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
60	0.000522	0.0395	pa1477	ccmC	-13.58	0.025601	178 -- 207	98 -- 123	heme exporter protein CcmC		_____________177____________________________208\n_____________\|______________________________\|\n5'-GCG...UUCCA_______C__UAAACAG__________U__AUUGG...UGC-3'\n______________AAGAGCC_UG_______AGCCUGAUGA_GA\n______________\|\|:\|:\|\|_\|\|_______\|\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUUUGG_AC_______UCGGACUACU_CU\n3'-UUU...CCCAG_______C__UAA______________C__CUAUU...GUU-5'\n_____________\|______________________________\|\n_____________124____________________________97\n	198 -- 204	101 -- 107	-23.0207 kcal/mol	7.19156 kcal/mol	2.25245 kcal/mol	177 208@LB@ \| \|@LB@5'-GCG...UUCCA C UAAACAG U AUUGG...UGC-3'@LB@ AAGAGCC UG AGCCUGAUGA GA@LB@ \|\|:\|:\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUUUUGG AC UCGGACUACU CU@LB@3'-UUU...CCCAG C UAA C CUAUU...GUU-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -23.0207 kcal/mol@LB@Unfolding Energy - mRNA 7.19156 kcal/mol@LB@Unfolding Energy - sRNA 2.25245 kcal/mol@LB@@LB@Position - mRNA 178 -- 207@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 101 -- 107@LB@
70	0.0007568	0.0493	pa3767	N/A	-16.77	0.002880	160 -- 178	98 -- 122	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________159_______________________179\n_____________\|_________________________\|\n5'-CAU...AUAUG_________________________CCAUC...GCG-3'\n______________GAGACCG______GCCUGAUGGGGA\n______________:\|:\|\|\|\|______\|\|\|\|\|\|\|\|:\|\|\|\n______________UUUUGGC______CGGACUACUCCU\n3'-UUU...CCAGU_______ACUAAU____________CUAUU...GUU-5'\n_____________\|_________________________\|\n_____________123_______________________97\n	172 -- 178	98 -- 104	-28.0357 kcal/mol	9.01481 kcal/mol	2.25226 kcal/mol	159 179@LB@ \| \|@LB@5'-CAU...AUAUG CCAUC...GCG-3'@LB@ GAGACCG GCCUGAUGGGGA@LB@ :\|:\|\|\|\| \|\|\|\|\|\|\|\|:\|\|\|@LB@ UUUUGGC CGGACUACUCCU@LB@3'-UUU...CCAGU ACUAAU CUAUU...GUU-5'@LB@ \| \|@LB@ 123 97@LB@@LB@@LB@Energy -16.77 kcal/mol@LB@Hybridization Energy -28.0357 kcal/mol@LB@Unfolding Energy - mRNA 9.01481 kcal/mol@LB@Unfolding Energy - sRNA 2.25226 kcal/mol@LB@@LB@Position - mRNA 160 -- 178@LB@Position - sRNA 98 -- 122@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 98 -- 104@LB@
84	0.001042	0.05699	pa3121	leuC	-8.58	0.330521	182 -- 193	98 -- 110	3-isopropylmalate dehydratase large subunit		_____________181___________194\n_____________\|_____________\|\n5'-GCA...AAAUG_____________AAUCC...UGC-3'\n______________AG_CUGAUGAGGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UC_GACUACUCCU\n3'-UUU...ACUAA__G__________CUAUU...GUU-5'\n_____________\|_____________\|\n_____________111___________97\n	187 -- 193	98 -- 104	-17.6185 kcal/mol	6.87469 kcal/mol	2.16105 kcal/mol	181 194@LB@ \| \|@LB@5'-GCA...AAAUG AAUCC...UGC-3'@LB@ AG CUGAUGAGGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ UC GACUACUCCU@LB@3'-UUU...ACUAA G CUAUU...GUU-5'@LB@ \| \|@LB@ 111 97@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -17.6185 kcal/mol@LB@Unfolding Energy - mRNA 6.87469 kcal/mol@LB@Unfolding Energy - sRNA 2.16105 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 98 -- 110@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 98 -- 104@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@
