Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03730

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: 1746
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25


Found at i:514 original size:228 final size:225

Alignment explanation


    Indices: 77--520  Score: 699
    Period size: 225  Copynumber: 2.0  Consensus size: 225

         67 CTCCTCTATC

                                 *  *                **                      
         77 AGGATGAAGCTAATGAAGAATGTCGTATAAATGGAAATGATGCCGGAGTATCAGAGGATGCCGGT
          1 AGGATGAAGCTAATGAAGAATATCATATAAATGGAAATGATAACGGAGTATCAGAGGATGCCGGT

                                    *                   *                    
        142 TTTAATCAAGATAAAGTTAATAATGATGATGATGTTGGTGGTAAGGACGATGAATTTGATGATGA
         66 TTTAATCAAGATAAAGTTAATAATAATGATGATGTTGGTGGTAAAGACGATGAATTTGATGATGA

             *                  *  *                                         
        207 AGATGAGGAGGAGGCTGATGGTGGTGGCAGTGGCGGAGGCATTTCTGGTCATTATGATAATGATG
        131 ACATGAGGAGGAGGCTGATGATGATGGCAGTGGCGGAGGCATTTCTGGTCATTATGATAATGATG

                                          
        272 TGATTCCTGATGATGTTGATAAGGTGGATG
        196 TGATTCCTGATGATGTTGATAAGGTGGATG

                            *            *    *                          *   
        302 AGGATGAAGCTAATGATGAATATCATATAGATGGCAATGATAACGGAGTATCAGAGGATGCTGGT
          1 AGGATGAAGCTAATGAAGAATATCATATAAATGGAAATGATAACGGAGTATCAGAGGATGCCGGT

                          *                      *         *     *           
        367 TTTAATCAAGATAATGTTAATAATAATGATGATGTTGTTGGTAAAGATGATGACTTTGATGATGA
         66 TTTAATCAAGATAAAGTTAATAATAATGATGATGTTGGTGGTAAAGACGATGAATTTGATGATGA

                             *                                               
        432 ACATGAAGATGAGGAGGGTGATGATGATGGCAGTGGCGGAGGCATTTCTGGTCATTATGATAATG
        131 ACATG-AG--GAGGAGGCTGATGATGATGGCAGTGGCGGAGGCATTTCTGGTCATTATGATAATG

                                    
        497 ATGTGATTCCTGATGATGTTGATA
        193 ATGTGATTCCTGATGATGTTGATA

        521 TGGAGGATAA


Statistics
Matches: 198,  Mismatches: 18, Indels: 3
        0.90            0.08        0.01

Matches are distributed among these distances:
 225  120  0.61
 226    2  0.01
 228   76  0.38

ACGTcount: A:0.32, C:0.07, G:0.31, T:0.30


Consensus pattern (225 bp):   
AGGATGAAGCTAATGAAGAATATCATATAAATGGAAATGATAACGGAGTATCAGAGGATGCCGGT
TTTAATCAAGATAAAGTTAATAATAATGATGATGTTGGTGGTAAAGACGATGAATTTGATGATGA
ACATGAGGAGGAGGCTGATGATGATGGCAGTGGCGGAGGCATTTCTGGTCATTATGATAATGATG
TGATTCCTGATGATGTTGATAAGGTGGATG
Done.