use strict;
use warnings;

my $source1  = '[TCG]GGGG[AT]'; # ambiguous
my $target1   = 'AGGGGC'; # No of mismatch = 2  on position 1 and 6
my $target2  = 'TGGGGC'; # No of mismatch = 1  on position 6 only

# Turn the source into a regexp that accepts any character at each
# position, but only captures the matches
(my $sourcepat = $source1) =~ s/(\[.*?\]|.)/(?:($1)|.)/g;

for ($target1, $target2) {
  # Substitute _ for undef in the matches returned
  my @result = map defined()?$_:'_', /$sourcepat/;
  print "$_: @result\n";
}
__DATA__
Output is:
AGGGGC: _ G G G G _
TGGGGC: T G G G G _