LSPrimer accepts a multiple squences alignment file that containing target and nontarget sequences as input, and picking a set of PCR primers that will sensitively and specifically amplify the homologs accross the target squences.
Please past your alignment file in the box below, or upload it directly. Your alinment file must containing target and nontarget sequences. Target sequences are the homologous sequences of a lineage. Nontarget sequences are the closely related sequences that are not belong to the target lineage. Alinment file must be FASTA format. Moreover, you must specify which sequence to be the template for primer design in the red box.

Enter Alignment

Past your alignment below (Alignment must be FASTA format. Only string of ACGTNacgtn can be recognized, '-' will be considered as gap symbol, other letters will be treated as N, numbers and blanks will be ignored):

Or upload your alignment file (FASTA format):