This appears to meet the spec?

#! perl -slw
use strict;

sub consensus {
    my( $aref ) = @_;
    my $result;
    my $xor = $aref->[0];
    $xor ^= $_ for @{ $aref }[ 1 .. $#$aref ];

    for my $o ( 0 .. length( $xor ) -1 ) {
        if( substr $xor, $o, 1 eq chr(0) ) {
            $result .= substr $aref->[0], $o, 1;
        }
        else {
            my %c; $c{ substr $_, $o, 1 }++ for @{ $aref };
            my @sorted = sort{ $c{ $b } <=> $c{ $a } } keys %c;
            my $add = join '', grep{ $c{ $_ } == $c{ $sorted[ 0 ] } } 
+@sorted;
            $add = "[$add]" if length( $add ) > 1;
            $result .= $add;
        }
    }
    return $result;
}

my @sets = (
    [ qw[AAAAA ATCGA ATAAA] ],
    [ qw[AAAAA AACGA ATAAA ATAAA] ],
    [ qw[ACCGTA ATCGTA ACTGGA ATCCGA ] ],
);

print "[@$_] : ", consensus( $_ ) for @sets;
__END__
P:\test>500962
[AAAAA ATCGA ATAAA] : ATAAA
[AAAAA AACGA ATAAA ATAAA] : A[AT]AAA
[ACCGTA ATCGTA ACTGGA ATCCGA] : A[TC]CG[TG]A
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