This one is inspired by moritz's solution, which only replaced the last "T" with a "K" in the first string. It has one less bit-op than my original, so should be a bit faster. (LOL... that one snuck up on me while typing) 
my $s = 'AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA';
my $t = 'ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA';

(my $del = $t) =~ tr/ACGTA-Z/\0\0\0\0_/;
(my $add = $t) =~ tr/ACGT/_/;

my $merged = ($s | $del) & $add;
say $merged;

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In reply to Re^3: merging dna sequences by Anonymous Monk
in thread merging dna sequences by garyboyd

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