Q: How can I disclose a sequence which contains less than 4 specifically defined amino acids, based on an ST.25 sequence listing?

For a sequence to be included in a WIPO ST.26-compliant sequence listing it must meet the minimum length requirement. See WIPO ST.26 paragraph 8. If you import an ST.25-compliant sequence listing into WIPO Sequence, this sequence will appear as 'intentionally skipped'. 

The advice provided in Scenario 3 of Annex VII of WIPO ST.26, which provides recommendations on how to avoid added or deleted matter, is to include the excluded sequences in the application body. 

note: "Specifically defined" definition can be found under DEFINITIONS Section (k) of  WIPO ST.26.