First, read davido's answer: Re: How can I count the number and kinds of letters at 1st, 2nd and 3rd positions of 3-letter words in a string?

Here, I put some code, as easy as possible (I hope) without complexe data structure:

#!perl
use strict;
use warnings;

my $seq = "ATCGGCGCCTAT" ;
my (%first,%second,%third);
#perlre
my @trilet = $seq =~ /.../g;
#perlsyn LOOP
foreach my $letter ('A','T','G','C') { #init
    $first{ $letter }=0;
    $second{ $letter }=0;
    $third{ $letter }=0;
}
foreach my $tri (@trilet) {
    #perlfunc : substr
    $first{ substr $tri,0,1 }++;
    $second{ substr $tri,1,1 }++;
    $third{  substr $tri,2,1 }++;
}
foreach my $letter ('A','T','G','C') {
    print "$letter=$first{$letter}; ";
}
print "\n";
foreach my $letter ('A','T','G','C') {
    print "$letter=$second{$letter}; ";
}
print "\n";
foreach my $letter ('A','T','G','C') {
    print "$letter=$third{$letter}; ";
}
print "\n";
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