in reply to What is the problem of subroutine "make_file" in my code?
is probably not doing what you intended. You probably mean the following:my @Motif = split(//,'$origin[$y]'); # This is a loop to get the motif + template from origin8
(note the missing single-quotes)# This is a loop to get the motif template from origin8 my @Motif = split(//,$origin[$y]);
Also it might help if you give us a short bit of the long_sequences.txt so we can run your code.