Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_01745

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, 705

Length: 1176
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22


Found at i:115 original size:24 final size:23

Alignment explanation


    Indices: 91--194  Score: 118
    Period size: 24  Copynumber: 4.3  Consensus size: 23

         81 GGGCAACAAT

                 *       *         
         91 GGGAATGGCAACAACAATGGTAA
          1 GGGAAGGGCAACAGCAATGGTAA

            *     *                 
        114 TGGATATGGCAACAGCAATGGTAA
          1 GGGA-AGGGCAACAGCAATGGTAA

               *                    
        138 GAGCAAGGGCAACAGCAATGGTAA
          1 G-GGAAGGGCAACAGCAATGGTAA

                      *             
        162 GGGCAAGGGCGACAGCAATGGTAA
          1 GGG-AAGGGCAACAGCAATGGTAA

                     
        186 GGGCAAGGG
          1 GGG-AAGGG

        195 GGACAGCGAC


Statistics
Matches: 71,  Mismatches: 7, Indels: 5
        0.86            0.08        0.06

Matches are distributed among these distances:
  23    4  0.06
  24   65  0.92
  25    2  0.03

ACGTcount: A:0.38, C:0.14, G:0.37, T:0.12


Consensus pattern (23 bp):   
GGGAAGGGCAACAGCAATGGTAA

Found at i:134 original size:12 final size:12

Alignment explanation


    Indices: 119--182  Score: 56
    Period size: 12  Copynumber: 5.3  Consensus size: 12

        109 GGTAATGGAT

                        
        119 ATGGCAACAGCA
          1 ATGGCAACAGCA

                *  *    
        131 ATGGTAAGAGCA
          1 ATGGCAACAGCA

             *          
        143 AGGGCAACAGCA
          1 ATGGCAACAGCA

                *  **   
        155 ATGGTAAGGGCA
          1 ATGGCAACAGCA

             *   *      
        167 AGGGCGACAGCA
          1 ATGGCAACAGCA

                
        179 ATGG
          1 ATGG

        183 TAAGGGCAAG


Statistics
Matches: 37,  Mismatches: 15, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
  12   37  1.00

ACGTcount: A:0.38, C:0.17, G:0.36, T:0.09


Consensus pattern (12 bp):   
ATGGCAACAGCA

Found at i:177 original size:48 final size:48

Alignment explanation


    Indices: 97--194  Score: 135
    Period size: 48  Copynumber: 2.0  Consensus size: 48

         87 CAATGGGAAT

                             *     *                        
         97 GGCAACAACAATGGTAATGGATATGGCAACAGCAATGGTAAGAGCAAG
          1 GGCAACAACAATGGTAAGGGATAGGGCAACAGCAATGGTAAGAGCAAG

                   *                    *              *     
        145 GGCAACAGCAATGGTAAGGGCA-AGGGCGACAGCAATGGTAAGGGCAAG
          1 GGCAACAACAATGGTAAGGG-ATAGGGCAACAGCAATGGTAAGAGCAAG

              
        193 GG
          1 GG

        195 GGACAGCGAC


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  48   43  0.98
  49    1  0.02

ACGTcount: A:0.38, C:0.15, G:0.36, T:0.11


Consensus pattern (48 bp):   
GGCAACAACAATGGTAAGGGATAGGGCAACAGCAATGGTAAGAGCAAG

Found at i:199 original size:24 final size:24

Alignment explanation


    Indices: 125--201  Score: 127
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        115 GGATATGGCA

                          *        *
        125 ACAGCAATGGTAAGAGCAAGGGCA
          1 ACAGCAATGGTAAGGGCAAGGGCG

                                    
        149 ACAGCAATGGTAAGGGCAAGGGCG
          1 ACAGCAATGGTAAGGGCAAGGGCG

                                  * 
        173 ACAGCAATGGTAAGGGCAAGGGGG
          1 ACAGCAATGGTAAGGGCAAGGGCG

                 
        197 ACAGC
          1 ACAGC

        202 GACGAAGGAA


Statistics
Matches: 50,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  24   50  1.00

ACGTcount: A:0.36, C:0.17, G:0.39, T:0.08


Consensus pattern (24 bp):   
ACAGCAATGGTAAGGGCAAGGGCG
Done.