I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download these sequences. However, when I click select all and then "get selected sequences", I am taken to a Genbank page containing the full genomes of the organisms, not just the bits that aligned. how can I download the sequences of just the bits that aligned?
I'm afraid that won't help; he wants sequences of only the aligned regions from the BLAST output.