Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_554 ID=scaffold_554-JGI_221_v2.0

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: 5923
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.31

Warning! 148 characters in sequence are not A, C, G, or T


Found at i:4826 original size:25 final size:25

Alignment explanation


    Indices: 4721--4839  Score: 84
    Period size: 25  Copynumber: 4.8  Consensus size: 25

       4711 AGCTGTATAA

                      *  *       *   
       4721 CGGGAAGCTCTTGCGAGCCAATTAT
          1 CGGGAAGCTCATGAGAGCCAAATAT

                  *                    
       4746 CGGGAATCTCAT-ACGAGCCATAA-A-
          1 CGGGAAGCTCATGA-GAGCCA-AATAT

                       *    *    *    
       4770 CGGGAAGCTCAAGAGAACC-ATTACT
          1 CGGGAAGCTCATGAGAGCCAAATA-T

              *      *               
       4795 CGAGAAGCTTATGAGAGCCAAATAT
          1 CGGGAAGCTCATGAGAGCCAAATAT

                   *  *         
       4820 CGGGAAGATCGTGAGAGCCA
          1 CGGGAAGCTCATGAGAGCCA

       4840 TATAACATGA


Statistics
Matches: 70,  Mismatches: 17, Indels: 14
        0.69            0.17        0.14

Matches are distributed among these distances:
  22    1  0.01
  23    1  0.01
  24   14  0.20
  25   50  0.71
  26    4  0.06

ACGTcount: A:0.34, C:0.22, G:0.27, T:0.18


Consensus pattern (25 bp):   
CGGGAAGCTCATGAGAGCCAAATAT
Done.