Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6038639

Input and runtime details for job 6038639 (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 6038639 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:35:57 CET 2018
?CopraRNA Started@ Fri Feb 16 20:19:35 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 21:35:30 CET 2018
?Post-Processing Finished@ Fri Feb 16 21:35:37 CET 2018
?Job Completed@ Fri Feb 16 21:35:51 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
55 0.02093 0.29 ct_785 rl34 -4.69 0.410747 264 -- 270 80 -- 86 50S ribosomal protein L34  
68 0.02545 0.29 ct_369 aroB -8.93 0.051509 264 -- 292 1 -- 31 3-dehydroquinate synthase  
23 0.006311 0.2093 ct_671 N/A -7.19 0.130787 265 -- 279 17 -- 34    
151 0.06398 0.3424 ct_647 N/A -6.81 0.158308 265 -- 281 12 -- 34    
141 0.05655 0.3262 ct_645 N/A -6.85 0.155161 266 -- 276 17 -- 28    
139 0.05609 0.3262 ct_291 ptsN_2 -9.13 0.046270 268 -- 291 36 -- 59 PTS fructose transporter subunit IIA  
22 0.005311 0.1984 ct_111 groES -5.40 0.305537 269 -- 283 17 -- 33 co-chaperonin GroES  
192 0.08479 0.363 ct_293 accD -5.01 0.360945 270 -- 276 79 -- 85 acetyl-CoA carboxylase carboxyltransferase subunit beta  
100 0.03658 0.3007 ct_875 N/A -4.31 0.472369 272 -- 278 28 -- 34    
152 0.064 0.3424 ct_749 alaS -4.53 0.436714 274 -- 290 41 -- 57 alanine--tRNA ligase  

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