Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
195	0.03271	0.5507	b3213	gltD	-10.79	0.067022	188 -- 211	38 -- 59	glutamate synthase 4Fe-4S protein small subunit		_____________187______________________212\n_____________\|________________________\|\n5'-AGC...CAGUA_______GC____AUGAG______UGUUU...AGC-3'\n______________AGGGGUA__AACA_____UCAGAA\n______________\|\|\|\|\|\|\|__\|\|\|\|_____\|\|\|\|\|\|\n______________UCCCCAU__UUGU_____AGUCUU\n3'-UUU...CUUUA_____________CUGUA______UACUU...UCG-5'\n_____________\|________________________\|\n_____________60_______________________37\n	188 -- 194	53 -- 59	-20.1632 kcal/mol	3.12506 kcal/mol	6.25108 kcal/mol	187 212@LB@ \| \|@LB@5'-AGC...CAGUA GC AUGAG UGUUU...AGC-3'@LB@ AGGGGUA AACA UCAGAA@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UCCCCAU UUGU AGUCUU@LB@3'-UUU...CUUUA CUGUA UACUU...UCG-5'@LB@ \| \|@LB@ 60 37@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -20.1632 kcal/mol@LB@Unfolding Energy - mRNA 3.12506 kcal/mol@LB@Unfolding Energy - sRNA 6.25108 kcal/mol@LB@@LB@Position - mRNA 188 -- 211@LB@Position - sRNA 38 -- 59@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 53 -- 59@LB@
128	0.0201	0.5155	b2782	mazF	-10.78	0.067406	32 -- 50	1 -- 23	mRNA interferase toxin antitoxin is MazE	b4225	_____________31______________________51\n_____________\|_______________________\|\n5'-AUC...CAAUC_______________________GAAGA...UCC-3'\n______________UGAAUA___UUGAUGAUGA_AGU\n______________\|:\|\|\|\|___\|\|:\|\|\|\|\|\|\|_\|\|:\n______________AUUUAU___AAUUACUACU_UCG\n3'-UUU...CCAUU______UUC__________A___-5'\n_____________\|______________________\|\n_____________24_____________________1\n	41 -- 47	5 -- 11	-13.6359 kcal/mol	2.75565 kcal/mol	0.105066 kcal/mol	31 51@LB@ \| \|@LB@5'-AUC...CAAUC GAAGA...UCC-3'@LB@ UGAAUA UUGAUGAUGA AGU@LB@ \|:\|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|:@LB@ AUUUAU AAUUACUACU UCG@LB@3'-UUU...CCAUU UUC A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -13.6359 kcal/mol@LB@Unfolding Energy - mRNA 2.75565 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 32 -- 50@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 5 -- 11@LB@
170	0.02787	0.531	b3184	yhbE	-10.77	0.067448	1 -- 31	11 -- 53	EamA family inner membrane putative transporter		______________1__________________________________________32\n______________\|__________________________________________\|\n___________5'-_________GUA_________AUU___________________AGGCC...UGG-3'\n______________AAGCAGACG_____AAGUGAA___CG__________AAGUUAA\n______________\|\|:\|\|\|\|\|:_____\|\|:\|\|\|\|___\|\|__________\|\|\|\|\|\|\|\n______________UUUGUCUGU_____UUUACUU___GC__________UUCAAUU\n3'-UUU...CCCCA_________AAGUC_______ACU__CAUUAUUUAU_______ACUAC...UCG-5'\n_____________\|___________________________________________\|\n_____________54__________________________________________10\n	25 -- 31	11 -- 17	-18.1985 kcal/mol	1.09209 kcal/mol	6.3325 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GUA AUU AGGCC...UGG-3'@LB@ AAGCAGACG AAGUGAA CG AAGUUAA@LB@ \|\|:\|\|\|\|\|: \|\|:\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUGUCUGU UUUACUU GC UUCAAUU@LB@3'-UUU...CCCCA AAGUC ACU CAUUAUUUAU ACUAC...UCG-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -18.1985 kcal/mol@LB@Unfolding Energy - mRNA 1.09209 kcal/mol@LB@Unfolding Energy - sRNA 6.3325 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
34	0.003196	0.3086	b0896	dmsC	-10.70	0.070045	189 -- 235	4 -- 59	dimethyl sulfoxide reductase anaerobic subunit C		_____________188_______________________________________________________236\n_____________\|_________________________________________________________\|\n5'-CUG...CCCGA___A____UG__________________________________CCGC_________CUUCA...AAG-3'\n______________AGG_GGUG___AGAUG___GGAAGUGGAUGGC____AUGAAUGG______UGAUGAU\n______________\|\|\|_\|\|\|:___\|\|\|::___:\|\|\|:\|\|:\|\|\|:\|____\|\|:\|\|\|::______\|\|\|\|\|\|\|\n______________UCC_CCAU___UCUGU___UCUUUACUUACUG____UAUUUAUU______ACUACUA\n3'-UUU...CUUUA________UUG_____AAG_____________CCAU________UCAAUU_______UCG-5'\n_____________\|_________________________________________________________\|\n_____________60________________________________________________________3\n	