To design RNA molecules using Tuschl's rules, select the option button next to Tuschl's Motif Pattern and then select one or more pattern checkboxes. The Designer will generate 19-nucleotide RNA sequences that match the selected pattern(s). For example, if you select the AA(N19)TT pattern, the Designer will search for an area of the sequence that begins with "AA" and ends with "TT," with 19 bases in between. Each pattern is listed using the following base code letters: A = Adenine; T = Thymine; R = Adenine or Guanine (Purines); Y = Thymine or Cytosine (Pyrimidines); N = Any.
Up to 10 designs will be generated for the selected target sequence.
Note: The Default Motif Pattern design algorithm will give the best results in most cases, and is highly recommended. The results using this algorithm may include some Tuschl's patterns; these will be noted on the results page.