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#!/usr/bin/perl -w
use strict;
...
my  $aln2 = $factory->align($seq_array_ref);  #final line that prints 
+to STDOUT
 
__END__

....some text, followed by.....
T-COFFEE, Version_1.37 (Wed Jul 11 14:38:06 PDT 2001)
...
seq_0           -------G-GG---------TGTTAT--TCAAGCAAAAAAA
seq_4           --TATTTGCAG---------TGATGTAATC-AGC-------
                          *                 *