Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01108.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: 7521
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32


Found at i:298 original size:12 final size:12

Alignment explanation


    Indices: 283--307  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        273 ACTATGGACT

                        
        283 TGATTATGATGA
          1 TGATTATGATGA

                        
        295 TGATTATGATGA
          1 TGATTATGATGA

             
        307 T
          1 T

        308 AACTACGACG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44


Consensus pattern (12 bp):   
TGATTATGATGA

Found at i:5506 original size:17 final size:17

Alignment explanation


    Indices: 5463--5507  Score: 56
    Period size: 17  Copynumber: 2.7  Consensus size: 17

       5453 GTTAAAAAAT

                            *
       5463 TGATTATTTTTATTTTT
          1 TGATTATTTTTATTTTA

             * *             
       5480 TTAATATTTTTATTTTA
          1 TGATTATTTTTATTTTA

                        
       5497 TGATT-TTTTTA
          1 TGATTATTTTTA

       5508 ATAATTTATT


Statistics
Matches: 23,  Mismatches: 5, Indels: 1
        0.79            0.17        0.03

Matches are distributed among these distances:
  16    6  0.26
  17   17  0.74

ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73


Consensus pattern (17 bp):   
TGATTATTTTTATTTTA

Found at i:5508 original size:25 final size:22

Alignment explanation


    Indices: 5466--5518  Score: 70
    Period size: 25  Copynumber: 2.3  Consensus size: 22

       5456 AAAAAATTGA

                                 * 
       5466 TTATTTTTATTTTTTTAATATTT
          1 TTATTTTTATTTTTTTAATA-AT

                                    
       5489 TTATTTTATGATTTTTTTAATAAT
          1 TTATTTT-T-ATTTTTTTAATAAT

                  
       5513 TTATTT
          1 TTATTT

       5519 GATTAAATGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  23    7  0.26
  24    8  0.30
  25   12  0.44

ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74


Consensus pattern (22 bp):   
TTATTTTTATTTTTTTAATAAT
Done.