Input and runtime details for job 5882223 (precomputed example)

Sequence input

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

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

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

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

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

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

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
66	0.001146	0.05856	b1657	ydhP	-3.95	0.782289	131 -- 139	49 -- 57	putative MFS transporter inner membrane protein		_____________130_______140\n_____________\|_________\|\n5'-UCG...UUUUU_G_______UGUCA...GCG-3'\n______________U_UGAUUGC\n______________\|_:\|\|\|\|:\|\n______________A_GCUAAUG\n3'-AUU...GGUUU_G_______CACUU...AUG-5'\n_____________\|_________\|\n_____________58________48\n	133 -- 139	49 -- 55	-6.30818 kcal/mol	2.04371 kcal/mol	0.318327 kcal/mol	130 140@LB@ \| \|@LB@5'-UCG...UUUUU G UGUCA...GCG-3'@LB@ U UGAUUGC@LB@ \| :\|\|\|\|:\|@LB@ A GCUAAUG@LB@3'-AUU...GGUUU G CACUU...AUG-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -3.95 kcal/mol@LB@Hybridization Energy -6.30818 kcal/mol@LB@Unfolding Energy - mRNA 2.04371 kcal/mol@LB@Unfolding Energy - sRNA 0.318327 kcal/mol@LB@@LB@Position - mRNA 131 -- 139@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 49 -- 55@LB@
76	0.001511	0.06993	b3465	rsmD	-10.43	0.033857	227 -- 244	49 -- 65	16S rRNA m(2)G966 methyltransferase SAM-dependent		_____________226________________245\n_____________\|__________________\|\n5'-UUG...GGCAG____________C_____UGGCG...GCC-3'\n______________CGGCCAAAUCCG_AUUAU\n______________\|:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________GUCGGUUUAGGC_UAAUG\n3'-AUU...UAUAA__________________CACUU...AUG-5'\n_____________\|__________________\|\n_____________66_________________48\n	232 -- 238	54 -- 60	-22.129 kcal/mol	5.5281 kcal/mol	6.19707 kcal/mol	226 245@LB@ \| \|@LB@5'-UUG...GGCAG C UGGCG...GCC-3'@LB@ CGGCCAAAUCCG AUUAU@LB@ \|:\|\|\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ GUCGGUUUAGGC UAAUG@LB@3'-AUU...UAUAA CACUU...AUG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -22.129 kcal/mol@LB@Unfolding Energy - mRNA 5.5281 kcal/mol@LB@Unfolding Energy - sRNA 6.19707 kcal/mol@LB@@LB@Position - mRNA 227 -- 244@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 54 -- 60@LB@
78	0.001629	0.07345	b2624	alpA	-3.42	0.861549	231 -- 237	49 -- 55	CP4-57 prophage; DNA-binding transcriptional activator		_____________230_____238\n_____________\|_______\|\n5'-CGC...UACUA_______CAGCG...AAU-3'\n______________CGGUUAC\n______________\|\|:\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	231 -- 237	49 -- 55	-7.04991 kcal/mol	3.33366 kcal/mol	0.311712 kcal/mol	230 238@LB@ \| \|@LB@5'-CGC...UACUA CAGCG...AAU-3'@LB@ CGGUUAC@LB@ \|\|:\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -7.04991 kcal/mol@LB@Unfolding Energy - mRNA 3.33366 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 231 -- 237@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 49 -- 55@LB@
98	0.002849	0.1023	b0772	ybhC	-6.17	0.383539	27 -- 33	49 -- 55	acyl-CoA thioesterase lipoprotein		_____________26______34\n_____________\|_______\|\n5'-UCA...CGCCU_______UGCGA...AUC-3'\n______________CGAUUAC\n______________\|\|\|\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	27 -- 33	49 -- 55	-7.86935 kcal/mol	1.39337 kcal/mol	0.311712 kcal/mol	26 34@LB@ \| \|@LB@5'-UCA...CGCCU UGCGA...AUC-3'@LB@ CGAUUAC@LB@ \|\|\|\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.86935 kcal/mol@LB@Unfolding Energy - mRNA 1.39337 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 27 -- 33@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 49 -- 55@LB@
123	0.004171	0.1178	b2989	yghU	-8.31	0.130595	46 -- 54	49 -- 57	putative S-transferase		_____________45________55\n_____________\|_________\|\n5'-UUA...UGUGC_________CUGCU...CGC-3'\n______________UCUGAUUAC\n______________\|\|:\|\|\|\|\|\|\n______________AGGCUAAUG\n3'-AUU...GGUUU_________CACUU...AUG-5'\n_____________\|_________\|\n_____________58________48\n	48 -- 54	49 -- 55	-9.38135 kcal/mol	0.766517 kcal/mol	0.318327 kcal/mol	45 55@LB@ \| \|@LB@5'-UUA...UGUGC CUGCU...CGC-3'@LB@ UCUGAUUAC@LB@ \|\|:\|\|\|\|\|\|@LB@ AGGCUAAUG@LB@3'-AUU...GGUUU CACUU...AUG-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -9.38135 kcal/mol@LB@Unfolding Energy - mRNA 0.766517 kcal/mol@LB@Unfolding Energy - sRNA 0.318327 kcal/mol@LB@@LB@Position - mRNA 46 -- 54@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 49 -- 55@LB@
