use strict;
use warnings;

my $str = 'A[ACGT]G[TG]G[ACT]C[AT]'; # or whatever

my $strings = [ $str ];

while ( index ( $$strings[0], '[' ) > -1 ) { 
  $strings = expand ( $strings ) ;
}
print "$_\n" for @$strings;

sub expand {
  my $arg = shift;
  my @to_expand = @$arg;

  my $idx1 = index $to_expand[0], '[';
  my $idx2 = index $to_expand[0], ']';

  my $post = substr $to_expand[0], $idx2 + 1;

  my @expanded;

  foreach my $item ( @to_expand ) {
    my $pre = substr $item, 0, $idx1;
    for ( $idx1 + 1 .. $idx2 - 1 ) {
      push @expanded, $pre . substr ( $item, $_, 1 ) . $post;
    }
  }
  return \@expanded;
}