Fix an integer $n$ and alphabet $\Sigma=\{0,1\}$. Define $DFA(n)$ to be the collection of all finite-state automata on $n$ states with starting state 1. We are considering all DFAs (not just connected, minimal, or non-degenerate ones); thus, $|DFA(n)| = n^{2n}2^n$.
Now consider two strings $x,y\in\Sigma^*$ and define $K(x,y)$ to be the number of elements of $DFA(n)$ that accept both $x$ and $y$.
Question: What is the complexity of computing $K(x,y)$?
This question has implications for machine learning.
Edit: Now that there's a bounty on this question, I suppose a bit more precision in the formulation is in order. For $n\ge1$, let $DFA(n)$ be the collection of $n^{2n}2^n$ automata, as defined above. For $x,y\in\{0,1\}^*$, define $K_n(x,y)$ to be the number of automata in $DFA(n)$ that accept both $x$ and $y$. Question: can $K_n(x,y)$ be computed in time $poly(n,|x|,|y|)$?