#!/usr/bin/env perl

use strict;
use warnings;

my %results;

{
    local $/ = '';

    while (my $record = <DATA>) {
        $record =~ s/\A>(.+?)$//m;
        my $entry = $1;
        $record =~ s/\s//gm;
        $results{$entry}{len} = length $record;

        for (0 .. $results{$entry}{len} - 1) {
            ++$results{$entry}{count}{substr $record, $_, 1};
        }
    }
}

use Data::Dump;
dd \%results;

__DATA__
>sp_0005
VQLQESGGGLVQAGGSLRLSCAASGRAVSMYNMGWFRQAPGQERELVAAISRGGSIYYA
DSVKGRFTISRDNAKNTLYLQMNNLKPEDTGVYQCRQGSTLGQGTQVTVSS

>sp_0017
HVQLVESGGGSVQAGGSLRLTCAASGFTFSNYYMSWVRQAPGKGLEWVSSIYSVGSNGYY
ADSVKGRSTISRDNAKNTLYLQMNSLKPEDTAVYYCAAEPGGSWWDAYSYWGQGTQVTVS S