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          $local_array[$seq_num] = Bio::Seq->new(-id=>$id, -seq=>$string);
      }
      @local_array = grep $_ , @local_array; # remove array entries with no match

      # Perform alignment on the local segments of the sequences which match "anchor"
      $aln = $factory->align(\@local_array);
      my $consensus  = $aln->consensus_string(); # Get consensus of local alignment

      if (scalar(@seqs_not_matched) ) {
          print " Sequences not matching $regex : @seqs_not_matched \n"
      } else {
          print " All sequences match $regex : @seqs_not_matched \n"
  }
      print "Consensus sequence of local alignment: $consensus \n";

      return 1;
  }

  #----------------
  sub clustalw_usage {
  #----------------

  #-----------------------
  # Prints usage information for general parameters.

      print STDERR <<"QQ_PARAMS_QQ";

   Command-line accessible script variables and commands:
   -------------------------------
   -h                 :  Display this usage info and exit.
   -in <str>          :  File containing input sequences in fasta format (default = $infile) .
   -do <str>          :  String listing examples to be executed. Default is to execute
                         all tests (ie default = '123')
   -param <str>   :  Parameter to be varied in example 1. Any clustalw parameter
                     which takes inteer values can be varied (default = 'ktuple')
   -start <int>   :  Initial value for varying parameter in example 1 (default = 1)
   -stop <int>    :  Final value for varying parameter (default = 3)
   -regex   <str> :  Regular expression for 'anchoring' alignment in example 3
                     (default = $regex)
   -ext <int>     :  Distance regexp anchor should be extended in each direction
                     for local alignment in example 3   (default = 30)

  In addition, any valid Clustalw parameter can be set using the syntax
  "parameter=>value" as in "ktuple=>3"

  So a typical command lines might be:
   > clustalw.pl -param=pairgap -start=2 -stop=3 -do=1 "ktuple=>3"
  or
   > clustalw.pl -ext=10 -regex='W[AST]F' -do=23 -in='t/cysprot1a.fa'

  QQ_PARAMS_QQ

  }

=head1 PARAMETER FOR ALIGNMENT COMPUTATION

=head2 KTUPLE

 Title       : KTUPLE
 Description : (optional) set the word size to be used in the alignment
               This is the size of exactly matching fragment that is used.
               INCREASE for speed (max= 2 for proteins; 4 for DNA),
               DECREASE for sensitivity.
               For longer sequences (e.g. >1000 residues) you may
               need to increase the default

=head2 TOPDIAGS

 Title       : TOPDIAGS
 Description : (optional) number of best diagonals to use
               The number of k-tuple matches on each diagonal
               (in an imaginary dot-matrix plot) is calculated.
               Only the best ones (with most matches) are used in
               the alignment.  This parameter specifies how many.
               Decrease for speed; increase for sensitivity.

=head2 WINDOW

 Title       : WINDOW
 Description : (optional) window size
               This is the number of diagonals around each of the 'best'
               diagonals that will be used.  Decrease for speed;
               increase for sensitivity.

=head2 PAIRGAP

 Title       : PAIRGAP
 Description : (optional) gap penalty for pairwise alignments
               This is a penalty for each gap in the fast alignments.
               It has little affect on the speed or sensitivity except
               for extreme values.

=head2 FIXEDGAP

 Title       : FIXEDGAP
 Description : (optional) fixed length gap penalty

=head2 FLOATGAP

 Title       : FLOATGAP
 Description : (optional) variable length gap penalty

=head2 MATRIX

 Title       : MATRIX
 Default     : PAM100 for DNA - PAM250 for protein alignment
 Description : (optional) substitution matrix used in the multiple
               alignments. Depends on the version of clustalw as to
               what default matrix will be used

               PROTEIN WEIGHT MATRIX leads to a new menu where you are
               offered a choice of weight matrices. The default for
               proteins in version 1.8 is the PAM series derived by
               Gonnet and colleagues. Note, a series is used! The
               actual matrix that is used depends on how similar the
               sequences to be aligned at this alignment step
               are. Different matrices work differently at each
               evolutionary distance.

               DNA WEIGHT MATRIX leads to a new menu where a single
               matrix (not a series) can be selected. The default is