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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 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.
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