Freiburg RNA Tools
CopomuS - Results
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CopomuS 6576753

Input and runtime details for job 6576753 (precomputed example)

Sequence Parameters

? RNA-1GCCACUGCUUUUCUUUGAUGUCCCCAUUUUGUGGAGCCCAUCAACCCCGCCAUUUCGGUUCAAGGUUGGUGGGUUUUUU
? Index first position of RNA-11
? RNA-2TCATGAAAGATAGTACTGTCGCCGCGTCTAAAATGCGCAAACGTGAACGCAATCGATTACGTAAATGATAGATATGTGAAACAAGACATATTTTTGTGAGCAATGATTTTTATAATAGGCTCCGCAGAAACACGAAATATTTAGAAACGCAAATTGCGTTCTTTTCACTCCCGCAAGGGATTTCAAACAGTGGCATACATATGAAAAAAACTTTACTCGCAGTCAGCGCAGCGCTGGCGCTCACCTCATCTTTTACTGCTAACGCAGCAGAAAATGATCAGCCGCAGTATTTGTCCGACT
? 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
?Processing 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: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6576753&toolName=CopomuS ( 30 days expiry )

The job description you specified

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

[csv]

? Identified and ranked mutation candidates

Show rows: 1-15 16-16 all
Sort by selecting a column name
mutation encoding rank idx(1) idx(2) ww mm mfeCover (ww+mm) E(ww|mm)+x <E(wm|mw) mfe(ww) mfe(wm) mfe(mw) mfe(mm)
C2G&G-8C 1 -8 2 CG GC 1 1 -15.57 -6.38 -6.8 -16.05
U6A&A-12U 2 -12 6 UA AU 1 1 -15.57 -4.94 -2.49 -12.82
C3G&G-9C 3 -9 3 CG GC 1 1 -15.57 -8.32 -9.29 -16.04
C23G&G-23C 4 -23 23 CG GC 1 1 -15.57 -11.51 -12.04 -18.48
U16A&A-16U 5 -16 16 UA AU 1 1 -15.57 -11.47 -12.15 -15.85
U15A&A-15U 6 -15 15 UA AU 1 1 -15.57 -12.59 -12.66 -15.38
A4U&U-10A 7 -10 4 AU UA 1 1 -15.57 -12.93 -7.4 -17.23
G17C&C-17G 8 -17 17 GC CG 1 1 -15.57 -10.1 -12.04 -14.55
C5G&G-11C 9 -11 5 CG GC 1 1 -15.57 -8.38 -13.17 -17.3
C22G&G-22C 10 -22 22 CG GC 1 1 -15.57 -13.57 -12.43 -18.93
U30A&A-26U 11 -26 30 UA AU 1 1 -15.57 -12.56 -10.09 -13.88
U21A&A-21U 12 -21 21 UA AU 1 1 -15.57 -14.4 -12.1 -16.53
U29A&A-25U 13 -25 29 UA AU 1 1 -15.57 -14.45 -13.43 -16.31
G31C&C-27G 14 -27 31 GC CG 1 0 -15.57 -14.59 -13.15 -16.73
G33C&C-29G 15 -29 33 GC CG 1 0 -15.57 -14.97 -13.17 -19.45
Rows: 1-15 16-16 all

Sequences for selected mutation


		

? Predicted mfe(ww) interaction of RNA1-RNA2

RNA-2
           -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
RNA-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