Finding often repeating substrings in multiple strings
Let's say you are looking for substrings that occur at least $c$ times in each string and have length at least $k$. Furthermore, lets say we're looking for maximally repeated substrings i.e. if $R$ is our solution set of substrings, there exists no pair $r_i, r_j\in R$ such that $r_i$ is a substring of $r_j$.

Offline option

Construct a generalized suffix tree from all input strings. Any node at depth at least $k$ that has at least $c$ leaves from each input string (i.e. at least $c$ $\$_1$ leaves, at least $c$ $\$_2$ leaves and so on) is $blue$ and each $blue$ node with no $blue$ children is also $red$. The set of substrings represented by $red$ nodes is the set of maximally repeated substrings. This runs in time $O(mn)$ where you have $n$ input strings of length at most $m$.