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
11	1.195e-05	0.004211	pa3638	N/A	-14.67	0.012752	102 -- 115	100 -- 120	tRNA(Ile)-lysidine synthase	_____________101___________________116\n_____________\|_____________________\|\n5'-GCG...GUUAC_____________________CUACG...CCA-3'\n______________GACC_______GCCUGAUGAG\n______________:\|\|\|_______\|\|\|\|\|\|\|\|\|\|\n______________UUGG_______CGGACUACUC\n3'-UUU...AGUUU____CACUAAU__________CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________121___________________99\n	109 -- 115	100 -- 106	-19.8992 kcal/mol	2.98005 kcal/mol	2.24919 kcal/mol	101 116@LB@ \| \|@LB@5'-GCG...GUUAC CUACG...CCA-3'@LB@ GACC GCCUGAUGAG@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUGG CGGACUACUC@LB@3'-UUU...AGUUU CACUAAU CUCUA...GUU-5'@LB@ \| \|@LB@ 121 99@LB@@LB@@LB@Energy -14.67 kcal/mol@LB@Hybridization Energy -19.8992 kcal/mol@LB@Unfolding Energy - mRNA 2.98005 kcal/mol@LB@Unfolding Energy - sRNA 2.24919 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 100 -- 120@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 100 -- 106@LB@
12	1.22e-05	0.004211	pa3312	N/A	-10.60	0.134070	231 -- 250	100 -- 119	3-hydroxyisobutyrate dehydrogenase	_____________230__________________251\n_____________\|____________________\|\n5'-CGG...CCUUC____GUCUC___________CGUGC...UGU-3'\n______________GCCG_____GGCCUGAUGGG\n______________:\|\|\|_____:\|\|\|\|\|\|\|\|:\|\n______________UGGC_____UCGGACUACUC\n3'-UUU...GUUUU____ACUAA___________CUCUA...GUU-5'\n_____________\|____________________\|\n_____________120__________________99\n	244 -- 250	100 -- 106	-24.2186 kcal/mol	11.3713 kcal/mol	2.24903 kcal/mol	230 251@LB@ \| \|@LB@5'-CGG...CCUUC GUCUC CGUGC...UGU-3'@LB@ GCCG GGCCUGAUGGG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UGGC UCGGACUACUC@LB@3'-UUU...GUUUU ACUAA CUCUA...GUU-5'@LB@ \| \|@LB@ 120 99@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -24.2186 kcal/mol@LB@Unfolding Energy - mRNA 11.3713 kcal/mol@LB@Unfolding Energy - sRNA 2.24903 kcal/mol@LB@@LB@Position - mRNA 231 -- 250@LB@Position - sRNA 100 -- 119@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 100 -- 106@LB@
16	3.003e-05	0.008352	pa2689	N/A	-17.00	0.002414	189 -- 205	100 -- 117	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________188________________206\n_____________\|__________________\|\n5'-CGG...CAUAA__A__A____________AACCU...UGG-3'\n______________CG_GA__AGCCUGAUGAG\n______________\|\|_\|\|__\|\|\|\|\|\|\|\|\|\|\|\n______________GC_CU__UCGGACUACUC\n3'-UUU...UUUUG__A__AA___________CUCUA...GUU-5'\n_____________\|__________________\|\n_____________118________________99\n	199 -- 205	100 -- 106	-22.2469 kcal/mol	3.0121 kcal/mol	2.23711 kcal/mol	188 206@LB@ \| \|@LB@5'-CGG...CAUAA A A AACCU...UGG-3'@LB@ CG GA AGCCUGAUGAG@LB@ \|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ GC CU UCGGACUACUC@LB@3'-UUU...UUUUG A AA CUCUA...GUU-5'@LB@ \| \|@LB@ 118 99@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -22.2469 kcal/mol@LB@Unfolding Energy - mRNA 3.0121 kcal/mol@LB@Unfolding Energy - sRNA 2.23711 kcal/mol@LB@@LB@Position - mRNA 189 -- 205@LB@Position - sRNA 100 -- 117@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 100 -- 106@LB@
