This lets you save the current pattern with the probe whose name is in the Probe text entry box. When reading in data, if any text is found following the clone name the box will be displayed in light blue, so you could edit this text in a tree update window to be more informative if you wanted. The current algorithm essentially tries to find loci such that the centres of all the positive YAC's are within the defined range. This is not strictly correct. The units are physical map bands.
Larger values allow more spread out clusters.
Applies to current keyset, which should contain probes with hybridisation data. It returns stats on how many clusters of various sorts there are, as a line on the terminal.