use strict;
use warnings;

my $DNA = "ATATCCCGATCAGG3TT!GCA\n";
chomp $DNA;
print "The length of the sequence is:\n", length($DNA), "\n";

my $nucleotideDNA = $DNA;
#my $count = $nucleotideDNA =~ tr/ATCG]//c;  # Remove and count invalids
my $count = $nucleotideDNA =~ tr/ATCG//cd;  # Remove and count invalids

my $locations;  # Find location of invalids in original string
$locations  .=  "$-[0], " while ( $DNA =~ /[^ATCG]/g );

print "There are $count non-valid nucleotides at locations:\n$locations \n";


OUTPUT:
The length of the sequence is:
21
There are 2 non-valid nucleotides at locations:
14, 17,