Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6527768

Input and runtime details for job 6527768 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 6527768 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:51 CET 2018
?Processing Started@ Fri Feb 16 15:25:20 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:38:58 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:39:05 CET 2018
?Job Completed@ Fri Feb 16 20:39:38 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

The job description you specified

MicA


Output download complete results [zip]

Downloadable files

[csv]
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[txt] [svg]


heatmap

? Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
1 0 0 b2687 luxS -86.29 0.000000 61 -- 132 1 -- 72 S-ribosylhomocysteine lyase  
2 9.051e-06 0.01532 b2745 truD -15.77 0.011349 54 -- 69 2 -- 17 tRNA(Glu) pseudouridine(13) synthase  
3 3.559e-05 0.03436 b0168 map -14.62 0.018437 228 -- 248 5 -- 21 methionine aminopeptidase  
4 4.059e-05 0.03436 b2748 ftsB -19.92 0.001892 154 -- 190 1 -- 44 cell division protein  
5 7.362e-05 0.04801 b0741 pal -13.90 0.024968 103 -- 115 3 -- 16 peptidoglycan-associated outer membrane lipoprotein  
6 9.655e-05 0.04801 b4175 hflC -9.47 0.148653 186 -- 211 5 -- 32 HflB protease modulator specific for phage lambda cII repressor  
7 9.926e-05 0.04801 b1113 ldtC -15.69 0.011765 184 -- 223 1 -- 45 L D-transpeptidase linking Lpp to murein  
8 0.000167 0.07068 b0814 ompX -11.11 0.078421 202 -- 223 1 -- 22 outer membrane protein X  
9 0.000195 0.07335 b1830 prc -15.09 0.015143 131 -- 161 7 -- 38 carboxy-terminal protease for penicillin-binding protein 3  
10 0.0002413 0.08171 b2594 rluD -15.70 0.011720 48 -- 64 5 -- 21 23S rRNA pseudouridine(1911 1915 1917) synthase  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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Results are computed with CopraRNA version 2.1.2