Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00004.F6

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, 1000

Length: 3831
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:1651 original size:7 final size:7

Alignment explanation


    Indices: 1625--1893  Score: 89
    Period size: 7  Copynumber: 39.0  Consensus size: 7

       1615 TCCAGCCAAT

                   
       1625 CCCTAAA
          1 CCCTAAA

              *    
       1632 CCTTAAA
          1 CCCTAAA

             *    *
       1639 CTCTAAC
          1 CCCTAAA

                  *
       1646 CCCTAAT
          1 CCCTAAA

             *     
       1653 CTCTAAA
          1 CCCTAAA

                   
       1660 CCCTAAA
          1 CCCTAAA

              *    
       1667 CCTTAAA
          1 CCCTAAA

            * *   *
       1674 TCATAAC
          1 CCCTAAA

                   
       1681 CCCTAAA
          1 CCCTAAA

              *  * 
       1688 CCTTATA
          1 CCCTAAA

             *   * 
       1695 -TCTATA
          1 CCCTAAA

                   
       1701 CCCTAAA
          1 CCCTAAA

             *     
       1708 CTCTAAA
          1 CCCTAAA

              *  * 
       1715 CCTTATA
          1 CCCTAAA

             **  * 
       1722 -TTTATA
          1 CCCTAAA

              *    
       1728 CCTTAAA
          1 CCCTAAA

              *    
       1735 CCTTAAA
          1 CCCTAAA

                 * 
       1742 CCCTAGA
          1 CCCTAAA

                   
       1749 -CCTAAA
          1 CCCTAAA

                   
       1755 CCCTAAA
          1 CCCTAAA

                   
       1762 -CCTAAA
          1 CCCTAAA

              *    
       1768 CCTTAAA
          1 CCCTAAA

            *      
       1775 ACCTAAA
          1 CCCTAAA

            *      
       1782 ACC-AAA
          1 CCCTAAA

                *  *
       1788 GCCCCAAG
          1 -CCCTAAA

                  *
       1796 CCCTAAG
          1 CCCTAAA

               *   
       1803 CCCCAAA
          1 CCCTAAA

            *     *
       1810 TCCTAAT
          1 CCCTAAA

              *   *
       1817 CCTTAAG
          1 CCCTAAA

              *   *
       1824 CCTTAAG
          1 CCCTAAA

              *    
       1831 CCTTAAA
          1 CCCTAAA

              *    
       1838 CCTTAAA
          1 CCCTAAA

             *     
       1845 CTCTAAA
          1 CCCTAAA

             *     
       1852 CTCTAAA
          1 CCCTAAA

            * *    
       1859 TCTTAAA
          1 CCCTAAA

              *    
       1866 CCTTAAA
          1 CCCTAAA

             *     
       1873 CACTAAA
          1 CCCTAAA

              *    
       1880 CCTTAAA
          1 CCCTAAA

              *    
       1887 CCATAAA
          1 CCCTAAA

       1894 TAAATAGTAA


Statistics
Matches: 198,  Mismatches: 58, Indels: 12
        0.74            0.22        0.04

Matches are distributed among these distances:
   6   23  0.12
   7  173  0.87
   8    2  0.01

ACGTcount: A:0.41, C:0.32, G:0.02, T:0.25


Consensus pattern (7 bp):   
CCCTAAA

Found at i:1716 original size:27 final size:26

Alignment explanation


    Indices: 1682--1772  Score: 110
    Period size: 27  Copynumber: 3.4  Consensus size: 26

       1672 AATCATAACC

                                      
       1682 CCTAAACCTTATATCTATACCCTAAA
          1 CCTAAACCTTATATCTATACCCTAAA

                           *      *    
       1708 CTCTAAACCTTATATTTATACCTTAAA
          1 C-CTAAACCTTATATCTATACCCTAAA

                     *  * *   *        
       1735 CCTTAAACCCTAGACCTAAACCCTAAA
          1 CC-TAAACCTTATATCTATACCCTAAA

                       
       1762 CCTAAACCTTA
          1 CCTAAACCTTA

       1773 AAACCTAAAA


Statistics
Matches: 54,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  26   10  0.19
  27   44  0.81

ACGTcount: A:0.38, C:0.31, G:0.01, T:0.30


Consensus pattern (26 bp):   
CCTAAACCTTATATCTATACCCTAAA

Found at i:1778 original size:27 final size:26

Alignment explanation


    Indices: 1626--1893  Score: 108
    Period size: 28  Copynumber: 9.7  Consensus size: 26

       1616 CCAGCCAATC

                               *      *
       1626 CCTAAACCTTAAACTCTAACCCCTAAT
          1 CCTAAACCTTAAAC-CTAAACCCTAAA

                     *           * *    *
       1653 CTCTAAACCCTAAACCTTAAATCATAACC
          1 C-CTAAACCTTAAACC-TAAACCCTAA-A

                       * *   *        
       1682 CCTAAACCTTATATCTATACCCTAAA
          1 CCTAAACCTTAAACCTAAACCCTAAA

                        * **  *   *    
       1708 CTCTAAACCTTATATTTATACCTTAAA
          1 C-CTAAACCTTAAACCTAAACCCTAAA

                     *  *              
       1735 CCTTAAACCCTAGACCTAAACCCTAAA
          1 CC-TAAACCTTAAACCTAAACCCTAAA

                                *      
       1762 CCTAAACCTTAAAACCTAAAACC-AAA
          1 CCTAAACCTT-AAACCTAAACCCTAAA

                *  *  *    *  *   *     *
       1788 GCCCCAAGCCCTAAGCCCCAAATCCTAAT
          1 --CCTAAACCTTAA-ACCTAAACCCTAAA

                  *      *         *    
       1817 CCTTAAGCCTTAAGCCTTAAACCTTAAA
          1 CC-TAAACCTTAAACC-TAAACCCTAAA

                             *      *    
       1845 CTCTAAA-CTCTAAATCTTAAACCTTAAA
          1 C-CTAAACCT-TAAA-CCTAAACCCTAAA

                                 
       1873 CACTAAACCTTAAACCATAAA
          1 C-CTAAACCTTAAACC-TAAA

       1894 TAAATAGTAA


Statistics
Matches: 182,  Mismatches: 42, Indels: 33
        0.71            0.16        0.13

Matches are distributed among these distances:
  26   12  0.07
  27   72  0.40
  28   91  0.50
  29    7  0.04

ACGTcount: A:0.41, C:0.32, G:0.02, T:0.25


Consensus pattern (26 bp):   
CCTAAACCTTAAACCTAAACCCTAAA

Done.