use strict;
use warnings;

my $source= '[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

my @tar = split //, $target1;
my @t = @tar;

for my $i (1..($#t+1))
{  
    my $a ='';    
    if ($source !~ /^\[/) #not ambiguous
    {
       ($a) =  $source =~ /^(.)/s;
        $source =~ s/^.//s;
        my $s = shift @tar;
        ($s eq $a) ? print "$s matches position $i in target\n" : print "$s not matches position $i in target\n";             
    }
    else         #ambiguous
    {
       ($a) =  $source =~ /^\[([^\]]*)/s;
        my @a = split //, $a;
        $source =~ s/^([^\]]*)\]//s;
        my $s = shift @tar;
        (my @m = grep /$s/, @a) ? print "[@a] matches position $i in target\n" : print "[@a] not matches position $i in target\n";       
    }
}