Please fill out the submission form and click the Submit button. Input fields marked with a * are required.
(Load Example Data: toy example or interaction of snoRNA mgU6-77 and U6 snRNA by selecting U6 Rfam seed alignment)

1st Multiple Sequence Alignment* 2nd Multiple Sequence Alignment*
This is the first alignment in FASTA format.
Either choose a MAF block or a customized query. [?]   
This is the second alignment in FASTA format.
Either choose an Rfam family or a customized query. [?]
Human (Hg18) 17way MULTIZ alignment: [?] Rfam 10.0 seed alignment: [?]
or enter alignment:
or upload the alignment file: Species in selected Rfam seed alignment:
(you may want to select at least 3 for 1st alignment)
Phylogenetic Tree
Calculate the score for a given tree in Newick format. [?]
1st RNA secondary structure 2nd RNA secondary structure
Intra-molecular structure of the first alignment
in dot-bracket notation. [?]
Intra-molecular structure of the second alignment
in dot-bracket notation. [?]
Maximal percentage of gaps in alignment column [?]
Intra-molecular base paired reliability threshold
for accessibility (Delta)
Minimal partial structure probability (Gamma) [?]
RNA(co)fold option: disallows pairs that occur isolated (noLP) [?]
Constraint stems get extended by inner and outer base pairs [?]
Reliability threshold of evolutionary constrained base pairs [?]
Reliability threshold of evolutionary constrained unpaired bases [?]
Weighting factor for single stranded probabilities (Alpha) [?]
Weighting factor for thermodynamic overlap (Beta) [?]
Job Name
Enter your e-mail adress if you want to receive a notification after the job has finished,
and give your job any custom name.