As I suggested:

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my $k = 15;
my %repo = (
    "readA" => "AAACATGAAAAGAAATGATGAAACAGA",
    "readB" => "AAATCATGAAACAGAGCCTCATCTCCC ",
);
my @order = (  "readB_1","readA_2");

#my $k = 25;
#my %repo = (
#    "readA" => "GCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCA",
#    "readB" => "TACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAAC",
#    "readC" => "GCTGAGGCAGGAGAATTGCTTGAACTTAGGGGATG",
#    "readD" => "TACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAAC",
#);
#my @order = ( "readA_1", "readB_2", "readC_1", "readD_2");

sub muster {
    local $^W;
    my( $bits ) = @_;
    my $muster = '';
    for my $p ( 0 .. length( $bits->[0] )-1 ) {
        my %uniq;
        ++$uniq{ substr $bits->[ $_ ], $p, 1 } for 0 .. $#$bits;
        if( keys %uniq > 1 ) {
            $muster .= '(' . join( ',', keys %uniq ) . ')';
        }
        else {
            $muster .= each %uniq;
        }
    }
    return $muster;
}

my( @heads, @bodys,  @tails );
while( @order ) {
    my( $s1, $p1, $s2, $p2 ) = map split( '_', shift @order ), 1 .. 2;
    ( $s1, $s2 ) = ( $s2, $s1 ) if $p1 > $p2;

    push @heads, substr $repo{ $s2 }, 0, length( $repo{ $s2 } ) - $k;
    push @bodys, substr $repo{ $s2 }, -$k;
    push @tails, substr $repo{ $s1 }, $k;
    push @bodys, substr $repo{ $s1 }, 0, $k;
}

my $head = muster( \@heads );
my $body = muster( \@bodys );
my $tail = muster( \@tails );

print $head, $body, $tail;

__END__
TACTC(A,G)GGAGGAGAATTGCTTGAACCTGGGAGGCA(T,C)T(A,G)GG(A,G)G(A,G)(T,C)(A
+,G)
TACTC(A,G)GGAGGCTGAGGCAGGAGAATTGCTTGAAC(T,C)T(A,G)GG(A,G)G(A,G)(T,C)(A
+,G)

AAACATGAAAAGAAAT(C,G)ATGAAACAGAGCCTCATCTCCC
AAACATGAAAAGAAAT(G,C)ATGAAACAGAGCCTCATCTCCC
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