Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold998

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: 3453
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1936 original size:6 final size:6

Alignment explanation


    Indices: 1927--2047  Score: 66
    Period size: 6  Copynumber: 20.0  Consensus size: 6

       1917 AACAAAAAAG

                                    **     **          *           
       1927 AAGAAA AAGAAA AAG--A AAGTGA AAGTGA AAGAAA ATGAAA AAGAAA
          1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA

                   ** *                 **        **  *            
       1973 AAGAAA TTGCAA AAGAAA AAGAAA TCGAAA AAGTGA GAGAAA AAGAAA
          1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA

             *                *           
       2021 ATGAAGAA AAGAAA ATTGAAA AAGAAA
          1 AAG-A-AA AAGAAA A-AGAAA AAGAAA

       2048 TTGAGATTTA


Statistics
Matches: 86,  Mismatches: 24, Indels: 10
        0.72            0.20        0.08

Matches are distributed among these distances:
   4    4  0.05
   6   71  0.83
   7    7  0.08
   8    4  0.05

ACGTcount: A:0.69, C:0.02, G:0.21, T:0.08


Consensus pattern (6 bp):   
AAGAAA

Found at i:2004 original size:18 final size:17

Alignment explanation


    Indices: 1921--2005  Score: 86
    Period size: 18  Copynumber: 5.0  Consensus size: 17

       1911 AATAAAAACA

                             
       1921 AAAAAG-AA-GAAAAAG
          1 AAAAAGAAATGAAAAAG

                           ** 
       1936 AAAAAGAAAGTGAAAGTG
          1 AAAAAGAAA-TGAAAAAG

               *             
       1954 AAAGA-AAATGAAAAAG
          1 AAAAAGAAATGAAAAAG

                        *     
       1970 AAAAAGAAATTGCAAAAG
          1 AAAAAGAAA-TGAAAAAG

                              
       1988 AAAAAGAAATCGAAAAAG
          1 AAAAAGAAAT-GAAAAAG

       2006 TGAGAGAAAA


Statistics
Matches: 56,  Mismatches: 8, Indels: 9
        0.77            0.11        0.12

Matches are distributed among these distances:
  15    6  0.11
  16   12  0.21
  17    7  0.12
  18   31  0.55

ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07


Consensus pattern (17 bp):   
AAAAAGAAATGAAAAAG

Done.