I too thought "bitwise string" but ended up with a different mix of operators: 
my $s = 'AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA';
my $t = 'ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA';

tr/ACGTA-Z/\0\0\0\0_/ for my ($s_, $t_) = ($s, $t);

my $merged = ($s | $t_) & ($t | $s_);
say $merged;

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In reply to Re^2: merging dna sequences by Anonymous Monk
in thread merging dna sequences by garyboyd

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