Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2271

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, 605

Length: 1009
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35


Found at i:727 original size:7 final size:7

Alignment explanation


    Indices: 715--819  Score: 53
    Period size: 7  Copynumber: 15.4  Consensus size: 7

        705 AACCCTGAAT

                   
        715 CCTTAAA
          1 CCTTAAA

                   
        722 CCTTAAA
          1 CCTTAAA

                *  
        729 CC-TGAA
          1 CCTTAAA

              *    
        735 CCCTAAA
          1 CCTTAAA

              *    
        742 CCCTAAA
          1 CCTTAAA

                    
        749 -CTCTAAA
          1 CCT-TAAA

                 *  
        756 TCCTTGAA
          1 -CCTTAAA

                    
        764 -CTCTAAA
          1 CCT-TAAA

                   
        771 CC-TAAA
          1 CCTTAAA

             *     
        777 CTTTAAA
          1 CCTTAAA

                *  
        784 CC-TCAA
          1 CCTTAAA

                    
        790 CAC-TAAA
          1 C-CTTAAA

                   
        797 -CTTAAA
          1 CCTTAAA

                   
        803 CCTTAAA
          1 CCTTAAA

            *  *   
        810 TCTCAAA
          1 CCTTAAA

               
        817 CCT
          1 CCT

        820 AAATCCTAAA


Statistics
Matches: 76,  Mismatches: 12, Indels: 20
        0.70            0.11        0.19

Matches are distributed among these distances:
   5    1  0.01
   6   21  0.28
   7   48  0.63
   8    4  0.05
   9    2  0.03

ACGTcount: A:0.41, C:0.31, G:0.02, T:0.26


Consensus pattern (7 bp):   
CCTTAAA

Found at i:741 original size:13 final size:13

Alignment explanation


    Indices: 725--829  Score: 70
    Period size: 13  Copynumber: 7.8  Consensus size: 13

        715 CCTTAAACCT

                   *   * 
        725 TAAACCTGAACCC
          1 TAAACCTAAACTC

                          
        738 TAAACCCTAAACTC
          1 TAAA-CCTAAACTC

                     *     
        752 TAAATCCTTGAACTC
          1 TAAA-CC-TAAACTC

                        *
        767 TAAACCTAAACTT
          1 TAAACCTAAACTC

                   *   * 
        780 TAAACCTCAACAC
          1 TAAACCTAAACTC

                 *       
        793 TAAACTTAAAC-C
          1 TAAACCTAAACTC

                 *         
        805 TTAAATCTCAAAC-C
          1 -TAAACCT-AAACTC

                       
        819 TAAATCCTAAA
          1 TAAA-CCTAAA

        830 TCTCGAGGTT


Statistics
Matches: 73,  Mismatches: 14, Indels: 10
        0.75            0.14        0.10

Matches are distributed among these distances:
  12    1  0.01
  13   40  0.55
  14   22  0.30
  15   10  0.14

ACGTcount: A:0.44, C:0.30, G:0.02, T:0.25


Consensus pattern (13 bp):   
TAAACCTAAACTC
Done.