Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00257.R1

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: 3294
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24


Found at i:2727 original size:15 final size:14

Alignment explanation


    Indices: 2703--2732  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       2693 ATAAACGGAA

                          
       2703 AGAGAAGGAGAAGG
          1 AGAGAAGGAGAAGG

                           
       2717 AGAGAAAGGAGAAGG
          1 AGAG-AAGGAGAAGG

             
       2732 A
          1 A

       2733 AAGAGAACGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.27
  15   11  0.73

ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00


Consensus pattern (14 bp):   
AGAGAAGGAGAAGG

Found at i:2760 original size:33 final size:31

Alignment explanation


    Indices: 2699--2781  Score: 79
    Period size: 33  Copynumber: 2.8  Consensus size: 31

       2689 AAAGATAAAC

                                 *         
       2699 GGAAAGAGAAGGAGAAGGAGAGAAAGGAGAA
          1 GGAAAGAGAAGGAGAAGGAGAAAAAGGAGAA

                             *                
       2730 GGAAAGAGAACGGGAGAGGGA-AAAAGAGGAGAA
          1 GGAAAGAGAA--GGAGAAGGAGAAAA-AGGAGAA

                                    
       2763 -G-AA-A-AAGGAGAAGGA-AAAA
          1 GGAAAGAGAAGGAGAAGGAGAAAA

       2782 GACAGGAAAC


Statistics
Matches: 46,  Mismatches: 3, Indels: 10
        0.78            0.05        0.17

Matches are distributed among these distances:
  27   12  0.26
  29    2  0.04
  30    1  0.02
  31   12  0.26
  32    4  0.09
  33   15  0.33

ACGTcount: A:0.57, C:0.01, G:0.42, T:0.00


Consensus pattern (31 bp):   
GGAAAGAGAAGGAGAAGGAGAAAAAGGAGAA

Found at i:2768 original size:14 final size:15

Alignment explanation


    Indices: 2708--2783  Score: 61
    Period size: 15  Copynumber: 5.1  Consensus size: 15

       2698 CGGAAAGAGA

                        *   
       2708 AGGAGAAGGAGAGAA-
          1 AGGAGAAGGA-AAAAG

                        *  
       2723 AGGAGAAGGAAAGAG
          1 AGGAGAAGGAAAAAG

                     *        
       2738 AACGGGAGAGGGAAAAAG
          1 -A--GGAGAAGGAAAAAG

                           
       2756 AGGAGAA-G-AAAA-
          1 AGGAGAAGGAAAAAG

                           
       2768 AGGAGAAGGAAAAAG
          1 AGGAGAAGGAAAAAG

             
       2783 A
          1 A

       2784 CAGGAAACAC


Statistics
Matches: 49,  Mismatches: 5, Indels: 14
        0.72            0.07        0.21

Matches are distributed among these distances:
  12    7  0.14
  13    5  0.10
  14    7  0.14
  15   16  0.33
  16    1  0.02
  17    1  0.02
  18   12  0.24

ACGTcount: A:0.57, C:0.01, G:0.42, T:0.00


Consensus pattern (15 bp):   
AGGAGAAGGAAAAAG
Done.