTGAA
          1 TGGAGATGGCTAAAGCACAGGAGAAGAGGAAGATTGCAGAAGAATTGAAGAAGAAGGCTGTTGAA

                     **     *  
        150 GAAAGAAAACATGCTGCTT
         66 GAAAGAAAATGTGCTGATT

                                   *                   * *           *       
        169 TGGAGATGGCTAAAGCACAGGAGCAGAGGAAGATTGCAGAAGAGTCGAAGAAGAAGGTTGTTGAA
          1 TGGAGATGGCTAAAGCACAGGAGAAGAGGAAGATTGCAGAAGAATTGAAGAAGAAGGCTGTTGAA

                              *  
        234 GAAAGAAAACATGTG--GCTT
         66 GAAAG-AAA-ATGTGCTGATT

                                   *   *                               *     
        253 TGGAGATGGCTAAAGCACAGGAGCAGAAGAAGATTGCAGAAGAGATT-AAGAAGAAGGCAGTTGA
          1 TGGAGATGGCTAAAGCACAGGAGAAGAGGAAGATTGCAGAAGA-ATTGAAGAAGAAGGCTGTTGA

                      **        
        317 AGAAAGAAAACATGCTGATT
         65 AGAAAGAAAATGTGCTGATT

             **        *    **   *                       ***                 
        337 TACAGATGGCTGAAGCGGAGGCGCAA-AGGAAGATTGCAGAAGAAACCAAGAAGAAGGCTGTTGA
          1 TGGAGATGGCTAAAGCACAGGAG-AAGAGGAAGATTGCAGAAGAATTGAAGAAGAAGGCTGTTGA

              *            *    
        401 AGCAAGAAAATGTGCCGATT
         65 AGAAAGAAAATGTGCTGATT

             *     *        
        421 TTGAGATCGCTAAAGC
          1 TGGAGATGGCTAAAGC

        437 GGAAGCAACT


Statistics
Matches: 307,  Mismatches: 38, Indels: 14
        0.86            0.11        0.04

Matches are distributed among these distances:
  82    3  0.01
  83    4  0.01
  84  292  0.95
  85    5  0.02
  86    3  0.01

ACGTcount: A:0.41, C:0.11, G:0.32, T:0.17


Consensus pattern (84 bp):   
TGGAGATGGCTAAAGCACAGGAGAAGAGGAAGATTGCAGAAGAATTGAAGAAGAAGGCTGTTGAA
GAAAGAAAATGTGCTGATT

Done.