Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07043

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, 914

Length: 1524
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21


Found at i:169 original size:12 final size:12

Alignment explanation


    Indices: 152--229  Score: 84
    Period size: 12  Copynumber: 6.5  Consensus size: 12

        142 CAGAAACTAC

                        
        152 AGGAAGTGGAAG
          1 AGGAAGTGGAAG

                   *    
        164 AGGAAGTAGAAG
          1 AGGAAGTGGAAG

                *  *    
        176 AGGAGGTTGAAG
          1 AGGAAGTGGAAG

             *    *     
        188 AAGAAGAGGAAG
          1 AGGAAGTGGAAG

            *    *      
        200 TGGAACTGGAAG
          1 AGGAAGTGGAAG

                  *     
        212 AGGAAGAGGAAG
          1 AGGAAGTGGAAG

                  
        224 AGGAAG
          1 AGGAAG

        230 AGGAGGAAGA


Statistics
Matches: 52,  Mismatches: 14, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  12   52  1.00

ACGTcount: A:0.45, C:0.01, G:0.46, T:0.08


Consensus pattern (12 bp):   
AGGAAGTGGAAG

Found at i:242 original size:6 final size:6

Alignment explanation


    Indices: 152--233  Score: 76
    Period size: 6  Copynumber: 13.7  Consensus size: 6

        142 CAGAAACTAC

                   *                         *  **      *           
        152 AGGAAG TGGAAG AGGAAG TA-GAAG AGGAGG TTGAAG AAGAAG AGGAAG
          1 AGGAAG AGGAAG AGGAAG -AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG

            *    * *                               
        200 TGGAAC TGGAAG AGGAAG AGGAAG AGGAAG AGGA
          1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGA

        234 GGAAGAGGAG


Statistics
Matches: 61,  Mismatches: 13, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
   5    1  0.02
   6   59  0.97
   7    1  0.02

ACGTcount: A:0.45, C:0.01, G:0.46, T:0.07


Consensus pattern (6 bp):   
AGGAAG

Found at i:1237 original size:27 final size:27

Alignment explanation


    Indices: 1207--1261  Score: 83
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1197 AGTGGGAGTG

                             *         
       1207 GGGTTCAACCCTGGAGTTGCTGCTGCT
          1 GGGTTCAACCCTGGAGTGGCTGCTGCT

                 *        *            
       1234 GGGTTTAACCCTGGGGTGGCTGCTGCT
          1 GGGTTCAACCCTGGAGTGGCTGCTGCT

             
       1261 G
          1 G

       1262 CACCAGCTTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.09, C:0.24, G:0.38, T:0.29


Consensus pattern (27 bp):   
GGGTTCAACCCTGGAGTGGCTGCTGCT
Done.