#!/usr/bin/env perl

use strict;
use warnings;
use Bio::AlignIO;
use Bio::SeqIO;
use Bio::Seq;

my $seqtt  = Bio::AlignIO->new(-file => "test.ali");

my $alntt=$seqtt->next_aln();
my $seqtemplate=$alntt->get_seq_by_pos(1);
my $seqtarget=$alntt->get_seq_by_pos(2);

printf "AlignID in: %5.2f, length: %s\n", $alntt->percentage_identity, $alntt->length();


for (my $k=1;$k<$alntt->length();$k++){
    my $col1=$alntt->column_from_residue_number( $seqtemplate->id(), $k);
    my $col2=$alntt->column_from_residue_number( $seqtarget->id(), $k);
    printf "%s:%d for seq 1 and %s:%d for seq 2\n", substr($seqtemplate->seq(),$col1,1), $col1, substr($seqtarget->seq(),$col2,1), $col2; 
                                              ;
    #my $col=$alntt->column_from_residue_number( $seqtarget->id(), $k);
}