The LocARNA web server will procude pairwise and multiple structural alignments of RNA sequences. LocARNA was developed in collaboration with the Bioinformatics Group Freiburg.

Simply paste or upload your sequences below and click Proceed. To get more information on the meaning of the options click the symbols. You can test the server using these sample sequences.

Paste or type your sequences in FASTA format here:

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Or upload a file in FASTA format:

 Basic options 

global local	type of alignment Make a global or local alignment.

Show advanced options

 Advanced options 

Scoring parameters
None RIBOSUM45_25 RIBOSUM45_30 RIBOSUM45_35 RIBOSUM45_40 RIBOSUM45_45 RIBOSUM45_50 RIBOSUM45_55 RIBOSUM45_60 RIBOSUM45_65 RIBOSUM45_70 RIBOSUM45_75 RIBOSUM45_80 RIBOSUM45_85 RIBOSUM45_90 RIBOSUM45_95 RIBOSUM50_25 RIBOSUM50_30 RIBOSUM50_35 RIBOSUM50_40 RIBOSUM50_45 RIBOSUM50_50 RIBOSUM50_55 RIBOSUM50_60 RIBOSUM50_65 RIBOSUM50_70 RIBOSUM50_75 RIBOSUM50_80 RIBOSUM50_85 RIBOSUM50_90 RIBOSUM50_95 RIBOSUM55_25 RIBOSUM55_30 RIBOSUM55_35 RIBOSUM55_40 RIBOSUM55_45 RIBOSUM55_50 RIBOSUM55_55 RIBOSUM55_60 RIBOSUM55_65 RIBOSUM55_70 RIBOSUM55_75 RIBOSUM55_80 RIBOSUM55_85 RIBOSUM55_90 RIBOSUM55_95 RIBOSUM60_25 RIBOSUM60_30 RIBOSUM60_35 RIBOSUM60_40 RIBOSUM60_45 RIBOSUM60_50 RIBOSUM60_55 RIBOSUM60_60 RIBOSUM60_65 RIBOSUM60_70 RIBOSUM60_75 RIBOSUM60_80 RIBOSUM60_85 RIBOSUM60_90 RIBOSUM60_95 RIBOSUM65_25 RIBOSUM65_30 RIBOSUM65_35 RIBOSUM65_40 RIBOSUM65_45 RIBOSUM65_50 RIBOSUM65_55 RIBOSUM65_60 RIBOSUM65_65 RIBOSUM65_70 RIBOSUM65_75 RIBOSUM65_80 RIBOSUM65_85 RIBOSUM65_90 RIBOSUM65_95 RIBOSUM70_25 RIBOSUM70_30 RIBOSUM70_35 RIBOSUM70_40 RIBOSUM70_45 RIBOSUM70_50 RIBOSUM70_55 RIBOSUM70_60 RIBOSUM70_65 RIBOSUM70_70 RIBOSUM70_75 RIBOSUM70_80 RIBOSUM70_85 RIBOSUM70_90 RIBOSUM70_95 RIBOSUM75_25 RIBOSUM75_30 RIBOSUM75_35 RIBOSUM75_40 RIBOSUM75_45 RIBOSUM75_50 RIBOSUM75_55 RIBOSUM75_60 RIBOSUM75_65 RIBOSUM75_70 RIBOSUM75_75 RIBOSUM75_80 RIBOSUM75_85 RIBOSUM75_90 RIBOSUM75_95 RIBOSUM80_25 RIBOSUM80_30 RIBOSUM80_35 RIBOSUM80_40 RIBOSUM80_45 RIBOSUM80_50 RIBOSUM80_55 RIBOSUM80_60 RIBOSUM80_65 RIBOSUM80_70 RIBOSUM80_75 RIBOSUM80_80 RIBOSUM80_85 RIBOSUM80_90 RIBOSUM80_95 RIBOSUM85_25 RIBOSUM85_30 RIBOSUM85_35 RIBOSUM85_40 RIBOSUM85_45 RIBOSUM85_50 RIBOSUM85_55 RIBOSUM85_60 RIBOSUM85_65 RIBOSUM85_70 RIBOSUM85_75 RIBOSUM85_80 RIBOSUM85_85 RIBOSUM85_90 RIBOSUM85_95 RIBOSUM90_25 RIBOSUM90_30 RIBOSUM90_35 RIBOSUM90_40 RIBOSUM90_45 RIBOSUM90_50 RIBOSUM90_55 RIBOSUM90_60 RIBOSUM90_65 RIBOSUM90_70 RIBOSUM90_75 RIBOSUM90_80 RIBOSUM90_85 RIBOSUM90_90 RIBOSUM90_95 RIBOSUM95_25 RIBOSUM95_30 RIBOSUM95_35 RIBOSUM95_40 RIBOSUM95_45 RIBOSUM95_50 RIBOSUM95_55 RIBOSUM95_60 RIBOSUM95_65 RIBOSUM95_70 RIBOSUM95_75 RIBOSUM95_80 RIBOSUM95_85 RIBOSUM95_90 RIBOSUM95_95 RIBOSUM100_25 RIBOSUM100_30 RIBOSUM100_35 RIBOSUM100_40 RIBOSUM100_45 RIBOSUM100_50 RIBOSUM100_55 RIBOSUM100_60 RIBOSUM100_65 RIBOSUM100_70 RIBOSUM100_75 RIBOSUM100_80 RIBOSUM100_85 RIBOSUM100_90 RIBOSUM100_95	use RIBOSUM matrix (instead of match/mismatch scores) LocARNA will use a RIBOSUM matrix instead of ordinary match/mismatch scores. Choose "None" for ordinary match/mismatch scores.
	Match score Score for two positions that are identical. This option will not be considered as long as "use RIBOSUM matrix" is not switched to "None".
	Mismatch score Score for two positions that are not identical. This option will not be considered as long as "use RIBOSUM matrix" is not switched to "None".
	Indel-opening score Score for opening a new gap.
	Indel score Score for extending a gap.
	Structure weight Weights score contribution of structure against sequence.
Heuristics for speed accuracy trade off
	Minimal pair probability Base-pairs that have a probability less than this threshold are not considered in the computation.
	Minimal probability for constructing the guide tree Same as minimal pair probability, but only for the guide tree computation. Base-pairs that have a probability less than this threshold are not considered in the guide tree computation.
	Maximal difference for sizes of matched arcs Maximal difference for sizes of matched arcs. Only arcs with less size difference can be structurally matched. Choose "none" to disable this heuristic.
Other parameters
	Clustalw output width Specifies the column width for the CLUSTAL W output.
	Alignment with stacking terms Consider stacking energies in the computation.
	avoid lonely base-pairs Predicted structures can contain isolated base pairs (helices of length 1), which may be undesirable. Check this box to avoid such lonely pairs.

Notification via e-mail upon completion of the job (optional):