26	6.892e-05	0.01177	pa0375	ftsX	-18.23	0.000891	153 -- 205	100 -- 144	cell division protein FtsX	_____________152___________________________________________________206\n_____________\|_____________________________________________________\|\n5'-CUG...AUGCU_____U____C__G_____A___UCGCU________GGAUGA___________CGCCA...CGU-3'\n______________GACCC_GCAG_GU_GCCGG_UCA_____GACCGUGA______GGCCUGAUGAG\n______________\|\|\|\|\|_\|\|\|:_\|\|_\|\|\|\|\|_\|\|\|_____:\|\|\|\|\|\|\|______:\|\|\|\|\|\|\|\|\|\|\n______________CUGGG_CGUU_CA_CGGCC_AGU_____UUGGCACU______UCGGACUACUC\n____3'-UUUUUUU_____C____U________C___UU___________AA_______________CUCUA...GUU-5'\n_____________\|_____________________________________________________\|\n_____________145___________________________________________________99\n	199 -- 205	100 -- 106	-59.0387 kcal/mol	20.5976 kcal/mol	20.2157 kcal/mol	152 206@LB@ \| \|@LB@5'-CUG...AUGCU U C G A UCGCU GGAUGA CGCCA...CGU-3'@LB@ GACCC GCAG GU GCCGG UCA GACCGUGA GGCCUGAUGAG@LB@ \|\|\|\|\| \|\|\|: \|\| \|\|\|\|\| \|\|\| :\|\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ CUGGG CGUU CA CGGCC AGU UUGGCACU UCGGACUACUC@LB@ 3'-UUUUUUU C U C UU AA CUCUA...GUU-5'@LB@ \| \|@LB@ 145 99@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -59.0387 kcal/mol@LB@Unfolding Energy - mRNA 20.5976 kcal/mol@LB@Unfolding Energy - sRNA 20.2157 kcal/mol@LB@@LB@Position - mRNA 153 -- 205@LB@Position - sRNA 100 -- 144@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 100 -- 106@LB@
52	0.0004019	0.03518	pa4012	N/A	-10.34	0.152385	122 -- 132	100 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________121_________133\n_____________\|___________\|\n5'-CAU...CGAUG___________CGUUG...GCU-3'\n______________AGCCUGAUGGG\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UCGGACUACUC\n3'-UUU...ACUAA___________CUCUA...GUU-5'\n_____________\|___________\|\n_____________111_________99\n	126 -- 132	100 -- 106	-17.6316 kcal/mol	5.13362 kcal/mol	2.15723 kcal/mol	121 133@LB@ \| \|@LB@5'-CAU...CGAUG CGUUG...GCU-3'@LB@ AGCCUGAUGGG@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UCGGACUACUC@LB@3'-UUU...ACUAA CUCUA...GUU-5'@LB@ \| \|@LB@ 111 99@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -17.6316 kcal/mol@LB@Unfolding Energy - mRNA 5.13362 kcal/mol@LB@Unfolding Energy - sRNA 2.15723 kcal/mol@LB@@LB@Position - mRNA 122 -- 132@LB@Position - sRNA 100 -- 110@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 100 -- 106@LB@
55	0.0004353	0.03637	pa0086	N/A	-16.64	0.003171	21 -- 37	100 -- 117	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________20_________________38\n_____________\|__________________\|\n5'-GGC...CAGAA____CA____________CCGGC...ACG-3'\n______________CGUG___GGCCUGAUGAG\n______________\|\|\|\|___:\|\|\|\|\|\|\|\|\|\|\n______________GCAC___UCGGACUACUC\n3'-UUU...UUUUG____UAA___________CUCUA...GUU-5'\n_____________\|__________________\|\n_____________118________________99\n	31 -- 37	100 -- 106	-24.5052 kcal/mol	5.62761 kcal/mol	2.23711 kcal/mol	20 38@LB@ \| \|@LB@5'-GGC...CAGAA CA CCGGC...ACG-3'@LB@ CGUG GGCCUGAUGAG@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ GCAC UCGGACUACUC@LB@3'-UUU...UUUUG UAA CUCUA...GUU-5'@LB@ \| \|@LB@ 118 99@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -24.5052 kcal/mol@LB@Unfolding Energy - mRNA 5.62761 kcal/mol@LB@Unfolding Energy - sRNA 2.23711 kcal/mol@LB@@LB@Position - mRNA 21 -- 37@LB@Position - sRNA 100 -- 117@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 100 -- 106@LB@
