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
59	0.0005101	0.0395	pa2173a	N/A	-13.53	0.026409	139 -- 150	107 -- 119		_____________138___________151\n_____________\|_____________\|\n5'-CAA...AACCU_____________AUGGG...CCC-3'\n______________GCCGUGAU_AGCC\n______________:\|\|\|\|\|\|\|_\|\|\|\|\n______________UGGCACUA_UCGG\n3'-UUU...GUUUU________A____ACUAC...GUU-5'\n_____________\|_____________\|\n_____________120___________106\n	140 -- 146	112 -- 118	-18.4805 kcal/mol	2.71645 kcal/mol	2.23484 kcal/mol	138 151@LB@ \| \|@LB@5'-CAA...AACCU AUGGG...CCC-3'@LB@ GCCGUGAU AGCC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UGGCACUA UCGG@LB@3'-UUU...GUUUU A ACUAC...GUU-5'@LB@ \| \|@LB@ 120 106@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -18.4805 kcal/mol@LB@Unfolding Energy - mRNA 2.71645 kcal/mol@LB@Unfolding Energy - sRNA 2.23484 kcal/mol@LB@@LB@Position - mRNA 139 -- 150@LB@Position - sRNA 107 -- 119@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 112 -- 118@LB@
68	0.0007335	0.0493	pa0794	N/A	-9.72	0.203453	182 -- 194	107 -- 118	aconitate hydratase	_____________181_____________________195\n_____________\|_______________________\|\n5'-CAU...ACACC________GAGUCCG____A___ACAGC...AGC-3'\n______________CCGUGAUU_______AGCC_UGA\n______________\|\|\|\|\|\|\|\|_______\|\|\|\|_\|\|\|\n______________GGCACUAA_______UCGG_ACU\n3'-UUU...UUUUU_______________________ACUCC...GUU-5'\n_____________\|_______________________\|\n_____________119_____________________106\n	183 -- 189	111 -- 117	-17.4679 kcal/mol	6.47077 kcal/mol	2.24144 kcal/mol	181 195@LB@ \| \|@LB@5'-CAU...ACACC GAGUCCG A ACAGC...AGC-3'@LB@ CCGUGAUU AGCC UGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ GGCACUAA UCGG ACU@LB@3'-UUU...UUUUU ACUCC...GUU-5'@LB@ \| \|@LB@ 119 106@LB@@LB@@LB@Energy -9.72 kcal/mol@LB@Hybridization Energy -17.4679 kcal/mol@LB@Unfolding Energy - mRNA 6.47077 kcal/mol@LB@Unfolding Energy - sRNA 2.24144 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 107 -- 118@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 111 -- 117@LB@
80	0.0008839	0.05078	pa0353	ilvD	-13.41	0.028361	174 -- 187	107 -- 121	dihydroxy-acid dehydratase	_____________173_____________188\n_____________\|_______________\|\n5'-UUC...AACCC_______________GCAGG...AGA-3'\n______________GAACC_UGAUUAGCC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________UUUGG_ACUAAUCGG\n3'-UUU...CAGUU_____C_________ACUAC...GUU-5'\n_____________\|_______________\|\n_____________122_____________106\n	181 -- 187	107 -- 113	-19.137 kcal/mol	3.4906 kcal/mol	2.23534 kcal/mol	173 188@LB@ \| \|@LB@5'-UUC...AACCC GCAGG...AGA-3'@LB@ GAACC UGAUUAGCC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UUUGG ACUAAUCGG@LB@3'-UUU...CAGUU C ACUAC...GUU-5'@LB@ \| \|@LB@ 122 106@LB@@LB@@LB@Energy -13.41 kcal/mol@LB@Hybridization Energy -19.137 kcal/mol@LB@Unfolding Energy - mRNA 3.4906 kcal/mol@LB@Unfolding Energy - sRNA 2.23534 kcal/mol@LB@@LB@Position - mRNA 174 -- 187@LB@Position - sRNA 107 -- 121@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 107 -- 113@LB@
