@all_seqs = ();
while(<>)
{
	if($_=~/(.*)\t(.*)/)
	{
		$id=$1;
		$seq=$2;

		push @all_seqs, $seq;
	}
}

for ($i=0; $i<=$#all_seqs; $i++)
{
	$seq_to_examine=$all_seqs[$i];
	@split_seq_to_examine=split(//, $seq_to_examine);	

	for($j=0; $j<=1108; $j++)
	{
		if ($split_seq_to_examine[$j] eq 'A') {$count_A++;}
		elsif ($split_seq_to_examine[$j] eq 'T') {$count_T++;}
		elsif ($split_seq_to_examine[$j] eq 'C') {$count_C++;}
		elsif ($split_seq_to_examine[$j] eq 'G') {$count_G++;}
		elsif ($split_seq_to_examine[$j] eq '-') {$count_non++;}

	print $j."\t".$count_A."\t".$count_T."\t".$count_C."\t".$count_G."\n";
	}
}