229 -- 235	4 -- 10	-34.4804 kcal/mol	17.4476 kcal/mol	6.33761 kcal/mol	188 236@LB@ \| \|@LB@5'-CUG...CCCGA A UG CCGC CUUCA...AAG-3'@LB@ AGG GGUG AGAUG GGAAGUGGAUGGC AUGAAUGG UGAUGAU@LB@ \|\|\| \|\|\|: \|\|\|:: :\|\|\|:\|\|:\|\|\|:\| \|\|:\|\|\|:: \|\|\|\|\|\|\|@LB@ UCC CCAU UCUGU UCUUUACUUACUG UAUUUAUU ACUACUA@LB@3'-UUU...CUUUA UUG AAG CCAU UCAAUU UCG-5'@LB@ \| \|@LB@ 60 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -34.4804 kcal/mol@LB@Unfolding Energy - mRNA 17.4476 kcal/mol@LB@Unfolding Energy - sRNA 6.33761 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 4 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 4 -- 10@LB@
141	0.0236	0.526	b3339	tufA	-10.69	0.070202	69 -- 84	1 -- 19	translation elongation factor EF-Tu 1	b3980	_____________68__________________85\n_____________\|___________________\|\n5'-AAU...AUUCC___________________GCCGA...CCA-3'\n______________UGAAGU__AUGAUGA_AGC\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________AUUUCA__UACUACU_UCG\n3'-UUU...UAUUU______AU_______A___-5'\n_____________\|__________________\|\n_____________20_________________1\n	75 -- 81	5 -- 11	-13.5879 kcal/mol	2.83361 kcal/mol	0.0638423 kcal/mol	68 85@LB@ \| \|@LB@5'-AAU...AUUCC GCCGA...CCA-3'@LB@ UGAAGU AUGAUGA AGC@LB@ \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ AUUUCA UACUACU UCG@LB@3'-UUU...UAUUU AU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -13.5879 kcal/mol@LB@Unfolding Energy - mRNA 2.83361 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 5 -- 11@LB@
97	0.01584	0.5059	b0116	lpd	-10.63	0.072174	157 -- 204	5 -- 49	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase		_____________156_______________________________________________205\n_____________\|_________________________________________________\|\n5'-CCG...CUGAA_____A_____U____CC_C___A________UAUA___GUC_______GUACU...UAA-3'\n______________AGACG__CGGG_AUGA__G_CGG_GAUAAAUA____GAG___AUGAUGA\n______________\|\|\|\|:__\|:\|:_\|\|\|\|__\|_\|\|\|_:\|\|\|\|\|\|\|____:\|\|___\|\|\|\|\|\|\|\n______________UCUGU__GUCU_UACU__C_GCC_UUAUUUAU____UUC___UACUACU\n3'-UUU...AUUUG_____AA____U____UA_U___A_______________AAU_______AUCG-5'\n_____________\|_________________________________________________\|\n_____________50________________________________________________4\n	198 -- 204	5 -- 11	-27.6335 kcal/mol	10.6788 kcal/mol	6.32229 kcal/mol	156 205@LB@ \| \|@LB@5'-CCG...CUGAA A U CC C A UAUA GUC GUACU...UAA-3'@LB@ AGACG CGGG AUGA G CGG GAUAAAUA GAG AUGAUGA@LB@ \|\|\|\|: \|:\|: \|\|\|\| \| \|\|\| :\|\|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|@LB@ UCUGU GUCU UACU C GCC UUAUUUAU UUC UACUACU@LB@3'-UUU...AUUUG AA U UA U A AAU AUCG-5'@LB@ \| \|@LB@ 50 4@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -27.6335 kcal/mol@LB@Unfolding Energy - mRNA 10.6788 kcal/mol@LB@Unfolding Energy - sRNA 6.32229 kcal/mol@LB@@LB@Position - mRNA 157 -- 204@LB@Position - sRNA 5 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
92	0.01497	0.5059	b1902	ftnB	-10.62	0.072498	12 -- 36	1 -- 25	ferritin B putative ferrous iron reservoir		_____________11________________________37\n_____________\|_________________________\|\n5'-UGA...GUAAA____U_____C________UUA___AUUUU...AAC-3'\n______________AAUA_AUAAA_UUGAUGAU___AGC\n______________\|\|\|\|_\|\|\|\|\|_\|\|:\|\|\|\|\|___\|\|\|\n______________UUAU_UAUUU_AAUUACUA___UCG\n3'-UUU...UGCCA____U_____C________CUA___-5'\n_____________\|________________________\|\n_____________26_______________________1\n	24 -- 30	7 -- 13	-13.6335 kcal/mol	2.89836 kcal/mol	0.112205 kcal/mol	11 37@LB@ \| \|@LB@5'-UGA...GUAAA U C UUA AUUUU...AAC-3'@LB@ AAUA AUAAA UUGAUGAU AGC@LB@ \|\|\|\| \|\|\|\|\| \|\|:\|\|\|\|\| \|\|\|@LB@ UUAU UAUUU AAUUACUA UCG@LB@3'-UUU...UGCCA U C CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -13.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.89836 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 12 -- 36@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 7 -- 13@LB@
