Utilities
Evaluate, display, and annotate the equilibrium properties of an ordered complex. The Utilities page accepts as input either sequence information, structure information, or both, performing diverse functions based on the information provided.
Nucleic acid type:
Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.
Update:
Update all calculations and graphics.
Temperature:
Enter the temperature (default 37 °C).
Structure:
Specify a secondary structure in dot-parens-plus notation (each unpaired base is represented by a dot, each base pair by matching parentheses, and each nick between strands by a plus). Structures must be connected and free of pseudoknots. For example:

..(((...((((((..+.)))))).((((....)))))))

yields:
Sequence:
Enter strand sequences with nicks betweem strands denoted “+”. T's or U's are acceptable for both RNA and DNA and will be appropriately converted. Each base can be any of the standard nucleic acid codes (depicted below for RNA; T replaces U for DNA).
NA,C,G,U
RA,G
YC,U
MA,C
KG,U
SC,G
WA,U
VA,C,G
HA,C,U
BC,G,U
DA,G,U
Specified secondary structure:
Depiction of the specified secondary structure in any of a variety of formats.
Pair probability plot:
Click the thumbnail for a larger version. Depicts equilibrium base-pairing probabilities for the ordered complex, treating all strands as distinct. By definition, these data are independent of concentration and of all other ordered complexes in solution. The area and color of each dot scale with the equilibrium probability of the corresponding base pair (probabilities below 0.001 are not depicted). With this convention, the plot is symmetric, with the upper and lower triangles separated by a diagonal line. The area and color of each dot in the column at right scale with the equilibrium probability that the corresponding base is unpaired.
Details:
Advanced options:
Select among available energy models, specify dangle treatments, and specify salt concentrations.
Download job:
Download all data and plots for the utilities job as a single compressed file.