Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3326

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: 26079
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:8803 original size:15 final size:16

Alignment explanation


    Indices: 8772--8808  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       8762 GAGCTGAGTT

                            
       8772 TGAGCT-AGCTAGAAA
          1 TGAGCTGAGCTAGAAA

              *             
       8787 TGTGCTGAGCT-GAAA
          1 TGAGCTGAGCTAGAAA

                   
       8802 TGAGCTG
          1 TGAGCTG

       8809 GAAACAATCT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  15   15  0.79
  16    4  0.21

ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24


Consensus pattern (16 bp):   
TGAGCTGAGCTAGAAA

Found at i:8937 original size:52 final size:52

Alignment explanation


    Indices: 8859--8959  Score: 166
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       8849 TATGCACATA

                         *              *               *       
       8859 TTTGAGCTTCAACTGAGCTAGAAATGAGGTCTTAAGCTACTGTCTATTATTG
          1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTATTG

                                                  *          
       8911 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
          1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTA

       8960 CGTTTTCTTA


Statistics
Matches: 45,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  52   45  1.00

ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34


Consensus pattern (52 bp):   
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTATTG

Found at i:14138 original size:20 final size:20

Alignment explanation


    Indices: 14115--14161  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      14105 GGGTTAAGAT

                            *   
      14115 TGAGCTGAATTGAGCTTGAG
          1 TGAGCTGAATTGAGCTCGAG

                *   *           
      14135 TGAGTTGACTTGAGCTCGAG
          1 TGAGCTGAATTGAGCTCGAG

                   
      14155 TGAGCTG
          1 TGAGCTG

      14162 GAAACGAGCT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30


Consensus pattern (20 bp):   
TGAGCTGAATTGAGCTCGAG

Found at i:15886 original size:48 final size:48

Alignment explanation


    Indices: 15831--15936  Score: 137
    Period size: 48  Copynumber: 2.2  Consensus size: 48

      15821 TTGTCTTTTC

                                               *               
      15831 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
          1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA

                      *      *                              
      15879 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
          1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA

                      
      15927 TTTCTTTTTC
          1 TTTCTTTTTC

      15937 CATGACACTC


Statistics
Matches: 52,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  48   40  0.77
  49    8  0.15
  50    4  0.08

ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59


Consensus pattern (48 bp):   
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA

Found at i:25038 original size:6 final size:6

Alignment explanation


    Indices: 25022--25071  Score: 50
    Period size: 6  Copynumber: 8.3  Consensus size: 6

      25012 GTTCAAAAGC

                   *             *                                   
      25022 TTTATT ATTATT TTTATT ATT-TT TTTATT TTT-TAT TTTAGTT TTTATT
          1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT-T TTTA-TT TTTATT

              
      25070 TT
          1 TT

      25072 AGAAAAATCA


Statistics
Matches: 36,  Mismatches: 4, Indels: 8
        0.75            0.08        0.17

Matches are distributed among these distances:
   5    5  0.14
   6   25  0.69
   7    5  0.14
   8    1  0.03

ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80


Consensus pattern (6 bp):   
TTTATT

Done.