YAPE::Regex::Explain might help you here:

(?m-isx:^.*$)

matches as follows:
  
NODE                     EXPLANATION
----------------------------------------------------------------------
(?m-isx:                 group, but do not capture (with ^ and $
                         matching start and end of line) (case-
                         sensitive) (with . not matching \n)
                         (matching whitespace and # normally):
----------------------------------------------------------------------
  ^                        the beginning of a "line"
----------------------------------------------------------------------
  .*                       any character except \n (0 or more times
                           (matching the most amount possible))
----------------------------------------------------------------------
  $                        before an optional \n, and the end of a
                           "line"
----------------------------------------------------------------------
)                        end of grouping
----------------------------------------------------------------------
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The .* does not match a newline character, and $ is optional. Perhaps you also want the /s modifier (perlre):

use warnings;
use strict;

"AAC\nGTT\n" =~ /^.*$/ms;

print $&; 

__END__

AAC
GTT
[download]