my @pairs = ( [qw/ATCG TAGC/], [qw/ACTG TGAT/] );

print "@$_: ", (dna_compare(@$_) ? "matched" : "didn't matched"), $/
  for @pairs;

sub dna_compare {
  my($dna, $comp) = @_;

  return !scalar grep {
    (substr($dna, $_, 1).substr($comp, $_, 1))
     !~ m< ^ (?: AT | TA | GC | CG ) \z >x;
  } 0 .. (length($dna) - 1);
}

__output__

ATCG TAGC: matched
ACTG TGAT: didn't matched