Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_02565

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, 313

Length: 522
ACGTcount: A:0.28, C:0.37, G:0.12, T:0.24


Found at i:206 original size:30 final size:30

Alignment explanation


    Indices: 160--518  Score: 322
    Period size: 30  Copynumber: 12.0  Consensus size: 30

        150 ATTGCTTCCG

                  *    *     **           
        160 CCATATGAGTATAAGTCGTCACCTCCACCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                   *                      
        190 CCATATACGTACAAGTCACCACCTCCACCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                   *               *  *   
        220 CCATATATGTACAAGTCACCACCACCTCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                       *     *  *        *
        250 CCATATAAGTATAAGTCTCCGCCTCCACCC
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                 * *         *     *      
        280 CCATACATGTACAAGTCGCCACCACCACCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                 *     **    *     *  *   
        310 CCATACAAGTATGAGTCGCCACCACCTCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                 *     **             *   
        340 CCATACAAGTATGAGTCACCACCTCCGCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                  **      *           *   
        370 CCATATGTGTACAAATCACCACCTCCGCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                  **      *        *  *   
        400 CCATATGTGTACAAATCACCACCACCTCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                  **                  *   
        430 CCATATGTGTACAAGTCACCACCTCCTCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                 *     **          *  *   
        460 CCATACAAGTATGAGTCACCACCACCTCCT
          1 CCATATAAGTACAAGTCACCACCTCCACCT

                 *                       
        490 CCATACAAGTACAAGTCACCACCTCCACC
          1 CCATATAAGTACAAGTCACCACCTCCACC

        519 CCCA


Statistics
Matches: 280,  Mismatches: 49, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30  280  1.00

ACGTcount: A:0.28, C:0.40, G:0.10, T:0.21


Consensus pattern (30 bp):   
CCATATAAGTACAAGTCACCACCTCCACCT

Found at i:240 original size:90 final size:90

Alignment explanation


    Indices: 160--512  Score: 391
    Period size: 90  Copynumber: 3.9  Consensus size: 90

        150 ATTGCTTCCG

                  *          **                * *               *           
        160 CCATATGAGTATAAGTCGTCACCTCCACCTCCATATACGTACAAGTCACCACCTCCACCTCCATA
          1 CCATATAAGTATAAGTCACCACCTCCACCTCCATACATGTACAAGTCACCACCACCACCTCCATA

            * *                      
        225 TATGTACAAGTCACCACCACCTCCT
         66 CAAGTACAAGTCACCACCACCTCCT

                             *  *        *                 *                 
        250 CCATATAAGTATAAGTCTCCGCCTCCACCCCCATACATGTACAAGTCGCCACCACCACCTCCATA
          1 CCATATAAGTATAAGTCACCACCTCCACCTCCATACATGTACAAGTCACCACCACCACCTCCATA

                  **    *            
        315 CAAGTATGAGTCGCCACCACCTCCT
         66 CAAGTACAAGTCACCACCACCTCCT

                 *      *             *        **       *        *  *        
        340 CCATACAAGTATGAGTCACCACCTCCGCCTCCATATGTGTACAAATCACCACCTCCGCCTCCATA
          1 CCATATAAGTATAAGTCACCACCTCCACCTCCATACATGTACAAGTCACCACCACCACCTCCATA

            ***      *               
        405 TGTGTACAAATCACCACCACCTCCT
         66 CAAGTACAAGTCACCACCACCTCCT

                  **   *              *          *   **             *        
        430 CCATATGTGTACAAGTCACCACCTCCTCCTCCATACAAGTATGAGTCACCACCACCTCCTCCATA
          1 CCATATAAGTATAAGTCACCACCTCCACCTCCATACATGTACAAGTCACCACCACCACCTCCATA

                              
        495 CAAGTACAAGTCACCACC
         66 CAAGTACAAGTCACCACC

        513 TCCACCCCCA


Statistics
Matches: 212,  Mismatches: 51, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  90  212  1.00

ACGTcount: A:0.29, C:0.40, G:0.10, T:0.22


Consensus pattern (90 bp):   
CCATATAAGTATAAGTCACCACCTCCACCTCCATACATGTACAAGTCACCACCACCACCTCCATA
CAAGTACAAGTCACCACCACCTCCT

Done.