Or, even more Perl-ish, with a bit less extra work (e.g. only one //g loop):

use Term::ANSIColor;
open(READ,"<dna.txt");
$m = 'AGGGGG';
$_ = do { local $/; <READ> };   # read whole file
s/\s+//g;                       # remove blanks
s{$m}{                          # search the string
    push @c, 1 - length($m) + pos;               # remember position
    color('bold green').$m.color('reset');       # remember to reset!
}eg;
print "$_\n";                   # print transformed string
print "NUMBER OF SITES THE MOTIF ($m) IS PRESENT: ".@c."\n";
print "AND THE POSITION IN THE STRING IS:", join(',', @c), "\n\n";
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