I echo brother kscwab's comments .. this sounds an awful lot like homework.

At the very least, break down what kind of pattern you are looking for. The regexp you've listed appears to look for

• ATG;
• ACGT repeated three times, which you capture into $1, then expect to repeat from three to five thousand times; and
• One of TAA, TAG and TGA.

It's a bit hard to figure out exactly what your code is, because you haven't mastered putting the code between code tags. If you can explain in more complete sentences what you are looking for, I'm sure we can guide you into completing the Perl that you need to get the job done.

For example, the triplet you are looking for at the end .. the 'T' appears at the beginning of each pattern, so you are really looking for

• T; followed by
• AA, AG or GA.