Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11429

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:0.20, C:0.48, G:0.16, T:0.16


Found at i:121 original size:24 final size:24

Alignment explanation


    Indices: 43--122  Score: 74
    Period size: 24  Copynumber: 3.3  Consensus size: 24

         33 AGACCCTTTT

                 *                  
         43 GCACCCCCACCGCCAGGGCATCCG
          1 GCACCACCACCGCCAGGGCATCCG

                    *        *  *    *
         67 GCACCACCTCCGCCA-GAC-CCCTTT
          1 GCACCACCACCGCCAGGGCATCC--G

              *                     
         91 GCTCCACCACCGCCAGGGCATCCG
          1 GCACCACCACCGCCAGGGCATCCG

                    
        115 GCACCACC
          1 GCACCACC

        123 TCCACCAGAC


Statistics
Matches: 41,  Mismatches: 11, Indels: 8
        0.68            0.18        0.13

Matches are distributed among these distances:
  22    2  0.05
  23    2  0.05
  24   33  0.80
  25    2  0.05
  26    2  0.05

ACGTcount: A:0.17, C:0.54, G:0.20, T:0.09


Consensus pattern (24 bp):   
GCACCACCACCGCCAGGGCATCCG

Found at i:142 original size:24 final size:24

Alignment explanation


    Indices: 67--147  Score: 76
    Period size: 24  Copynumber: 3.4  Consensus size: 24

         57 AGGGCATCCG

                                    
         67 GCACCACCTCCGCCAGACCCCTTT
          1 GCACCACCTCCGCCAGACCCCTTT

              *     *        *  *    *
         91 GCTCCACCACCGCCAGGGCATCC--G
          1 GCACCACCTCCGCCA-GAC-CCCTTT

                       *            
        115 GCACCACCTCCACCAGACCCCTTT
          1 GCACCACCTCCGCCAGACCCCTTT

                     
        139 GCACCACCT
          1 GCACCACCT

        148 ATGTTTGGGC


Statistics
Matches: 42,  Mismatches: 11, Indels: 8
        0.69            0.18        0.13

Matches are distributed among these distances:
  22    2  0.05
  23    2  0.05
  24   34  0.81
  25    2  0.05
  26    2  0.05

ACGTcount: A:0.19, C:0.53, G:0.15, T:0.14


Consensus pattern (24 bp):   
GCACCACCTCCGCCAGACCCCTTT

Found at i:158 original size:48 final size:48

Alignment explanation


    Indices: 22--146  Score: 214
    Period size: 48  Copynumber: 2.6  Consensus size: 48

         12 CGGGCATCCT

                             *        *                     
         22 CCACCTCCACCAGACCCTTTTGCACCCCCACCGCCAGGGCATCCGGCA
          1 CCACCTCCACCAGACCCCTTTGCACCACCACCGCCAGGGCATCCGGCA

                    *              *                        
         70 CCACCTCCGCCAGACCCCTTTGCTCCACCACCGCCAGGGCATCCGGCA
          1 CCACCTCCACCAGACCCCTTTGCACCACCACCGCCAGGGCATCCGGCA

                                         
        118 CCACCTCCACCAGACCCCTTTGCACCACC
          1 CCACCTCCACCAGACCCCTTTGCACCACC

        147 TATGTTTGGG


Statistics
Matches: 71,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  48   71  1.00

ACGTcount: A:0.18, C:0.54, G:0.15, T:0.13


Consensus pattern (48 bp):   
CCACCTCCACCAGACCCCTTTGCACCACCACCGCCAGGGCATCCGGCA
Done.