Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00732.P2

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: 21262
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:12274 original size:19 final size:19

Alignment explanation


    Indices: 12228--12275  Score: 62
    Period size: 19  Copynumber: 2.6  Consensus size: 19

      12218 GTATATATTT

                               
      12228 TAAA-TTTATTTAGATAGA
          1 TAAATTTTATTTAGATAGA

                 *      *      
      12246 TAAATCTTATTTGGATAGA
          1 TAAATTTTATTTAGATAGA

               *       
      12265 TAAGTTTTATT
          1 TAAATTTTATT

      12276 CATATTCTAG


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  18    4  0.16
  19   21  0.84

ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48


Consensus pattern (19 bp):   
TAAATTTTATTTAGATAGA

Found at i:12337 original size:43 final size:43

Alignment explanation


    Indices: 12289--12381  Score: 152
    Period size: 43  Copynumber: 2.2  Consensus size: 43

      12279 ATTCTAGAAA

                                                        
      12289 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
          1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC

                          *             *              
      12332 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
          1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC

                   
      12375 TATTTTC
          1 TATTTTC

      12382 CCAATTAGGA


Statistics
Matches: 47,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  43   46  0.98
  44    1  0.02

ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52


Consensus pattern (43 bp):   
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC

Found at i:17004 original size:19 final size:19

Alignment explanation


    Indices: 16958--17005  Score: 55
    Period size: 19  Copynumber: 2.6  Consensus size: 19

      16948 GTATATATTT

                               
      16958 TAAA-TTTATTTAGGTAGA
          1 TAAATTTTATTTAGGTAGA

                 *              
      16976 TAAATCTTATTT-GGATAGA
          1 TAAATTTTATTTAGG-TAGA

               *       
      16995 TAAGTTTTATT
          1 TAAATTTTATT

      17006 CATATTCTAG


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  18    6  0.24
  19   19  0.76

ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48


Consensus pattern (19 bp):   
TAAATTTTATTTAGGTAGA

Found at i:17067 original size:43 final size:43

Alignment explanation


    Indices: 17019--17111  Score: 152
    Period size: 43  Copynumber: 2.2  Consensus size: 43

      17009 ATTCTAGAAA

                                                        
      17019 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
          1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC

                          *             *              
      17062 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
          1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC

                   
      17105 TATTTTC
          1 TATTTTC

      17112 CCAATTAAGA


Statistics
Matches: 47,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  43   46  0.98
  44    1  0.02

ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52


Consensus pattern (43 bp):   
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Done.