可以四个一起。
网页上有说明“Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your sequences. To get the CDS annotation in the output, use only the NCBI accession or gi number for either the query or subject. Reformat the results and check 'CDS feature' to display that annotation.”
也就是说在上下的输入位置，可以同时输入一个以上的序列。如果上下同时输入2个，就是4个序列了。
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