Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10267

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: 1923
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29


Found at i:1817 original size:3 final size:3

Alignment explanation


    Indices: 1809--1862  Score: 63
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1799 AACAATTGGG

                        *       *       *       *       *                  
       1809 TGA TGA TGA AGA TGA AGA TGA AGA TGA AGA TGA AGA TGA TGA TGA TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA

                   
       1857 TGA TGA
          1 TGA TGA

       1863 GTTCTGTTCT


Statistics
Matches: 41,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24


Consensus pattern (3 bp):   
TGA

Found at i:1860 original size:12 final size:12

Alignment explanation


    Indices: 1809--1862  Score: 81
    Period size: 12  Copynumber: 4.5  Consensus size: 12

       1799 AACAATTGGG

                        
       1809 TGATGATGAAGA
          1 TGATGATGAAGA

               *        
       1821 TGAAGATGAAGA
          1 TGATGATGAAGA

               *        
       1833 TGAAGATGAAGA
          1 TGATGATGAAGA

                     *  
       1845 TGATGATGATGA
          1 TGATGATGAAGA

                  
       1857 TGATGA
          1 TGATGA

       1863 GTTCTGTTCT


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  12   39  1.00

ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24


Consensus pattern (12 bp):   
TGATGATGAAGA

Found at i:1862 original size:6 final size:6

Alignment explanation


    Indices: 1813--1859  Score: 76
    Period size: 6  Copynumber: 7.8  Consensus size: 6

       1803 ATTGGGTGAT

                                                    *      *      
       1813 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAT GATGAT GATGA
          1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGA

       1860 TGAGTTCTGT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   6   40  1.00

ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21


Consensus pattern (6 bp):   
GATGAA
Done.