Probe Match against Small Subunit rRNAs

This analysis returns an overview of the matches between a probe and its potential target, as a list and as a phylogenetic overview. Probe Match will not design an oligonucleotide probe for you; however, it will help you evaluate a specified probe sequence with the rRNA sequences in the RDP database. View an output example, learn what to avoid, and read about known issues with the software.

Probe Match was written by Niels Larsen and is based on a pattern matcher by Ross Overbeek.

Probe Specification

The form below is for entering the probe sequence; type or paste it into the box(es) below. You may break the probe into adjacent fragments and specify the maximum number of mismatches, insertions and deletions for each. The sort option determines which fragment is used to sort the output. If you prefer to specify the target sequence instead of the probe sequence, change Probe to Target.

The Probe Target sequence is in its 5'->3' direction.

Sort Probe sequence fragment Mis Ins Del [Caution] Min. stem length: Cation conc. (M): Min. loop size: Formamide (%): Max. loop size:

Probe Match Options

Display results using a Prokaryotic Eukaryotic Mitochondrial tree. [Note] This option is only used if the Phylogenetic view box below is checked.

Target view and/or Phylogenetic view and/or Count matches Show matches or Show non-matches

Results by Electronic Mail If you want to receive the results via e-mail, enter your electronic mail address below.

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