Use this form for searching for a short sequence (such as a primer or probe) within the aligned sequence data. This tool is most useful for determining the character position of 16S rDNA PCR primers/probes within the aligned prokMSA. The output will also summarize the phylogenetic scope of the oligonucleotide by using a pattern match which does not account for cross hybridization potential.

If you would like to try another method you may want to check-out ARB Probe Match Online, ARB-PMO, instead. Soon that web site will fullfill your probe design needs as well.