135	0.004796	0.125	b3634	coaD	-9.06	0.083023	69 -- 85	49 -- 66	pantetheine-phosphate adenylyltransferase		_____________68_________________86\n_____________\|__________________\|\n5'-GGA...UUUAC________CG________CGUAG...UUC-3'\n______________UCA_CCGA__CCGAUUAC\n______________\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|\n______________AGU_GGUU__GGCUAAUG\n3'-AUU...UUAUA___C____UA________CACUU...AUG-5'\n_____________\|__________________\|\n_____________67_________________48\n	79 -- 85	49 -- 55	-17.7938 kcal/mol	2.54845 kcal/mol	6.20469 kcal/mol	68 86@LB@ \| \|@LB@5'-GGA...UUUAC CG CGUAG...UUC-3'@LB@ UCA CCGA CCGAUUAC@LB@ \|\|\| \|\|:\| \|\|\|\|\|\|\|\|@LB@ AGU GGUU GGCUAAUG@LB@3'-AUU...UUAUA C UA CACUU...AUG-5'@LB@ \| \|@LB@ 67 48@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -17.7938 kcal/mol@LB@Unfolding Energy - mRNA 2.54845 kcal/mol@LB@Unfolding Energy - sRNA 6.20469 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 49 -- 66@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 49 -- 55@LB@
158	0.00634	0.1412	b3598	yibI	-10.19	0.039756	289 -- 298	49 -- 58	DUF3302 family inner membrane protein	b3587	_____________288________299\n_____________\|__________\|\n5'-CGU...CCCUU__________CA-3'\n______________AUCUGAUUGC\n______________\|\|\|:\|\|\|\|:\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	292 -- 298	49 -- 55	-10.9433 kcal/mol	0.440755 kcal/mol	0.318367 kcal/mol	288 299@LB@ \| \|@LB@5'-CGU...CCCUU CA-3'@LB@ AUCUGAUUGC@LB@ \|\|\|:\|\|\|\|:\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -10.9433 kcal/mol@LB@Unfolding Energy - mRNA 0.440755 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
162	0.006534	0.1413	b3771	ilvD	-6.87	0.280008	44 -- 51	49 -- 56	dihydroxyacid dehydratase		_____________43_______52\n_____________\|________\|\n5'-GCG...GUGGC________CAAAC...GUA-3'\n______________CCGGUUAC\n______________\|\|\|:\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	45 -- 51	49 -- 55	-9.72973 kcal/mol	2.55538 kcal/mol	0.317884 kcal/mol	43 52@LB@ \| \|@LB@5'-GCG...GUGGC CAAAC...GUA-3'@LB@ CCGGUUAC@LB@ \|\|\|:\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -6.87 kcal/mol@LB@Hybridization Energy -9.72973 kcal/mol@LB@Unfolding Energy - mRNA 2.55538 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 44 -- 51@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 49 -- 55@LB@
165	0.006672	0.1423	b1651	gloA	-7.94	0.160716	101 -- 108	49 -- 56	glyoxalase I Ni-dependent		_____________100______109\n_____________\|________\|\n5'-UGG...CUAUA________CCGAC...AAA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	102 -- 108	49 -- 55	-10.6899 kcal/mol	2.44421 kcal/mol	0.317884 kcal/mol	100 109@LB@ \| \|@LB@5'-UGG...CUAUA CCGAC...AAA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -10.6899 kcal/mol@LB@Unfolding Energy - mRNA 2.44421 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 101 -- 108@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 49 -- 55@LB@
168	0.006917	0.1448	b3070	yqjH	-8.25	0.134865	172 -- 181	49 -- 58	putative siderophore interacting protein		_____________171________182\n_____________\|__________\|\n5'-ACU...GAUAU__________CAUCA...AGC-3'\n______________AUCUGAUUAC\n______________\|\|\|:\|\|\|\|\|\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	175 -- 181	49 -- 55	-10.8722 kcal/mol	2.31397 kcal/mol	0.318367 kcal/mol	171 182@LB@ \| \|@LB@5'-ACU...GAUAU CAUCA...AGC-3'@LB@ AUCUGAUUAC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -10.8722 kcal/mol@LB@Unfolding Energy - mRNA 2.31397 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 172 -- 181@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 49 -- 55@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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