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: https://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	Additional homologs
25	0.0006298	0.08814	stm3161	metC	-13.21	0.223681	190 -- 249	35 -- 90	cystathionine beta-lyase		_____________189__________________250\n_____________\|____________________\|\n5'-CAA...AACUG_________G__________AAAAA...CAC-3'\n______________GUAAACGCA__GACGCAGCA\n______________\|:\|\|\|\|:\|\|__:\|\|:\|\|:\|\|\n______________CGUUUGUGU__UUGUGUUGU\n3'-UUU...GUUAA_________UG_________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________34\n	243 -- 249	71 -- 77	-21.5854 kcal/mol	5.07977 kcal/mol	3.80671 kcal/mol	189 250@LB@ \| \|@LB@5'-CAA...AACUG G AAAAA...CAC-3'@LB@ GUAAACGCA GACGCAGCA@LB@ \|:\|\|\|\|:\|\| :\|\|:\|\|:\|\|@LB@ CGUUUGUGU UUGUGUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -21.5854 kcal/mol@LB@Unfolding Energy - mRNA 5.07977 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 71 -- 77@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@
159	0.008305	0.1845	stm3625	yhjV	-13.06	0.235438	203 -- 240	55 -- 86	transporter		_____________202________________________241\n_____________\|__________________________\|\n5'-UUA...UAUUU_____________CUCUA________CGACA...UCU-3'\n______________UGGGCAG__GGGG______UGCAGGA\n______________\|\|\|:\|\|\|__:\|\|\|______\|:\|\|\|\|\|\n______________ACCUGUC__UCCC______AUGUCCU\n3'-UUU...GUGAU_______UG____AUUUAC_______UCACU...UCA-5'\n_____________\|__________________________\|\n_____________87_________________________54\n	202 -- 208	139 -- 145	-24.2103 kcal/mol	7.6176 kcal/mol	3.71206 kcal/mol	202 241@LB@ \| \|@LB@5'-UUA...UAUUU CUCUA CGACA...UCU-3'@LB@ UGGGCAG GGGG UGCAGGA@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ ACCUGUC UCCC AUGUCCU@LB@3'-UUU...GUGAU UG AUUUAC UCACU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -13.06 kcal/mol@LB@Hybridization Energy -24.2103 kcal/mol@LB@Unfolding Energy - mRNA 7.6176 kcal/mol@LB@Unfolding Energy - sRNA 3.71206 kcal/mol@LB@@LB@Position - mRNA 203 -- 240@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 139 -- 145@LB@
133	0.006689	0.1774	stm0831	dps	-13.05	0.236755	141 -- 176	159 -- 184	DNA starvation/stationary phase protection protein Dps		_____________140________________________177\n_____________\|__________________________\|\n5'-CAU...UUACC___CA_______AACU__________AAUUG...UUA-3'\n______________CAC__AACAGCA____CGUC_UAACC\n______________\|\|\|__\|\|\|\|:\|\|____\|:\|\|_:\|\|\|\|\n______________GUG__UUGUUGU____GUAG_GUUGG\n3'-UUU...CGUUU____________GUU_____U_____CAUUC...UCA-5'\n_____________\|__________________________\|\n_____________185________________________158\n	37 -- 43	76 -- 82	-18.4678 kcal/mol	1.39739 kcal/mol	8.25195 kcal/mol	140 177@LB@ \| \|@LB@5'-CAU...UUACC CA AACU AAUUG...UUA-3'@LB@ CAC AACAGCA CGUC UAACC@LB@ \|\|\| \|\|\|\|:\|\| \|:\|\| :\|\|\|\|@LB@ GUG UUGUUGU GUAG GUUGG@LB@3'-UUU...CGUUU GUU U CAUUC...UCA-5'@LB@ \| \|@LB@ 185 158@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -18.4678 kcal/mol@LB@Unfolding Energy - mRNA 1.39739 kcal/mol@LB@Unfolding Energy - sRNA 8.25195 kcal/mol@LB@@LB@Position - mRNA 141 -- 176@LB@Position - sRNA 159 -- 184@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 76 -- 82@LB@
185	0.01043	0.1967	stm1700	fabI	-13.03	0.238331	75 -- 107	38 -- 76	enoyl-[acyl-carrier-protein] reductase		_____________74______________________________108\n_____________\|_______________________________\|\n5'-AGU...AGCGU____C______C___________________UAUAA...CUG-3'\n______________GACA_ACGGGG________CA_GGAGUGGGA\n______________\|\|\|\|_\|\|:\|\|\|________\|\|_\|:\|\|\|\|::\|\n______________CUGU_UGUCCC________GU_CUUCACUUU\n3'-UUU...GAUAC____C______AUUUACAU__C_________UUCCC...UCA-5'\n_____________\|_______________________________\|\n_____________77______________________________37\n	96 -- 102	134 -- 140	-20.8604 kcal/mol	6.05685 kcal/mol	6.0649 kcal/mol	74 108@LB@ \| \|@LB@5'-AGU...AGCGU C C UAUAA...CUG-3'@LB@ GACA ACGGGG CA GGAGUGGGA@LB@ \|\|\|\| \|\|:\|\|\| \|\| \|:\|\|\|\|::\|@LB@ CUGU UGUCCC GU CUUCACUUU@LB@3'-UUU...GAUAC C AUUUACAU C UUCCC...UCA-5'@LB@ \| \|@LB@ 77 37@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -20.8604 kcal/mol@LB@Unfolding Energy - mRNA 6.05685 kcal/mol@LB@Unfolding Energy - sRNA 6.0649 kcal/mol@LB@@LB@Position - mRNA 75 -- 107@LB@Position - sRNA 38 -- 76@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 134 -- 140@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@
