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 = $e};'
Number of bases - 30
A = 5; C = 5; G = 7; T = 9; err = 4
knoppix@Microknoppix:~$

[download]

I hope this is helpful.

Cheers,

JohnGG

In reply to Re: Request to detect the mistake in a perl script for finding inter-substring distance from a large text file by johngg
in thread Request to detect the mistake in a perl script for finding inter-substring distance from a large text file by supriyoch_2008

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