perl -MData::Dump -lnE "$ar[0]++; $ar[pos]{$1}++  while /(.)/g;
                      END{ dd @ar }" freq.txt
(
  4,                             # el 0 is the lines count
  { A => 3, B => 1 },            # el 1 contains occurences found at position 1
  { A => 4 },                    # el 2 .. so on
  { A => 1, B => 2, C => 1 },
  { B => 4 },
  { B => 1, C => 2, D => 1 },
)