Welcome to the Multilign Web Server

The Multilign server takes three or more sequences, either DNA or RNA, and folds them into their common lowest free energy conformations. Additionally, it creates an alignment file of the 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.

If you plan to leave this page while waiting for calculations to complete, please make sure you have entered a valid email address below. Leaving this page without entering a valid email address will render results inaccessible.

If you need specific help using the Multilign server, please click here.

February 14, 2018:
RNAstructure tools have been updated to version 6.0.1 which includes several improvements.
Please contact us with any questions or issues regarding this update.

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 Nucleic Acid Type:

Select Multilign Options:

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

Designate Address to Email Results: