Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_548 ID=scaffold_548-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: 7539
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.27

Warning! 1706 characters in sequence are not A, C, G, or T


Found at i:2596 original size:14 final size:15

Alignment explanation


    Indices: 2563--2600  Score: 60
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       2553 GAGAGAAGAA

                           
       2563 AAAAAGAAATGAGAG
          1 AAAAAGAAATGAGAG

                           
       2578 AAAAAGAAATGAGA-
          1 AAAAAGAAATGAGAG

            *        
       2592 TAAAAGAAA
          1 AAAAAGAAA

       2601 AAGAAAATGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14    8  0.36
  15   14  0.64

ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08


Consensus pattern (15 bp):   
AAAAAGAAATGAGAG
Done.