A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account

CoFold is a thermodynamics-based RNA secondary structure folding algorithm that takes co-transcriptional folding in account. This has been shown to significantly improve the state-of-art in terms of prediction accuracy, especially for long sequences greater than 1000 nt in length.

Sequence Input

Enter a single nucleotide sequence (with optional fasta header, up to 50kb):

Or upload a fasta file:


Thermodynamic energy parameters

Turner, 1999 [ref]

Andronescu, 2007 [ref]

Scaling parameters



  • Please be patient when submitting long sequences. A 1500 nt sequence will take roughly 20 seconds, and a 3000 nt sequence may take up to 3 minutes.
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