Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21704

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, 409

Length: 683
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.22


Found at i:276 original size:30 final size:30

Alignment explanation


    Indices: 241--406  Score: 226
    Period size: 30  Copynumber: 5.5  Consensus size: 30

        231 ACCCCAGTTT

                   *               *       
        241 CAACTCCTCCACCCAG-TTCTCCTCCTCCCG
          1 CAACTCCACCA-CCAGCTTCTCCACCTCCCG

                         *              * 
        271 CAACTCCACCACCTGCTTCTCCACCTCCTG
          1 CAACTCCACCACCAGCTTCTCCACCTCCCG

                      *                 * 
        301 CAACTCCACCTCCAGCTTCTCCACCTCCTG
          1 CAACTCCACCACCAGCTTCTCCACCTCCCG

                      *                   
        331 CAACTCCACCTCCAGCTTCTCCACCTCCCG
          1 CAACTCCACCACCAGCTTCTCCACCTCCCG

             *     *                      
        361 CCACTCCTCCACCAGCTTCTCCACCTCCCG
          1 CAACTCCACCACCAGCTTCTCCACCTCCCG

             *              
        391 CCACTCCACCACCAGC
          1 CAACTCCACCACCAGC

        407 GACCCCCCCA


Statistics
Matches: 124,  Mismatches: 11, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
  29    3  0.02
  30  121  0.98

ACGTcount: A:0.16, C:0.57, G:0.07, T:0.20


Consensus pattern (30 bp):   
CAACTCCACCACCAGCTTCTCCACCTCCCG

Found at i:277 original size:15 final size:15

Alignment explanation


    Indices: 259--400  Score: 104
    Period size: 15  Copynumber: 9.5  Consensus size: 15

        249 CCACCCAGTT

                *     *    
        259 CTCCTCCTCCCGCAA
          1 CTCCACCTCCTGCAA

                   *     **
        274 CTCCACCACCTGCTT
          1 CTCCACCTCCTGCAA

                           
        289 CTCCACCTCCTGCAA
          1 CTCCACCTCCTGCAA

                      *  **
        304 CTCCACCTCCAGCTT
          1 CTCCACCTCCTGCAA

                           
        319 CTCCACCTCCTGCAA
          1 CTCCACCTCCTGCAA

                      *  **
        334 CTCCACCTCCAGCTT
          1 CTCCACCTCCTGCAA

                      *  * 
        349 CTCCACCTCCCGCCA
          1 CTCCACCTCCTGCAA

                *  *  *  **
        364 CTCCTCCACCAGCTT
          1 CTCCACCTCCTGCAA

                      *  * 
        379 CTCCACCTCCCGCCA
          1 CTCCACCTCCTGCAA

                   
        394 CTCCACC
          1 CTCCACC

        401 ACCAGCGACC


Statistics
Matches: 97,  Mismatches: 30, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  15   97  1.00

ACGTcount: A:0.15, C:0.58, G:0.06, T:0.21


Consensus pattern (15 bp):   
CTCCACCTCCTGCAA

Found at i:418 original size:45 final size:45

Alignment explanation


    Indices: 259--421  Score: 146
    Period size: 45  Copynumber: 3.6  Consensus size: 45

        249 CCACCCAGTT

                *     *  *                          *    
        259 CTCCTCCTCCCGCAACTCCACCACCTGCTTCTCCACCTCCTGCAA
          1 CTCCACCTCCAGCCACTCCACCACCTGCTTCTCCACCTCCAGCAA

                         **       *     **             **
        304 CTCCACCTCCAGCTTCTCCACCTCCTGCAACTCCACCTCCAGCTT
          1 CTCCACCTCCAGCCACTCCACCACCTGCTTCTCCACCTCCAGCAA

                      *        *     *              *  * 
        349 CTCCACCTCCCGCCACTCCTCCACCAGCTTCTCCACCTCCCGCCA
          1 CTCCACCTCCAGCCACTCCACCACCTGCTTCTCCACCTCCAGCAA

                   *     *  *  *        
        394 CTCCACCACCAGCGACCCCCCCACCTGC
          1 CTCCACCTCCAGCCACTCCACCACCTGC

        422 AACTCCTCCT


Statistics
Matches: 91,  Mismatches: 27, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  45   91  1.00

ACGTcount: A:0.15, C:0.58, G:0.07, T:0.19


Consensus pattern (45 bp):   
CTCCACCTCCAGCCACTCCACCACCTGCTTCTCCACCTCCAGCAA

Found at i:427 original size:60 final size:60

Alignment explanation


    Indices: 241--430  Score: 238
    Period size: 60  Copynumber: 3.2  Consensus size: 60

        231 ACCCCAGTTT

                                   *                    *                
        241 CAACTCCTCCACCCAG-TTCTCCTCCTCCCGCAACTCCACCACCTGCTTCTCCACCTCCTG
          1 CAACTCCTCCA-CCAGCTTCTCCACCTCCCGCAACTCCACCACCAGCTTCTCCACCTCCTG

                   *  *                 *           *                 * 
        301 CAACTCCACCTCCAGCTTCTCCACCTCCTGCAACTCCACCTCCAGCTTCTCCACCTCCCG
          1 CAACTCCTCCACCAGCTTCTCCACCTCCCGCAACTCCACCACCAGCTTCTCCACCTCCTG

             *                             *              ** *  *  *    
        361 CCACTCCTCCACCAGCTTCTCCACCTCCCGCCACTCCACCACCAGCGACCCCCCCACCTG
          1 CAACTCCTCCACCAGCTTCTCCACCTCCCGCAACTCCACCACCAGCTTCTCCACCTCCTG

                      
        421 CAACTCCTCC
          1 CAACTCCTCC

        431 TGCTACCCCA


Statistics
Matches: 109,  Mismatches: 20, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  59    4  0.04
  60  105  0.96

ACGTcount: A:0.16, C:0.57, G:0.07, T:0.19


Consensus pattern (60 bp):   
CAACTCCTCCACCAGCTTCTCCACCTCCCGCAACTCCACCACCAGCTTCTCCACCTCCTG
Done.