I have been trying to do clustalx for my sequences of Polyketide synthase. Many of my sequences have two Acyl Carrier protein (ACP) domains. The problem is that clustal x is not accepting the file. However I had tried to change the name of both the domains to avoid ambiguity, I also did BLAST for those domains, no results. I although tried eliminating one ACP domain from the sequences having two which was accepted, but this won\t answer my query. Any help?

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