86	0.001073	0.05733	pa0916	N/A	-12.39	0.051807	188 -- 200	107 -- 119	ribosomal protein S12 methylthiotransferase RimO	_____________187___________201\n_____________\|_____________\|\n5'-GUC...CGCCU____A________AUGUC...GCU-3'\n______________ACCG_GGUUAGCC\n______________\|\|\|\|_\|:\|\|\|\|\|\|\n______________UGGC_CUAAUCGG\n3'-UUU...GUUUU____A________ACUAC...GUU-5'\n_____________\|_____________\|\n_____________120___________106\n	194 -- 200	107 -- 113	-18.1643 kcal/mol	3.54951 kcal/mol	2.23484 kcal/mol	187 201@LB@ \| \|@LB@5'-GUC...CGCCU A AUGUC...GCU-3'@LB@ ACCG GGUUAGCC@LB@ \|\|\|\| \|:\|\|\|\|\|\|@LB@ UGGC CUAAUCGG@LB@3'-UUU...GUUUU A ACUAC...GUU-5'@LB@ \| \|@LB@ 120 106@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -18.1643 kcal/mol@LB@Unfolding Energy - mRNA 3.54951 kcal/mol@LB@Unfolding Energy - sRNA 2.23484 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 107 -- 119@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 107 -- 113@LB@
134	0.002678	0.0912	pa1421	gbuA	-12.45	0.050008	184 -- 195	107 -- 120	guanidinobutyrase	_____________183____________196\n_____________\|______________\|\n5'-UCC...ACAAC______________ACCCC...CCG-3'\n______________GACCGUGA__GGCC\n______________:\|\|\|\|\|\|\|__:\|\|\|\n______________UUGGCACU__UCGG\n3'-UUU...AGUUU________AA____ACUAC...GUU-5'\n_____________\|______________\|\n_____________121____________106\n	185 -- 191	113 -- 119	-18.3112 kcal/mol	3.63401 kcal/mol	2.2351 kcal/mol	183 196@LB@ \| \|@LB@5'-UCC...ACAAC ACCCC...CCG-3'@LB@ GACCGUGA GGCC@LB@ :\|\|\|\|\|\|\| :\|\|\|@LB@ UUGGCACU UCGG@LB@3'-UUU...AGUUU AA ACUAC...GUU-5'@LB@ \| \|@LB@ 121 106@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -18.3112 kcal/mol@LB@Unfolding Energy - mRNA 3.63401 kcal/mol@LB@Unfolding Energy - sRNA 2.2351 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 107 -- 120@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 113 -- 119@LB@
146	0.003267	0.1028	pa0918	N/A	-13.83	0.021920	192 -- 207	107 -- 122	cytochrome b561	_____________191______________208\n_____________\|________________\|\n5'-CCA...GAGAA___________G____GGAAA...AAC-3'\n______________GGAACCGUGAU_AGCU\n______________::\|\|\|\|\|\|\|\|\|_\|\|\|:\n______________UUUUGGCACUA_UCGG\n3'-UUU...CCAGU___________A____ACUAC...GUU-5'\n_____________\|________________\|\n_____________123______________106\n	196 -- 202	112 -- 118	-20.0543 kcal/mol	3.98833 kcal/mol	2.23582 kcal/mol	191 208@LB@ \| \|@LB@5'-CCA...GAGAA G GGAAA...AAC-3'@LB@ GGAACCGUGAU AGCU@LB@ ::\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ UUUUGGCACUA UCGG@LB@3'-UUU...CCAGU A ACUAC...GUU-5'@LB@ \| \|@LB@ 123 106@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -20.0543 kcal/mol@LB@Unfolding Energy - mRNA 3.98833 kcal/mol@LB@Unfolding Energy - sRNA 2.23582 kcal/mol@LB@@LB@Position - mRNA 192 -- 207@LB@Position - sRNA 107 -- 122@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 112 -- 118@LB@
