vectorstrip is useful for stripping vector sequence from the ends of sequences of interest.
Here are several examples of running vectorstrip. The vectorfile and the sequence files used in these example are given below. In each case, the same fragment has been cloned into the XhoI site of the polylinker of each vector. The cloned fragment is represented in lowercase, and the vector sequence is represented in uppercase. This makes it easy to see the sequence trimming.
Mandatory qualifiers (bold if not always prompted):