if statement only executes once in for loop even though condition in true

I'm writing a program that takes a file name and a number (n) from command line arguments. It reads a DNA sequence then finds and outputs the subsequences of length n with the highest frequency of C and G. Here's the code:

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
import java.util.Collections;
import java.util.Scanner;

public class CGIslands {
    public static void main(String args[]) {

        // check arguments

        if(args.length != 2) {
            System.err.println("ERROR: expected file name and an integer");
            System.exit(1);
        }

        int n = Integer.parseInt(args[1]);
        String fileName = args[0];
        Scanner s = null;
        String sequence = "";

        // read in sequence

        try {
            s = new Scanner(new File(fileName));
            } catch (FileNotFoundException e) {
                e.printStackTrace();
                }

        while(s.hasNext()) {
            sequence = sequence + s.next();
        }

        s.close();

        int numOfSubseq = sequence.length() - n + 1;
        double CGCount = 0;
        Double[] frequencyArr = new Double[numOfSubseq];
        Double[] countArr = new Double[numOfSubseq];

        for (int i = 0; i < numOfSubseq; i++) {

            CGCount = 0;

            for (int j = 0; j < n; j++) {

                if (sequence.charAt(i + j) == 'C' || sequence.charAt(i + j) == 'G') {
                    CGCount++;
                }
            }

            countArr[i] = CGCount;
            frequencyArr[i] = CGCount / n;
        }




        // print output

        System.out.println("n = " + n);
        System.out.format("Highest frequency: %.0f / %d = %.2f%%\n", Collections.max(Arrays.asList(countArr)), n, Collections.max(Arrays.asList(frequencyArr)) * 100);
        System.out.println("CG Islands:");

        for (int i = 0; i < numOfSubseq; i++) {
            System.out.println(countArr[i] + " " + Collections.max(Arrays.asList(countArr)));
            if (countArr[i] == Collections.max(Arrays.asList(countArr))) {
                System.out.format("%d thru %d: %s\n", i + 1, i + n, sequence.substring(i, i + n));
            }
        }


    }
}

Command line arguments:

inputFile.txt 4

inputFile.txt:

CCAATACCGT

The part I'm having trouble with is here:

for (int i = 0; i < numOfSubseq; i++) {

    if (countArr[i] == Collections.max(Arrays.asList(countArr))) {
       System.out.format("%d thru %d: %s\n", i + 1, i + n, sequence.substring(i, i + n));
    }
}

I've checked the values of both and they both equal 3.0 twice, but the if statement is only run once.

Output:

n = 4
Highest frequency: 3 / 4 = 75.00%
CG Islands:
6 thru 9: ACCG

Expected:

n = 4
Highest frequency: 3 / 4 = 75.00%
CG Islands:
6 thru 9: ACCG
7 thru 10: CCGT

Any ideas why the second one isn't printed even though the condition is still true?