Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00040.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, 1000

Length: 1684
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29


Found at i:435 original size:6 final size:6

Alignment explanation


    Indices: 421--471  Score: 66
    Period size: 6  Copynumber: 8.5  Consensus size: 6

        411 GAAAGATGAC

                *                                      * *       * 
        421 GGTGGT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GATCAT GGTGGT
          1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT

               
        469 GGT
          1 GGT

        472 CATGATGATA


Statistics
Matches: 39,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   6   39  1.00

ACGTcount: A:0.14, C:0.02, G:0.51, T:0.33


Consensus pattern (6 bp):   
GGTGAT

Found at i:474 original size:12 final size:12

Alignment explanation


    Indices: 426--480  Score: 65
    Period size: 12  Copynumber: 4.6  Consensus size: 12

        416 ATGACGGTGG

                      * 
        426 TGGTGATGGTGA
          1 TGGTGATGGTCA

                      * 
        438 TGGTGATGGTGA
          1 TGGTGATGGTCA

                    *   
        450 TGGTGATGATCA
          1 TGGTGATGGTCA

                 *      
        462 TGGTGGTGGTCA
          1 TGGTGATGGTCA

              *    
        474 TGATGAT
          1 TGGTGAT

        481 AATAATGATG


Statistics
Matches: 37,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  12   37  1.00

ACGTcount: A:0.18, C:0.04, G:0.44, T:0.35


Consensus pattern (12 bp):   
TGGTGATGGTCA

Found at i:476 original size:18 final size:18

Alignment explanation


    Indices: 426--477  Score: 59
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        416 ATGACGGTGG

                      *   * * 
        426 TGGTGATGGTGATGGTGA
          1 TGGTGATGGTCATGATCA

                      *       
        444 TGGTGATGGTGATGATCA
          1 TGGTGATGGTCATGATCA

                 *          
        462 TGGTGGTGGTCATGAT
          1 TGGTGATGGTCATGAT

        478 GATAATAATG


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   30  1.00

ACGTcount: A:0.17, C:0.04, G:0.44, T:0.35


Consensus pattern (18 bp):   
TGGTGATGGTCATGATCA
Done.