Build a hash of arrays - one array for each letter:

use strict;
use warnings;

my %frequencies;
my $maxCol = 0;

while (<DATA>) {
    chomp;

    my ($name, $seq) = split;
    
    next unless defined $seq;
    
    my @letters = split '', $seq;
    
    ++$frequencies{$letters[$_]}[$_] for 0 .. $#letters;
    $maxCol = $#letters if $maxCol < $#letters;
}

for my $letter (qw"A T G C") {
    $frequencies{$letter}[$_] ||= 0 for 0 .. $maxCol;
    print "$letter @{$frequencies{$letter}}\n";
}

__DATA__
fred  ATGTTGTAT
fred1 ATCTTATAT
fred2 ATCTTATAT
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Prints:

A 3 0 0 0 0 2 0 3 0
T 0 3 0 3 3 0 3 0 3
G 0 0 1 0 0 1 0 0 0
C 0 0 2 0 0 0 0 0 0
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