#!/usr/bin/perl
use strict;
use warnings;
use Syntax::Construct qw{ // };

my $endpos = 0;
my ($startpos, $count);
my %occurrences;

my $file = $ARGV[0];
open(DATA, $file);
while (<DATA>) {
    if (/^CLUSTAL.*/) {next;}
    if (/^ +$/) {
	$startpos = $endpos + 1;
	$count = 0;
    }
    elsif (/\s+ ([-actg]+) \s*$/x) {
        ++$count;
        my @nucleotides = split //, $1;
	$endpos = $endpos + length $1 if $startpos == $endpos + 1;
        for my $pos (0 .. $#nucleotides) {
            ++$occurrences{ $nucleotides[$pos] }[$startpos + $pos]
                unless '-' eq $nucleotides[$pos];
        }
    }
}

for my $pos (1 .. $endpos) {
    print "$pos\t";
    for my $nucleotide (sort keys %occurrences) {
        printf "%s\t%0.1f\t", uc $nucleotide, 100 * ($occurrences{$nucleotide}[$pos] // 0) / $count;
    }
    print "\n";
}


##</code><code>##

CLUSTAL O(1.2.1) multiple sequence alignment


gnl|hbvcds|AB014370_PreC_P-A       ------------------------------------------------------------
gnl|hbvcds|AB064314_PreC_P-A       ------------------------------------------------------------
gnl|hbvcds|AB014384_C_P-C          ------------------------------------------------------------
gnl|hbvcds|AB014385_C_P-C          ------------------------------------------------------------
gnl|hbvcds|AB048701_PreS1_P-D      atggggcagaatctttccaccagcaatcctctgggattctttcccgaccatcagttggat
gnl|hbvcds|AB078031_PreS1_P-D      atggggcagaatctttccaccagcaaccctctgggattctttcccgaccaccagttggat
gnl|hbvcds|AB030513_S_P-A          -----------------------------------------------------------a
gnl|hbvcds|AB064314_S_P-A          -----------------------------------------------------------c
gnl|hbvcds|AB194947_PreS2_P-E      -----------------------------------------------------------g
gnl|hbvcds|AB194948_PreS2_P-E      -----------------------------------------------------------g
                                                                                               

gnl|hbvcds|AB014370_PreC_P-A       tagagtctcctgagcattgctcacctcaccatactgcactcaggcaagccattctctgct
gnl|hbvcds|AB064314_PreC_P-A       tagagtctcctgagcattgctcacctcaccatacggcactcaggcaagccattctctgct
gnl|hbvcds|AB014384_C_P-C          tagagtctccggaacattgttcacctcaccatacagcactcaggcaagctattctgtgtt
gnl|hbvcds|AB014385_C_P-C          tagagtctccggaacattgttcacctcaccatacagcactcaggcaagctattctgtgtt
gnl|hbvcds|AB048701_PreS1_P-D      gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact
gnl|hbvcds|AB078031_PreS1_P-D      gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact
gnl|hbvcds|AB030513_S_P-A          gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact
gnl|hbvcds|AB064314_S_P-A          gggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggact
gnl|hbvcds|AB194947_PreS2_P-E      gggtttttcttgttgacaaaaatcctcacaataccgcagagtctagactcgtggtggact
gnl|hbvcds|AB194948_PreS2_P-E      gggtttttcttgttgacaaaaatcctcacaataccgcagagtctagactcgtggtggact
                                     *  * **  *   *       ****** **** ***        *    *  *    *