Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38870

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, 813

Length: 1356
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28


Found at i:979 original size:6 final size:6

Alignment explanation


    Indices: 968--1050  Score: 58
    Period size: 6  Copynumber: 13.8  Consensus size: 6

        958 CATGCTCACC

                                  * *        *  *   *      *       
        968 ATCATG ATCATG ATCATG ACCGTG ATCATC ACCATC ATCATC ATCATG
          1 ATCATG ATCATG ATCATG ATCATG ATCATG ATCATG ATCATG ATCATG

             *      *   *  *      *   *             
       1016 AACATG AGCATA AACATG ACCATC ATCATG ATCAT
          1 ATCATG ATCATG ATCATG ATCATG ATCATG ATCAT

       1051 ACTCATGACC


Statistics
Matches: 60,  Mismatches: 17, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
   6   60  1.00

ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27


Consensus pattern (6 bp):   
ATCATG

Found at i:983 original size:12 final size:12

Alignment explanation


    Indices: 968--1060  Score: 62
    Period size: 12  Copynumber: 7.8  Consensus size: 12

        958 CATGCTCACC

                   *    
        968 ATCATGATCATG
          1 ATCATGACCATG

                     *  
        980 ATCATGACCGTG
          1 ATCATGACCATG

                 *     *
        992 ATCATCACCATC
          1 ATCATGACCATG

                 * *    
       1004 ATCATCATCATG
          1 ATCATGACCATG

             *     *   *
       1016 AACATGAGCATA
          1 ATCATGACCATG

             *         *
       1028 AACATGACCATC
          1 ATCATGACCATG

                   *    
       1040 ATCATGATCAT-
          1 ATCATGACCATG

                      
       1051 ACTCATGACC
          1 A-TCATGACC

       1061 CAGGAGTTTC


Statistics
Matches: 64,  Mismatches: 16, Indels: 2
        0.78            0.20        0.02

Matches are distributed among these distances:
  11    1  0.02
  12   63  0.98

ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26


Consensus pattern (12 bp):   
ATCATGACCATG
Done.