Q: How can I disclose a sequence which contains less than 4 specifically defined amino acids, based on an earlier 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, any sequence containing less than 4 specifically defined amino acids will appear as 'intentionally skipped', both in the project and in the generated sequence listing. 

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: the definition for "specifically defined" can be found under Paragraph 3 Section (k) of  WIPO ST.26.