#/usr/bin/perl
my $search = 'TTGACA';
open FILE, $ARGV[0] or die "can't open file\n";
local $/;
$data = <FILE>;
$data =~ s/[^GNUCAT]//g;  # or similar ;-)
close FILE;
my $count = () = $data =~ m/$search/g;
print "String $search occured $count times\n\n";