Input and runtime details for job 7743500 (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 7743500 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:00 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:27:12 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 06:56:30 CET 2018
	Post-Processing Finished		@ Sat Feb 17 06:56:38 CET 2018
	Job Completed		@ Sat Feb 17 06:57:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
141	0.002959	0.09644	pa5519	N/A	-12.18	0.058415	260 -- 272	100 -- 118	acyl-CoA thioesterase	pa2693	_____________259_________________273\n_____________\|___________________\|\n5'-GGG...CCCGC___________________AGAAA...ACA-3'\n______________CCGU______CCUGAUGAG\n______________\|\|\|\|______\|\|\|\|\|\|\|\|\|\n______________GGCA______GGACUACUC\n3'-UUU...UUUUU____CUAAUC_________CUCUA...GUU-5'\n_____________\|___________________\|\n_____________119_________________99\n	266 -- 272	100 -- 106	-18.4857 kcal/mol	4.06476 kcal/mol	2.24889 kcal/mol	259 273@LB@ \| \|@LB@5'-GGG...CCCGC AGAAA...ACA-3'@LB@ CCGU CCUGAUGAG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GGCA GGACUACUC@LB@3'-UUU...UUUUU CUAAUC CUCUA...GUU-5'@LB@ \| \|@LB@ 119 99@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -18.4857 kcal/mol@LB@Unfolding Energy - mRNA 4.06476 kcal/mol@LB@Unfolding Energy - sRNA 2.24889 kcal/mol@LB@@LB@Position - mRNA 260 -- 272@LB@Position - sRNA 100 -- 118@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 100 -- 106@LB@
77	0.0008517	0.05078	pa4366	sodB	-3.26	0.982782	263 -- 269	117 -- 123	superoxide dismutase		_____________262_____270\n_____________\|_______\|\n5'-GAC...UCCGC_______CUGGA...ACA-3'\n______________AGAAACC\n______________\|:\|\|\|\|\|\n______________UUUUUGG\n3'-UUU...CCCAG_______CACUA...GUU-5'\n_____________\|_______\|\n_____________124_____116\n	263 -- 269	117 -- 123	-5.6152 kcal/mol	1.17222 kcal/mol	1.17573 kcal/mol	262 270@LB@ \| \|@LB@5'-GAC...UCCGC CUGGA...ACA-3'@LB@ AGAAACC@LB@ \|:\|\|\|\|\|@LB@ UUUUUGG@LB@3'-UUU...CCCAG CACUA...GUU-5'@LB@ \| \|@LB@ 124 116@LB@@LB@@LB@Energy -3.26 kcal/mol@LB@Hybridization Energy -5.6152 kcal/mol@LB@Unfolding Energy - mRNA 1.17222 kcal/mol@LB@Unfolding Energy - sRNA 1.17573 kcal/mol@LB@@LB@Position - mRNA 263 -- 269@LB@Position - sRNA 117 -- 123@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 117 -- 123@LB@
67	0.0007208	0.0493	pa0304	spuH	-8.66	0.319981	266 -- 281	40 -- 54	polyamine transporter PotI		_____________265______________282\n_____________\|________________\|\n5'-CAA...CCGAU_______C_G______UAUUC...CCA-3'\n______________GCUGAUC_U_GUGAUC\n______________\|\|\|\|\|\|\|_\|_\|:\|\|:\|\n______________CGACUAG_A_CGCUGG\n3'-UUU...AUGGC_________G______UCAAC...GUU-5'\n_____________\|________________\|\n_____________55_______________39\n	266 -- 272	48 -- 54	-20.1848 kcal/mol	3.44761 kcal/mol	8.07324 kcal/mol	265 282@LB@ \| \|@LB@5'-CAA...CCGAU C G UAUUC...CCA-3'@LB@ GCUGAUC U GUGAUC@LB@ \|\|\|\|\|\|\| \| \|:\|\|:\|@LB@ CGACUAG A CGCUGG@LB@3'-UUU...AUGGC G UCAAC...GUU-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -20.1848 kcal/mol@LB@Unfolding Energy - mRNA 3.44761 kcal/mol@LB@Unfolding Energy - sRNA 8.07324 kcal/mol@LB@@LB@Position - mRNA 266 -- 281@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 48 -- 54@LB@
