The following are guidelines for setting the endpoints and clone site of the vector:
•If you have many input reads, consider specifying a segment rather than the whole vector, since searching for the whole vector sequence increases the likelihood of finding a false match. A portion of the vector comprising approximately 1 kb upstream and downstream from the clone site is usually sufficient.
•Entering a clone site will increase the accuracy of the vector trimming. However, the trimming algorithm does not require the exact position of the cloning site.
•Nested deletion sequencers should develop a new vector sequence that approximates the sequence created with the tailing procedure. If you use an unmodified vector sequence, each constituent fragment would lose its vector sequence, but the nucleotides added during tailing would remain. This could destroy the consensus sequence at every end of a constituent fragment.
•Similarly, if you use adaptors for cloning, remember to add the adaptor sequence to the vector sequence at the appropriate position so that the vector catalog entry matches the insertion site precisely.