For example, if you want to get intergenic sequences which have a specific noncoding RNA like "TPP" in specfic genome like "NC_000913": First select the checkboxes for:
"DNA fragment" or/and "description" in the "fragment" section (because this is where you find the information on chromosome)
"start", "end", "strand", "sequence" in the "gap5" section (because this is where you will get the sequence and other related information for the region in 5-prime of the genes)
"description", in the "RNA familly " section (because this is where you will get the sequence RNA known)
"start", "end", "strand", in the "RNA_known" section (because this is where you will get the RNA positions for Known RNA)
After, choose the condition to which you want to limit your search:
Choose "description" of the "RNA_familly " section, choose "find the pattern" and write "TPP".
Choose "DNA fragment" of the "fragment " section, choose "find the pattern" and write "NC_000913".