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my $a = "ABABA";
my $b = "BB--B-BB";
...
my $a_pos = 0;
$new =~ s:[^-]:substr($a, $a_pos++, 1):ge;
print "New is $new\n";

my $a = "ABABA";
my $b = "BB--B-BB";
substr($a, pos($b)-1, 0, '-') while ($b =~ /-/g);

print "A is now $a\n";