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

##</code><code>##

#! perl -sw
use strict;
# ... your existing code....

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

my ($total, $p) = (0, 0);
do {
  $total = 0;
#NOTE: Extra $'s v ........................................v
  print substr( $$strings[$_]}, $p, 60 ) . "\n" for 0 .. $#$strings;
  print "\n";
  $p+=60;
  $total += length($_) - $p for @$strings; # And here!
} while( $total > 0 );
__END__