Does it explicitly print to STDOUT, or just to the currently selected handle?

If the latter, and you have v5.8.x you could do something like (untested) 

my $buf;
open( my $fh, '>', \$buf ) or die "Write to buffer failed\n";
my $hold = select( $fh );
my  $aln2 = $factory->align($seq_array_ref);
select $hold;
# find desired line in $buf
my ($score) = $buf =~ /SCORE (\d+)/;

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the lowliest monk

In reply to Re: Parsing Text from Object Header that prints to STDOUT by tlm
in thread Parsing Text from Object Header that prints to STDOUT by monkfan

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