Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
153	0.008123	0.1845	stm2512	xseA	-14.57	0.138273	215 -- 252	42 -- 82	exodeoxyribonuclease VII large subunit	_____________214________253\n_____________\|__________\|\n5'-CGU...UUUUU__________GCCUU...GCG-3'\n______________ACCGUAAGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UGGCAUUCGG\n3'-UUU...AGUGU__________UUUUC...UCA-5'\n_____________\|__________\|\n_____________83_________41\n	234 -- 240	56 -- 62	-17.1871 kcal/mol	1.1981 kcal/mol	7.48121 kcal/mol	214 253@LB@ \| \|@LB@5'-CGU...UUUUU GCCUU...GCG-3'@LB@ ACCGUAAGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UGGCAUUCGG@LB@3'-UUU...AGUGU UUUUC...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -17.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.1981 kcal/mol@LB@Unfolding Energy - sRNA 7.48121 kcal/mol@LB@@LB@Position - mRNA 215 -- 252@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 56 -- 62@LB@
56	0.002144	0.1363	pslt006	repA	-15.36	0.103288	219 -- 279	36 -- 87	DNA replication	_____________218_____________________280\n_____________\|_______________________\|\n5'-ACU...ACACC_______UGUU____U_______CGACA...CCC-3'\n______________CGAACAC_____CAC__CAUUAC\n______________\|:\|\|\|\|\|_____\|\|\|__\|\|\|:\|\|\n______________GUUUGUG_____GUG__GUAGUG\n3'-UUU...UUAAC_______UUGUU___UU______UUGGC...UCA-5'\n_____________\|_______________________\|\n_____________88______________________35\n	225 -- 231	83 -- 89	-15.7114 kcal/mol	3.78124 kcal/mol	5.66809 kcal/mol	218 280@LB@ \| \|@LB@5'-ACU...ACACC UGUU U CGACA...CCC-3'@LB@ CGAACAC CAC CAUUAC@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|@LB@ GUUUGUG GUG GUAGUG@LB@3'-UUU...UUAAC UUGUU UU UUGGC...UCA-5'@LB@ \| \|@LB@ 88 35@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -15.7114 kcal/mol@LB@Unfolding Energy - mRNA 3.78124 kcal/mol@LB@Unfolding Energy - sRNA 5.66809 kcal/mol@LB@@LB@Position - mRNA 219 -- 279@LB@Position - sRNA 36 -- 87@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 83 -- 89@LB@
179	0.009806	0.1951	stm3912	rep	-13.00	0.240883	219 -- 287	22 -- 83	ATP-dependent DNA helicase Rep	_____________218__________________________288\n_____________\|____________________________\|\n5'-AGU...UCCCA____UUUAAAUCCC______________CUGUC...CCA-3'\n______________UGCG__________GGC_CAACAACACG\n______________\|\|\|:__________::\|_\|\|\|\|\|\|\|\|\|:\n______________ACGU__________UUG_GUUGUUGUGU\n3'-UUU...GGUUA_________________U__________UGUAG...UCA-5'\n_____________\|____________________________\|\n_____________84___________________________21\n	222 -- 228	74 -- 80	-15.5311 kcal/mol	3.54327 kcal/mol	3.73631 kcal/mol	218 288@LB@ \| \|@LB@5'-AGU...UCCCA UUUAAAUCCC CUGUC...CCA-3'@LB@ UGCG GGC CAACAACACG@LB@ \|\|\|: ::\| \|\|\|\|\|\|\|\|\|:@LB@ ACGU UUG GUUGUUGUGU@LB@3'-UUU...GGUUA U UGUAG...UCA-5'@LB@ \| \|@LB@ 84 21@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -15.5311 kcal/mol@LB@Unfolding Energy - mRNA 3.54327 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 219 -- 287@LB@Position - sRNA 22 -- 83@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 74 -- 80@LB@
195	0.01085	0.197	stm0549	fimZ	-13.17	0.226725	219 -- 235	155 -- 171	DNA-binding response regulator	_____________218___________236\n_____________\|_____________\|\n5'-CAG...CUGUU_____________AACAC...UGA-3'\n______________AUCAUUAUGGACG\n______________\|\|\|\|:\|\|\|\|\|\|\|:\n______________UAGUGAUACCUGU\n3'-UUU...GUAAU_____________CUGUC...UCA-5'\n_____________\|_____________\|\n_____________172___________154\n	225 -- 231	159 -- 165	-17.3187 kcal/mol	3.33371 kcal/mol	3.42647 kcal/mol	218 236@LB@ \| \|@LB@5'-CAG...CUGUU AACAC...UGA-3'@LB@ AUCAUUAUGGACG@LB@ \|\|\|\|:\|\|\|\|\|\|\|:@LB@ UAGUGAUACCUGU@LB@3'-UUU...GUAAU CUGUC...UCA-5'@LB@ \| \|@LB@ 172 154@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -17.3187 kcal/mol@LB@Unfolding Energy - mRNA 3.33371 kcal/mol@LB@Unfolding Energy - sRNA 3.42647 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 155 -- 171@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
