Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02561.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, 499

Length: 833
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.25


Found at i:467 original size:27 final size:24

Alignment explanation


    Indices: 436--489  Score: 72
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        426 TATTCGGGAA

                                       
        436 TGGTGGAGGATATGACGGCGGAGGCGG
          1 TGGTGGAGGATAT---GGCGGAGGCGG

                  *                 
        463 TGGTGGCGGATATGGCGGAGGCGG
          1 TGGTGGAGGATATGGCGGAGGCGG

               
        487 TGG
          1 TGG

        490 AGGATATGGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  24   14  0.54
  27   12  0.46

ACGTcount: A:0.15, C:0.11, G:0.57, T:0.17


Consensus pattern (24 bp):   
TGGTGGAGGATATGGCGGAGGCGG

Found at i:503 original size:24 final size:24

Alignment explanation


    Indices: 437--504  Score: 70
    Period size: 24  Copynumber: 2.8  Consensus size: 24

        427 ATTCGGGAAT

                                      
        437 GGTGGAGGATATGACGGCGGAGGCGG
          1 GGTGGAGGATATGA-GGCGGAGGC-G

                  *                  
        463 TGGTGGCGGATAT--GGCGGAGGC-
          1 -GGTGGAGGATATGAGGCGGAGGCG

                                
        485 GGTGGAGGATATGGAGGCGG
          1 GGTGGAGGATAT-GAGGCGG

        505 TGGCCGATAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 9
        0.77            0.04        0.19

Matches are distributed among these distances:
  21   11  0.31
  24   14  0.39
  27   11  0.31

ACGTcount: A:0.18, C:0.10, G:0.57, T:0.15


Consensus pattern (24 bp):   
GGTGGAGGATATGAGGCGGAGGCG

Found at i:507 original size:39 final size:39

Alignment explanation


    Indices: 464--582  Score: 184
    Period size: 39  Copynumber: 3.0  Consensus size: 39

        454 CGGAGGCGGT

                                                   
        464 GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC
          1 GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC

                  *                                
        503 GGTGGCCGATATGGCGGAGGCGGTGGAGGATATGGAGGC
          1 GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC

                                *        *           
        542 GGTGGCGGATATGGCGGCGGTGGCGGTGGTGGATATGGAGG
          1 GGTGGCGGATAT---GGCGGAGGCGGTGGAGGATATGGAGG

        583 TTGACGCTGA


Statistics
Matches: 73,  Mismatches: 4, Indels: 3
        0.91            0.05        0.04

Matches are distributed among these distances:
  39   49  0.67
  42   24  0.33

ACGTcount: A:0.16, C:0.11, G:0.56, T:0.17


Consensus pattern (39 bp):   
GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC

Found at i:548 original size:24 final size:23

Alignment explanation


    Indices: 515--582  Score: 65
    Period size: 24  Copynumber: 3.1  Consensus size: 23

        505 TGGCCGATAT

                 *                  
        515 GGCGGAGGCGGTGGAGGATATGGA
          1 GGCGGTGGCGGTGG-GGATATGGA

                                  *
        539 GGCGGTGGC-----GGATATGGC
          1 GGCGGTGGCGGTGGGGATATGGA

                                    
        557 GGCGGTGGCGGTGGTGGATATGGA
          1 GGCGGTGGCGGTGG-GGATATGGA

              
        581 GG
          1 GG

        583 TTGACGCTGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 12
        0.70            0.06        0.24

Matches are distributed among these distances:
  18   17  0.49
  24   18  0.51

ACGTcount: A:0.15, C:0.10, G:0.59, T:0.16


Consensus pattern (23 bp):   
GGCGGTGGCGGTGGGGATATGGA

Found at i:565 original size:18 final size:18

Alignment explanation


    Indices: 458--567  Score: 112
    Period size: 18  Copynumber: 5.8  Consensus size: 18

        448 TGACGGCGGA

                 *            
        458 GGCGGTGGTGGCGGATAT
          1 GGCGGCGGTGGCGGATAT

                          *      
        476 GGCGGAGGCGGTGGAGGATAT
          1 GGC---GGCGGTGGCGGATAT

              *         *     
        497 GGAGGCGGTGGCCGATAT
          1 GGCGGCGGTGGCGGATAT

                          *      
        515 GGCGGAGGCGGTGGAGGATAT
          1 GGC---GGCGGTGGCGGATAT

              *               
        536 GGAGGCGGTGGCGGATAT
          1 GGCGGCGGTGGCGGATAT

                          
        554 GGCGGCGGTGGCGG
          1 GGCGGCGGTGGCGG

        568 TGGTGGATAT


Statistics
Matches: 75,  Mismatches: 11, Indels: 12
        0.77            0.11        0.12

Matches are distributed among these distances:
  18   45  0.60
  21   30  0.40

ACGTcount: A:0.15, C:0.13, G:0.57, T:0.15


Consensus pattern (18 bp):   
GGCGGCGGTGGCGGATAT
Done.