Freiburg RNA Tools
LocARNA - Results
LocARNA 3558571

Input and runtime details for job 3558571 (precomputed example)

Sequence and Structure

? Sequence Input in FASTA Format[.fa]


? Alignment TypeGlobal
? Alignment Modeno

Alignment Scoring

? Structure Weight200
? Indel Opening Score-800
? Indel Score-50
? Use RIBOSUMyes
? Match Score50
? Mismatch Score0

RNA Folding

? Local folding: max. base pair span150
? Temperature in °C37.0
? Energy parameter set (Vienna package)
? Upload dot plotsnot provided

Heuristics for speed/accuracy tradeoff

? Minimal Pair Probability5.0E-4
? Minimal Probability for Guide Tree Construction0.005
? Maximal Difference for Sizes of Matched Arcs30
? Maximal Difference for Alignment Edges60

Other Parameters

? Ignore Constraintsno
? Disallow Lonely Pairsyes
? Use alifold consensus dot plotsno
? Consistency Transformation (LocARNA-P only)no
? Keep Sequence Input Orderno
? Stockholm alignment outputyes

Job ID 3558571 (server version 4.4.4)

?Job Submitted & Queued@ Thu Jun 08 13:26:36 CEST 2017
?LocARNA Started@ Thu Jun 08 13:26:48 CEST 2017
?LocARNA Finished & Post-Processing@ Thu Jun 08 13:26:50 CEST 2017
?Post-Processing Finished@ Thu Jun 08 13:26:55 CEST 2017
?Job Completed@ Thu Jun 08 13:26:55 CEST 2017
 DIRECT ACCESS: ( 30 days expiry )

Description of the job

tRNA alignment with fixed structure

Output download complete results [zip]

? Alignment annotated with RNAalifold consensus structure

download alignment [ClustalW] [Stockholm] [FASTA] [structure] [structure-pairs] download alignment figure [.pdf] [.ps] [.png]

Bases are encoded by IUPAC codes. For interpretation of the colors see this legend. For a detailed description of the output, please see the help page.

? Guide tree and Intermediate Alignments

download guide tree [NEWICK format] [.svg] download [similarity matrix]
guide tree

Intermediate Alignments

? RNAalifold consensus structure

download consensus figure [.pdf] [.ps] [.png]

For interpretation of the colors see this legend. For a detailed description of the output, please see the help page.

Color Legend

Color legend
Compatible base pairs are colored, where the hue shows the number of different types C-G, G-C, A-U, U-A, G-U or U-G of compatible base pairs in the corresponding columns. In this way the hue shows sequence conservation of the base pair. The saturation decreases with the number of incompatible base pairs. Thus, it indicates the structural conservation of the base pair.

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

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When using LocARNA please cite :

Results are computed with LocARNA version 1.9.1 linking Vienna RNA package 2.3.2