Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3182

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: 11792
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30


Found at i:11702 original size:27 final size:28

Alignment explanation


    Indices: 11639--11788  Score: 205
    Period size: 28  Copynumber: 5.4  Consensus size: 28

      11629 GAGATTGGCG

                       *     *   *  *    
      11639 CTAAGTGTGCGGGTTTAAATTGTACAGCA
          1 CTAAGTGTGCGAGTTT-GATTATATAGCA

                                  *     
      11668 CTAAGTGTGCGAG-TTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                  *     
      11695 CTAAGTGTGCGAGTTTGATTATGTAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                                        
      11723 CTAAGTGTGCGAGTTTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

                      *                 
      11751 CTAAGTGTGCAAG-TTGATTATATAGCA
          1 CTAAGTGTGCGAGTTTGATTATATAGCA

              *        
      11778 CTGAGTGTGCG
          1 CTAAGTGTGCG

      11789 GACT


Statistics
Matches: 111,  Mismatches: 9, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
  27   44  0.40
  28   55  0.50
  29   12  0.11

ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33


Consensus pattern (28 bp):   
CTAAGTGTGCGAGTTTGATTATATAGCA

Found at i:11729 original size:55 final size:55

Alignment explanation


    Indices: 11664--11788  Score: 198
    Period size: 55  Copynumber: 2.3  Consensus size: 55

      11654 TAAATTGTAC

                                      *               *           * 
      11664 AGCACTAAGTGTGCGAG-TTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAG-TTGATTATAT

                                                                   
      11719 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTGATTATAT
          1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTGATTATAT

                  *        
      11774 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

      11789 GACT


Statistics
Matches: 65,  Mismatches: 4, Indels: 2
        0.92            0.06        0.03

Matches are distributed among these distances:
  55   40  0.62
  56   25  0.38

ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33


Consensus pattern (55 bp):   
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTGATTATAT
Done.