(Analysis by Danny Mittal)

For convenience, let $S$ be the given string.

Subtask 1 ($|S| \leq 10$)

There are at most $4^{10} \approx 10^6$ possible genomes, so we can just try each one to see if it produces something consistent with the input after Farmer John's edits. This runs in $O(|S|4^{|S|})$.

Subtask 2 ($|S| \leq 10^2$)

Consider dividing the result of Farmer's John's edits back into the substrings of the genome after he had reversed them (but before he had concatenated them). Such a division could only correspond to one starting genome, which we could get by reversing the substrings back and concatenating them. However, not every division is valid (corresponds to some starting genome). In order for a division to be valid, it must satisfy two properties:

• For any two consecutive substrings $s$ and $t$ in our division, the first letter of $s$ and the last letter of $t$, which were adjacent before Farmer John reversed the substrings, must be equal in order for Farmer John to have split the genome there.
• Any substring $s$ must not have two adjacent letters within itself that are equal, because if it did, Farmer John would have split the genome there as well.

Given these conditions, we can solve this problem using DP. It is useful to first compute a preliminary DP that for each substring $S[j\ldots k]$ and letters $l, m$ computes the amount of ways to replace the question marks in $s[j\ldots k]$ with letters so that $s[j\ldots k]$ starts with $l$, ends with $m$, and satisfies our second condition, i. e. doesn't contain any two adjacent equal letters. This DP is fairly straightforward to compute in $O(|S|^2)$.

After that, we will perform our main DP, where for each index $k$ and letter $l$, we compute the number of divisions of $S[1\ldots k]$ such that the last substring in the division begins with $l$. To transition, we try each possible ending index $j$ of the previous substring in our division. By making use of our preliminary DP values for $s[j + 1\ldots k]$, we can do this in constant time for each $(j, k)$, making this DP, and thus the overall algorithm, $O(|S|^2)$ as well.

Subtask 3 ($|S| \leq 10^5$)

To solve this subtask, we will optimize our solution to the previous subtask.

In our new DP, we will instead, for each $k$, count divisions of $S[1 \ldots k]$ which may be incomplete, in that the last letter of the last substring may not match the first character of the second-to-last substring. This means that in addition to keeping track of the first letter $l$ of the last substring, we also need to keep track of the last letter $m$ of the last substring as well as the first letter $n$ of the second-to-last substring. We will refer to said DP value as $dp_{k, n, l, m}$.

The optimization comes from the transitions necessary for this DP. Instead of going through all previous indexes $j$, our transition is either extending the last substring in our division up to $k - 1$ by one character, or adding a new substring consisting of a single character to our division up to $k - 1$.

In the first type of transition, the letters $n$ and $l$ stay the same, and the last two letters in the substring we are extending must not be equal in order to satisfy our second condition, so we simply add $dp_{k - 1, n, l, m}$ to $dp_{k, n, l, m'}$ for all $n, l, m, m'$ such that $m \neq m'$ and $m'$ is a valid letter for $S_k$.

In the second type of transition, the old values of $n$ and $m$ must match in order to satisfy our first condition, so we add $dp_{k - 1, m, l, m}$ to $dp_{k, l, m', m'}$ for all $m, l, m'$ such that $m'$ is a valid letter for $S_k$.

To compute our final answer, we simply need to ensure that we have $n = m$, so our answer is the sum over $dp_{|S|, m, l, m}$ for all $m, l$.

For each $k$, we compute at most $4^4 + 4^3$ transitions, which is constant (and still small enough), making our algorithm $O(|S|)$.

import java.io.BufferedReader;
import java.io.IOException;

public class BovineGenomicsII {
public static final long MOD = 1000000007;
public static final char[] BASES = "AGCT".toCharArray();

public static void main(String[] args) throws IOException {
long[][][][] dp = new long[s.length][4][4][4];
for (int n = 0; n < 4; n++) {
for (int l = 0; l < 4; l++) {
if (s[0] == '?' || s[0] == BASES[l]) {
dp[0][n][l][l] = 1L;
}
}
}
for (int k = 1; k < s.length; k++)
for (int m2 = 0; m2 < 4; m2++)
if (s[k] == '?' || s[k] == BASES[m2]) {
for (int n = 0; n < 4; n++) {
for (int l = 0; l < 4; l++) {
for (int m = 0; m < 4; m++) {
if (m != m2) {
dp[k][n][l][m2] += dp[k-1][n][l][m];
dp[k][n][l][m2] %= MOD;
}
if (n == m) {
dp[k][l][m2][m2] += dp[k-1][n][l][m];
dp[k][l][m2][m2] %= MOD;
}
}
}
}
}