The problem here is the word order: In a usual sentence (main clause or subordinate clause), the word order is Subject-Predicate[P]-Object (O): "He told me where you are."
Even in an interrogative clauses, this word order remains: "Can you(S) tell(V) me where you are?". (Can here is an auxiliary verb that helps to keep the actual order (hv-S-V-O), if there's no auxliary like c
Where are you? = What is your location? = Where are you located? If your friend calls you in need of help: "Come and get me immediately!", you might ask "Where are you?". This is very common.
Where you are? = a short form of "Is it where you are?" ("it" refers to some place you were talking about earlier.) = Is it in the same place as you are? Suppose you and your friend