Let $X_r$ be a finite type Dynkin diagram, and $\ell$ be a positive integer greater than or equal to two. The $Y$-system of type $X_r$ with level $\ell$ is a system of algebraic relations, whose solutions have been proved to have periodicity. For any pair $(X_r, \ell)$, we define an integer sequence called exponents using formulation of the $Y$-system by cluster algebras. We give a conjectural formula expressing the exponents by the root system of type $X_r$, and prove this conjecture for $(A_1,\ell)$ and $(A_r, 2)$ cases. We point out that a specialization of this conjecture gives a relationship between the exponents and the asymptotic dimension of an integrable highest weight module of an affine Lie algebra. We also give a point of view from $q$-series identities for this relationship.