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my %match = map { $_ => 1 } qw(GCGAT CACGT);

...
    s/N//; # remove the first N in the string
    print "match: $line" if $match{substr($_, 0, 5)}
}

my $pattern = join('|', qw(GCGAT CACGT));
$pattern = qr/^(?:$pattern)/;
...
    s/N//; # remove the first N in the string
    print "match: $line" if $_ =~ $pattern;
}