Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14463

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, 200

Length: 267
ACGTcount: A:0.45, C:0.11, G:0.28, T:0.16


Found at i:226 original size:24 final size:24

Alignment explanation


    Indices: 190--264  Score: 89
    Period size: 24  Copynumber: 3.1  Consensus size: 24

        180 GGGACCTGCT

                 *  *                
        190 AAAGAAGAGAAGAAAGATGACAAA-
          1 AAAGACGAAAAGAAAGATGA-AAAG

                    *       *       
        214 AAAGACGATAAGAAAGGTGAAAAG
          1 AAAGACGAAAAGAAAGATGAAAAG

                          *         
        238 AAAGACGAAAAGAAGGATGAAAAG
          1 AAAGACGAAAAGAAAGATGAAAAG

               
        262 AAA
          1 AAA

        265 TGA


Statistics
Matches: 44,  Mismatches: 6, Indels: 2
        0.85            0.12        0.04

Matches are distributed among these distances:
  23    3  0.07
  24   41  0.93

ACGTcount: A:0.64, C:0.04, G:0.27, T:0.05


Consensus pattern (24 bp):   
AAAGACGAAAAGAAAGATGAAAAG

Found at i:229 original size:12 final size:12

Alignment explanation


    Indices: 199--264  Score: 62
    Period size: 12  Copynumber: 5.5  Consensus size: 12

        189 TAAAGAAGAG

                    *    
        199 AAGAAAGATGACA
          1 AAGAAAGACGA-A

                       *
        212 AA-AAAGACGAT
          1 AAGAAAGACGAA

                   **   
        223 AAGAAAGGTGAA
          1 AAGAAAGACGAA

                        
        235 AAGAAAGACGAA
          1 AAGAAAGACGAA

                 *  *   
        247 AAGAAGGATGAA
          1 AAGAAAGACGAA

                  
        259 AAGAAA
          1 AAGAAA

        265 TGA


Statistics
Matches: 42,  Mismatches: 10, Indels: 3
        0.76            0.18        0.05

Matches are distributed among these distances:
  11    2  0.05
  12   38  0.90
  13    2  0.05

ACGTcount: A:0.64, C:0.05, G:0.26, T:0.06


Consensus pattern (12 bp):   
AAGAAAGACGAA
Done.