use strict;
use warnings;
use autodie;

open FH, '<', 'test.dat';
    my $data = do {local $/; <FH>};
close FH;

open FH2, '>', 'seq.dat';

if ($data =~ /Name:\s(.*)?.*Nucleotide\sSequence:\s(.*)?/xms)
{
    print "Yes!\n";
    print FH2 $1, $2, "\n\n";
}

close FH2;