140	0.02319	0.526	b3615	waaH	-10.58	0.073933	178 -- 212	1 -- 47	LPS(HepIII)-glucuronic acid glycosyltransferase		_____________177______________________________________________213\n_____________\|________________________________________________\|\n5'-GAU...GGAUA____________C____U_______UU________________AC___ACCAA...GGA-3'\n______________AC_UUCAGAGGU____G_CGGUAAU___________AUGAUGA__AGC\n______________\|\|_\|\|\|\|\|\|::\|____\|_\|\|\|\|\|\|\|___________\|\|\|\|\|\|\|__\|\|\|\n______________UG_AAGUCUUUA____C_GCCAUUA___________UACUACU__UCG\n3'-UUU...UUGUC__U_________CUUA_U_______UUUAUUUCAAU_______A____-5'\n_____________\|_______________________________________________\|\n_____________48______________________________________________1\n	201 -- 207	5 -- 11	-24.9941 kcal/mol	8.09222 kcal/mol	6.32011 kcal/mol	177 213@LB@ \| \|@LB@5'-GAU...GGAUA C U UU AC ACCAA...GGA-3'@LB@ AC UUCAGAGGU G CGGUAAU AUGAUGA AGC@LB@ \|\| \|\|\|\|\|\|::\| \| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UG AAGUCUUUA C GCCAUUA UACUACU UCG@LB@3'-UUU...UUGUC U CUUA U UUUAUUUCAAU A -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -24.9941 kcal/mol@LB@Unfolding Energy - mRNA 8.09222 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@LB@
26	0.001686	0.211	b0091	murC	-10.53	0.075719	174 -- 220	1 -- 48	UDP-N-acetylmuramate:L-alanine ligase		_____________173______________________________________________221\n_____________\|________________________________________________\|\n5'-CAG...CGUAU__AUUUA______U___________A_______UACACAACAAU____AAAAC...GCG-3'\n______________GA_____AGAAGU_AAUGGC_GUAA_GAAUGAA___________UGGC\n______________\|\|_____\|\|\|\|:\|_\|\|\|\|:\|_\|\|\|\|_:\|\|\|:\|\|___________\|:\|\|\n______________CU_____UCUUUA_UUACUG_CAUU_UUUAUUU___________AUCG\n3'-UUU...UUUGU__GUAAG______C______C____A_______CAAUUACUACU____-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	199 -- 205	16 -- 22	-22.2946 kcal/mol	5.44296 kcal/mol	6.32011 kcal/mol	173 221@LB@ \| \|@LB@5'-CAG...CGUAU AUUUA U A UACACAACAAU AAAAC...GCG-3'@LB@ GA AGAAGU AAUGGC GUAA GAAUGAA UGGC@LB@ \|\| \|\|\|\|:\| \|\|\|\|:\| \|\|\|\| :\|\|\|:\|\| \|:\|\|@LB@ CU UCUUUA UUACUG CAUU UUUAUUU AUCG@LB@3'-UUU...UUUGU GUAAG C C A CAAUUACUACU -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -22.2946 kcal/mol@LB@Unfolding Energy - mRNA 5.44296 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 174 -- 220@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
182	0.03007	0.5424	b3131	agaR	-10.52	0.076061	148 -- 177	28 -- 59	transcriptional repressor of the aga regulon		_____________147______________________________178\n_____________\|________________________________\|\n5'-CAG...UAGAA___C__U________AAAC_____________AAAGU...AGG-3'\n______________AGG_GU_AAUAGGCA____GAAAUGAA__ACG\n______________\|\|\|_\|\|_\|\|:\|\|:\|\|____\|\|\|\|\|\|\|\|__\|\|\|\n______________UCC_CA_UUGUCUGU____CUUUACUU__UGC\n3'-UUU...CUUUA___C__U________AAGU________AC___CAUUA...UCG-5'\n_____________\|________________________________\|\n_____________60_______________________________27\n	167 -- 173	34 -- 40	-23.0737 kcal/mol	6.26419 kcal/mol	6.28754 kcal/mol	147 178@LB@ \| \|@LB@5'-CAG...UAGAA C U AAAC AAAGU...AGG-3'@LB@ AGG GU AAUAGGCA GAAAUGAA ACG@LB@ \|\|\| \|\| \|\|:\|\|:\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCC CA UUGUCUGU CUUUACUU UGC@LB@3'-UUU...CUUUA C U AAGU AC CAUUA...UCG-5'@LB@ \| \|@LB@ 60 27@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -23.0737 kcal/mol@LB@Unfolding Energy - mRNA 6.26419 kcal/mol@LB@Unfolding Energy - sRNA 6.28754 kcal/mol@LB@@LB@Position - mRNA 148 -- 177@LB@Position - sRNA 28 -- 59@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 34 -- 40@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)

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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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