You can do what you want, in a slightly complex way. The query window
is no use to you, as others have said.
You must create objects in the "Restriction" class, which normally has
restriction sites. It is best to make a file of them, and read them
in. To see what the file should look like, use "Ace dump" on a set of
restriction site objects from the Main KeySet window. You should give
the new objects names that do not just contain ACGT -- though not
strictly necessary it will help avoid confusion. Now if get write
access from the main menu, and read your file in from the "Read .ace
files" window, also accessed via the main menu.
Next you want to make a keyset of all your motifs, preferably by them
having a shared name element, e.g. RAP1, RAP2 etc., so you can give a
template RAP* in the main window, and get the list you want in the
Main KeySet window. The pink "Selected KeySet" box should be on in
the window containing your keyset of motifs. If not, then click
something in the window.
Finally, you can now use the "Motif KeySet" button in the DNA_Analysis
window, and when you do a search it will search with all the patterns
in your keyset, which is what you wanted, I think. Although this
sounds complicated it allows you to seach with any set of patterns,
and store the patterns with names for future use. The "Max mismatch"
button should still work to allow mismatches.