Clones are exact DNA replcas of the original correct? Would there be any differences in a DNA test against a clone and the original sire? 

The normal way a clone is done is with a random mare's egg.  Which they harvest from the mare and remove the nuclious from. They then replace the nuclious with the donor material. The egg shell is all that remains of the mare's DNA. This shell carries Mitochondrial DNA that is passed from female to her female offspring. Since the mare is not from the same family as the donor, that makes the clone a 95% match to the donor.  If they get an egg from a mare that is from the same female family as the donor this difference disappears.  That said the testing done by the breed associations to determine parentage is not sensitive enough to determine the difference in the MtDNA. There are tests that can determine this 5% difference in DNA but they are not done in the normal course of breed parentage testing. One would have to know the need to do the test with a higher sensitivity before testing. 

Once the clone is alive and if it's a stallion the foals by this clone stallion will ALL have the same DNA contribution as the donor stallions foals since the clone stallion is not passing MtDNA to his foals because he doesn't have any egg shells. So there is no way to tell if the foals are by the donor or the clone.

Thank you! Exactly the answer I was looking for. Not that I am saying anyone is doing it, I was just curious if it was possible to pass off or register horses as being by a sire that are actually by a clone of said sire. 

It absolutely is possible. That's a concern. 

That was an awesome explanation!

What all studs out there have been cloned at this point?  I know the big ones - Scamper, Frenchmans Guy, etc... Are there more now?

HotShot, Latte, Feature Mr Jess, Royal Blue Boon, High Brow Cat, Topper, Storm Cat, Smart Little Lena,

Royal Blue Boon is a mare, isn't she??

Yes. I believe Dashing Phoebe was also cloned.

Taylor Fit (gelding) was also cloned.

Good gravy that's quite a list.

That’s all I thought of off the top of my head. There’s way more than that if you add Gem Twist, the 6 polo ponies and all the bucking horses. Plus a lot of people don’t want the public to know when they clone something so it’s kept quiet.

I really don't see the point in cloning a stallion when you can't register the foals by the clone through AQHA.

And yet none of the clones have been able to do what the original did.  

The 6 cloned polo ponies are actually doing very well. There’s talk of the Tomorillo clone (named Tomotillo) being in the Olympics in 2024 or so.  Guess time will tell.

I know the cutters didn’t do so hot. I’m not even sure if they are running Another Shot. I know the Latte clone is looking pretty good so far. 

Viagen said they clone roughly 100 horses every year. The guy with the polo ponies is with a company that has done 200 since 2009. There are way more clones out there than we realize. You can bet that as soon as one hits performance wise, they’ll be crowing from the rooftops.

So the host mare or the egg donor mare doesn't have any influence?  I still think that upbringing / inviroment would have to play some kind of role in how one turns out.

I absolutely think that upbringing has a lot to do with it- look at Scamper's clone, Charmayne started him on the barrels and he didn't take to it like Scamper did. I personally wouldn't breed to a cloned stallion for fear I would get semen from a clone. Some people don't mind, but I would feel jipped because I would want to know I'm getting semen from the stallion himself, that's been there, done that. You can't replicate upbringing and personality based on that, and I want the grit and mindset from the stallion himself. My husband said he wouldn't mind if we got semen from the clone and not the stallion himself because it's technically the same, but I disagree. 

Clayton doesn’t look or travel like Scamper did. Most clones do resemble the original. Clayton really didn’t.

I think the OP was originally posting that the DNA could be the same as the original stud. There has to be additional testing to that. I think the the OP was asking was just that  

If a stud was a clone and put in the ‘back woods’ so to speak... that the seman of the clone would test (under the current testing... without further testing) as THE original stud.Yes, it would.  

IF... unscrupulous stud owners wanted to ‘hide’ the cloned stud they COULD pass the ‘frozen’ seman of the cloned stud off as the original stud.. under current testing.  

AQHA would have to do further testing at that point to prove the original vs. the clone. 

I THINK that is what the OP was getting at.

I REALLY think this could happen the way the OP said.

And a BIG YES... that scenario is extemely concerning. 

I read a book with this same scenario--original sire could no longer produce viable semen and an "unknown" clone was used.  For the life of me can't remember the name of the book. . . 

Yep.

And no one would be the wiser.

People would not know that they were actually getting seman from the clone under the current DNA testing. 

Mitrochondrial DNA is passed from the female to ALL of her offspring. Since AQHA does prove parentage on the female side as well the mitochondrial DNA is tested also.  With genes, think of a BINGO game.  You draw numbers out that fit into different catagories.  Someone wins and you put all the numbers (genes) back in the bowl and start all over.  The next game will not have the same numbers called, making each individual different but you still have the same gene pool. That is why clones do not look exactly the same or have the same abilities  

I was was just watching a thing on TV about tracking criminals’ DNA through these genealogical sites. The testing is very precise.