Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
177	0.009845	0.1869	b3241	aaeA	-6.34	0.565531	229 -- 235	29 -- 35	p-hydroxybenzoic acid efflux system component	_____________228_____236\n_____________\|_______\|\n5'-UCC...CUCCC_______CAUCA...CCG-3'\n______________GUACGGC\n______________\|\|\|\|:\|\|\n______________CAUGUCG\n3'-UUU...AGGAC_______AUCGU...UCG-5'\n_____________\|_______\|\n_____________36______28\n	229 -- 235	29 -- 35	-10.2139 kcal/mol	2.71034 kcal/mol	1.16584 kcal/mol	228 236@LB@ \| \|@LB@5'-UCC...CUCCC CAUCA...CCG-3'@LB@ GUACGGC@LB@ \|\|\|\|:\|\|@LB@ CAUGUCG@LB@3'-UUU...AGGAC AUCGU...UCG-5'@LB@ \| \|@LB@ 36 28@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.2139 kcal/mol@LB@Unfolding Energy - mRNA 2.71034 kcal/mol@LB@Unfolding Energy - sRNA 1.16584 kcal/mol@LB@@LB@Position - mRNA 229 -- 235@LB@Position - sRNA 29 -- 35@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 29 -- 35@LB@
80	0.002475	0.104	b2468	aegA	-11.19	0.098238	223 -- 245	11 -- 33	putative oxidoreductase FeS binding subunit/NAD/FAD-binding subunit	_____________222_____________________246\n_____________\|_______________________\|\n5'-UCU...GGCCA_____C____AUGUC________CAUGC...UGA-3'\n______________ACAGU_AGCA_____UGGGUUGU\n______________\|\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|:\|\n______________UGUCG_UCGU_____ACCCAAUA\n3'-UUU...GACCA_____A____AAAAU________CAAAA...UCG-5'\n_____________\|_______________________\|\n_____________34______________________10\n	239 -- 245	11 -- 17	-21.0997 kcal/mol	8.44489 kcal/mol	1.46958 kcal/mol	222 246@LB@ \| \|@LB@5'-UCU...GGCCA C AUGUC CAUGC...UGA-3'@LB@ ACAGU AGCA UGGGUUGU@LB@ \|\|\|\|: \|\|\|\| \|\|\|\|\|\|:\|@LB@ UGUCG UCGU ACCCAAUA@LB@3'-UUU...GACCA A AAAAU CAAAA...UCG-5'@LB@ \| \|@LB@ 34 10@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -21.0997 kcal/mol@LB@Unfolding Energy - mRNA 8.44489 kcal/mol@LB@Unfolding Energy - sRNA 1.46958 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 11 -- 33@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 11 -- 17@LB@
168	0.00897	0.1795	b3139	agaC	-13.68	0.025868	233 -- 273	1 -- 39	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________232________________________________________274\n_____________\|__________________________________________\|\n5'-AAC...UUAUC_____CG_________U___GUUC____GAU__A________UGGAA...CGA-3'\n______________CCUGG__GC_GUUAGU_UUU____UGGG___UG_UUUUUGGC\n______________\|\|\|\|\|__:\|_\|:\|\|\|:_\|\|\|____\|\|\|\|___\|\|_\|\|\|\|::\|\|\n______________GGACC__UG_CGAUCG_AAA____ACCC___AC_AAAAGUCG\n3'-UUU...ACCAA_____A___U______U___AU______AAU__A________-5'\n_____________\|_________________________________________\|\n_____________40________________________________________1\n	267 -- 273	1 -- 7	-31.3276 kcal/mol	13.0397 kcal/mol	4.60651 kcal/mol	232 274@LB@ \| \|@LB@5'-AAC...UUAUC CG U GUUC GAU A UGGAA...CGA-3'@LB@ CCUGG GC GUUAGU UUU UGGG UG UUUUUGGC@LB@ \|\|\|\|\| :\| \|:\|\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|::\|\|@LB@ GGACC UG CGAUCG AAA ACCC AC AAAAGUCG@LB@3'-UUU...ACCAA A U U AU AAU A -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -31.3276 kcal/mol@LB@Unfolding Energy - mRNA 13.0397 kcal/mol@LB@Unfolding Energy - sRNA 4.60651 kcal/mol@LB@@LB@Position - mRNA 233 -- 273@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
