Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00357.F2

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, 495

Length: 825
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29


Found at i:382 original size:24 final size:24

Alignment explanation


    Indices: 355--413  Score: 63
    Period size: 21  Copynumber: 2.6  Consensus size: 24

        345 ATGACAATGA

                                     
        355 TGATGAGGAAGATGAAGCA-GCAGG
          1 TGATGAGGAAGATGAAG-ATGCAGG

                   *                
        379 TGAT---CAAGATGAAGATGCAGG
          1 TGATGAGGAAGATGAAGATGCAGG

               *          
        400 TGAGGAGGAAGATG
          1 TGATGAGGAAGATG

        414 GATCAGGTGA


Statistics
Matches: 28,  Mismatches: 3, Indels: 8
        0.72            0.08        0.21

Matches are distributed among these distances:
  20    1  0.04
  21   17  0.61
  24   10  0.36

ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15


Consensus pattern (24 bp):   
TGATGAGGAAGATGAAGATGCAGG

Found at i:387 original size:21 final size:21

Alignment explanation


    Indices: 363--402  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        353 GATGATGAGG

                                  
        363 AAGATGAAGCA-GCAGGTGATC
          1 AAGATGAAG-ATGCAGGTGATC

                               
        384 AAGATGAAGATGCAGGTGA
          1 AAGATGAAGATGCAGGTGA

        403 GGAGGAAGAT


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

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15


Consensus pattern (21 bp):   
AAGATGAAGATGCAGGTGATC

Found at i:569 original size:9 final size:9

Alignment explanation


    Indices: 557--597  Score: 64
    Period size: 9  Copynumber: 4.6  Consensus size: 9

        547 GGAAGGTGAA

                     
        557 GAAGAAGAG
          1 GAAGAAGAG

                     
        566 GAAGAAGAG
          1 GAAGAAGAG

                    *
        575 GAAGAAGAT
          1 GAAGAAGAG

              *      
        584 GAGGAAGAG
          1 GAAGAAGAG

                 
        593 GAAGA
          1 GAAGA

        598 GCTTCAGCCA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   9   28  1.00

ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02


Consensus pattern (9 bp):   
GAAGAAGAG

Found at i:569 original size:12 final size:12

Alignment explanation


    Indices: 554--598  Score: 54
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        544 CGAGGAAGGT

                    *  *
        554 GAAGAAGAAGAG
          1 GAAGAAGAGGAA

                        
        566 GAAGAAGAGGAA
          1 GAAGAAGAGGAA

                 *      
        578 GAAGATGAGGAA
          1 GAAGAAGAGGAA

              *      
        590 GAGGAAGAG
          1 GAAGAAGAG

        599 CTTCAGCCAC


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  12   28  1.00

ACGTcount: A:0.53, C:0.00, G:0.44, T:0.02


Consensus pattern (12 bp):   
GAAGAAGAGGAA

Done.