Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2991

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: 12376
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32


Found at i:2222 original size:22 final size:21

Alignment explanation


    Indices: 2191--2235  Score: 63
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       2181 AGGTGTTTTC

                      **         
       2191 TTTTAAAAGATGACTTAATAA
          1 TTTTAAAAGAAAACTTAATAA

                                  
       2212 TTTTATAAAGAAAACTTAATAA
          1 TTTTA-AAAGAAAACTTAATAA

              
       2234 TT
          1 TT

       2236 ATTAGAGTTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    5  0.24
  22   16  0.76

ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40


Consensus pattern (21 bp):   
TTTTAAAAGAAAACTTAATAA

Found at i:11478 original size:28 final size:28

Alignment explanation


    Indices: 11410--11508  Score: 128
    Period size: 28  Copynumber: 3.5  Consensus size: 28

      11400 CATGAGATTG

                          *     *   *  * 
      11410 GCACTAAGTGTGCGGGTTTAAATTGTACA
          1 GCACTAAGTGTGCGAGTTT-GATTATATA

                                        
      11439 GCACTAAGTGTGCGAGTTTGATTATATA
          1 GCACTAAGTGTGCGAGTTTGATTATATA

                                         
      11467 GCACTAAGTGTGCGAG-TTGAATTATATA
          1 GCACTAAGTGTGCGAGTTTG-ATTATATA

                 *        
      11495 GCACTGAGTGTGCG
          1 GCACTAAGTGTGCG

      11509 GACTTAATAT


Statistics
Matches: 64,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  27    3  0.05
  28   43  0.67
  29   18  0.28

ACGTcount: A:0.27, C:0.13, G:0.28, T:0.31


Consensus pattern (28 bp):   
GCACTAAGTGTGCGAGTTTGATTATATA
Done.