Ah Prettybox. The program with so many options that is hard to figure
out how to do what you want to accomplish. :-)
1) Set your primary sequence (your 'top' sequence) so that it has a very
high weight, say 100. Leave the other sequences at a weight of 1.
2) Run Prettybox with a /PLUality=101
Doing this will cause Prettybox to shade the primary sequence and any
matching secondary sequences only when the primary sequence matches any
secondary sequence. There will be no shading when only secondary
sequences match each other, i.e., when the primary sequence doesn't
match any other sequence.
This should accomplish what you want. Another possiblity is to use the
PrettyBox.MRK file to tell the program which regions to mark; although I
don't think this will really do what you want.
If you really get desperate it is always possible to hand edit the
PrettyBox output files before sending them to your Postscript-compatible
printer. Run PrettyBox with the /OUTput=file option and then use your
favorite editor to change the some of the "(black)" words to "(white)"
Rick Westerman System Manager of the Ag Campus Lab. for
westerm at purdue.edu Computational Biology (ACLCB) & Sys. Mgr.
Phone: (317) 494-0505 of the Biochemistry department BCHM bldg.
FAX: (317) 494-7897 Purdue Univ. W. Lafayette, IN 47907