Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00341.N3

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: 2184
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35


Found at i:829 original size:3 final size:3

Alignment explanation


    Indices: 821--877  Score: 105
    Period size: 3  Copynumber: 19.0  Consensus size: 3

        811 TTGTTAGGAG

                                                                         * 
        821 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                       
        869 TTA TTA TTA
          1 TTA TTA TTA

        878 ATATAATTAG


Statistics
Matches: 52,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   52  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TTA

Found at i:882 original size:15 final size:15

Alignment explanation


    Indices: 823--886  Score: 101
    Period size: 15  Copynumber: 4.3  Consensus size: 15

        813 GTTAGGAGTT

                          *
        823 ATTATTATTATTATT
          1 ATTATTATTATTATA

                          *
        838 ATTATTATTATTATT
          1 ATTATTATTATTATA

                           
        853 ATTATTATTATTATA
          1 ATTATTATTATTATA

                      *    
        868 ATTATTATTAATATA
          1 ATTATTATTATTATA

                
        883 ATTA
          1 ATTA

        887 GTAATAAATA


Statistics
Matches: 47,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   47  1.00

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (15 bp):   
ATTATTATTATTATA

Found at i:886 original size:12 final size:12

Alignment explanation


    Indices: 821--892  Score: 83
    Period size: 12  Copynumber: 6.0  Consensus size: 12

        811 TTGTTAGGAG

                     *  
        821 TTATTATTATTA
          1 TTATTATTAATA

                     *  
        833 TTATTATTATTA
          1 TTATTATTAATA

                     *  
        845 TTATTATTATTA
          1 TTATTATTAATA

                         
        857 TTATTATT-ATAA
          1 TTATTATTAAT-A

                        
        869 TTATTATTAATA
          1 TTATTATTAATA

             *    *     
        881 TAATTAGTAATA
          1 TTATTATTAATA

        893 AATAATTTCA


Statistics
Matches: 55,  Mismatches: 3, Indels: 4
        0.89            0.05        0.06

Matches are distributed among these distances:
  11    1  0.02
  12   52  0.95
  13    2  0.04

ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60


Consensus pattern (12 bp):   
TTATTATTAATA
Done.