Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00505.F1

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, 656

Length: 1094
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27


Found at i:749 original size:6 final size:6

Alignment explanation


    Indices: 700--741  Score: 75
    Period size: 6  Copynumber: 7.0  Consensus size: 6

        690 GATGCGAAAC

                                      *                     
        700 CAGAAG CAGAAG CAGAAG CAGAAA CAGAAG CAGAAG CAGAAG
          1 CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG

        742 AAACAGAAGA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.52, C:0.17, G:0.31, T:0.00


Consensus pattern (6 bp):   
CAGAAG

Found at i:752 original size:12 final size:12

Alignment explanation


    Indices: 695--741  Score: 67
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        685 AAGATGATGC

                         
        695 GAAACCAGAAGCA
          1 GAAA-CAGAAGCA

               *        
        708 GAAGCAGAAGCA
          1 GAAACAGAAGCA

                        
        720 GAAACAGAAGCA
          1 GAAACAGAAGCA

               *      
        732 GAAGCAGAAG
          1 GAAACAGAAG

        742 AAACAGAAGA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  12   28  0.90
  13    3  0.10

ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00


Consensus pattern (12 bp):   
GAAACAGAAGCA

Found at i:762 original size:21 final size:21

Alignment explanation


    Indices: 719--764  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        709 AAGCAGAAGC

                       * *       
        719 AGAAACAGAAGCAGAAGCAGA
          1 AGAAACAGAAGAAAAAGCAGA

                            * *  
        740 AGAAACAGAAGAAAAATCTGA
          1 AGAAACAGAAGAAAAAGCAGA

                
        761 AGAA
          1 AGAA

        765 GCTGGTGCAG


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.61, C:0.11, G:0.24, T:0.04


Consensus pattern (21 bp):   
AGAAACAGAAGAAAAAGCAGA
Done.