Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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_000913 Escherichia coli str. K-12 substr. MG1655

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
191	0.0398	0.6177	b4335	yjiM	-5.72	0.281824	283 -- 290	47 -- 54	putative 2-hydroxyglutaryl-CoA dehydratase		_____________282______291\n_____________\|________\|\n5'-CGG...GGAUC________CGCGG...UUC-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	284 -- 290	47 -- 53	-8.85878 kcal/mol	2.24401 kcal/mol	0.897871 kcal/mol	282 291@LB@ \| \|@LB@5'-CGG...GGAUC CGCGG...UUC-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -8.85878 kcal/mol@LB@Unfolding Energy - mRNA 2.24401 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 47 -- 53@LB@
192	0.04008	0.6177	b2822	recC	-5.02	0.370915	179 -- 195	44 -- 57	exonuclease V (RecBCD complex) gamma chain		_____________178_______________196\n_____________\|_________________\|\n5'-AGU...CCGAA_______U__UC_____CCGCU...AGA-3'\n______________UCGUCAG_AG__AGGAG\n______________:\|\|\|\|\|:_\|\|__\|\|\|\|:\n______________GGCAGUU_UC__UCCUU\n3'-UUU...AACCG_________________AAAGU...ACA-5'\n_____________\|_________________\|\n_____________58________________43\n	179 -- 185	51 -- 57	-11.1502 kcal/mol	3.39036 kcal/mol	2.73756 kcal/mol	178 196@LB@ \| \|@LB@5'-AGU...CCGAA U UC CCGCU...AGA-3'@LB@ UCGUCAG AG AGGAG@LB@ :\|\|\|\|\|: \|\| \|\|\|\|:@LB@ GGCAGUU UC UCCUU@LB@3'-UUU...AACCG AAAGU...ACA-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -5.02 kcal/mol@LB@Hybridization Energy -11.1502 kcal/mol@LB@Unfolding Energy - mRNA 3.39036 kcal/mol@LB@Unfolding Energy - sRNA 2.73756 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 51 -- 57@LB@
193	0.04043	0.6177	b1180	ycgM	-6.42	0.210248	289 -- 296	47 -- 54	putative isomerase/hydrolase		_____________288______297\n_____________\|________\|\n5'-GAU...ACAUA________AUGG-3'\n______________UUAAAGAG\n______________\|:\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	290 -- 296	47 -- 53	-7.63974 kcal/mol	0.325787 kcal/mol	0.897871 kcal/mol	288 297@LB@ \| \|@LB@5'-GAU...ACAUA AUGG-3'@LB@ UUAAAGAG@LB@ \|:\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -7.63974 kcal/mol@LB@Unfolding Energy - mRNA 0.325787 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
194	0.04051	0.6177	b0814	ompX	-6.96	0.165642	107 -- 118	50 -- 61	outer membrane protein X		_____________106__________119\n_____________\|____________\|\n5'-CUG...UGAAA____________CAUCA...CAC-3'\n______________UGGCCCGUUAGA\n______________\|\|\|\|\|\|\|\|:\|:\|\n______________ACCGGGCAGUUU\n3'-UUU...CGAUA____________CUCCU...ACA-5'\n_____________\|____________\|\n_____________62___________49\n	111 -- 117	51 -- 57	-20.1081 kcal/mol	2.98628 kcal/mol	10.1573 kcal/mol	106 119@LB@ \| \|@LB@5'-CUG...UGAAA CAUCA...CAC-3'@LB@ UGGCCCGUUAGA@LB@ \|\|\|\|\|\|\|\|:\|:\|@LB@ ACCGGGCAGUUU@LB@3'-UUU...CGAUA CUCCU...ACA-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -20.1081 kcal/mol@LB@Unfolding Energy - mRNA 2.98628 kcal/mol@LB@Unfolding Energy - sRNA 10.1573 kcal/mol@LB@@LB@Position - mRNA 107 -- 118@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 51 -- 57@LB@
195	0.04073	0.6177	b3166	truB	-9.24	0.058593	189 -- 197	45 -- 53	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase		_____________188_______198\n_____________\|_________\|\n5'-GGC...GACAG_________CUAAU...AAC-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	191 -- 197	45 -- 51	-13.1895 kcal/mol	3.02734 kcal/mol	0.917553 kcal/mol	188 198@LB@ \| \|@LB@5'-GGC...GACAG CUAAU...AAC-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -13.1895 kcal/mol@LB@Unfolding Energy - mRNA 3.02734 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 45 -- 51@LB@
