Welcome to the Predict a Secondary Structure Common to Three or More Sequences Web Server

The Predict a Secondary Structure Common to Three or More Sequences server takes three or more sequences and folds them into their common lowest free energy conformations. The Predict a Secondary Structure Common to Three or More Sequences server combines the capabilities of Multilign and TurboFold to create distinct sets of possible structures for multiple sequences. Note that sequences must be entered as a group in this server. Sequences can be entered either as a FASTA file with multiple sequences, or manually in the sequence box. Note also that the server assumes the sequences are RNA.

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Select Sequences Input:

- OR -
Enter your sequence content below (replaces upload if present).
Sequence content should be entered in FASTA format, with a proper FASTA header on a line preceding each sequence.
Please enter headers and nucleotides only, no comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.




Select General Options:

If a default value is left blank, the value is treated as if it was not changed at all.



Select Multilign Options:

If a default value is left blank, the value is treated as if it was not changed at all.




Select TurboFold Options:


If a default value is left blank, the value is treated as if it was not changed at all.

General Options



Maximum Expected Accuracy Mode Options



Pseudoknots Mode Options


Threshold Mode Options




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