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

[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
71 0.003482 0.1727 b4046 zur -8.96 0.216158 254 -- 300 53 -- 94 transcriptional repressor Zn(II)-binding  
72 0.00375 0.1804 b0386 proC -10.69 0.102749 216 -- 233 53 -- 70 pyrroline-5-carboxylate reductase NAD(P)-binding  
73 0.003782 0.1804 b3560 glyQ -10.80 0.098141 7 -- 31 51 -- 74 glycine tRNA synthetase alpha subunit  
74 0.003792 0.1804 b2520 yfhM -12.28 0.050623 263 -- 298 53 -- 91 bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein  
75 0.003854 0.1809 b0606 ahpF -8.17 0.297536 59 -- 82 64 -- 85 alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding  
76 0.003978 0.182 b0336 codB -6.71 0.504284 39 -- 48 1 -- 11 cytosine transporter  
77 0.00398 0.182 b2411 ligA -14.36 0.019662 79 -- 95 70 -- 86 DNA ligase NAD(+)-dependent  
78 0.004296 0.1855 b3258 panF -10.37 0.118507 142 -- 153 52 -- 62 pantothenate:sodium symporter  
79 0.004357 0.1855 b0008 talB -10.61 0.106795 240 -- 280 50 -- 88 transaldolase B  
80 0.004451 0.1855 b3578 yiaN -12.19 0.052777 198 -- 212 52 -- 66 2 3-diketo-L-gulonate TRAP transporter large permease protein  

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