Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


Output download complete results [zip]

Downloadable files

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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
91 0.004841 0.1855 b3194 mlaE -9.16 0.198986 180 -- 189 67 -- 76 ABC transporter maintaining OM lipid asymmetry inner membrane permease protein  
92 0.004911 0.1855 b3732 atpD -9.01 0.211333 117 -- 128 1 -- 11 F1 sector of membrane-bound ATP synthase beta subunit  
93 0.005014 0.1855 b0091 murC -15.25 0.013117 8 -- 30 73 -- 94 UDP-N-acetylmuramate:L-alanine ligase  
94 0.005015 0.1855 b2703 srlE -7.35 0.404948 254 -- 271 70 -- 86 glucitol/sorbitol-specific enzyme IIB component of PTS  
95 0.005084 0.1855 b3182 dacB -12.18 0.052827 253 -- 263 2 -- 12 D-alanyl-D-alanine carboxypeptidase  
96 0.005105 0.1855 b0870 ltaE -12.99 0.036706 93 -- 116 68 -- 88 L-allo-threonine aldolase PLP-dependent  
97 0.005188 0.1855 b3060 ttdR -16.80 0.006462 125 -- 147 67 -- 90 transcriptional activator of ttdABT b1799
98 0.005208 0.1855 b4174 hflK -10.42 0.116019 265 -- 284 65 -- 83 modulator for HflB protease specific for phage lambda cII repressor  
99 0.005465 0.1855 b0767 pgl -9.37 0.182441 275 -- 291 70 -- 86 6-phosphogluconolactonase  
100 0.00547 0.1855 b2451 eutA -10.77 0.099200 8 -- 32 56 -- 86 reactivating factor for ethanolamine ammonia lyase  

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