106	0.001743	0.07531	pa4019	N/A	-13.63	0.024857	269 -- 289	98 -- 119	aromatic acid decarboxylase		_____________268_____________________290\n_____________\|_______________________\|\n5'-CCG...CGCUU___C______________C____AGAGC...AGG-3'\n______________GCU__GAUU_GCCUGGUG_AGGA\n______________:\|:__\|\|\|\|_\|\|\|\|\|:\|\|_\|\|\|\|\n______________UGG__CUAA_CGGACUAC_UCCU\n3'-UUU...GUUUU___CA____U_____________CUAUU...GUU-5'\n_____________\|_______________________\|\n_____________120_____________________97\n	278 -- 284	102 -- 108	-22.0172 kcal/mol	6.14115 kcal/mol	2.25153 kcal/mol	268 290@LB@ \| \|@LB@5'-CCG...CGCUU C C AGAGC...AGG-3'@LB@ GCU GAUU GCCUGGUG AGGA@LB@ :\|: \|\|\|\| \|\|\|\|\|:\|\| \|\|\|\|@LB@ UGG CUAA CGGACUAC UCCU@LB@3'-UUU...GUUUU CA U CUAUU...GUU-5'@LB@ \| \|@LB@ 120 97@LB@@LB@@LB@Energy -13.63 kcal/mol@LB@Hybridization Energy -22.0172 kcal/mol@LB@Unfolding Energy - mRNA 6.14115 kcal/mol@LB@Unfolding Energy - sRNA 2.25153 kcal/mol@LB@@LB@Position - mRNA 269 -- 289@LB@Position - sRNA 98 -- 119@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 102 -- 108@LB@
40	0.0001908	0.02192	pa5015	aceE	-12.88	0.038887	273 -- 297	101 -- 123	pyruvate dehydrogenase subunit E1		_____________272________________________298\n_____________\|__________________________\|\n5'-CCU...AAGGU________C_CUC_____________CCC-3'\n______________GAAGACCG_G___AUUA_CCUGAUGA\n______________:\|\|:\|\|\|\|_\|___\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UUUUUGGC_C___UAAU_GGACUACU\n3'-UUU...CCCAG________A________C________CCUCU...GUU-5'\n_____________\|__________________________\|\n_____________124________________________100\n	291 -- 297	101 -- 107	-21.2393 kcal/mol	6.11337 kcal/mol	2.24445 kcal/mol	272 298@LB@ \| \|@LB@5'-CCU...AAGGU C CUC CCC-3'@LB@ GAAGACCG G AUUA CCUGAUGA@LB@ :\|\|:\|\|\|\| \| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUUUGGC C UAAU GGACUACU@LB@3'-UUU...CCCAG A C CCUCU...GUU-5'@LB@ \| \|@LB@ 124 100@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -21.2393 kcal/mol@LB@Unfolding Energy - mRNA 6.11337 kcal/mol@LB@Unfolding Energy - sRNA 2.24445 kcal/mol@LB@@LB@Position - mRNA 273 -- 297@LB@Position - sRNA 101 -- 123@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 101 -- 107@LB@
112	0.001904	0.07812	pa5310	N/A	-10.92	0.114175	276 -- 285	74 -- 83	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________275________286\n_____________\|__________\|\n5'-CGA...CCCUC__________CCAGC...CGC-3'\n______________UCCGGCUGCG\n______________\|\|\|\|:\|\|\|\|\|\n______________AGGCUGACGC\n3'-UUU...UUCUC__________ACCCA...GUU-5'\n_____________\|__________\|\n_____________84_________73\n	279 -- 285	74 -- 80	-18.1359 kcal/mol	3.11348 kcal/mol	4.10139 kcal/mol	275 286@LB@ \| \|@LB@5'-CGA...CCCUC CCAGC...CGC-3'@LB@ UCCGGCUGCG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ AGGCUGACGC@LB@3'-UUU...UUCUC ACCCA...GUU-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -18.1359 kcal/mol@LB@Unfolding Energy - mRNA 3.11348 kcal/mol@LB@Unfolding Energy - sRNA 4.10139 kcal/mol@LB@@LB@Position - mRNA 276 -- 285@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 74 -- 80@LB@
101	0.001673	0.07499	pa1787	acnB	-10.32	0.154094	277 -- 296	100 -- 121	aconitate hydratase B		_____________276_____________________297\n_____________\|_______________________\|\n5'-UAC...CGAAC______CA___________C___CUGC-3'\n______________AGACCG_____GGCCUGGU_GAG\n______________\|:\|\|\|\|_____:\|\|\|\|\|:\|_\|\|\|\n______________UUUGGC_____UCGGACUA_CUC\n3'-UUU...CAGUU______ACUAA____________CUCUA...GUU-5'\n_____________\|_______________________\|\n_____________122_____________________99\n	286 -- 292	103 -- 109	-20.0253 kcal/mol	7.46245 kcal/mol	2.24936 kcal/mol	276 297@LB@ \| \|@LB@5'-UAC...CGAAC CA C CUGC-3'@LB@ AGACCG GGCCUGGU GAG@LB@ \|:\|\|\|\| :\|\|\|\|\|:\| \|\|\|@LB@ UUUGGC UCGGACUA CUC@LB@3'-UUU...CAGUU ACUAA CUCUA...GUU-5'@LB@ \| \|@LB@ 122 99@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -20.0253 kcal/mol@LB@Unfolding Energy - mRNA 7.46245 kcal/mol@LB@Unfolding Energy - sRNA 2.24936 kcal/mol@LB@@LB@Position - mRNA 277 -- 296@LB@Position - sRNA 100 -- 121@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 103 -- 109@LB@
