Trimming a specific region from a reference
I have sequences alignment of about ~2 kb long, and would like to trim a specific unique region that is 11 bases long. Is there a tool that I can use, that can locate and align my region of interest (as a reference), to the alignment and then trim the specific region? I have about 200 alignments that are ~2 kb long and just want to extract that specific 11 bases long region in all the files using a tool that can process in batch.
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Your explanation is not clear as to exactly what you are trying to do. Are you looking to trim your alignments (or the reference)? If this is sanger sequence data then you may be able to use Jalview or MEGA6 for this in an interactive mode (not batch).