Depending upon your data, simply checking first that the strings don't match can make it much faster :
#String length is assumed to be equal
my ($k,$l) = @_;
# next line added
return 0 if $k eq $l;
my $len = length ($k);
my $num_mismatch = 0;
for (my $i=0; $i<$len; $i++)
++$num_mismatch if substr($k, $i, 1) ne substr($l, $i, 1);
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