You did not constrain where any of the triplets could match. You could replace 

while ($seq =~ /GCT/ig) { $GCT++; }

[download]

with 

while ($seq =~ /\G(?:...)*?GCT/sig) { $GCT++; }

[download]

or with 

while ($seq =~ /\G(...)/sg) { $GCT++ if uc($1) eq 'GCT'; }

[download]

but lets take one further and use 

while ($seq =~ /\G(...)/sg) { $counts{uc($1)}++; }

[download]

That reduces your program to 

my %counts;
++counts{uc($_)} for $seq =~ /.../sg;

for       my $l1 (qw( T C A G )) {
   for    my $l2 (qw( T C A G )) {
      for my $l3 (qw( T C A G )) {
         my $k = "$l1$l2$l3";
         my $v = $counts{$k} || 0;
         print("$k=$v;");
      }
      print("\n");
   }
}

[download]

In reply to Re: How can I get correct result in counting 3-letter words? by ikegami
in thread How can I get correct result in counting 3-letter words? by supriyoch_2008

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