my @cols;
while (<DATA>) {
	chomp;
	my ($id, @markers) = split;
	for my $i (0..$#markers) {
		$cols[$i]{$markers[$i]}++;
	}
}

for my $i (0..$#cols) {
	print "column $i\n";
	print "$_ $cols[$i]{$_} " for sort keys %{$cols[$i]}; 
	print "\n";
}

__DATA__
3851 A A G G T T A A C C
3854 A A G G T T A A C C
3871 A A G G T T A A G G