123.java

Map<Integer, Integer> Result= new HashMap<>();
int condition = Math.max(sample.size(), fileTwo.size());

for(int counter=1; counter<=condition; counter++)
{
  int match=0;
  for(String fileTwoPostionValue : fileTwo.get(String.valueOf(counter)))
  {
      if(sample.get(String.valueOf(counter)).contains(fileTwoPostionValue))
      {
          match++;
      }
  }
  Result.put(counter.toString(), match);
}