Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_659 ID=scaffold_659-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: 5564
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.28

Warning! 698 characters in sequence are not A, C, G, or T


Found at i:1366 original size:30 final size:29

Alignment explanation


    Indices: 1332--1401  Score: 70
    Period size: 30  Copynumber: 2.3  Consensus size: 29

       1322 GAAGCTAAAT

                            *              
       1332 TGAGCTCAAATAG-GTGGAATTGAGCTCAAG
          1 TGAGCT-AAATAGAGTCGAATTGAGCT-AAG

                    * *                  
       1362 TGAGCTAATTGGAGTCGAATTGAGCTAAG
          1 TGAGCTAAATAGAGTCGAATTGAGCTAAG

            *          
       1391 GGAGCTGAAAT
          1 TGAGCT-AAAT

       1402 TGAGCTGCAG


Statistics
Matches: 33,  Mismatches: 5, Indels: 4
        0.79            0.12        0.10

Matches are distributed among these distances:
  29   12  0.36
  30   21  0.64

ACGTcount: A:0.33, C:0.11, G:0.31, T:0.24


Consensus pattern (29 bp):   
TGAGCTAAATAGAGTCGAATTGAGCTAAG
Done.