$first_data = "first.txt";
open(DAT,$first_data) || die("Could not open file!");
@seq1 = <DAT>;

$second_file = "second.txt";
open (RF,$second_file) || die("Could not open file!");
@seq2 = <RF>;

my %hash = (
array1=>[@seq1],
array2=>[@seq2]
);

foreach my $value (%hash) {
    if($seq1 =~ $seq2){next;}
    else {print $value;
          exit;}
}