#!/usr/bin/env perl

#  https://www.perlmonks.org/?node_id=11113020

use Data::Dumper;
    $Data::Dumper::Sortkeys=1;                       # make it easier 
+to find "things" in the "dumps"
# Yes we'll take all the help we can get
use strict;
use warnings;

# Read the data one line at a time
while (<DATA>) {                                      # Same as while 
+($_=<DATA>) {
    # And get rid of the $INPUT_LINE_SEPARATOR (\n);
    chomp;                                            # Same as chomp(
+$_);
    warn Data::Dumper->Dump([\$_],[qw(*_)]),' ';      # Let's see what
+ we have ... there shouldn't be a trailing \n
    (my $bad=$_)=~ tr/[ATCG]/ /;
    warn Data::Dumper->Dump([\$_],[qw(*_)]),' ';      # So all the val
+id ones are gone
    if ($bad !~ m{^\s+$}) {                           # Are there any 
+bad ones?
        print "line: $.\n"                            # Yes - so print
+ the offending line number
        print "$_\n";                                 # The offending 
+line
        print "$bad\n";                               # The offending 
+character(s) in the line
        $bad=~ s{\w}{print 1+pos($bad),','}eg;        # Look for a "ch
+aracter" if you find one print its "location'
        print "\n";
        };
    };
__END__
TAAGAACAATAAGAACAA
TAAGAACAATAAUAACAA
TAYGAACAkTAAGAACzz
[download]

Yields

perl 3020a.pl 2> nul
TAAGAACAATAAUAACAA
            U
13,
TAYGAACAkTAAGAACzz
  Y     k       zz
3,9,17,18,
[download]