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Nucleic acid type:
RNA DNA
Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.
Temperature: °C
Enter the temperature (default 37 °C).
Update all calculations and graphics.
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:
MFE:
Use the MFE structure as the specified structure.
updating...
Cursor
0
Position of the cursor within the ordered complex.
 

Link
Link structure and sequence specifications, keeping their lengths the same.
Export structure information to the Design page, carrying available sequence information as sequence constraints for the redesign. This is useful when re-dimensioning duplex and loop lengths in a target secondary structure while retaining sequence information for a portion of the design.
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
Export sequence information to the Analysis page (e.g., to check for the formation of unintended ordered complexes in the context of a dilute solution).
Specified structure
Depiction of the specified secondary structure in any of a variety of formats.
Pair probabilities
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.
Format
Depict helicity
Depict with ideal helical geometry (A-form helices for RNA, B-form helices for DNA).
Base style
Depict bases as either circles or tick marks.
Circle
Tick
Base shading
Shade each base according to: probability (the probability that it adopts the depicted paired or unpaired state at equilibrium), identity (A = green, U/T = red, G = black, C = blue, all others = gray), or none (all bases are black).
Probability
Identity
None
Annotation
Annotate the drawing with any of: base letters, base numbers, top text, bottom text.
Draw numbers
Draw letters
Draw top title
Draw bottom text
Draw legend
Top text:
Bottom text:
Details
Sequence properties
Properties of the specified sequence information.
Min. free energy: kcal/mol
Free energy of the ordered complex (-kT log Q).
Free energy: kcal/mol
Free Energy of ordered complex ΔG = −kT log Q.
Num. of structures:
Number of structures in Ω(π)
BaseNumber%
A
The percentage of nucleotides in the sequence that are adenine.
C
The percentage of nucleotides in the sequence that are cytosine.
G
The percentage of nucleotides in the sequence that are guanine.
U
The percentage of nucleotides in the sequence that are uracil/thymine.
Other
The percentage of nucleotides in the sequence that are Other.
Sequence/structure properties
Properties of the specified structure and sequence information.
Free energy: kcal/mol
Free energy of the specified secondary structure.
Sequence/Structure Pfunc:
Partition function, Q, of given (unpseudoknotted) secondary structure and sequence
Probability:
The probability for the formation of this structure.
Ensemble defect: nt
The average number of nucleotides that are incorrectly paired at equilibrium relative to the specified secondary structure, evaluated over the Boltzmann-weighted ensemble of (unpseudoknotted) secondary structures (0 is best, N is worst, for a strand with N bases).
Normalized ensemble defect: %
The average percentage of nucleotides that are incorrectly paired at equilibrium relative to the specified secondary structure, evaluated over the Boltzmann-weighted ensemble of (unpseudoknotted) secondary structures (0% is best, 100% is worst).
Nucleotides: 0 nt
The number of nucleotides.
Advanced options
RNA energy parameters:
For RNA, there are two parameter sets: (Serra and Turner, 1995; default) and (Mathews et al., 1999; valid only at 37 °C). For DNA, there is one parameter set: (SantaLucia 1998).
Dangle treatment:
  None: no dangle energies are considered.
  Some (default): a dangle energy is incorporated for each unpaired base flanking a duplex (a base flanking two duplexes contributes only the minimum of the two possible dangle energies).
  All: a dangle energy is incorporated for each base flanking a duplex regardless of whether it is paired.
Na+:
1.0 M
For RNA, the salt concentrations are 1.0 M Na+ and 0.0 M Mg++. For DNA, the user-defined salt concentrations can be set in the ranges 0.05 – 1.1 M Na+ (SantaLucia and Hicks, 2004; default 1.0 M) and 0.0 – 0.2 M Mg++ (Koehler and Peyret, 2005; default 0.0 M).
Mg++:
0.0 M  
For RNA, the salt concentrations are 1.0 M Na+ and 0.0 M Mg++. For DNA, the user-defined salt concentrations can be set in the ranges 0.05 – 1.1 M Na+ (SantaLucia and Hicks, 2004; default 1.0 M) and 0.0 – 0.2 M Mg++ (Koehler and Peyret, 2005; default 0.0 M).