144	0.006813	0.158	b0111	ampE	-6.38	0.559697	294 -- 300	1 -- 7	ampicillin resistance inner membrane protein; putative signaling protein in beta-lactamase regulation	_____________293____300\n_____________\|______\|\n5'-CUU...CGUUC_______-3'\n______________UUUCGGC\n______________\|\|\|\|:\|\|\n______________AAAGUCG\n3'-UUU...UACAA_______-5'\n_____________\|______\|\n_____________8______1\n	294 -- 300	1 -- 7	-7.27697 kcal/mol	0.0992979 kcal/mol	0.796773 kcal/mol	293 300@LB@ \| \|@LB@5'-CUU...CGUUC -3'@LB@ UUUCGGC@LB@ \|\|\|\|:\|\|@LB@ AAAGUCG@LB@3'-UUU...UACAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -6.38 kcal/mol@LB@Hybridization Energy -7.27697 kcal/mol@LB@Unfolding Energy - mRNA 0.0992979 kcal/mol@LB@Unfolding Energy - sRNA 0.796773 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@LB@
106	0.003955	0.1254	b1767	ansA	-7.74	0.383564	250 -- 272	11 -- 34	cytoplasmic L-asparaginase 1	_____________249______________________273\n_____________\|________________________\|\n5'-UGC...CGGGA______GUUCCGAGCA________AUACC...GCC-3'\n______________UGCAGC___________GGGUUAU\n______________\|:\|\|\|\|___________\|\|\|\|\|\|\|\n______________AUGUCG___________CCCAAUA\n3'-UUU...GGACC______AUCGUAAAAUA_______CAAAA...UCG-5'\n_____________\|________________________\|\n_____________35_______________________10\n	266 -- 272	11 -- 17	-16.5796 kcal/mol	7.36686 kcal/mol	1.47152 kcal/mol	249 273@LB@ \| \|@LB@5'-UGC...CGGGA GUUCCGAGCA AUACC...GCC-3'@LB@ UGCAGC GGGUUAU@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|@LB@ AUGUCG CCCAAUA@LB@3'-UUU...GGACC AUCGUAAAAUA CAAAA...UCG-5'@LB@ \| \|@LB@ 35 10@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -16.5796 kcal/mol@LB@Unfolding Energy - mRNA 7.36686 kcal/mol@LB@Unfolding Energy - sRNA 1.47152 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 11 -- 34@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 11 -- 17@LB@
68	0.001845	0.09081	b2957	ansB	-14.03	0.020893	243 -- 268	22 -- 43	periplasmic L-asparaginase 2	_____________242________________________269\n_____________\|__________________________\|\n5'-AGC...UUAUG______AG_________AU_______ACCCA...GGA-3'\n______________GGUUUU__UGGUGCAGC__UGGCAUU\n______________\|\|\|\|::__\|\|\|\|:\|\|\|\|__\|:\|\|\|\|\|\n______________CCAAGG__ACCAUGUCG__AUCGUAA\n3'-UUU...CUCCA__________________________AAUAC...UCG-5'\n_____________\|__________________________\|\n_____________44_________________________21\n	262 -- 268	22 -- 28	-26.4763 kcal/mol	7.8858 kcal/mol	4.55803 kcal/mol	242 269@LB@ \| \|@LB@5'-AGC...UUAUG AG AU ACCCA...GGA-3'@LB@ GGUUUU UGGUGCAGC UGGCAUU@LB@ \|\|\|\|:: \|\|\|\|:\|\|\|\| \|:\|\|\|\|\|@LB@ CCAAGG ACCAUGUCG AUCGUAA@LB@3'-UUU...CUCCA AAUAC...UCG-5'@LB@ \| \|@LB@ 44 21@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -26.4763 kcal/mol@LB@Unfolding Energy - mRNA 7.8858 kcal/mol@LB@Unfolding Energy - sRNA 4.55803 kcal/mol@LB@@LB@Position - mRNA 243 -- 268@LB@Position - sRNA 22 -- 43@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 22 -- 28@LB@
166	0.008687	0.1759	b3210	arcB	-6.83	0.499810	260 -- 284	24 -- 46	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________259_______________________285\n_____________\|_________________________\|\n5'-UGC...GGUCU____C_C____CAAUGUU_______CUGGC...UUC-3'\n______________GGUG_G_UUCU_______GCUGGCG\n______________\|\|\|\|_\|_\|\|\|:_______\|\|\|:\|\|:\n______________CCAC_C_AAGG_______CGAUCGU\n3'-UUU...UUCCU___________ACCAUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	278 -- 284	24 -- 30	-17.917 kcal/mol	6.53164 kcal/mol	4.55813 kcal/mol	259 285@LB@ \| \|@LB@5'-UGC...GGUCU C C CAAUGUU CUGGC...UUC-3'@LB@ GGUG G UUCU GCUGGCG@LB@ \|\|\|\| \| \|\|\|: \|\|\|:\|\|:@LB@ CCAC C AAGG CGAUCGU@LB@3'-UUU...UUCCU ACCAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -17.917 kcal/mol@LB@Unfolding Energy - mRNA 6.53164 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 260 -- 284@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 24 -- 30@LB@
