This reply would be better if it actually compiled. Line 19 (the first print in the if body) is missing a semi-colon - obviously not the code you ran to produce the given output!

It would also be better to use a manifest variable instead of the default variable in the while statement so both the intent and scope are clearer. Bundling an assignment and operation on a variable into one line probably isn't best practice in an example for someone new to Perl ((my $bad=$_)=~ tr/[ATCG]/ /;).

Do you really expect $bad=~ s{\w}{print 1+pos($bad),','}eg; to make sense to an entry level Perl user, even with the comment?