76	0.0008254	0.04991	pa0029	N/A	-13.54	0.026240	35 -- 51	100 -- 123	sulfate transporter	_____________34_______________________52\n_____________\|________________________\|\n5'-GCU...ACAUG________________________CGACG...UGG-3'\n______________GAGAACC_______GCCUGAUGAG\n______________:\|:\|\|\|\|_______\|\|\|\|\|\|\|\|\|\|\n______________UUUUUGG_______CGGACUACUC\n3'-UUU...CCCAG_______CACUAAU__________CUCUA...GUU-5'\n_____________\|________________________\|\n_____________124______________________99\n	45 -- 51	100 -- 106	-21.4793 kcal/mol	5.69273 kcal/mol	2.24995 kcal/mol	34 52@LB@ \| \|@LB@5'-GCU...ACAUG CGACG...UGG-3'@LB@ GAGAACC GCCUGAUGAG@LB@ :\|:\|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUUUUGG CGGACUACUC@LB@3'-UUU...CCCAG CACUAAU CUCUA...GUU-5'@LB@ \| \|@LB@ 124 99@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -21.4793 kcal/mol@LB@Unfolding Energy - mRNA 5.69273 kcal/mol@LB@Unfolding Energy - sRNA 2.24995 kcal/mol@LB@@LB@Position - mRNA 35 -- 51@LB@Position - sRNA 100 -- 123@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 100 -- 106@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@
118	0.002082	0.07999	pa5066	hisI	-12.42	0.050876	194 -- 221	100 -- 123	phosphoribosyl-AMP cyclohydrolase	_____________193__________________________222\n_____________\|____________________________\|\n5'-CGA...CGUGG_______A___AAGAC_____G______AUUCA...GGA-3'\n______________AAAGACC_UGA_____UGGCU_GAUGAG\n______________\|\|\|:\|\|\|_\|\|\|_____\|:\|\|:_\|\|\|\|\|\|\n______________UUUUUGG_ACU_____AUCGG_CUACUC\n3'-UUU...CCCAG_______C___A_________A______CUCUA...GUU-5'\n_____________\|____________________________\|\n_____________124__________________________99\n	194 -- 200	117 -- 123	-21.0853 kcal/mol	6.41847 kcal/mol	2.24995 kcal/mol	193 222@LB@ \| \|@LB@5'-CGA...CGUGG A AAGAC G AUUCA...GGA-3'@LB@ AAAGACC UGA UGGCU GAUGAG@LB@ \|\|\|:\|\|\| \|\|\| \|:\|\|: \|\|\|\|\|\|@LB@ UUUUUGG ACU AUCGG CUACUC@LB@3'-UUU...CCCAG C A A CUCUA...GUU-5'@LB@ \| \|@LB@ 124 99@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -21.0853 kcal/mol@LB@Unfolding Energy - mRNA 6.41847 kcal/mol@LB@Unfolding Energy - sRNA 2.24995 kcal/mol@LB@@LB@Position - mRNA 194 -- 221@LB@Position - sRNA 100 -- 123@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 117 -- 123@LB@
132	0.002652	0.0912	pa0364	N/A	-15.84	0.005742	174 -- 193	100 -- 122	oxidoreductase	_____________173_____________________194\n_____________\|_______________________\|\n5'-AUU...AGCCC_______CC______________UGCAU...UGG-3'\n______________GAAGCCG____UAGCCUGA_GAG\n______________:\|\|:\|\|\|____\|\|\|\|\|\|\|\|_\|\|\|\n______________UUUUGGC____AUCGGACU_CUC\n3'-UUU...CCAGU_______ACUA________A___CUCUA...GUU-5'\n_____________\|_______________________\|\n_____________123_____________________99\n	184 -- 190	104 -- 110	-22.8122 kcal/mol	4.73034 kcal/mol	2.24976 kcal/mol	173 194@LB@ \| \|@LB@5'-AUU...AGCCC CC UGCAU...UGG-3'@LB@ GAAGCCG UAGCCUGA GAG@LB@ :\|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ UUUUGGC AUCGGACU CUC@LB@3'-UUU...CCAGU ACUA A CUCUA...GUU-5'@LB@ \| \|@LB@ 123 99@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -22.8122 kcal/mol@LB@Unfolding Energy - mRNA 4.73034 kcal/mol@LB@Unfolding Energy - sRNA 2.24976 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 100 -- 122@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 104 -- 110@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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