#! perl -slw
use strict;

my $genome1 =
'ACACTTGCATACTGATCATGACTTGACACACTTGCATACTGATCATGACTTGACACACTTGCATACTGATCATGACTTGACACACTTGCATACTGATCATGACTTGAC';
my $genome2 =
'ACTACGACTGCATGACTCCGATGACTGACTACGACTGCATGACTCCGATGACTGACTACGACTGCATGACTCCGATGACTGACTACGACTGCATGACTCCGATGACTG';

my $mismatches = get_mismatches ($genome1, $genome2);

my @strings = ($genome1, $mismatches, $genome2);

for (my $x = 0; $x < length ($strings [0]); $x +=60)   {
	 print join ("\n", map (substr ($strings[$_], $x, 60), 0..2 )) . "\n";
}

exit;

sub get_mismatches {
	($genome1, $genome2) = @_;
	my $mismatches = '';
	my $length= length ($genome1);
	my $position;
	my $count = 0;

	for ($position = 0; $position < $length; ++$position)  {
		if (substr($genome1, $position, 1) eq substr ($genome2, $position, 1)) {
			$mismatches .= "-";
		}
		else {
			$mismatches .= "*";
		}
	}
	return $mismatches;
}

__END__
C:\test>214064
ACACTTGCATACTGATCATGACTTGACACACTTGCATACTGATCATGACTTGACACACTT
--*****-****---****--******--*****-****---****--******--****
ACTACGACTGCATGACTCCGATGACTGACTACGACTGCATGACTCCGATGACTGACTACG

GCATACTGATCATGACTTGACACACTTGCATACTGATCATGACTTGAC
*-****---****--******--*****-****---****--******
ACTGCATGACTCCGATGACTGACTACGACTGCATGACTCCGATGACTG


C:\test>