Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00941.P1

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: 6147
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34


Found at i:3768 original size:6 final size:6

Alignment explanation


    Indices: 3757--3807  Score: 52
    Period size: 6  Copynumber: 8.8  Consensus size: 6

       3747 CAGGCCCAGA

                                               *    *      *      *
       3757 AAAAAG AAAAAG AAAAAG --AAAG AAAAAG GAAAAC AAAAAC AAAAAC
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG

                 
       3803 AAAAA
          1 AAAAA

       3808 AAAGGGTACA


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
   4    4  0.10
   6   36  0.90

ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Found at i:3780 original size:16 final size:15

Alignment explanation


    Indices: 3756--3811  Score: 58
    Period size: 16  Copynumber: 3.5  Consensus size: 15

       3746 GCAGGCCCAG

                           
       3756 AAAAAAGAAAAAGAA
          1 AAAAAAGAAAAAGAA

                              
       3771 AAAGAAAGAAAAAGGAAA
          1 AAA-AAAGAAAAA-G-AA

                   *     *  
       3789 ACAAAAACAAAAACAA
          1 A-AAAAAGAAAAAGAA

                   
       3805 AAAAAAG
          1 AAAAAAG

       3812 GGTACAAGAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  15    8  0.24
  16   12  0.35
  17    1  0.03
  18   11  0.32
  19    2  0.06

ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00


Consensus pattern (15 bp):   
AAAAAAGAAAAAGAA

Found at i:3794 original size:28 final size:27

Alignment explanation


    Indices: 3758--3812  Score: 74
    Period size: 28  Copynumber: 2.0  Consensus size: 27

       3748 AGGCCCAGAA

                *     *     *           
       3758 AAAAGAAAAAGAAAAAGAAAGAAAAAGG
          1 AAAACAAAAACAAAAACAAA-AAAAAGG

                                       
       3786 AAAACAAAAACAAAAACAAAAAAAAGG
          1 AAAACAAAAACAAAAACAAAAAAAAGG

       3813 GTACAAGAGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  27    7  0.29
  28   17  0.71

ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00


Consensus pattern (27 bp):   
AAAACAAAAACAAAAACAAAAAAAAGG
Done.