Shell Programming and Scripting

Hi All, here's a question from newbie

I have a data like this, which set of small DNA sequences separated by new line

I usually have to count frequency of each character in whole data, which I do with

Code:

awk -F "" '{ for ( i=1; i<=NF; i++) freq[$i]++} END {for (a in freq) print a, freq[a]}'

Now I am almost clueless when I need to count frequency of characters at each position, I am trying to present example with subset of data below
Any ideas, help is most appreciated. Please tell me if I am not clearly stating the problem.

Thank you,

Amit