Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5882223

Input and runtime details for job 5882223 (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 5882223 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:29:59 CET 2018
?CopraRNA Started@ Fri Feb 16 20:39:56 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 03:02:39 CET 2018
?Post-Processing Finished@ Sat Feb 17 03:02:47 CET 2018
?Job Completed@ Sat Feb 17 03:03:15 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[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
17 5.719e-05 0.01183 b3675 yidG -12.05 0.010096 82 -- 130 1 -- 56 inner membrane protein  
41 0.000458 0.03766 b3679 yidK -16.91 0.000078 119 -- 159 1 -- 60 putative transporter  
50 0.0006038 0.04249 b3755 yieP -5.20 0.556147 189 -- 196 25 -- 32 putative transcriptional regulator  
118 0.003907 0.1165 b3827 yigM -8.32 0.129405 260 -- 268 1 -- 9 putative inner membrane EamA-like transporter  
112 0.003594 0.1129 b3866 yihI -3.87 0.795256 171 -- 194 53 -- 75 activator of Der GTPase  
88 0.002339 0.09349 b3878 yihQ -11.00 0.022508 260 -- 267 1 -- 8 putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase b3656
52 0.0006736 0.04557 b3964 yijD -9.23 0.074829 177 -- 192 43 -- 57 DUF1422 family inner membrane protein  
178 0.007695 0.1511 b4567 yjjZ -7.25 0.231371 185 -- 218 2 -- 33 uncharacterized protein  
103 0.003241 0.1101 b0837 yliI -8.40 0.123505 223 -- 230 4 -- 11 soluble aldose sugar dehydrogenase  
168 0.006917 0.1448 b3070 yqjH -8.25 0.134865 172 -- 181 49 -- 58 putative siderophore interacting 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)

Job resubmission

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Feeds the job parameters to the input page to resubmit the job.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2