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# warning windows doublequotes
perl -lnE "$ar[0]++; $ar[pos]{$1}++  while /(.)/g;
...
4       B       1.00
5       B       0.25    C       0.50    D       0.25

perl -MData::Dump -lnE "$ar[0]++; $ar[pos]{$1}++  while /(.)/g;
                      END{ dd @ar }" freq.txt
...
  { B => 1, C => 2, D => 1 },
)

perl -MO=Deparse -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
...
    ;
}
-e syntax OK