End reads were used to design markers and one end marker was positioned onto a map by HAPPY mapping (b).
The clone was then oriented by screening, using PCR, adjacent mapped clones for the presence or absence of the un-anchored marker or by screening the clone for adjacent mapped markers.
Where no match was found in adjacent clones, the entire library could be screened for clones which contained markers either side of the gap (c).
Even after screening multiple large insert libraries, a few gaps remain suggesting that the sequences are not stable in bacterial vectors.
In this manner, large-insert clone-based maps for all eight chromosome were made.