122	0.002226	0.08331	pa4286	N/A	-14.46	0.014621	171 -- 194	98 -- 121	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________170_______________________195\n_____________\|_________________________\|\n5'-GGU...GAGCC________CC________AA_____AGAAU...GGC-3'\n______________GAGCCGUG___AGCCUGG__GAGGA\n______________:\|:\|\|\|\|\|___\|\|\|\|\|\|:__\|\|\|\|\|\n______________UUUGGCAC___UCGGACU__CUCCU\n3'-UUU...CAGUU________UAA_______A______CUAUU...GUU-5'\n_____________\|_________________________\|\n_____________122_______________________97\n	181 -- 187	104 -- 110	-28.256 kcal/mol	11.5428 kcal/mol	2.25186 kcal/mol	170 195@LB@ \| \|@LB@5'-GGU...GAGCC CC AA AGAAU...GGC-3'@LB@ GAGCCGUG AGCCUGG GAGGA@LB@ :\|:\|\|\|\|\| \|\|\|\|\|\|: \|\|\|\|\|@LB@ UUUGGCAC UCGGACU CUCCU@LB@3'-UUU...CAGUU UAA A CUAUU...GUU-5'@LB@ \| \|@LB@ 122 97@LB@@LB@@LB@Energy -14.46 kcal/mol@LB@Hybridization Energy -28.256 kcal/mol@LB@Unfolding Energy - mRNA 11.5428 kcal/mol@LB@Unfolding Energy - sRNA 2.25186 kcal/mol@LB@@LB@Position - mRNA 171 -- 194@LB@Position - sRNA 98 -- 121@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 104 -- 110@LB@
133	0.002661	0.0912	pa2511	N/A	-14.22	0.017134	181 -- 210	98 -- 119	transcriptional regulator		_____________180____________________________211\n_____________\|______________________________\|\n5'-CGG...GCCUU______UCGAGU___GAACCA_________CCCAU...CGC-3'\n______________GCCGUG______GCC______UGAUGAGGA\n______________:\|\|\|\|\|______\|\|\|______\|\|\|\|\|\|\|\|\|\n______________UGGCAC______CGG______ACUACUCCU\n3'-UUU...GUUUU______UAAU____________________CUAUU...GUU-5'\n_____________\|______________________________\|\n_____________120____________________________97\n	204 -- 210	98 -- 104	-24.6889 kcal/mol	8.22136 kcal/mol	2.25153 kcal/mol	180 211@LB@ \| \|@LB@5'-CGG...GCCUU UCGAGU GAACCA CCCAU...CGC-3'@LB@ GCCGUG GCC UGAUGAGGA@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UGGCAC CGG ACUACUCCU@LB@3'-UUU...GUUUU UAAU CUAUU...GUU-5'@LB@ \| \|@LB@ 120 97@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -24.6889 kcal/mol@LB@Unfolding Energy - mRNA 8.22136 kcal/mol@LB@Unfolding Energy - sRNA 2.25153 kcal/mol@LB@@LB@Position - mRNA 181 -- 210@LB@Position - sRNA 98 -- 119@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 98 -- 104@LB@
145	0.003161	0.1002	pa4147	acoR	-9.16	0.260996	230 -- 255	98 -- 121	transcriptional regulator AcoR	pa4021	_____________229_________________________256\n_____________\|___________________________\|\n5'-UAG...CAUGU________UC_____G__UCC______ACGCC...UCG-3'\n______________GGACUGUG___AGCC_UG___UGAGGA\n______________::\|\|:\|\|\|___\|\|\|\|_\|\|___\|\|\|\|\|\|\n______________UUUGGCAC___UCGG_AC___ACUCCU\n3'-UUU...CAGUU________UAA_______U________CUAUU...GUU-5'\n_____________\|___________________________\|\n_____________122_________________________97\n	231 -- 237	114 -- 120	-22.6885 kcal/mol	11.2814 kcal/mol	2.25186 kcal/mol	229 256@LB@ \| \|@LB@5'-UAG...CAUGU UC G UCC ACGCC...UCG-3'@LB@ GGACUGUG AGCC UG UGAGGA@LB@ ::\|\|:\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|@LB@ UUUGGCAC UCGG AC ACUCCU@LB@3'-UUU...CAGUU UAA U CUAUU...GUU-5'@LB@ \| \|@LB@ 122 97@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -22.6885 kcal/mol@LB@Unfolding Energy - mRNA 11.2814 kcal/mol@LB@Unfolding Energy - sRNA 2.25186 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 98 -- 121@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 114 -- 120@LB@
