Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02659.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: 2269
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28


Found at i:329 original size:21 final size:21

Alignment explanation


    Indices: 303--342  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        293 GATGGTGATA

                                  
        303 AAAAG-AGTAAAAAGAAGAAAG
          1 AAAAGAAG-AAAAAGAAGAAAG

                      *        
        324 AAAAGAAGAATAAGAAGAA
          1 AAAAGAAGAAAAAGAAGAA

        343 TAAGAAGGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  21   15  0.88
  22    2  0.12

ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05


Consensus pattern (21 bp):   
AAAAGAAGAAAAAGAAGAAAG

Found at i:363 original size:21 final size:21

Alignment explanation


    Indices: 339--387  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        329 AAGAATAAGA

                *                 
        339 AGAATAAGAAGGAG-AAAAAAG
          1 AGAAAAAGAA-GAGCAAAAAAG

                                 
        360 AGAAAAAGAAGAGCAAAAAAG
          1 AGAAAAAGAAGAGCAAAAAAG

             *     
        381 AAAAAAA
          1 AGAAAAA

        388 ATACGATGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20    3  0.12
  21   22  0.88

ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02


Consensus pattern (21 bp):   
AGAAAAAGAAGAGCAAAAAAG

Found at i:387 original size:30 final size:31

Alignment explanation


    Indices: 312--388  Score: 75
    Period size: 30  Copynumber: 2.5  Consensus size: 31

        302 AAAAAGAGTA

                       *          *        *
        312 AAAAGAAGAAAGAAAAGAAGAATAAGAAGAAT
          1 AAAA-AAGAAAAAAAAGAAGAAAAAGAAGAAC

              *  *  *                    * 
        344 AAGAAGGAGAAAAAAG-AGAAAAAGAAGAGC
          1 AAAAAAGAAAAAAAAGAAGAAAAAGAAGAAC

                           
        374 AAAAAAGAAAAAAAA
          1 AAAAAAGAAAAAAAA

        389 TACGATGAAA


Statistics
Matches: 35,  Mismatches: 10, Indels: 2
        0.74            0.21        0.04

Matches are distributed among these distances:
  30   23  0.66
  31    9  0.26
  32    3  0.09

ACGTcount: A:0.74, C:0.01, G:0.22, T:0.03


Consensus pattern (31 bp):   
AAAAAAGAAAAAAAAGAAGAAAAAGAAGAAC
Done.