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Optional gap feature:

FT   gap             {X..Y}
FT                   /estimated_length={unknown or known}

Unknown length is represented with 100Ns in the sequence. For known length, please replace with the number of Ns.

http://www.ebi.ac.uk/ena/submit/entry-upload-templates

More information on the assembly_gap feature

Feature Key           assembly_gap


Definition            gap between two components of a genome or transcriptome assembly;

Mandatory qualifiers  /estimated_length=unknown or <integer>
		      /gap_type="TYPE"
                      /linkage_evidence="TYPE" (Note: Mandatory only if the 
                      /gap_type is "within scaffold" or "repeat within
                      scaffold".If there are multiple types of linkage_evidence
                      they will appear as multiple /linkage_evidence="TYPE"
                      qualifiers. For all other types of assembly_gap
                      features, use of the /linkage_evidence qualifier is 
                      invalid.)
                      Mandatory qualifiers under assembly_gap feature for transcriptome
                      shotgun assemblies (TSA):
                      /estimated_length=<integer>
                      /gap_type="within scaffold" and /linkage_evidence="TYPE" where TYPE
                      can not be "unspecified";                     

Comment               the location span of the assembly_gap feature for an unknown gap has 
                      to be specified by the submitter; the specified gap length has to be 
                      reasonable (less or = 1000) and will be indicated as "n"'s in sequence.
                      However, the value for the estimated_length of assembly_gap features 
                      within a single (non-CON) transcriptome record must be an integer 
                      and can not be "unknown";