Easily fixed by remembering all indices, e.g. like this:

#!/usr/bin/perl -w
use strict;

chomp(my @sequences = <DATA>);

my (%sequences, $i);
push @{$sequences{$_}}, $i++ for @sequences;

for (keys %sequences) {
    my $complement = reverse;
    $complement =~ tr/GCAT/CGTA/;
    print "$_ complements sequence nr @{$sequences{$complement}}\n" if
        $sequences{$complement};
}

__DATA__
GATTACA
GATTACA
TTAGCAA
CATCATC
TTGCTAA
TGTAATC
GATGATG
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