190	0.01053	0.1967	stm4032	N/A	-12.98	0.242168	37 -- 92	31 -- 85	lipase	stm0490	_____________36__________________93\n_____________\|___________________\|\n5'-CUU...UCGCG____G______G_______GAGGG...GCU-3'\n______________AACA_AAUAUU_AUGACCG\n______________\|\|\|\|_\|\|:\|\|:_\|::\|\|\|\|\n______________UUGU_UUGUAG_UGUUGGC\n3'-UUU...UGUUG____G______________AUUCG...UCA-5'\n_____________\|___________________\|\n_____________86__________________30\n	283 -- 289	62 -- 68	-14.8704 kcal/mol	1.51414 kcal/mol	6.51321 kcal/mol	36 93@LB@ \| \|@LB@5'-CUU...UCGCG G G GAGGG...GCU-3'@LB@ AACA AAUAUU AUGACCG@LB@ \|\|\|\| \|\|:\|\|: \|::\|\|\|\|@LB@ UUGU UUGUAG UGUUGGC@LB@3'-UUU...UGUUG G AUUCG...UCA-5'@LB@ \| \|@LB@ 86 30@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -14.8704 kcal/mol@LB@Unfolding Energy - mRNA 1.51414 kcal/mol@LB@Unfolding Energy - sRNA 6.51321 kcal/mol@LB@@LB@Position - mRNA 37 -- 92@LB@Position - sRNA 31 -- 85@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 62 -- 68@LB@
182	0.01014	0.1966	stm3011	galR	-12.96	0.243649	22 -- 54	60 -- 90	transcriptional regulator GalR		_____________21_________________________________________55\n_____________\|__________________________________________\|\n_________5'-AC____C____U____UGCCA______AAUC__________UU_GCAAA...GGC-3'\n______________CUGA_UCGC_GGCC_____GCAGAC____GCAACAGCGC__C\n______________\|\|\|\|_\|\|\|\|_\|:\|\|_____\|\|\|:\|\|____:\|\|\|\|\|:\|:\|__\|\n______________GACU_AGCG_CUGG_____CGUUUG____UGUUGUUGUG__G\n3'-UUU...CACCA____U____U____UUAA_____________________UU_UAGUG...UCA-5'\n_____________\|__________________________________________\|\n_____________91_________________________________________59\n	35 -- 41	75 -- 81	-39.0068 kcal/mol	12.9734 kcal/mol	13.5432 kcal/mol	21 55@LB@ \| \|@LB@ 5'-AC C U UGCCA AAUC UU GCAAA...GGC-3'@LB@ CUGA UCGC GGCC GCAGAC GCAACAGCGC C@LB@ \|\|\|\| \|\|\|\| \|:\|\| \|\|\|:\|\| :\|\|\|\|\|:\|:\| \|@LB@ GACU AGCG CUGG CGUUUG UGUUGUUGUG G@LB@3'-UUU...CACCA U U UUAA UU UAGUG...UCA-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -39.0068 kcal/mol@LB@Unfolding Energy - mRNA 12.9734 kcal/mol@LB@Unfolding Energy - sRNA 13.5432 kcal/mol@LB@@LB@Position - mRNA 22 -- 54@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 75 -- 81@LB@
55	0.002114	0.1363	stm0887	artJ	-12.89	0.249853	160 -- 177	72 -- 90	arginine ABC transporter substrate-binding protein		_____________159_________________178\n_____________\|___________________\|\n5'-AUG...AUGCC___________________CAUAA...CGU-3'\n______________GCAGACACGGC_GCAUAAU\n______________\|\|\|:\|\|\|\|::\|_:\|\|:\|\|:\n______________CGUUUGUGUUG_UGUGUUG\n3'-UUU...GUUAA___________U_______UAGUG...UCA-5'\n_____________\|___________________\|\n_____________91__________________71\n	171 -- 177	72 -- 78	-21.0424 kcal/mol	4.03353 kcal/mol	3.80362 kcal/mol	159 178@LB@ \| \|@LB@5'-AUG...AUGCC CAUAA...CGU-3'@LB@ GCAGACACGGC GCAUAAU@LB@ \|\|\|:\|\|\|\|::\| :\|\|:\|\|:@LB@ CGUUUGUGUUG UGUGUUG@LB@3'-UUU...GUUAA U UAGUG...UCA-5'@LB@ \| \|@LB@ 91 71@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -21.0424 kcal/mol@LB@Unfolding Energy - mRNA 4.03353 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 160 -- 177@LB@Position - sRNA 72 -- 90@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 72 -- 78@LB@
148	0.007836	0.1845	stm2318	nuoL	-12.84	0.254324	144 -- 178	37 -- 76	NADH-quinone oxidoreductase subunit L		_____________143___________________179\n_____________\|_____________________\|\n5'-GGG...AGACC_____U____U__________UUCUC...UUG-3'\n______________GAUGG_CAGG___GAUGUACA\n______________\|\|::\|_\|\|\|\|___:\|\|\|\|\|\|\|\n______________CUGUC_GUCC___UUACAUGU\n3'-UUU...GAUAC_____U____CAU________CCUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________36\n	82 -- 88	142 -- 148	-19.9967 kcal/mol	7.20144 kcal/mol	3.50251 kcal/mol	143 179@LB@ \| \|@LB@5'-GGG...AGACC U U UUCUC...UUG-3'@LB@ GAUGG CAGG GAUGUACA@LB@ \|\|::\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUGUC GUCC UUACAUGU@LB@3'-UUU...GAUAC U CAU CCUUC...UCA-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -19.9967 kcal/mol@LB@Unfolding Energy - mRNA 7.20144 kcal/mol@LB@Unfolding Energy - sRNA 3.50251 kcal/mol@LB@@LB@Position - mRNA 144 -- 178@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 142 -- 148@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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