Kamino Factory

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.Arrays;
import java.util.Scanner;

public class KaminoFactory {
    public static void main(String[] args) throws IOException {
        Scanner scanner = new Scanner(System.in);

        BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));

        int size = Integer.parseInt(reader.readLine());

        String input = "";

        int bestSequenceIndex = Integer.MAX_VALUE;
        int bestSequenceSum = 0;
        int bestSequenceIndexRow = 0;
        int bestSequenceIndexRowOutput = 0;
        String sequenceOutput = "";

        while (!"Clone them!".equals(input = reader.readLine())) {
            ++bestSequenceIndexRow;
            String[] data = Arrays.stream(input.split("!+"))                          // String[] data = input.split("!+");
                    .filter(e -> !e.equals(""))
                    .toArray(String[]::new);

            int[] sequenceDNA = new int[size];
            int index = 0;
            for (int i = 0; i < data.length; i++) {
                sequenceDNA[index++] = Integer.parseInt(data[i]);
            }
            int maxCount = 0;
            int sequenceIndex = 0;
            for (int i = 0; i < sequenceDNA.length; i++) {
                int currentCount = 0;
                for (int j = i; j < sequenceDNA.length; j++) {
                    if (sequenceDNA[i] == sequenceDNA[j]) {
                        currentCount++;
                        if (currentCount > maxCount) {
                            maxCount = currentCount;
                            sequenceIndex = i;
                        }
                    } else {
                        break;
                    }
                }
            }
            int sequenceSum = 0;
            for (int i = 0; i < sequenceDNA.length; i++) {
                if (sequenceDNA[i] == 1) {
                    sequenceSum += sequenceDNA[i];
                }
            }
            if (sequenceIndex < bestSequenceIndex || sequenceSum > bestSequenceSum) {
                sequenceOutput = "";
                bestSequenceIndex = sequenceIndex;
                bestSequenceSum = sequenceSum;
                bestSequenceIndexRowOutput = bestSequenceIndexRow;
                for (int i = 0; i < sequenceDNA.length; i++) {
                    sequenceOutput += sequenceDNA[i] + " ";
                }
            }
        }
        System.out.println(String.format("Best DNA sample %d with sum: %d.",
                bestSequenceIndexRowOutput, bestSequenceSum));
        System.out.println(sequenceOutput.trim());
    }
}