150	0.003458	0.106	pa5558	atpF	-11.25	0.096505	215 -- 228	107 -- 120	ATP synthase subunit B	_____________214____________229\n_____________\|______________\|\n5'-CUC...AAUGC____C_________AGUCC...UGC-3'\n______________AACC_UGAUUGGCC\n______________\|\|\|\|_\|\|\|\|\|:\|\|\|\n______________UUGG_ACUAAUCGG\n3'-UUU...AGUUU____C_________ACUAC...GUU-5'\n_____________\|______________\|\n_____________121____________106\n	222 -- 228	107 -- 113	-18.4292 kcal/mol	4.95427 kcal/mol	2.2351 kcal/mol	214 229@LB@ \| \|@LB@5'-CUC...AAUGC C AGUCC...UGC-3'@LB@ AACC UGAUUGGCC@LB@ \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUGG ACUAAUCGG@LB@3'-UUU...AGUUU C ACUAC...GUU-5'@LB@ \| \|@LB@ 121 106@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -18.4292 kcal/mol@LB@Unfolding Energy - mRNA 4.95427 kcal/mol@LB@Unfolding Energy - sRNA 2.2351 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 107 -- 120@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 107 -- 113@LB@
174	0.00444	0.1171	pa4756	carB	-14.46	0.014655	252 -- 264	107 -- 119	carbamoyl phosphate synthase large subunit	_____________251___________265\n_____________\|_____________\|\n5'-GGU...GCCCC_____________AGGCC...CCU-3'\n______________AUCGUGAUUGGCC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\n______________UGGCACUAAUCGG\n3'-UUU...GUUUU_____________ACUAC...GUU-5'\n_____________\|_____________\|\n_____________120___________106\n	258 -- 264	107 -- 113	-20.5807 kcal/mol	3.88907 kcal/mol	2.23484 kcal/mol	251 265@LB@ \| \|@LB@5'-GGU...GCCCC AGGCC...CCU-3'@LB@ AUCGUGAUUGGCC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|@LB@ UGGCACUAAUCGG@LB@3'-UUU...GUUUU ACUAC...GUU-5'@LB@ \| \|@LB@ 120 106@LB@@LB@@LB@Energy -14.46 kcal/mol@LB@Hybridization Energy -20.5807 kcal/mol@LB@Unfolding Energy - mRNA 3.88907 kcal/mol@LB@Unfolding Energy - sRNA 2.23484 kcal/mol@LB@@LB@Position - mRNA 252 -- 264@LB@Position - sRNA 107 -- 119@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 107 -- 113@LB@
4	5.154e-07	0.0005922	pa1581	sdhC	-15.05	0.009907	206 -- 221	108 -- 123	succinate dehydrogenase subunit C	_____________205______________222\n_____________\|________________\|\n5'-ACG...GUGAA___________A____AAACG...CUG-3'\n______________AAAAGCCGUGA_UAGC\n______________\|\|\|\|:\|\|\|\|\|\|_\|\|\|\|\n______________UUUUUGGCACU_AUCG\n3'-UUU...CCCAG___________A____GACUA...GUU-5'\n_____________\|________________\|\n_____________124______________107\n	210 -- 216	113 -- 119	-19.67 kcal/mol	2.45872 kcal/mol	2.16544 kcal/mol	205 222@LB@ \| \|@LB@5'-ACG...GUGAA A AAACG...CUG-3'@LB@ AAAAGCCGUGA UAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UUUUUGGCACU AUCG@LB@3'-UUU...CCCAG A GACUA...GUU-5'@LB@ \| \|@LB@ 124 107@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -19.67 kcal/mol@LB@Unfolding Energy - mRNA 2.45872 kcal/mol@LB@Unfolding Energy - sRNA 2.16544 kcal/mol@LB@@LB@Position - mRNA 206 -- 221@LB@Position - sRNA 108 -- 123@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 113 -- 119@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@

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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