Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11234

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: 2169
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25


Found at i:666 original size:27 final size:27

Alignment explanation


    Indices: 552--666  Score: 133
    Period size: 27  Copynumber: 4.3  Consensus size: 27

        542 AGACTGATGA

                      *                 
        552 TCCAAAGCC-CAGGTTGGAGAATGAGGG
          1 TCCAAAGCCTGAGG-TGGAGAATGAGGG

                         *             
        579 TCCAAAGCCTGAGTTGGAGAATGAGGG
          1 TCCAAAGCCTGAGGTGGAGAATGAGGG

             *       *          *      
        606 TTCAAAGCCCGAGGTGGAGAGTGAGGG
          1 TCCAAAGCCTGAGGTGGAGAATGAGGG

              *           *         * *
        633 TCTAAAGCCTGAGGGGGAGAATGATGA
          1 TCCAAAGCCTGAGGTGGAGAATGAGGG

                   
        660 TCCAAAG
          1 TCCAAAG

        667 GGCCAGCTGC


Statistics
Matches: 73,  Mismatches: 14, Indels: 2
        0.82            0.16        0.02

Matches are distributed among these distances:
  27   71  0.97
  28    2  0.03

ACGTcount: A:0.30, C:0.16, G:0.37, T:0.17


Consensus pattern (27 bp):   
TCCAAAGCCTGAGGTGGAGAATGAGGG

Found at i:666 original size:54 final size:54

Alignment explanation


    Indices: 546--666  Score: 163
    Period size: 54  Copynumber: 2.2  Consensus size: 54

        536 AGTTCAAGAC

                                                          **      
        546 TGATGATCCAAAGCCCAGGTTGGAGAATGAGGGTCCAAAGCCTGAGTTGGAGAA
          1 TGATGATCCAAAGCCCAGGTTGGAGAATGAGGGTCCAAAGCCTGAGGGGGAGAA

               * * *                   *        *                  
        600 TGAGGGTTCAAAGCCCGAGG-TGGAGAGTGAGGGTCTAAAGCCTGAGGGGGAGAA
          1 TGATGATCCAAAGCCC-AGGTTGGAGAATGAGGGTCCAAAGCCTGAGGGGGAGAA

                         
        654 TGATGATCCAAAG
          1 TGATGATCCAAAG

        667 GGCCAGCTGC


Statistics
Matches: 56,  Mismatches: 10, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  54   53  0.95
  55    3  0.05

ACGTcount: A:0.31, C:0.15, G:0.37, T:0.17


Consensus pattern (54 bp):   
TGATGATCCAAAGCCCAGGTTGGAGAATGAGGGTCCAAAGCCTGAGGGGGAGAA
Done.