Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2344

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: 35727
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34


Found at i:15236 original size:25 final size:25

Alignment explanation


    Indices: 15197--15246  Score: 66
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      15187 ATGATGGTAC

                           **        
      15197 ATGATATATTGATATTTTGAAATGG
          1 ATGATATATTGATATAATGAAATGG

                                      
      15222 ATGATATA-TGTATATAATGAAATGG
          1 ATGATATATTG-ATATAATGAAATGG

      15247 TAAGATAATG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  24    2  0.09
  25   20  0.91

ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40


Consensus pattern (25 bp):   
ATGATATATTGATATAATGAAATGG

Found at i:16042 original size:17 final size:16

Alignment explanation


    Indices: 16020--16051  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

      16010 TTCCAGATTA

                             
      16020 TTGGAAGCTCGATCGGG
          1 TTGGAAGCTC-ATCGGG

                           
      16037 TTGGAAGCTCATCGG
          1 TTGGAAGCTCATCGG

      16052 AGATTTTATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.19, C:0.19, G:0.38, T:0.25


Consensus pattern (16 bp):   
TTGGAAGCTCATCGGG

Found at i:21057 original size:25 final size:25

Alignment explanation


    Indices: 21027--21076  Score: 75
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      21017 ATGATGGTAC

                             *        
      21027 ATGATATAT-TGATATATTGAAATGG
          1 ATGATATATGTG-TATAATGAAATGG

                                     
      21052 ATGATATATGTGTATAATGAAATGG
          1 ATGATATATGTGTATAATGAAATGG

      21077 TAAGATTATG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   21  0.91
  26    2  0.09

ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38


Consensus pattern (25 bp):   
ATGATATATGTGTATAATGAAATGG

Found at i:21086 original size:25 final size:25

Alignment explanation


    Indices: 21029--21086  Score: 66
    Period size: 25  Copynumber: 2.3  Consensus size: 25

      21019 GATGGTACAT

                           *         *
      21029 GATATAT-TGATATATTGAAATGGAT
          1 GATATATGTG-TATAATGAAATGGAA

                                      
      21054 GATATATGTGTATAATGAAATGGTAA
          1 GATATATGTGTATAATGAAATGG-AA

                    
      21080 GAT-TATG
          1 GATATATG

      21087 ATATGTATCA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  25   23  0.79
  26    6  0.21

ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38


Consensus pattern (25 bp):   
GATATATGTGTATAATGAAATGGAA
Done.