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Your dog is not "alpha" nor is he "dominant" and describing him as such only adds useless labels that don't help you solve the problem.
As it has been mentioned, the dog should not have free run of the house. In fact, I would crate it and begin house-training as it was a brand new dog. This means scheduled feedings, water, crating and supervised elimination breaks. At no time should the dog be unsupervised.
House soiling is one of the main reasons people give when abandoning dogs and really there is no excuse when a systematic approach can solve the problem.
..... you have had him medically checked for infections, and other problems?
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