We also have seen this problem. We always assumed it was some type of
cloning anomaly during the ligation. Adding DMSO helps once in a while,
but not very often. Our suggestion to our users who has this problem is to
sequence from the other end or to reclone the insert.
Tom Stelick
DNA Sequencing Lab
BioResource Center
Cornell University
DNA_Services at cornell.eduhttp://brcweb.bio.cornell.edu