open IN,  '<', 'sample.fa'    or die "Could not open 'sample.fa' because: $!";
open OUT, '>', 'modsample.fa' or die "Could not open 'modsample.fa' because: $!";

my $previous;
while ( my $line = <IN> ) {
    if ( $previous && $line =~ /mamma/ && $line =~ /mia/ ) {
        print OUT $previous, $line;
        }
    else {
        print ".";
        }
    $previous = $line
    }