87	0.004009	0.1596	stm2067	sbcB	-11.70	0.367652	220 -- 292	35 -- 90	exodeoxyribonuclease I	_____________219_____________________293\n_____________\|_______________________\|\n5'-AUU...AUGUA______U________________AUUGG...CCG-3'\n______________CGAACA_UAGCA__ACAAUAUCA\n______________\|:\|\|\|\|_:\|:\|\|__\|\|\|\|:\|\|\|\|\n______________GUUUGU_GUUGU__UGUUGUAGU\n3'-UUU...UUAAC____________UG_________GUUGG...UCA-5'\n_____________\|_______________________\|\n_____________91______________________34\n	110 -- 116	68 -- 74	-17.8808 kcal/mol	2.08887 kcal/mol	5.27986 kcal/mol	219 293@LB@ \| \|@LB@5'-AUU...AUGUA U AUUGG...CCG-3'@LB@ CGAACA UAGCA ACAAUAUCA@LB@ \|:\|\|\|\| :\|:\|\| \|\|\|\|:\|\|\|\|@LB@ GUUUGU GUUGU UGUUGUAGU@LB@3'-UUU...UUAAC UG GUUGG...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -17.8808 kcal/mol@LB@Unfolding Energy - mRNA 2.08887 kcal/mol@LB@Unfolding Energy - sRNA 5.27986 kcal/mol@LB@@LB@Position - mRNA 220 -- 292@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 68 -- 74@LB@
43	0.001574	0.1267	stm4453	treC	-17.28	0.050040	221 -- 269	37 -- 81	trehalose- 6-P hydrolase	_____________220____________________270\n_____________\|______________________\|\n5'-CGU...CGCAC_______AA_____________UAUUC...GCG-3'\n______________UUGCAGG__ACAACAAU__GAC\n______________\|\|\|\|\|::__\|\|\|\|\|\|\|:__:\|\|\n______________AACGUUU__UGUUGUUG__UUG\n3'-UUU...UGGUU_______G_________UG___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________82_____________________36\n	196 -- 202	77 -- 83	-15.8671 kcal/mol	3.0955 kcal/mol	3.80821 kcal/mol	220 270@LB@ \| \|@LB@5'-CGU...CGCAC AA UAUUC...GCG-3'@LB@ UUGCAGG ACAACAAU GAC@LB@ \|\|\|\|\|:: \|\|\|\|\|\|\|: :\|\|@LB@ AACGUUU UGUUGUUG UUG@LB@3'-UUU...UGGUU G UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -17.28 kcal/mol@LB@Hybridization Energy -15.8671 kcal/mol@LB@Unfolding Energy - mRNA 3.0955 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 221 -- 269@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 77 -- 83@LB@
92	0.004229	0.1596	stm0669	phoL	-19.39	0.022083	221 -- 286	36 -- 89	putative phosphate starvation-inducible protein ATP-binding	_____________220__________________________________________________________________287\n_____________\|____________________________________________________________________\|\n5'-AAA...CGAUA_________G__GAACAGUUUGAAUAUA____C______AAUUAC___UU____________CA____CCGUC...GCC-3'\n______________CAGACACAA_AG________________GACA_UCGCGA_______CC__GAGCCCG_CAGA__ACGC\n______________\|\|:\|\|\|\|\|\|_\|:________________:\|\|\|_\|\|:\|:\|_______\|\|__:\|\|\|\|\|:_\|\|\|\|__\|\|\|\|\n______________GUUUGUGUU_UU________________UUGU_AGUGUU_______GG__UUCGGGU_GUCU__UGCG\n3'-UUU...UUAAC_________G__GUG________________________GGCAUUC__UU_______A____UG____UAAGG...UCA-5'\n_____________\|____________________________________________________________________\|\n_____________90___________________________________________________________________35\n	270 -- 276	47 -- 53	-43.5648 kcal/mol	9.30805 kcal/mol	22.4875 kcal/mol	220 287@LB@ \| \|@LB@5'-AAA...CGAUA G GAACAGUUUGAAUAUA C AAUUAC UU CA CCGUC...GCC-3'@LB@ CAGACACAA AG GACA UCGCGA CC GAGCCCG CAGA ACGC@LB@ \|\|:\|\|\|\|\|\| \|: :\|\|\| \|\|:\|:\| \|\| :\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ GUUUGUGUU UU UUGU AGUGUU GG UUCGGGU GUCU UGCG@LB@3'-UUU...UUAAC G GUG GGCAUUC UU A UG UAAGG...UCA-5'@LB@ \| \|@LB@ 90 35@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -43.5648 kcal/mol@LB@Unfolding Energy - mRNA 9.30805 kcal/mol@LB@Unfolding Energy - sRNA 22.4875 kcal/mol@LB@@LB@Position - mRNA 221 -- 286@LB@Position - sRNA 36 -- 89@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 47 -- 53@LB@
