Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01017.F10

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: 3024
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31


Found at i:196 original size:8 final size:8

Alignment explanation


    Indices: 183--208  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

        173 TATATTTGAA

                    
        183 GAAGAAAG
          1 GAAGAAAG

                    
        191 GAAGAAAG
          1 GAAGAAAG

                    
        199 GAAGAAAG
          1 GAAGAAAG

              
        207 GA
          1 GA

        209 GGCAGGAATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (8 bp):   
GAAGAAAG

Found at i:1826 original size:32 final size:30

Alignment explanation


    Indices: 1767--1840  Score: 87
    Period size: 32  Copynumber: 2.4  Consensus size: 30

       1757 GGTCTAATTA

                             *            
       1767 AAAATTTT-AAAATTTTTGTGAGATTAATG
          1 AAAATTTTCAAAATTTTAGTGAGATTAATG

             *                       *     *
       1796 AGAATTTTCAAATATTTTAAGTGAGCTTAATT
          1 AAAATTTTCAAA-ATTTT-AGTGAGATTAATG

                         
       1828 AAAATTTTCAAAA
          1 AAAATTTTCAAAA

       1841 AAATTAGAAA


Statistics
Matches: 37,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  29    7  0.19
  30    3  0.08
  31    6  0.16
  32   21  0.57

ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42


Consensus pattern (30 bp):   
AAAATTTTCAAAATTTTAGTGAGATTAATG

Found at i:2728 original size:22 final size:22

Alignment explanation


    Indices: 2700--2759  Score: 120
    Period size: 22  Copynumber: 2.7  Consensus size: 22

       2690 ATTGCCAAAA

                                  
       2700 GGGAGGGAAAAGGGGGTTTCCC
          1 GGGAGGGAAAAGGGGGTTTCCC

                                  
       2722 GGGAGGGAAAAGGGGGTTTCCC
          1 GGGAGGGAAAAGGGGGTTTCCC

                            
       2744 GGGAGGGAAAAGGGGG
          1 GGGAGGGAAAAGGGGG

       2760 CTTCTCATTG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   38  1.00

ACGTcount: A:0.25, C:0.10, G:0.55, T:0.10


Consensus pattern (22 bp):   
GGGAGGGAAAAGGGGGTTTCCC
Done.