If you only needed to know if the complement string was (or was not) a true complement of the original, perhaps the simplest way would be to re-complement the complement and check for equality. The re-complementation can be acheived very easily using Perl's tr/// operator. eg.

 
my $dna = 'ACGTACGT';
my $cmp = 'TGCATGCA';
(my $recmp = $cmp) =~ tr[ACGT][TGCA];
print 'Matched' if $recmp eq $dna;
[download]

However, as you want to know what the failures were, you can still use the technique to simplify the process of finding them by creating the re-complemented string and then detecting the differences. You could do this with substr

#! perl -slw
use strict;

while( !eof DATA ) {
    my $dna = <DATA>;
    my $cmp = <DATA>;
    (my $temp = $cmp) =~ tr[ACGT][TGCA];
    if ($dna eq $temp) {
        print "$cmp is an accurate compliment of \n$dna";
    } elsif (length $dna != length $cmp) {
        print "$cmp is a different length to \n$dna";
    } else {
        for my $pos(0 .. length $dna) {
            my $c1 = substr($dna, $pos, 1);
            my $c2 = substr($cmp, $pos, 1);
            print "$c1-$c2 (pos:$pos) is a mismatch"
                unless $c1 eq (substr($temp, $pos, 1));
        }
    }
}


__DATA__
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCAG
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCA
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCCTAGGCTATATCTGCAGACGATCAGCAGCAAACGGATATCGGATCTAG
+GATCGATCAG
[download]

Output

C:\test>243661
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCAG
 is an accurate compliment of
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC

TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCA
 is a different length to
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC

C-C (pos:22) is a mismatch
A-G (pos:25) is a mismatch
A-A (pos:59) is a mismatch
G-G (pos:70) is a mismatch

C:\test>
[download]

Or you could go one stage further and use Perl's bit-wise string manipulations to find the differences and use the resultant string to indicate those differences in a simple manner.

#! perl -sw
use strict;

while( !eof DATA ) {
    my $dna = <DATA>;
    my $cmp = <DATA>;
    (my $temp = $cmp) =~ tr[ACGT][TGCA];

    if ($dna eq $temp) {
        print "\nNo mismatches found\n";
        print $dna;
        print $cmp;
    } else {
        ($temp ^= $dna) =~s[[^\0]][*]g;
        print "\nAsterists (*) indicate mismatches\n";
        print $dna;
        print $temp, $/;
        print $cmp;
    }
}


__DATA__
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCAG
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCA
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCCTAGGCTATATCTGCAGACGATCAGCAGCAAACGGATATCGGATCTAG
+GATCGATCAG
[download]

Output

C:\test>243661-2

No mismatches found
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCAG

Asterists (*) indicate mismatches
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
                                                                      
+         **
TGACCATGTATCGATCGATATCGTATGCTATATCTGCAGACGATCAGCAGCAAACGGATTTCGGATCTAG
+CATCGATCA

Asterists (*) indicate mismatches
ACTGGTACATAGCTAGCTATAGCATACGATATAGACGTCTGCTAGTCGTCGTTTGCCTAAAGCCTAGATC
+GTAGCTAGTC
                      *  *                                 *          
+*
TGACCATGTATCGATCGATATCCTAGGCTATATCTGCAGACGATCAGCAGCAAACGGATATCGGATCTAG
+GATCGATCAG

C:\test>
[download]