Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1051

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: 12595
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29


Found at i:42 original size:20 final size:20

Alignment explanation


    Indices: 17--66  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 20

          7 TGGCTTAAAA

                                
         17 TTGGTAGTGGATTGTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

                                
         37 TTGGTAGTGG---GTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

            *            
         54 GTGGTAGTGGATT
          1 TTGGTAGTGGATT

         67 AGTGGATGGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  17   16  0.62
  20   10  0.38

ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46


Consensus pattern (20 bp):   
TTGGTAGTGGATTGTTGTTG

Found at i:4665 original size:20 final size:20

Alignment explanation


    Indices: 4640--4689  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 20

       4630 TGGCTTAAAA

                                
       4640 TTGGTAGTGGATTGTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

                                
       4660 TTGGTAGTGG---GTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

            *            
       4677 GTGGTAGTGGATT
          1 TTGGTAGTGGATT

       4690 AGTGGATGGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  17   16  0.62
  20   10  0.38

ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46


Consensus pattern (20 bp):   
TTGGTAGTGGATTGTTGTTG

Found at i:7143 original size:20 final size:20

Alignment explanation


    Indices: 7118--7167  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 20

       7108 TGGCTTAAAA

                                
       7118 TTGGTAGTGGATTGTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

                                
       7138 TTGGTAGTGG---GTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

            *            
       7155 GTGGTAGTGGATT
          1 TTGGTAGTGGATT

       7168 AGTGGATGGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  17   16  0.62
  20   10  0.38

ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46


Consensus pattern (20 bp):   
TTGGTAGTGGATTGTTGTTG

Found at i:11772 original size:20 final size:20

Alignment explanation


    Indices: 11747--11796  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 20

      11737 TGGCTTAAAA

                                
      11747 TTGGTAGTGGATTGTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

                                
      11767 TTGGTAGTGG---GTTGTTG
          1 TTGGTAGTGGATTGTTGTTG

            *            
      11784 GTGGTAGTGGATT
          1 TTGGTAGTGGATT

      11797 AGTGGATGGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  17   16  0.62
  20   10  0.38

ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46


Consensus pattern (20 bp):   
TTGGTAGTGGATTGTTGTTG

Found at i:12392 original size:39 final size:39

Alignment explanation


    Indices: 12338--12440  Score: 143
    Period size: 39  Copynumber: 2.6  Consensus size: 39

      12328 TTTTATGTGG

                     *         *           *   * * 
      12338 GAAGATCAGTTTGATGAGATGAGCAAAGATGTATCGGGT
          1 GAAGATCAGATTGATGAGACGAGCAAAGATGAATCAGAT

                *                     *            
      12377 GAAGGTCAGATTGATGAGACGAGCAATGATGAATCAGAT
          1 GAAGATCAGATTGATGAGACGAGCAAAGATGAATCAGAT

                                     
      12416 GAAGATCAGATTGATGAGACGAGCA
          1 GAAGATCAGATTGATGAGACGAGCA

      12441 GTGAGGCATC


Statistics
Matches: 56,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  39   56  1.00

ACGTcount: A:0.37, C:0.10, G:0.32, T:0.21


Consensus pattern (39 bp):   
GAAGATCAGATTGATGAGACGAGCAAAGATGAATCAGAT
Done.