TIMTOWTDI

#!/usr/bin/env perl 
use strict;
use warnings;
use Test::More tests => 3;

my $have = 'aabbccddaaffddnnaa';
my $want = 'aabbccddeeffddnnaa';
my $aa   = $have;

# perldoc perlre
$aa =~ s/daaf/deef/;
is ($aa, $want, 'Match explicit surrounds');

# perldoc perlre
$aa = $have;
$aa =~ s/(.)aa(.)/$1ee$2/;
is ($aa, $want, 'Match non-terminal surrounds');

# perldoc -f substr
$aa = $have;
substr ($aa, length($aa)/2 - 1, 2, 'ee');
is ($aa, $want, 'Replace middle 2 chars of even-length string');
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Since you've given no algorithm to determine what to replace choose whichever suits.