Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00229.F3

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: 3417
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30


Found at i:2869 original size:72 final size:72

Alignment explanation


    Indices: 2776--2916  Score: 246
    Period size: 72  Copynumber: 2.0  Consensus size: 72

       2766 AGTCCGAGCG

                                                                   *         
       2776 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCTCGG
          1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG

                   
       2841 GCTCGTC
         66 GCTCGTC

                       *    *                         *                      
       2848 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCAGGCAATGACAATTTCTCGG
          1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG

                
       2913 GCTC
         66 GCTC

       2917 ATCGGGGGGC


Statistics
Matches: 65,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  72   65  1.00

ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34


Consensus pattern (72 bp):   
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
GCTCGTC

Found at i:3010 original size:33 final size:32

Alignment explanation


    Indices: 2964--3036  Score: 85
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       2954 GGGTCGTACA

                                              
       2964 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
          1 CACCGCAGCATAGCA-CTGC-CCCGGCCCATATC

                   **                  *    
       2997 CACCGCATTATAGCACTGCCCCGGCCCGTATC
          1 CACCGCAGCATAGCACTGCCCCGGCCCATATC

               *    
       3029 CACTGCAG
          1 CACCGCAG

       3037 TACTCCACTC


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  32   20  0.59
  33   14  0.41

ACGTcount: A:0.21, C:0.45, G:0.18, T:0.16


Consensus pattern (32 bp):   
CACCGCAGCATAGCACTGCCCCGGCCCATATC
Done.