Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1253

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: 7050
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32


Found at i:1228 original size:16 final size:16

Alignment explanation


    Indices: 1195--1224  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       1185 TAAATTCCAA

                            
       1195 ATTTTTTAATTTTAAT
          1 ATTTTTTAATTTTAAT

                           
       1211 ATTTTTT-ATTTTAA
          1 ATTTTTTAATTTTAA

       1225 ATATAATAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (16 bp):   
ATTTTTTAATTTTAAT

Found at i:1750 original size:20 final size:20

Alignment explanation


    Indices: 1725--1764  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1715 TCAAATCAAA

                  *             
       1725 TTTAAATTTAAATAAAAAAT
          1 TTTAAACTTAAATAAAAAAT

                                
       1745 TTTAAACTTAAATAAAAAAT
          1 TTTAAACTTAAATAAAAAAT

       1765 AAATTTTTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38


Consensus pattern (20 bp):   
TTTAAACTTAAATAAAAAAT

Found at i:2063 original size:20 final size:19

Alignment explanation


    Indices: 2038--2106  Score: 66
    Period size: 20  Copynumber: 3.4  Consensus size: 19

       2028 ATGAAAAATT

                                
       2038 ATATATTTAGTATTTAAAAA
          1 ATATATTTA-TATTTAAAAA

                             *  
       2058 ATATATATTATATTTAATAA
          1 ATATAT-TTATATTTAAAAA

            *   *                
       2078 TTATTTTTAATAATTTAAAAA
          1 ATATATTT-AT-ATTTAAAAA

                    
       2099 TATATATT
          1 -ATATATT

       2107 GCATTAATTA


Statistics
Matches: 39,  Mismatches: 6, Indels: 6
        0.76            0.12        0.12

Matches are distributed among these distances:
  19    2  0.05
  20   21  0.54
  21   11  0.28
  22    5  0.13

ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51


Consensus pattern (19 bp):   
ATATATTTATATTTAAAAA
Done.