my @instances = ( 'AAAAA  ATCGA',
                  'ATCGA  AAAAA',
                  'ATAAA  AAAAA',
                 );

##</code><code>##

my @instances2 = ( 'AAAAA  ATCGA',
                   'ATCGA',
                   'ATAAA  AAAAA',
                 );
# consensus :       ATAAA  A[AT][CA][GA]A

##</code><code>##

my @instances3 = ( 'AAAAA  ATCGA TTTT',
                   'ATCGA        TATA ',
                   'ATAAA  AAAAA ATTA ',
                 );
# consensus :      ATAAA  A[AT][CA][GA]A TTTA