Because you have a subsequent in the sentence, you should use is. Without the subsequent, you would use are. But the phrase "alignment and subsequent segregation" treats the whole process as a single entity, like fish and chips or macaroni and cheese.
From Google books:
According to this approach, phosphate precipitation and subsequent removal from wastewater is mediated by microbial activity in the aeration tank of the activated sludge process.
Though by midsummer, when the fall in prices it had predicted had not materialised, the Society recanted of its pessimism, and declared that a stock market fall and subsequent depression was not on the cards ...