152	0.003562	0.1073	pa3096	xcpY	-9.37	0.238148	248 -- 259	98 -- 110	type II secretion system protein L		_____________247___________260\n_____________\|_____________\|\n5'-ACC...GCGGG_____________ACUGG...GCG-3'\n______________GGCC_GAUGGGGA\n______________:\|\|\|_\|\|\|\|:\|\|\|\n______________UCGG_CUACUCCU\n3'-UUU...ACUAA____A________CUAUU...GUU-5'\n_____________\|_____________\|\n_____________111___________97\n	253 -- 259	98 -- 104	-17.5774 kcal/mol	6.04509 kcal/mol	2.16105 kcal/mol	247 260@LB@ \| \|@LB@5'-ACC...GCGGG ACUGG...GCG-3'@LB@ GGCC GAUGGGGA@LB@ :\|\|\| \|\|\|\|:\|\|\|@LB@ UCGG CUACUCCU@LB@3'-UUU...ACUAA A CUAUU...GUU-5'@LB@ \| \|@LB@ 111 97@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -17.5774 kcal/mol@LB@Unfolding Energy - mRNA 6.04509 kcal/mol@LB@Unfolding Energy - sRNA 2.16105 kcal/mol@LB@@LB@Position - mRNA 248 -- 259@LB@Position - sRNA 98 -- 110@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 98 -- 104@LB@
158	0.003862	0.1123	pa4780	N/A	-10.69	0.128339	184 -- 207	98 -- 122	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________183________________________208\n_____________\|__________________________\|\n5'-AGG...CCCGA_______C_______A_C_____A__CACCC...UGG-3'\n______________GGAACCG_G__UAGC_C_GAUGA_GA\n______________::\|\|\|\|\|_\|__\|\|\|\|_\|_\|\|\|\|\|_\|\|\n______________UUUUGGC_C__AUCG_G_CUACU_CU\n3'-UUU...CCAGU_______A_UA______A_____C__CUAUU...GUU-5'\n_____________\|__________________________\|\n_____________123________________________97\n	184 -- 190	116 -- 122	-18.2775 kcal/mol	5.33909 kcal/mol	2.25226 kcal/mol	183 208@LB@ \| \|@LB@5'-AGG...CCCGA C A C A CACCC...UGG-3'@LB@ GGAACCG G UAGC C GAUGA GA@LB@ ::\|\|\|\|\| \| \|\|\|\| \| \|\|\|\|\| \|\|@LB@ UUUUGGC C AUCG G CUACU CU@LB@3'-UUU...CCAGU A UA A C CUAUU...GUU-5'@LB@ \| \|@LB@ 123 97@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -18.2775 kcal/mol@LB@Unfolding Energy - mRNA 5.33909 kcal/mol@LB@Unfolding Energy - sRNA 2.25226 kcal/mol@LB@@LB@Position - mRNA 184 -- 207@LB@Position - sRNA 98 -- 122@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 116 -- 122@LB@
185	0.004884	0.1213	pa2528	N/A	-11.72	0.074904	177 -- 197	98 -- 118	resistance-nodulation-cell division (RND) efflux membrane fusion protein		_____________176___________________198\n_____________\|_____________________\|\n5'-CUU...CGCCU____UCUA_______A__A__ACCAU...UGG-3'\n______________CCGU____AGCCUGA_GA_GA\n______________\|\|\|\|____\|\|\|\|\|\|\|_\|\|_\|\|\n______________GGCA____UCGGACU_CU_CU\n3'-UUU...UUUUU____CUAA_______A__C__CUAUU...GUU-5'\n_____________\|_____________________\|\n_____________119___________________97\n	185 -- 191	104 -- 110	-18.0515 kcal/mol	4.07956 kcal/mol	2.25139 kcal/mol	176 198@LB@ \| \|@LB@5'-CUU...CGCCU UCUA A A ACCAU...UGG-3'@LB@ CCGU AGCCUGA GA GA@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\| \|\|@LB@ GGCA UCGGACU CU CU@LB@3'-UUU...UUUUU CUAA A C CUAUU...GUU-5'@LB@ \| \|@LB@ 119 97@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -18.0515 kcal/mol@LB@Unfolding Energy - mRNA 4.07956 kcal/mol@LB@Unfolding Energy - sRNA 2.25139 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 98 -- 118@LB@Position Seed - mRNA 185 -- 191@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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