The first thing that jumps out of the code is that you are initialising and incrementing elements of %first, %second and %third but only printing results from %first.

• Read and heed Re: How can I count the number and kinds of letters at 1st, 2nd and 3rd positions of 3-letter words in a string?
• Use strict.
  No, I don't see anything critical that strict would have caught in this instance, but the only benefit of intentionally omitting it is the saving of a few keystrokes. The cost is missing the information it often offers.
• Comment out lines 5 through 17 and run your code again. Look for any variation from the output you show here. Think about what that implies.

You've been offered the tools to learn how to do this yourself; you've been given solutions to most of the many questions you've asked en route to this one. Please consider either using these gifts to good effect... or hire a programmer.

It's difficult to explain in english that... I don't undertand what is really your problem. The code in Re: How can I count the number and kinds of letters at 1st, 2nd and 3rd positions of 3-letter words in a string? is not very nice but it is simple and I don't understand the aim of your corrections.

You said: I didn't write "use strict" at the beginning of the code intentionally. -- Don't do that! It's baaaad! use strict; is your best friend!

It seems you don't what to use an hash. Why ? $A1,$G1...$C3: 12 variables!!!

Finnaly, my script was probably not so simple and I propose another one, with one hash and keys like "A1" or "G3".

#!perl
use strict;
use warnings;

my $seq = "ATCGGCGCCTAT" ;
my %poscount;

my @trilet = $seq =~ /.../g;
#print join "\n",@trilet;

foreach my $let ('A','T','G','C') { #init
    $poscount{$let.'1'}=0;
    $poscount{$let.'2'}=0;
    $poscount{$let.'3'}=0;
}

foreach my $tri (@trilet) {
    print "processing '$tri'\n";
    my $let1 = substr $tri,0,1;
    $poscount{$let1.'1'}++;
    print $let1,"1++\t";
    my $let2 = substr $tri,1,1;
    $poscount{$let2.'2'}++;
    print $let2,"2++\t";
    my $let3 = substr $tri,2,1;
    $poscount{$let3.'3'}++;
    print $let3,"3++\n\n";
}

foreach my $pos (1,2,3) {
    foreach my $let ('A','T','G','C') {
        my $letpos = $let.$pos;
        print "$letpos=$poscount{$letpos}; "
    }
    print "\n";
}
__END__
processing 'ATC'
A1++    T2++    C3++

processing 'GGC'
G1++    G2++    C3++

processing 'GCC'
G1++    C2++    C3++

processing 'TAT'
T1++    A2++    T3++

A1=1; T1=1; G1=2; C1=0; 
A2=1; T2=1; G2=1; C2=1; 
A3=0; T3=1; G3=0; C3=3;
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