102	0.003761	0.123	b0928	aspC	-10.71	0.122473	105 -- 118	20 -- 33	aspartate aminotransferase PLP-dependent	_____________104____________119\n_____________\|______________\|\n5'-CGU...CAAAA_____CU_______CAUCA...UUG-3'\n______________ACAGC__GCGUUUU\n______________\|\|\|\|\|__\|\|:\|\|\|\|\n______________UGUCG__CGUAAAA\n3'-UUU...GACCA_____AU_______UACCC...UCG-5'\n_____________\|______________\|\n_____________34_____________19\n	112 -- 118	20 -- 26	-14.5276 kcal/mol	2.38321 kcal/mol	1.43447 kcal/mol	104 119@LB@ \| \|@LB@5'-CGU...CAAAA CU CAUCA...UUG-3'@LB@ ACAGC GCGUUUU@LB@ \|\|\|\|\| \|\|:\|\|\|\|@LB@ UGUCG CGUAAAA@LB@3'-UUU...GACCA AU UACCC...UCG-5'@LB@ \| \|@LB@ 34 19@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -14.5276 kcal/mol@LB@Unfolding Energy - mRNA 2.38321 kcal/mol@LB@Unfolding Energy - sRNA 1.43447 kcal/mol@LB@@LB@Position - mRNA 105 -- 118@LB@Position - sRNA 20 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 20 -- 26@LB@
145	0.006858	0.158	b2079	baeR	-14.59	0.014658	61 -- 107	1 -- 46	response regulator in two-component regulatory system with BaeS	_____________60________________________________________________108\n_____________\|_________________________________________________\|\n5'-CAG...CCAGC__C______G__C__G________A____CC__AACAU____GA_____ACAUA...CGA-3'\n______________GG_GGUUCC_GG_UG_GGCUGGCG_UUUG__UG_____UGUU____AGC\n______________\|\|_\|\|\|\|\|\|_\|\|_\|:_:\|\|\|:\|\|:_\|\|\|:__\|\|_____\|\|\|\|____\|\|\|\n______________CC_CCAAGG_CC_AU_UCGAUCGU_AAAU__AC_____ACAA____UCG\n3'-UUU...UUCCU__A______A_____G________A________CCAAU____AAAG___-5'\n_____________\|________________________________________________\|\n_____________47_______________________________________________1\n	78 -- 84	24 -- 30	-36.7072 kcal/mol	17.5074 kcal/mol	4.60935 kcal/mol	60 108@LB@ \| \|@LB@5'-CAG...CCAGC C G C G A CC AACAU GA ACAUA...CGA-3'@LB@ GG GGUUCC GG UG GGCUGGCG UUUG UG UGUU AGC@LB@ \|\| \|\|\|\|\|\| \|\| \|: :\|\|\|:\|\|: \|\|\|: \|\| \|\|\|\| \|\|\|@LB@ CC CCAAGG CC AU UCGAUCGU AAAU AC ACAA UCG@LB@3'-UUU...UUCCU A A G A CCAAU AAAG -5'@LB@ \| \|@LB@ 47 1@LB@@LB@@LB@Energy -14.59 kcal/mol@LB@Hybridization Energy -36.7072 kcal/mol@LB@Unfolding Energy - mRNA 17.5074 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 61 -- 107@LB@Position - sRNA 1 -- 46@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 24 -- 30@LB@
93	0.003115	0.1126	b2595	bamD	-5.90	0.625252	19 -- 35	31 -- 48	BamABCDE complex OM biogenesis lipoprotein	_____________18_________________36\n_____________\|__________________\|\n5'-CUG...UGACC___U_______C______CCGUU...AUG-3'\n______________GAG_UGGUUUU_GG_ACA\n______________\|\|\|_\|\|\|\|\|::_\|\|_\|\|\|\n______________CUC_ACCAAGG_CC_UGU\n3'-UUU...GAUUC___C_______A__A___CGAUC...UCG-5'\n_____________\|__________________\|\n_____________49_________________30\n	23 -- 29	38 -- 44	-14.3523 kcal/mol	5.2001 kcal/mol	3.25694 kcal/mol	18 36@LB@ \| \|@LB@5'-CUG...UGACC U C CCGUU...AUG-3'@LB@ GAG UGGUUUU GG ACA@LB@ \|\|\| \|\|\|\|\|:: \|\| \|\|\|@LB@ CUC ACCAAGG CC UGU@LB@3'-UUU...GAUUC C A A CGAUC...UCG-5'@LB@ \| \|@LB@ 49 30@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -14.3523 kcal/mol@LB@Unfolding Energy - mRNA 5.2001 kcal/mol@LB@Unfolding Energy - sRNA 3.25694 kcal/mol@LB@@LB@Position - mRNA 19 -- 35@LB@Position - sRNA 31 -- 48@LB@Position Seed - mRNA 23 -- 29@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)

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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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