Likely, substr is all you need, if you already know what parts overlap and what parts do not overlap. Once you have the non-overlapping parts, you can go through them character by character and if they match, you output that character, and if they don't match, you output the pair. I think there can only be two pairs anyway, so a fancy trick would be to use binary XOR on the "nonmatched" parts:

use strict;

my @nonmatched = qw(TACTCAGGAG TACTCGGGAG);
my $difference = $nonmatched[0] ^ $nonmatched[ 1 ];

# Replace all zeroes (= matches) by the original string:
$difference =~ s/\0/substr($nonmatched[0],pos($difference),1)/ge;

# Replace the "weird" parts with the proper pairs
my %pairs = (
    'C' ^ 'T' => '(C,T)',
    'A' ^ 'G' => '(A,G)',
);

$difference =~ s/(.)/$pairs{$1} || $1/ge;

print $difference;
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