Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00919.M1

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: 10406
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30


Found at i:5299 original size:21 final size:21

Alignment explanation


    Indices: 5273--5313  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5263 GAATAGGGCA

                    *     *      
       5273 GATGATGATATGGCTGATGAG
          1 GATGATGACATGGCAGATGAG

                                
       5294 GATGATGACATGGCAGATGA
          1 GATGATGACATGGCAGATGA

       5314 TGGGGAGGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.32, C:0.07, G:0.37, T:0.24


Consensus pattern (21 bp):   
GATGATGACATGGCAGATGAG

Found at i:5324 original size:12 final size:12

Alignment explanation


    Indices: 5309--5355  Score: 58
    Period size: 12  Copynumber: 3.9  Consensus size: 12

       5299 TGACATGGCA

                   *    
       5309 GATGATGGGGAG
          1 GATGATGAGGAG

                       *
       5321 GATGATGAGGAT
          1 GATGATGAGGAG

                      * 
       5333 GATGATGAGGGG
          1 GATGATGAGGAG

              *        
       5345 GAGGATGAGGA
          1 GATGATGAGGA

       5356 TGAGGATATA


Statistics
Matches: 29,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   29  1.00

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


Consensus pattern (12 bp):   
GATGATGAGGAG

Found at i:5336 original size:24 final size:24

Alignment explanation


    Indices: 5309--5358  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       5299 TGACATGGCA

                           *         
       5309 GATGATG-GGGAGGATGATGAGGAT
          1 GATGATGAGGG-GGAGGATGAGGAT

                                    
       5333 GATGATGAGGGGGAGGATGAGGAT
          1 GATGATGAGGGGGAGGATGAGGAT

              
       5357 GA
          1 GA

       5359 GGATATAGCT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  24   21  0.88
  25    3  0.12

ACGTcount: A:0.30, C:0.00, G:0.52, T:0.18


Consensus pattern (24 bp):   
GATGATGAGGGGGAGGATGAGGAT

Found at i:5354 original size:6 final size:6

Alignment explanation


    Indices: 5324--5362  Score: 51
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       5314 TGGGGAGGAT

                        *         **                     
       5324 GATGAG GATGAT GATGAG GGGGAG GATGAG GATGAG GAT
          1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GAT

       5363 ATAGCTGAAG


Statistics
Matches: 27,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.31, C:0.00, G:0.51, T:0.18


Consensus pattern (6 bp):   
GATGAG

Done.