Freiburg RNA Tools
CopomuS - Results
CopomuS 6576753

Input and runtime details for job 6576753 (precomputed example)

Sequence Parameters

? RNA-1
? Index first position of RNA-11
? RNA-2
? Index first position of RNA-2-200

Mutation Parameters

? Mutation candidates base pairs from mfe interaction only
? Ignore AU base pairsno
? Ignore GU base pairsno
? Ignore GC base pairsno
? Ignore lonely base pairsyes
? Ignore helix endsyes
? Ignore helix ends of mfeno
? Mutations to generate flip (e.g. GC to CG)

Evaluation Parameters

? Classification combination mfeCover + E
? Sorting within final classes minDeltaE

IntaRNA Parameters

? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? No lonely base pairsyes
? No GU at helix endsyes
? Min. number of basepairs in seed6
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (RNA-1)not provided
? Seed position (RNA-2)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes
? Temperature for energy computation37.0
? Access. RNA-1: folding window size150
? Access. RNA-1: max. basepair distance100
? Access. RNA-2: folding window size150
? Access. RNA-2: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 6576753 (server version trunk)

?Job Submitted & Queued@ Thu Feb 06 15:34:59 CET 2020
?CopomuS Started@ Thu Feb 06 15:36:29 CET 2020
?CopomuS Finished & Post-Processing@ Thu Feb 06 15:36:53 CET 2020
?Post-Processing Finished@ Thu Feb 06 15:36:53 CET 2020
?Job Completed@ Thu Feb 06 15:36:55 CET 2020
 DIRECT ACCESS: ( 30 days expiry )

Description of the job

Verification of RybB-tsx interaction in Salmonella by Papenfort et al. (2010) was originally using C2G:G-8C. (note, here we use tsx sequence = genomic region [-200,+100] around start codon)

Verification of RybB-tsx interaction in Salmonella by Papenfort et al. (2010) was originally using C2G&G-8C. (note, here we use tsx sequence = genomic region [-200,+100] around start codon)

? Output download complete results [zip]

Downloadable files


? Identified and ranked mutation candidates

Show rows: 1-15 16-16 all
Sort by selecting a column name. Rows: 1-15 16-16 all

Sequences for selected mutation


? Predicted mfe(ww) interaction of RNA1-RNA2

           -30                                -7
             |                                |
5'-UCA...ACUC      ----    UU     ------       AUAC...ACU-3'
             CCGCAA    GGGA  UCAAA      CAGUGGC
             ++++++    ||||  |||||      +++++++
             GGUGUU    CCCU  AGUUU      GUCACCG
3'-UUU...CCGA      UUAC    GU     CUUUUC       -5'
             |                                |
            34                                1

interaction energy = -15.57 kcal/mol

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When using CopomuS please cite :

Results are computed with CopomuS version dev using IntaRNA 3.1.5