Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2387

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: 12883
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30


Found at i:6077 original size:27 final size:27

Alignment explanation


    Indices: 6043--6220  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       6033 TAAATTGTAC

                                       
       6043 AGCACTAAGTGTGCGATTTGACTATGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

            *               **   *     
       6070 TGCACTAAGTGTGCGAAATGAATATG-
          1 AGCACTAAGTGTGCGATTTGACTATGT

                             *     *   *
       6096 ATGCACTAAGTGTGCGAATTGACCATGC
          1 A-GCACTAAGTGTGCGATTTGACTATGT

            *                           
       6124 GGCACTAAGTGTGCGAGTTTGACTATGT
          1 AGCACTAAGTGTGCGA-TTTGACTATGT

                                 *  *  
       6152 AGCACTAAGTGTGCGATTTGATTACGT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                            *    *   * 
       6179 AGCACTAAGTGTGCGAGTTGATTATAT
          1 AGCACTAAGTGTGCGATTTGACTATGT

                  *        
       6206 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       6221 GACTCAATAT


Statistics
Matches: 129,  Mismatches: 19, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  27  106  0.82
  28   23  0.18

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGATTTGACTATGT

Found at i:6157 original size:82 final size:81

Alignment explanation


    Indices: 6044--6199  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       6034 AAATTGTACA

                                      *                       *              
       6044 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
          1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG

                             
       6108 TGCGAATTGACCATGCG
         65 TGCGAATTGACCATGCG

                                                       **   *                
       6125 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
          1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG

                 *    
       6190 TGCGAGTTGA
         65 TGCGAATTGA

       6200 TTATATAGCA


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:6211 original size:82 final size:81

Alignment explanation


    Indices: 6040--6220  Score: 229
    Period size: 82  Copynumber: 2.2  Consensus size: 81

       6030 GGGTAAATTG

                                          *                       *          
       6040 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
          1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA

                            
       6105 GTGTGCGAATTGACCA
         66 GTGTGCGAATTGACCA

             * *                                           **   *            
       6121 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
          1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT

                      *    ** 
       6185 AAGTGTGCGAGTTGATTA
         64 AAGTGTGCGAATTGACCA

              *      *        
       6203 TATAGCACTGAGTGTGCG
          1 TACAGCACTAAGTGTGCG

       6221 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:0.30


Consensus pattern (81 bp):   
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.