Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15018

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, 207

Length: 345
ACGTcount: A:0.15, C:0.29, G:0.39, T:0.18


Found at i:25 original size:9 final size:9

Alignment explanation


    Indices: 7--75  Score: 61
    Period size: 9  Copynumber: 7.7  Consensus size: 9

          1 ATGGGA

                 *   
          7 CCAGGTGGG
          1 CCAGGAGGG

                     
         16 CCAGGAGGG
          1 CCAGGAGGG

                *     
         25 CCACCG-GGG
          1 CCA-GGAGGG

                    *
         34 CCAGGAGGA
          1 CCAGGAGGG

               **     
         43 CCTCCG-GGG
          1 CC-AGGAGGG

                     
         52 CCAGGAGGG
          1 CCAGGAGGG

                     
         61 CCAGGAGGG
          1 CCAGGAGGG

                  
         70 CCAGGA
          1 CCAGGA

         76 TGGGGCGGTC


Statistics
Matches: 47,  Mismatches: 9, Indels: 8
        0.73            0.14        0.12

Matches are distributed among these distances:
   8    2  0.04
   9   43  0.91
  10    2  0.04

ACGTcount: A:0.19, C:0.29, G:0.49, T:0.03


Consensus pattern (9 bp):   
CCAGGAGGG

Found at i:36 original size:18 final size:18

Alignment explanation


    Indices: 13--63  Score: 84
    Period size: 18  Copynumber: 2.8  Consensus size: 18

          3 GGGACCAGGT

                              
         13 GGGCCAGGAGGGCCACCG
          1 GGGCCAGGAGGGCCACCG

                       *  *   
         31 GGGCCAGGAGGACCTCCG
          1 GGGCCAGGAGGGCCACCG

                           
         49 GGGCCAGGAGGGCCA
          1 GGGCCAGGAGGGCCA

         64 GGAGGGCCAG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   29  1.00

ACGTcount: A:0.18, C:0.31, G:0.49, T:0.02


Consensus pattern (18 bp):   
GGGCCAGGAGGGCCACCG

Found at i:70 original size:18 final size:17

Alignment explanation


    Indices: 13--75  Score: 72
    Period size: 18  Copynumber: 3.5  Consensus size: 17

          3 GGGACCAGGT

                              
         13 GGGCCAGGAGGGCCACCG
          1 GGGCCAGGAGGGCCA-CG

                       *   *  
         31 GGGCCAGGAGGACCTCCG
          1 GGGCCAGGAGGGCC-ACG

                           * 
         49 GGGCCAGGAGGGCCAGG
          1 GGGCCAGGAGGGCCACG

                      
         66 AGGGCCAGGA
          1 -GGGCCAGGA

         76 TGGGGCGGTC


Statistics
Matches: 38,  Mismatches: 5, Indels: 4
        0.81            0.11        0.09

Matches are distributed among these distances:
  17    1  0.03
  18   37  0.97

ACGTcount: A:0.19, C:0.29, G:0.51, T:0.02


Consensus pattern (17 bp):   
GGGCCAGGAGGGCCACG

Found at i:219 original size:39 final size:39

Alignment explanation


    Indices: 73--206  Score: 198
    Period size: 39  Copynumber: 3.4  Consensus size: 39

         63 AGGAGGGCCA

                                                   *
         73 GGATGGGGCGGTCCTCCACCCGGACCAGGAGGG-CCACCA
          1 GGATGGGGCGGTCCTCCACCCGGACCAGG-GGGACCACCG

                                         *         
        112 GGATGGGGCGGTCCTCCACCCGGACCAGGAGGACCACCG
          1 GGATGGGGCGGTCCTCCACCCGGACCAGGGGGACCACCG

                    *        *                     
        151 GGATGGGGGGGTCCTCCTCCCGGACCAGGGGGACCACCG
          1 GGATGGGGCGGTCCTCCACCCGGACCAGGGGGACCACCG

              *        *     
        190 GGGTGGGGCGGCCCTCC
          1 GGATGGGGCGGTCCTCC

        207 GGTCGGACCA


Statistics
Matches: 86,  Mismatches: 8, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  38    2  0.02
  39   84  0.98

ACGTcount: A:0.14, C:0.35, G:0.42, T:0.09


Consensus pattern (39 bp):   
GGATGGGGCGGTCCTCCACCCGGACCAGGGGGACCACCG
Done.