I like bitwise operators :)

use strict;
use warnings;

my @targets = qw(AGGGGC TGGGGC);
my @sources = (<DATA>);

chomp @sources;
for my $source (@sources) {
  my @fields = grep length, split /(\[[^[\]]+\]|[^[\]]+)/, $source;
  my @cells = map {(index $_, '[') == 0 ? $_ : split ''} @fields;
  my $matchStr = join '', map {/\[/ ? "\x80" : $_} @fields;

  for my $target (@targets) {
    my @segments = grep length, split /(\x00+|.)/, $target ^ $matchStr
+;
    my $index = 0;

    for my $field (@segments) {
      next if length ($field) > 1 or $field eq "\x00";

      # Only here for an ambiguous char
      my $str = $cells[$index];
      my $chr = substr $target, $index, 1;

      next if $chr =~ /$str/;
      print "Mismatch at index $index in $source against $target\n";
    }
      continue {
      $index += length $field;
    }
  }
}

__DATA__
[TCG]GGGG[AT]
TGGGGT
[AC][TCG]GGG[AT]
[download]

Prints:

Mismatch at index 0 in [TCG]GGGG[AT] against AGGGGC
Mismatch at index 5 in [TCG]GGGG[AT] against AGGGGC
Mismatch at index 5 in [TCG]GGGG[AT] against TGGGGC
Mismatch at index 0 in TGGGGT against AGGGGC
Mismatch at index 5 in TGGGGT against AGGGGC
Mismatch at index 5 in TGGGGT against TGGGGC
Mismatch at index 5 in [AC][TCG]GGG[AT] against AGGGGC
Mismatch at index 0 in [AC][TCG]GGG[AT] against TGGGGC
Mismatch at index 5 in [AC][TCG]GGG[AT] against TGGGGC
[download]