A better way to count your bases would be to use tr.
knoppix@Microknoppix:~$ perl -Mstrict -wE '
> my $dna = q{CCATGNGTTATGNGTTACACGTNGTNTACG};
> my $b = length $dna;
> my $A = $dna =~ tr{A}{};
> my $C = $dna =~ tr{C}{};
> my $G = $dna =~ tr{G}{};
> my $T = $dna =~ tr{T}{};
> my $e = $b - ( $A + $C + $G + $T );
> say qq{Number of bases - $b};
> say qq{A = $A; C = $C; G = $G; T = $T; err = $e};'
Number of bases - 30
A = 5; C = 5; G = 7; T = 9; err = 4
knoppix@Microknoppix:~$
I hope this is helpful.
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