Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_520 ID=scaffold_520-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: 6121
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:3384 original size:18 final size:18

Alignment explanation


    Indices: 3363--3406  Score: 54
    Period size: 17  Copynumber: 2.5  Consensus size: 18

       3353 AATTCAACAT

                              
       3363 ATTTATAAAATTTTCAAA
          1 ATTTATAAAATTTTCAAA

                    *     *   
       3381 ATTTAT-ATATTTTTAAA
          1 ATTTATAAAATTTTCAAA

             *       
       3398 AATTATAAA
          1 ATTTATAAA

       3407 TATTCTAAAA


Statistics
Matches: 21,  Mismatches: 4, Indels: 2
        0.78            0.15        0.07

Matches are distributed among these distances:
  17   14  0.67
  18    7  0.33

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (18 bp):   
ATTTATAAAATTTTCAAA

Found at i:3398 original size:17 final size:17

Alignment explanation


    Indices: 3372--3419  Score: 51
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       3362 TATTTATAAA

                      *      
       3372 ATTTTCAAAATTTATAT
          1 ATTTTCAAAAATTATAT

                 *          *
       3389 ATTTTTAAAAATTATAA
          1 ATTTTCAAAAATTATAT

              *           
       3406 ATATTCTAAAAATT
          1 ATTTTC-AAAAATT

       3420 CTAAAAAATA


Statistics
Matches: 25,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  17   18  0.72
  18    7  0.28

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (17 bp):   
ATTTTCAAAAATTATAT
Done.