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Branched sequences must be included in a sequence listing by separating them into linear components. WIPO Sequence will not take a branched sequence and separate the components for the applicant.
ST ST.26 Annex VI is a guidance document which provides various example sequences, advises whether they should form part of an ST.26 sequence listing and how to provide this information. Example 7(a)-1 has an example of a branched nucleotide sequence listing and Examples 7(b)-2 & 3 are examples of a branched amino acid sequence listing.