196	0.04084	0.6177	b3137	kbaY	-7.51	0.129887	187 -- 200	37 -- 51	tagatose 6-phosphate aldolase 1 kbaY subunit	b2096	_____________186_____________201\n_____________\|_______________\|\n5'-CAC...GGCAU_______UCG_____AUGAG...CGA-3'\n______________AAGAGGA____CAUU\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________UUCUCCU____GUAA\n3'-UUU...GCAGU_______UAAA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________52______________36\n	187 -- 193	45 -- 51	-11.4071 kcal/mol	2.82588 kcal/mol	1.07049 kcal/mol	186 201@LB@ \| \|@LB@5'-CAC...GGCAU UCG AUGAG...CGA-3'@LB@ AAGAGGA CAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ UUCUCCU GUAA@LB@3'-UUU...GCAGU UAAA AAAAA...ACA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -11.4071 kcal/mol@LB@Unfolding Energy - mRNA 2.82588 kcal/mol@LB@Unfolding Energy - sRNA 1.07049 kcal/mol@LB@@LB@Position - mRNA 187 -- 200@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
197	0.04129	0.6177	b1205	ychH	-8.72	0.074776	153 -- 162	43 -- 52	DUF2583 family putative inner membrane protein		_____________152________163\n_____________\|__________\|\n5'-CAA...AUAAG__________AUUCC...UAC-3'\n______________GAAGAGGGGU\n______________:\|\|\|\|\|\|::\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	156 -- 162	43 -- 49	-11.7568 kcal/mol	2.17132 kcal/mol	0.865937 kcal/mol	152 163@LB@ \| \|@LB@5'-CAA...AUAAG AUUCC...UAC-3'@LB@ GAAGAGGGGU@LB@ :\|\|\|\|\|\|::\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.7568 kcal/mol@LB@Unfolding Energy - mRNA 2.17132 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 153 -- 162@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 43 -- 49@LB@
198	0.04148	0.6177	b1067	yceH	-6.24	0.226874	185 -- 202	38 -- 56	UPF0502 family protein		_____________184_________________203\n_____________\|___________________\|\n5'-GCA...CCGGC__C___________C____GAAAU...GUG-3'\n______________CG_UAAGGAG_AAU_UCAU\n______________\|\|_:\|\|:\|\|\|_\|\|\|_\|\|\|\|\n______________GC_GUUUCUC_UUA_AGUA\n3'-UUU...ACCGG__A_______C___A____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	188 -- 194	47 -- 53	-10.8881 kcal/mol	3.47135 kcal/mol	1.17918 kcal/mol	184 203@LB@ \| \|@LB@5'-GCA...CCGGC C C GAAAU...GUG-3'@LB@ CG UAAGGAG AAU UCAU@LB@ \|\| :\|\|:\|\|\| \|\|\| \|\|\|\|@LB@ GC GUUUCUC UUA AGUA@LB@3'-UUU...ACCGG A C A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -10.8881 kcal/mol@LB@Unfolding Energy - mRNA 3.47135 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 185 -- 202@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
199	0.0417	0.6177	b4070	nrfA	-7.95	0.106497	2 -- 16	44 -- 55	nitrite reductase formate-dependent cytochrome		_____________1_______________17\n_____________\|_______________\|\n__________5'-U___GAA_________GAUAC...CAA-3'\n______________GUU___AAAGAGGAA\n______________\|\|:___\|\|\|\|\|\|\|\|\|\n______________CAG___UUUCUCCUU\n3'-UUU...CCGGG_______________AAAGU...ACA-5'\n_____________\|_______________\|\n_____________56______________43\n	10 -- 16	44 -- 50	-11.2989 kcal/mol	2.40804 kcal/mol	0.941432 kcal/mol	1 17@LB@ \| \|@LB@ 5'-U GAA GAUAC...CAA-3'@LB@ GUU AAAGAGGAA@LB@ \|\|: \|\|\|\|\|\|\|\|\|@LB@ CAG UUUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -11.2989 kcal/mol@LB@Unfolding Energy - mRNA 2.40804 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 2 -- 16@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 44 -- 50@LB@
200	0.04173	0.6177	b3155	yhbQ	-7.74	0.117248	9 -- 16	50 -- 57	GIY-YIG nuclease superfamily protein		_____________8________17\n_____________\|________\|\n___5'-UUUUUCUU________AUGUA...GCG-3'\n______________CCGUCAAA\n______________\|\|\|\|\|\|\|\|\n______________GGCAGUUU\n3'-UUU...AACCG________CUCCU...ACA-5'\n_____________\|________\|\n_____________58_______49\n	10 -- 16	50 -- 56	-10.5697 kcal/mol	0.110673 kcal/mol	2.72137 kcal/mol	8 17@LB@ \| \|@LB@ 5'-UUUUUCUU AUGUA...GCG-3'@LB@ CCGUCAAA@LB@ \|\|\|\|\|\|\|\|@LB@ GGCAGUUU@LB@3'-UUU...AACCG CUCCU...ACA-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -10.5697 kcal/mol@LB@Unfolding Energy - mRNA 0.110673 kcal/mol@LB@Unfolding Energy - sRNA 2.72137 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 50 -- 56@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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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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