Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00405.N1

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, 593

Length: 989
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26


Found at i:854 original size:8 final size:8

Alignment explanation


    Indices: 816--853  Score: 67
    Period size: 8  Copynumber: 4.8  Consensus size: 8

        806 AAAAAGAGAT

                    
        816 AAGAAGGG
          1 AAGAAGGG

                    
        824 AAGAAGGG
          1 AAGAAGGG

                    
        832 AAGAAGGG
          1 AAGAAGGG

                  * 
        840 AAGAAGAG
          1 AAGAAGGG

                  
        848 AAGAAG
          1 AAGAAG

        854 AAGAAAGAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   8   29  1.00

ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00


Consensus pattern (8 bp):   
AAGAAGGG

Found at i:955 original size:14 final size:14

Alignment explanation


    Indices: 906--968  Score: 58
    Period size: 14  Copynumber: 4.4  Consensus size: 14

        896 TGAGAGAAGA

                          
        906 AAAAAGAA--AAAG
          1 AAAAAGAAGGAAAG

                             
        918 AAAAAGAGAAGGAGAAG
          1 -AAAA-AGAAGGA-AAG

              *    *    * 
        935 AAGAAGAGGGAAGG
          1 AAAAAGAAGGAAAG

                          
        949 AAAAAGAAGGAAAG
          1 AAAAAGAAGGAAAG

                  
        963 AAAAAG
          1 AAAAAG

        969 GTGTTATTTG


Statistics
Matches: 40,  Mismatches: 6, Indels: 7
        0.75            0.11        0.13

Matches are distributed among these distances:
  13    4  0.10
  14   23  0.57
  15    6  0.15
  16    4  0.10
  17    3  0.08

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (14 bp):   
AAAAAGAAGGAAAG

Found at i:955 original size:17 final size:17

Alignment explanation


    Indices: 911--968  Score: 50
    Period size: 19  Copynumber: 3.4  Consensus size: 17

        901 GAAGAAAAAA

                      *       
        911 GAAAAAGAAAAAGAGAAG
          1 GAAAAAG-AAGAGAGAAG

                          *    
        929 GAGAAGAAGAAGAGGGAAG
          1 GA-AA-AAGAAGAGAGAAG

                             
        948 GAAAAAGAAG-GA-AA-
          1 GAAAAAGAAGAGAGAAG

                   
        962 GAAAAAG
          1 GAAAAAG

        969 GTGTTATTTG


Statistics
Matches: 35,  Mismatches: 3, Indels: 8
        0.76            0.07        0.17

Matches are distributed among these distances:
  14    7  0.20
  15    2  0.06
  16    1  0.03
  17    6  0.17
  18    4  0.11
  19   12  0.34
  20    3  0.09

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (17 bp):   
GAAAAAGAAGAGAGAAG
Done.