Many bacterial complete genomes have been sequenced with small plasmids of less than 5kb.  If I use BLAST to search for plasmids similar to my plasmid of interest, I find a few dozen, but some are the reverse complement strand relative to others, and each has a different "base number one" in the GenBank entries.  I know how to make the reverse complement, and I can clip the 3' end off and paste it on the 5' end to get the data ready to align, but it seems to me that there may already be an automated tool for this.

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