First, I do not replicate your stated challenge. You say "that the $1 is unspecified", but when I get your posted code, I get: 
GTTTCTCCCATCTCTCCATCGGCATAAAAATACAGAATGATC

[download]
which, while it is not correct, is not unspecified. Am I misunderstanding your statement, or are you seeing something different from your code? Make sure that your examples match up to the issues you are encountering.

If I run stevieb's solution, I get 

GTTTCTCCCATCTCTCCATCGGCA
ATC

[download]
which would seem to meet your spec. The bigger question is what happens for nested cases? What is your expected output for 
my $seq = 'ATGATGTGATGA';

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Also, I note a reference to codons, which implies that your tests should be considering a stride of 3 rather than an arbitrary position. Does this matter for your case?

#11929 First ask yourself `How would I do this without a computer?' Then have the computer do it the same way.

In reply to Re: Regular expressions by kennethk
in thread Regular expressions by lairel

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