Объединить разделенный строки

HashMap<String, String> data = new HashMap<>();
data.put(">DNA_CHAIN_ID_6404", "CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG")

 private HashMap<String, String> concatStrings(String filePath) throws IOException {
        ArrayList<String> keys = new ArrayList<>();
        ArrayList<String> concatenatedStrings = new ArrayList<>();
        HashMap<String, String> data = new HashMap<>();
 
        BufferedReader in = new BufferedReader(new FileReader(filePath));
 
        String line;
        String concatenatedString = "";
 
        while ((line = in.readLine()) != null) {
            while (!line.startsWith(">")) { //until a string doesn't start with the ">" sign it's a part of a DNA chain
                concatenatedString = concatenatedString + line.trim(); //save a piece
                line = in.readLine(); //retrieve a next piece of the DNA chain
                if (line == null) //if nothing to read further - break;
                    break;
            }
 
            if(line!=null) //if there is still something to read in file, conduct the following control
            if (line.startsWith(">")) //if a string starts with ">" it's an id from DB
                keys.add(line); //add to IDs
 
            if (!concatenatedString.startsWith(">") && !concatenatedString.equals("")) { //if a string is not empty and doesn't start with ">", then it's definitely a DNA chain
                concatenatedStrings.add(concatenatedString);//add to values
                concatenatedString = ""; //reset value
            }
        }
 
        for (int i = 0; i < keys.size(); i++)
            data.put(keys.get(i), concatenatedStrings.get(i)); //add everything to map
 
        return data;
    }

public static void main(String[] args) {
        String in = ">DNA_CHAIN_ID_6404\n" +
                "CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC\n" +
                "TCCCACTAATAATTCTGAGG\n" +
                ">DNA_CHAIN_ID_5959\n" +
                "CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT\n" +
                "ATATCCATTTGTCAGCAGACACGC\n" +
                ">DNA_CHAIN_ID_0808\n" +
                "CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC\n" +
                "TGGGAACCTGCGGGCAGTAGGTGGAAT";
        
        in = in.replaceAll("\\W", "");
        in = in.replaceAll("(DNA.+?\\d+?)(?:[A-Z])", " $1 ");
        Map<String, String> map = new HashMap<>();
 
        String[] items = in.trim().split(" ");
        for (int i = 0; i < items.length; i += 2) {
            map.put(items[i], items[i + 1]);
        }
        // ....
        for (Map.Entry<String, String> pair : map.entrySet()) {
            System.out.printf("Key: %s\nValue: %s\n", pair.getKey(), pair.getValue());
        }
    }

public static void main(String[] args) {
        try (Scanner fileStrReader = new Scanner(new File("input.txt"))) {
            String lastIdDna = "";
            String curIdDna = "w";
            StringBuilder boxForVals = new StringBuilder();
            while (fileStrReader.hasNextLine()) {
                String curStr = fileStrReader.nextLine();
                if (curStr.startsWith(">DNA_CHAIN_ID")) {
                    curIdDna = curStr;
                    if (!curIdDna.equals(lastIdDna) && !lastIdDna.isEmpty()) {
                        System.out.printf("%s --> %s%n", lastIdDna, boxForVals.toString());
                        boxForVals.delete(0, boxForVals.toString().length() - 1);
                    }
                } else boxForVals.append(curStr);
                lastIdDna = curIdDna;
            }
            System.out.printf("%s --> %s%n", lastIdDna, boxForVals.toString());
        }catch (FileNotFoundException e) {e.printStackTrace();}
    }