Primer Aligner

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Purpose: PrimAlign will generate an alignment of your nucleotide sequence against our curated sequence alignment.

Details: This tool can be used to align primers, functional domains, or any nucleotide sequence of interest. To perform such an analysis using protein sequences, see Epilign.

Input should consist of a single nucleotide sequence. The output you receive will include a map of the reference genome with your sequence plotted, a summary of the changes in your sequence relative to each of the alignment sequences, a display of the alignment of your sequence, and an option to download the alignment.