Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g01120.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, 1000

Length: 3868
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29


Found at i:49 original size:23 final size:23

Alignment explanation


    Indices: 6--49  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

          1 ACGAT

                *           *      
          6 CCTTTTCTTCTTAACATTCTCTA
          1 CCTTATCTTCTTAACACTCTCTA

                                  
         29 CCTTATCTTCTTCAAC-CTCTC
          1 CCTTATCTTCTT-AACACTCTC

         50 CCTTCTTTCT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  23   15  0.83
  24    3  0.17

ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48


Consensus pattern (23 bp):   
CCTTATCTTCTTAACACTCTCTA

Found at i:3182 original size:12 final size:12

Alignment explanation


    Indices: 3167--3216  Score: 64
    Period size: 12  Copynumber: 4.2  Consensus size: 12

       3157 CAAAGTTGTT

                    *   
       3167 GATGAAGAGGAA
          1 GATGAAGACGAA

                *   *   
       3179 GATGGAGAGGAA
          1 GATGAAGACGAA

              *         
       3191 GACGAAGACGAA
          1 GATGAAGACGAA

                        
       3203 GATGAAGACGAA
          1 GATGAAGACGAA

              
       3215 GA
          1 GA

       3217 GGATGATGAT


Statistics
Matches: 33,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  12   33  1.00

ACGTcount: A:0.48, C:0.06, G:0.40, T:0.06


Consensus pattern (12 bp):   
GATGAAGACGAA

Found at i:3224 original size:18 final size:18

Alignment explanation


    Indices: 3166--3225  Score: 68
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       3156 ACAAAGTTGT

                     *         
       3166 TGATGAAGAGGAAGATGGA
          1 TGATGAAGACGAAGA-GGA

               *           *  
       3185 -GAGGAAGACGAAGACGA
          1 TGATGAAGACGAAGAGGA

            *                 
       3202 AGATGAAGACGAAGAGGA
          1 TGATGAAGACGAAGAGGA

                  
       3220 TGATGA
          1 TGATGA

       3226 TGATGATGTT


Statistics
Matches: 34,  Mismatches: 6, Indels: 3
        0.79            0.14        0.07

Matches are distributed among these distances:
  17    2  0.06
  18   32  0.94

ACGTcount: A:0.45, C:0.05, G:0.40, T:0.10


Consensus pattern (18 bp):   
TGATGAAGACGAAGAGGA
Done.