use strict;

use Getopt::Std;  #Invokes Get options package
our ($opt_c,$opt_e);
getopts('ce:');


my @seq = <>;
chomp(@seq);
my $seq = join("", @seq);


our %re = (
      'BamHI'  => 'GGATCC 1', # G | GATCC
      'EcoRI'  => 'GAATTC 1', # G | AATTC
      'EcoRII' => 'CCWGG 0',  #   | CCWGG
);

my @enz = split(/\b(\s+)\b/,$re{$opt_e});
my $enzseq = $enz[0];
my $cut = $enz[2];
print "The restriction site is: $enzseq\n\n";

while($seq =~ /($enzseq)/ig) {
    my $site = pos($seq),"\n";
    print "$site\n";
}