152	0.008087	0.1845	stm0213	dapD	-12.65	0.271269	222 -- 289	49 -- 104	2 3 4 5-tetrahydropyridine-2 6-dicarboxylate N-succinyltransferase	_____________221______________________290\n_____________\|________________________\|\n5'-UUU...UUAAC_________GUU___G________UGAGA...AGG-3'\n______________AAUGCAGCA___ACA_AACGUUAU\n______________\|\|::\|\|:\|\|___\|\|\|_\|\|\|:\|:\|:\n______________UUGUGUUGU___UGU_UUGUAGUG\n3'-UUU...AACGU_______________G________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________105______________________48\n	202 -- 208	79 -- 85	-17.6746 kcal/mol	3.78795 kcal/mol	5.3513 kcal/mol	221 290@LB@ \| \|@LB@5'-UUU...UUAAC GUU G UGAGA...AGG-3'@LB@ AAUGCAGCA ACA AACGUUAU@LB@ \|\|::\|\|:\|\| \|\|\| \|\|\|:\|:\|:@LB@ UUGUGUUGU UGU UUGUAGUG@LB@3'-UUU...AACGU G UUGGC...UCA-5'@LB@ \| \|@LB@ 105 48@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -17.6746 kcal/mol@LB@Unfolding Energy - mRNA 3.78795 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 222 -- 289@LB@Position - sRNA 49 -- 104@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 79 -- 85@LB@
59	0.00232	0.14	stm4105	metF	-16.51	0.066936	223 -- 245	40 -- 59	methylenetetrahydrofolate reductase [NAD(P)H]	_____________222__________________246\n_____________\|____________________\|\n5'-AAG...UUUAC__________AUA_______GCGAU...GCA-3'\n______________AACACAACAA___AUAACAU\n______________\|\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________UUGUGUUGUU___UGUUGUA\n3'-UUU...AACGU__________G_________GUGUU...UCA-5'\n_____________\|____________________\|\n_____________60___________________39\n	175 -- 181	70 -- 76	-16.6304 kcal/mol	0.675865 kcal/mol	3.87174 kcal/mol	222 246@LB@ \| \|@LB@5'-AAG...UUUAC AUA GCGAU...GCA-3'@LB@ AACACAACAA AUAACAU@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ UUGUGUUGUU UGUUGUA@LB@3'-UUU...AACGU G GUGUU...UCA-5'@LB@ \| \|@LB@ 60 39@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 0.675865 kcal/mol@LB@Unfolding Energy - sRNA 3.87174 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 40 -- 59@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 70 -- 76@LB@
143	0.007336	0.182	stm2276	ubiG	-14.65	0.134291	225 -- 278	36 -- 81	2-octaprenyl-6-hydroxy phenol methylase	_____________224_________________279\n_____________\|___________________\|\n5'-CAC...CGGCA____________CA_____UUUGC...AAU-3'\n______________GUAGAUAUAACG__GCGAC\n______________\|:\|:\|:\|:\|\|\|:__:\|:\|\|\n______________CGUUUGUGUUGU__UGUUG\n3'-UUU...GUUAA____________UG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________82__________________35\n	134 -- 140	80 -- 86	-18.0681 kcal/mol	5.41873 kcal/mol	3.80362 kcal/mol	224 279@LB@ \| \|@LB@5'-CAC...CGGCA CA UUUGC...AAU-3'@LB@ GUAGAUAUAACG GCGAC@LB@ \|:\|:\|:\|:\|\|\|: :\|:\|\|@LB@ CGUUUGUGUUGU UGUUG@LB@3'-UUU...GUUAA UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -18.0681 kcal/mol@LB@Unfolding Energy - mRNA 5.41873 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 225 -- 278@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 80 -- 86@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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