Here's a variation on rjt's approach that uses a different method to compare the reversed, complemented strings, and then flags locations of non-reverse-complementarity: 

>perl -wMstrict -le
"die 'Please enter exactly two sequences' unless @ARGV == 2;
 ;;
 my ($seq1, $seq2) = map uc, @ARGV;
 die 'Please enter only ATCG sequences' if grep /[^ATCG]/, $seq1, $seq
+2;
 ;;
 die 'Sequence lengths differ' if length $seq1 != length $seq2;
 ;;
 (my $comp = $seq2) =~ tr/ATCG/TAGC/;
 my $mask = $seq1 ^ reverse $comp;
 ;;
 if ($mask !~ m{ [^\000] }xms) {
   print 'The sequences are reverse-complementary';
   exit;
   }
 ;;
 $mask =~ tr{\000-\377}{_^};
 print 'Sequences are non-reverse-complementary at these locations:';
 print qq{@ARGV};
 print qq{$mask }, ''.reverse $mask;
"  GGGGaaaaaaCatttatatat  atatataaatttttATtcccc
Sequences are non-reverse-complementary at these locations:
GGGGaaaaaaCatttatatat atatataaatttttATtcccc
______^___^__________ __________^___^______

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In reply to Re: Reverse Complement by AnomalousMonk
in thread Reverse Complement by stamp1982

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