Hash to the rescue.

However, some 3 letter words occur more than onces, it shows correctly!

#!/usr/bin/perl 
use warnings;
use strict;

my $a="NTCA TCC TCGTCTTTCTTTTTATTGTACTATTAATAGTGCTGTTGATGGCTACTCCTGCTT
+CCACAT
CAACAGCGACGCCGGCGTATAATCATTATGACAACCACGACTAACAATAAAAAGAGCAGTAGAAGGCCCC
+CGC
CTCACGTAGTCGTGGTTGCAGCCGCGGCTGACGATGAAGAGGGAGGCGGGGGT N";

 $a=~s/\s+?//g;
 my %has_dat;
   foreach my $alpha(split//,$a){
      $has_dat{$alpha}++ if $alpha eq  ('A'|'T'|'G'|'C') or $alpha ne 
+ ('A'|'T'|'G'|'C');
   }
     print $_,'=',$has_dat{$_},' ' for keys %has_dat;

   print "\nLength: ",length($a),$/;

    %has_dat=(); 
   while($a=~m/\G(\w{3})/gc){
        $has_dat{$1}++;
     }
      my $counter=0;
     foreach (sort keys %has_dat){
        if($counter==5){print "\n";$counter=0;}
        print $_,'=',$has_dat{$_},' ';++$counter;
    }
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