Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2492

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, 556

Length: 928
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27


Found at i:734 original size:5 final size:6

Alignment explanation


    Indices: 724--846  Score: 50
    Period size: 6  Copynumber: 20.0  Consensus size: 6

        714 AAAAGACATT

                              **  *                **         ** * 
        724 GAAAAA GAAAAA GAAATT GCAAAA GAAAAA GAAATC GAAAAA GTGAGA
          1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA

                        *                *      *     **   *  *       
        772 GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAT GAAATT GAGAAT GAAAAA
          1 GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA GAAAAA GAAAAA

                **                      
        823 -AAATT GAAAAA GAAAAA GAGAAAA
          1 GAAAAA GAAAAA GAAAAA GA-AAAA

        847 AAGAAATTGA


Statistics
Matches: 84,  Mismatches: 28, Indels: 9
        0.69            0.23        0.07

Matches are distributed among these distances:
   5    3  0.04
   6   66  0.79
   7   11  0.13
   8    4  0.05

ACGTcount: A:0.68, C:0.02, G:0.20, T:0.11


Consensus pattern (6 bp):   
GAAAAA

Found at i:734 original size:18 final size:18

Alignment explanation


    Indices: 708--841  Score: 89
    Period size: 18  Copynumber: 7.7  Consensus size: 18

        698 TTGGAGAAAT

                *       *     
        708 AAAATAAAAAGACATTGA
          1 AAAAGAAAAAGAAATTGA

                             *
        726 AAAAGAAAAAGAAATTGC
          1 AAAAGAAAAAGAAATTGA

                           *  
        744 AAAAGAAAAAGAAATCGA
          1 AAAAGAAAAAGAAATTGA

                 ** *     **  
        762 AAAAGTGAGAGAAAAAGA
          1 AAAAGAAAAAGAAATTGA

               *           *  
        780 AAATG---AAGAAA-AGA
          1 AAAAGAAAAAGAAATTGA

                *     *        
        794 AAATTGAAAATGAAATTGA
          1 AAA-AGAAAAAGAAATTGA

            *  *              
        813 GAATGAAAAA-AAATTGA
          1 AAAAGAAAAAGAAATTGA

                        
        830 AAAAGAAAAAGA
          1 AAAAGAAAAAGA

        842 GAAAAAAGAA


Statistics
Matches: 92,  Mismatches: 18, Indels: 12
        0.75            0.15        0.10

Matches are distributed among these distances:
  14    6  0.07
  15    7  0.08
  17   15  0.16
  18   60  0.65
  19    4  0.04

ACGTcount: A:0.68, C:0.02, G:0.18, T:0.12


Consensus pattern (18 bp):   
AAAAGAAAAAGAAATTGA

Found at i:828 original size:17 final size:17

Alignment explanation


    Indices: 806--839  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        796 ATTGAAAATG

                   *  *      
        806 AAATTGAGAATGAAAAA
          1 AAATTGAAAAAGAAAAA

                             
        823 AAATTGAAAAAGAAAAA
          1 AAATTGAAAAAGAAAAA

        840 GAGAAAAAAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15


Consensus pattern (17 bp):   
AAATTGAAAAAGAAAAA
Done.