94	0.001308	0.06355	pa1587	lpdG	-9.92	0.185926	282 -- 296	75 -- 91	2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase		_____________281_______________297\n_____________\|_________________\|\n5'-GUG...UGGGC____________C____AUCG-3'\n______________CUGAAGA__CCG_CUGC\n______________\|\|\|\|\|\|\|__\|\|\|_\|\|\|\|\n______________GACUUCU__GGC_GACG\n3'-UUU...UAUUA_______CA___U____CACCC...GUU-5'\n_____________\|_________________\|\n_____________92________________74\n	282 -- 288	85 -- 91	-18.2743 kcal/mol	2.47066 kcal/mol	5.88668 kcal/mol	281 297@LB@ \| \|@LB@5'-GUG...UGGGC C AUCG-3'@LB@ CUGAAGA CCG CUGC@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|@LB@ GACUUCU GGC GACG@LB@3'-UUU...UAUUA CA U CACCC...GUU-5'@LB@ \| \|@LB@ 92 74@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -18.2743 kcal/mol@LB@Unfolding Energy - mRNA 2.47066 kcal/mol@LB@Unfolding Energy - sRNA 5.88668 kcal/mol@LB@@LB@Position - mRNA 282 -- 296@LB@Position - sRNA 75 -- 91@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 85 -- 91@LB@
119	0.002082	0.07999	pa4053	ribE	-9.84	0.193218	284 -- 298	103 -- 117	6 7-dimethyl-8-ribityllumazine synthase		_____________283_____________299\n_____________\|_______________\|\n5'-UGC...UUCGU_____AA________CA-3'\n______________CGUGG__AGCCUGGU\n______________\|\|\|\|:__\|\|\|\|\|\|:\|\n______________GCACU__UCGGACUA\n3'-UUU...UUUUG_____AA________CUCCU...GUU-5'\n_____________\|_______________\|\n_____________118_____________102\n	292 -- 298	103 -- 109	-17.5695 kcal/mol	5.50648 kcal/mol	2.23013 kcal/mol	283 299@LB@ \| \|@LB@5'-UGC...UUCGU AA CA-3'@LB@ CGUGG AGCCUGGU@LB@ \|\|\|\|: \|\|\|\|\|\|:\|@LB@ GCACU UCGGACUA@LB@3'-UUU...UUUUG AA CUCCU...GUU-5'@LB@ \| \|@LB@ 118 102@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -17.5695 kcal/mol@LB@Unfolding Energy - mRNA 5.50648 kcal/mol@LB@Unfolding Energy - sRNA 2.23013 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 103 -- 117@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 103 -- 109@LB@
198	0.005468	0.1268	pa5463	N/A	-11.00	0.109950	289 -- 298	38 -- 47	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________288________299\n_____________\|__________\|\n5'-GUU...GGUGG__________CA-3'\n______________UCGCGACCAG\n______________\|\|\|\|\|\|\|\|\|\|\n______________AGCGCUGGUC\n3'-UUU...ACUAG__________AACUC...GUU-5'\n_____________\|__________\|\n_____________48_________37\n	292 -- 298	38 -- 44	-19.1199 kcal/mol	4.44679 kcal/mol	3.68214 kcal/mol	288 299@LB@ \| \|@LB@5'-GUU...GGUGG CA-3'@LB@ UCGCGACCAG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AGCGCUGGUC@LB@3'-UUU...ACUAG AACUC...GUU-5'@LB@ \| \|@LB@ 48 37@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.1199 kcal/mol@LB@Unfolding Energy - mRNA 4.44679 kcal/mol@LB@Unfolding Energy - sRNA 3.68214 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 38 -- 47@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 38 -- 44@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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service.

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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