not really sure what is a motif here, but this can't stop me to fail, of course XDD ... please, save the facepalms for the end, thanks ;-)

Only a draft, unworking and untested...but can give you some ideas

use 5.010;

my ($file, $motif) = @ARGV;

my $warn = <<'EOF';
     Number or arguments incorrect, Please run this program 
     with 2 arguments, a file and a motif to count the number 
     of letters between any two motifs: i.e. 
     perl script.pl myfile mymotif
EOF

if (scalar @ARGV != 2) {print $warn}

if (scalar @ARGV == 2){

open (my $DNAFILE, '<', $file) 
        or die "I need that you provide a file. Cannot open file $!";

## $DNAFILE = join( '', @DNA); 
## don't understand this line ... can you explain this?

$DNAFILE =~ s/\s//g;  # Remove whitespace, ok

if ( $DNAFILE =~ /$motif/ ) {
     print "\nI found it!\n";
      
       # Count number of nt between two motifs
 
my $string ="@DNA"; # same question, explain please, why do you need t
+his?
 ## mmmh... are you trying to say "\@DNA"?

     say "Lengths are:", $_ for map { sprintf("%d", length) } split /$
+motif/, $string;

# Count number of motifs

my $count=($string =~ m/$motif/g);

print "Number of motifs: $count.\n\n";

close DNAFILE;

} else { print "The motif: $motif was not found in the file $file.\n"}

} # first else block



__END__
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Your turn

(Updated: problem with $warn fixed)