However, Clark was able to slot him in behind a solid tempo and when he got to the outside, Alligator Blood ($11) accelerated clear to score by a length over the luckless Private Eye ($17), with Rothfire ($11) sticking on after leading, another 1-3/4 lengths away.
"On straightening, it was a matter of being patient, letting him build through his gears and I thought all he has to do is find off the bridle and he showed a great turn of foot," Clark said.
"I haven't had a lot to do with the horse's career but that was a pretty special performance.
"It's great to ride another Group 1 winner for Gai and Adrian, Gai's 150th, her first Stradbroke and I'm sure they'd be stoked."
Private Eye's jockey Brenton Avdulla ran into traffic jams in the straight and felt the topweight would have made a race of it with even luck.
"He went huge and was probably stiff not to win," Avdulla said.
"The low draw helped him early but the things around him didn't take him anywhere and the winner was off and gone."
Favourite Eleven Eleven finished last with Hugh Bowman saying everything went wrong from the time the horse got into the gates.
"He got a bit upset in the barriers with a bit going on and I didn't have time to settle him," Bowman said.
"During the race it was chaotic to say the least, and he didn't appreciate it unfortunately."
Alligator Blood was the 16th major Waterhouse and Bott have won since forming their partnership, adding to the 134 Waterhouse captured as a trainer in her own right.