#!/usr/bin/perl
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::LocatableSeq;

my $seq1=new Bio::LocatableSeq(
-seq=>"ABCDEFG-",
-id=>"t1",
-start=>1,
-end=>8
);

my $seq2=new Bio::LocatableSeq(
-seq=>"BCZEFGIH",
-id=>"t2",
-start=>1,
-end=>8
);
my $seq3=new Bio::LocatableSeq(
-seq=>"KBCDEGH-",
-id=>"t3",
-start=>1,
-end=>8);


$aln=Bio::SimpleAlign->new();
$aln->add_seq($seq1);
$aln->add_seq($seq2);
$aln->add_seq($seq3);


#$factory= Bio::Tools::Run::Alignment::Clustalw->new();
#$aln=$factory->align(\@seq_array);

#$threshold=50;
$str=$aln->consensus_string($threshold);
#printf $aln->length,"\n";
#printf $aln->no_residues,"\n";
#printf $aln->no_sequences,"\n";
#printf $aln->percentage_identity,"\n";
printf $seq1->seq(),"\n";printf("\n");
printf $seq2->seq(),"\n";printf("\n");
printf $seq3->seq(),"\n";printf("\n");
printf("$str\n");
printf $aln->match_line(),"\n";
printf $aln->match(),"\n";