Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2318

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: 16444
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Found at i:1689 original size:27 final size:27

Alignment explanation


    Indices: 1655--1830  Score: 196
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       1645 TAAATTGTAC

                                       
       1655 AGCACTAAGTGTGCGATTTGACTATGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

            *               **   *     
       1682 TGCACTAAGTGTGCGAAATGAATATG-
          1 AGCACTAAGTGTGCGATTTGACTATGT

                             *     *   *
       1708 ATGCACTAAGTGTGCGAATTGACCATGC
          1 A-GCACTAAGTGTGCGATTTGACTATGT

            *                           
       1736 GGCACTAAGTGTGCGAGTTTGACTATGT
          1 AGCACTAAGTGTGCGA-TTTGACTATGT

                                 *  *  
       1764 AGCACTAAGTGTGCGATTTGATTACGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                            *        * 
       1791 AGCACTAAGTGTGCGAGTTGA--ATAT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                  *        
       1816 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       1831 GACTCAATAT


Statistics
Matches: 127,  Mismatches: 19, Indels: 8
        0.82            0.12        0.05

Matches are distributed among these distances:
  25   16  0.13
  27   88  0.69
  28   23  0.18

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGATTTGACTATGT

Found at i:1769 original size:82 final size:81

Alignment explanation


    Indices: 1656--1811  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       1646 AAATTGTACA

                                      *                       *              
       1656 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
          1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG

                             
       1720 TGCGAATTGACCATGCG
         65 TGCGAATTGACCATGCG

                                                       **   *                
       1737 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
          1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG

                 *    
       1802 TGCGAGTTGA
         65 TGCGAATTGA

       1812 ATATAGCACT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   15  0.22
  82   51  0.76
  83    1  0.01

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (81 bp):   
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG

Found at i:9677 original size:27 final size:27

Alignment explanation


    Indices: 9643--9820  Score: 198
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       9633 TAAATTGTAC

                                       
       9643 AGCACTAAGTGTGCGATTTGACTATGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

            *               **   *     
       9670 TGCACTAAGTGTGCGAAATGAATATG-
          1 AGCACTAAGTGTGCGATTTGACTATGT

                             *     *   *
       9696 ATGCACTAAGTGTGCGAATTGACCATGC
          1 A-GCACTAAGTGTGCGATTTGACTATGT

            *                           
       9724 GGCACTAAGTGTGCGAGTTTGACTATGT
          1 AGCACTAAGTGTGCGA-TTTGACTATGT

                                 *  *  
       9752 AGCACTAAGTGTGCGATTTGATTACGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                            *         * 
       9779 AGCACTAAGTGTGCGAGTTGA-TGATAT
          1 AGCACTAAGTGTGCGATTTGACT-ATGT

                  *        
       9806 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       9821 GACTCAATAT


Statistics
Matches: 128,  Mismatches: 19, Indels: 8
        0.83            0.12        0.05

Matches are distributed among these distances:
  26    1  0.01
  27  104  0.81
  28   23  0.18

ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGATTTGACTATGT

Found at i:9757 original size:82 final size:81

Alignment explanation


    Indices: 9644--9799  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       9634 AAATTGTACA

                                      *                       *              
       9644 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
          1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG

                             
       9708 TGCGAATTGACCATGCG
         65 TGCGAATTGACCATGCG

                                                       **   *                
       9725 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
          1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG

                 *    
       9790 TGCGAGTTGA
         65 TGCGAATTGA

       9800 TGATATAGCA


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   15  0.22
  82   51  0.76
  83    1  0.01

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (81 bp):   
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG

Found at i:9811 original size:82 final size:81

Alignment explanation


    Indices: 9640--9820  Score: 229
    Period size: 82  Copynumber: 2.2  Consensus size: 81

       9630 GGGTAAATTG

                                          *                       *          
       9640 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
          1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA

                            
       9705 GTGTGCGAATTGACCA
         66 GTGTGCGAATTGACCA

             * *                                           **   *            
       9721 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
          1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT

                      *    ** 
       9785 AAGTGTGCGAGTTGATGA
         64 AAGTGTGCGAATTGACCA

              *      *        
       9803 TATAGCACTGAGTGTGCG
          1 TACAGCACTAAGTGTGCG

       9821 GACTCAATAT


Statistics
Matches: 84,  Mismatches: 14, Indels: 3
        0.83            0.14        0.03

Matches are distributed among these distances:
  81   18  0.21
  82   66  0.79

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (81 bp):   
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.