# warning windows doublequotes
perl -lnE "$ar[0]++; $ar[pos]{$1}++  while /(.)/g;
     END{ foreach $row (1..$#ar){print join qq(\t),$row,map{$_,sprintf('%.2f',$ar[$row]{$_}/$ar[0] )} sort keys %{$ar[$row]}} }" freq.txt

1       A       0.75    B       0.25
2       A       1.00
3       A       0.25    B       0.50    C       0.25
4       B       1.00
5       B       0.25    C       0.50    D       0.25