Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00406.N1

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, 324

Length: 540
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24


Found at i:176 original size:72 final size:72

Alignment explanation


    Indices: 83--223  Score: 228
    Period size: 72  Copynumber: 2.0  Consensus size: 72

         73 AGTCCGAGCG

                                                                   *         
         83 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCCCGG
          1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG

                   
        148 GCTCGTC
         66 GCTCGTC

                       *    *                         *  *               *   
        155 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCGGGCAATGACAATTTCTCGG
          1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG

                
        220 GCTC
         66 GCTC

        224 ATCGGGGGGC


Statistics
Matches: 63,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  72   63  1.00

ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33


Consensus pattern (72 bp):   
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
GCTCGTC

Found at i:317 original size:33 final size:33

Alignment explanation


    Indices: 271--344  Score: 87
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        261 GGGTCGTACA

                                *             
        271 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
          1 CACCGCAGCATAGCA-CTGCCCCCGGCCCATATC

                   **                   *    
        304 CACCGCATTATAGCACTGCCCCCGGCCCGTATC
          1 CACCGCAGCATAGCACTGCCCCCGGCCCATATC

               *    
        337 CACTGCAG
          1 CACCGCAG

        345 TACTCCACTC


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    2  0.06
  33   32  0.94

ACGTcount: A:0.20, C:0.46, G:0.18, T:0.16


Consensus pattern (33 bp):   
CACCGCAGCATAGCACTGCCCCCGGCCCATATC
Done.