#! perl -slw
use strict;

my $s = 'XXQQGGYYNNQGYNNNNQNGGNGGNGGGQQQNNN';

print $s; 
print ' ' x( pos( $s ) - length( $1) ), $1 
    while $s =~ m[
        (                     ## Capture to $1
        
            (?:             ## A group
                ([QGYN])    ## of these characters
                (?!\2{2})   ## repeated no more than twice in successi
+on
            ){3,6}          ## 3 to 6 characters in length
            ?                 ## Remove for greedy matching.    
        )
]xg;

## Condensed and greedy
print $s; 
print ' ' x( pos( $s ) - length( $1) ), $1 
    while $s =~ m[( (?: ([QGYN]) (?!\2{2}) ){3,6} ) ]xg;

__END__
[20:37:58.32] P:\test>temp
XXQQGGYYNNQGYNNNNQNGGNGGNGGGQQQNNN
  QQG
     GYY
        NNQ
               NNQ
                  NGG
                     NGG
XXQQGGYYNNQGYNNNNQNGGNGGNGGGQQQNNN
  QQGGYY
        NNQGY
               NNQNGG
                     NGGN
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