S4 ABIC
S1 AB-C
S2 A--C

##</code><code>##

S4 ABICID
S2 A--C-D
S1 AB-C-D

##</code><code>##

# With major improvement by "canonizable" Adrade :-)

sub align_v3
{
    my ($hashref,$seq) = @_;
    my @in = split(/\s/,$seq);
    my $test = join('(.*?)',@in);
    
    my @hyph_padded_seq;
    my @sequences;

   my $reduce;
   for (keys %$hashref) { $reduce = length(${$hashref->{$_}}[0]); 
   last; }

    for my $key( sort {$a cmp $b} keys(%$hashref))
    {

        my $string = join('',@{$hashref->{$key}});
       
        if($string =~ $test)
        {
           push(@sequences, $hashref->{$key});
        }

    }

    my $regex = '.*'.join('(.*)',@in).'.*';
    my @in_the_running;
    my $biglen = 0;

    for (@sequences) 
    {
        my @letters = @$_; # split(//,$_);

        s/.*($in[0].*$in[$#in]).*/$1/;

        my ($first, $last) = (0,0);
        for (@letters) { last if $_ eq $in[0]; $first++; }
        for (reverse @letters) { last if $_ eq $in[$#in];
        $last++; 
       }
        $last = $#letters - $last;

        @letters = @letters[$first..$last];
        my $asstr = join('',@letters);


        if ((my @gaps) = ($asstr =~ m/$regex/o))
        {
            my $len = length(join('',@gaps)) / $reduce;
            if ($len > $biglen) 
            { 
                unshift(@in_the_running, [ @letters ]); 
                $biglen = length(join('',@gaps)); 

            }
            elsif ($len == $biglen)
            {
                unshift(@in_the_running, [ @letters ]);

            }
            else 
            { 
                push(@in_the_running, [ @letters ]);
            }
        }
    }


    #print @{$in_the_running[0]}, "\n";
    push @hyph_padded_seq, join('',@{$in_the_running[0]}); 

    my @base = @{$in_the_running[0]};

    for my $seqno (1..$#in_the_running) 
    {
        # my @seq = split(//,$in_the_running[$seqno]);
        my @seq = @{$in_the_running[$seqno]};
        my $count = $#base;
        my @disp;

        for my $q (reverse @base) 
        {

          if (($seq[$#seq] eq $q) || ($count == $#seq))
          {
              push(@disp, pop(@seq));
          }
          else 
          { 
              push(@disp, '-' x $reduce);
          }
          $count--;
        }
        push @hyph_padded_seq, join('', reverse(@disp));
        #print reverse(@disp), "\n";
   }
     
    return @hyph_padded_seq; 
}

# A hash version can be found here: http://paste.phpfi.com/61624