use 5.026;
use warnings;

open my $dnaFH, q{<}, \ <<__EOD__ or die $!;
TAAGAACAATAAGAACAAGAACAATAA
GAACAATAAGXAATAAGAAXXAACAAGAACAATAA
ACAATAAAAGAACAATAAGAA
__EOD__

while ( my $sequence = <$dnaFH> )
{
    chomp $sequence;
    my $length = length $sequence;
    say qq{Sequence: $sequence -- Length $length};
    if ( $sequence =~ m{^[ACGT]+$} )
    {
        say q{     Sequence is GOOD!};
    }
    else
    {
        my @badPosns;
        push @badPosns, pos $sequence
           while $sequence =~ m{(?x) (?= ( [^ACGT] ) )}g;
        my $nBad = scalar @badPosns;
        my $perc = sprintf q{%.2f}, $nBad / $length * 100;
        say qq{     Sequence is BAD at @badPosns};
        say qq{     $nBad bad positions, $perc\% of total};
    }
}

close $dnaFH or die $!;