Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_543 ID=scaffold_543-JGI_221_v2.0

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: 7242
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.26

Warning! 1344 characters in sequence are not A, C, G, or T


Found at i:3206 original size:13 final size:12

Alignment explanation


    Indices: 3188--3223  Score: 54
    Period size: 13  Copynumber: 2.8  Consensus size: 12

       3178 TGGCCTCTCC

                         
       3188 TTTTCTTTTTCCT
          1 TTTTCTTTTT-CT

                        
       3201 TTTTCTTTTTCT
          1 TTTTCTTTTTCT

                       
       3213 TTTCTCTTTTT
          1 TTT-TCTTTTT

       3224 TATTTTTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  12    5  0.23
  13   17  0.77

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (12 bp):   
TTTTCTTTTTCT

Found at i:3209 original size:5 final size:6

Alignment explanation


    Indices: 3188--3223  Score: 54
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       3178 TGGCCTCTCC

                                                     
       3188 TTTTCT TTTTCCT TTTTCT TTTTCT TTTCTCT TTTT
          1 TTTTCT TTTT-CT TTTTCT TTTTCT TTT-TCT TTTT

       3224 TATTTTTATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   6   16  0.57
   7   12  0.43

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (6 bp):   
TTTTCT
Done.