$ perl -Mstrict -Mwarnings -E '
my $ref = q{AATTTGGGCTACT};
my $qry = q{AAATTCGGCTACA};

my $xor = $ref ^ $qry;

my @offsets;
push @offsets, pos $xor while $xor =~ m{(?=[^\x00])}g;

say join q{ }, map { ( $_ + 1 ) . substr $qry, $_, 1 } @offsets;'
3A 6C 13A
$