#!/usr/bin/env perl

use strict;
use warnings;

my $DNA = <STDIN>;
chomp($DNA);

my $lengthseq = length $DNA;
print "The length of the sequence is: $lengthseq\n";

my (@nucleotideDNA, @nonvalid);

for my $pos (0 .. $lengthseq - 1) {
    my $nucleotide = substr $DNA, $pos, 1;

    if ($nucleotide =~ /^[ACGT]$/) {
        push @nucleotideDNA, $pos+1 . ":\t$nucleotide";
    }
    else {
        push @nonvalid, $pos+1 . ":\t$nucleotide";
    }
}

print "*** nucleotideDNA ***\n";
print "$_\n" for @nucleotideDNA;
print "*** nonvalid ***\n";
print "$_\n" for @nonvalid;

##</code><code>##

$ ./pm_11113020_parse_dna.pl
XACGTYTGCAZ
The length of the sequence is: 11
*** nucleotideDNA ***
2:      A
3:      C
4:      G
5:      T
7:      T
8:      G
9:      C
10:     A
*** nonvalid ***
1:      X
6:      Y
11:     Z

##</code><code>##

for my $pos (0 .. $#DNA) { ... }