Report CpG rich areas emboss newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto Sequence Window Size Step size (shift) Minimum length Minimum average observed to expected ratio Minimum average percentage of G plus C

You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html