for (Alignment leftAlignment : leftAlignmentList) {
int index = startIndex;
Iterator<Alignment> rightIterator =
rightAlignmentList.listIterator(index);
while(rightIterator.hasNext()) {
Alignment rightAlignment = rightIterator.next();
if (leftAlignment.equals(rightAlignment)) {
rightOnlyAlignmentList.addAll(
rightAlignmentList.subList(startIndex, index));
startIndex = index + 1;
break;