Searching genome with specifed number of Ns between two known sequences - (Jan/16/2012 )

Do you know if there's a way to search a genome in BLAST for sequences separated by, say, 5-30 N? E.g. AAAA (N)_5-30 TTTT?

just input your sequence. i'd use global alignment rather than local for that kind of purpose. at least i believe so... it's been over 4 years since i did proper bioinformatics...

Yes, you can just insert nnnnnnn into your query sequence. Try BLAT http://genome.ucsc.edu/cgi-bin/hgBlat