Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09558

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: 2592
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25


Found at i:2026 original size:12 final size:12

Alignment explanation


    Indices: 2011--2060  Score: 64
    Period size: 12  Copynumber: 4.2  Consensus size: 12

       2001 CAAAGTTGTT

                    *   
       2011 GATGAAGAGGAA
          1 GATGAAGACGAA

                *   *   
       2023 GATGGAGAGGAA
          1 GATGAAGACGAA

              *         
       2035 GACGAAGACGAA
          1 GATGAAGACGAA

                        
       2047 GATGAAGACGAA
          1 GATGAAGACGAA

              
       2059 GA
          1 GA

       2061 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:2068 original size:18 final size:18

Alignment explanation


    Indices: 2010--2069  Score: 68
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       2000 ACAAAGTTGT

                     *         
       2010 TGATGAAGAGGAAGATGGA
          1 TGATGAAGACGAAGA-GGA

               *           *  
       2029 -GAGGAAGACGAAGACGA
          1 TGATGAAGACGAAGAGGA

            *                 
       2046 AGATGAAGACGAAGAGGA
          1 TGATGAAGACGAAGAGGA

                  
       2064 TGATGA
          1 TGATGA

       2070 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.