$sequence =~ /(ATG.*?(?<=TAA|TAG|TGA))/g

##</code><code>##

ATGGTTTCTCCCATCTCTCCATCGGCATAA
ATGA

##</code><code>##

my @from;
my $pos = -1;
push @from, $pos while -1 != ($pos = index $sequence, 'ATG', $pos + 1);

my @to;
for my $end (qw( TAA TAG TGA )) {
    $pos = -1;
    push @to, $pos + 3 while -1 != ($pos = index $sequence, $end, $pos + 1);
}

for my $f (@from) {
    for my $t (@to) {
        say substr $sequence, $f, $t - $f if $t > $f;
    }
}
__END__
Output:

ATGGTTTCTCCCATCTCTCCATCGGCATAA
ATGGTTTCTCCCATCTCTCCATCGGCATAAAAATACAGAATGATCTAA
ATGGTTTCTCCCATCTCTCCATCGGCATAAAAATACAGAATGA
ATGATCTAA
ATGA