Quick Help (more help is available)
RDP's ProbeMatch finds sequences matching your probe in the RDP's database. A list of probes is available at sites such as Probebase. Use programs such as Primrose or ARB to assist you with phylogenetic probe design.
Probe: Please enter your probe(s) in the 5' to 3' direction. Only IUPAC codons can be used, including ambiguity codons. A probe must be less than 64 bases in length.
Restrict to Domain: Search only Bacteria, Archaea or Fungi sequences, if desired.
Restrict to Region: Only search sequences with sequence data in the specified E. coli region (GenBank J01695) for Bacteria or Archaea , or S. cerevisiae (GanBank NC_001144.5:455571..451786) for Fungi. There are many partial 16S sequences in the RDP database that may be missing data in the region your probe targets. This function can be useful if you're interested in what sequences your probe does not match. The coverage of the number of RDP sequences spanning each base position for each domain can be found on resources.