I'm guessing that you'll need to chomp the value of $CorE after you've read it in from STDIN. You're trying to match on just the value 'C', when perl is probably seeing 'C\n' as its value.
Just as a suggestion, you may also want to consider ignoring the case of the input. For example if someone enters 'c' then it doesn't pass the conditional. You could use a simple regex such as if ($CorE =~ /^C/i) which would also eliminate the need for chomping.