Hi there!

Just a few mistakes:

<FILE>; # ignore first line
my @words = (A, C, G, T); #letters to search
my @file = do {local $/; split (//, <FILE>); }; #split each letter int
+o an array

foreach $file (@file){
    foreach $words (@words){
        if ($file eq $words){
             $word_list{$file}++;
        }
    }
}
@pairs = sort {$a->[1] <=> $b->[1]}
         map {[ $_ => $word_list{$_}]}
         keys %word_list;

print "word $_->[0] = $_->[1]\n" for @pairs;
[download]

You were only splitting on the first line of the file, and there was a typo on the last line. The code above will hopefully work as you intended.