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
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins	_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@LB@
106	0.02162	0.6177	b1831	proQ	-7.28	0.143813	159 -- 202	38 -- 75	RNA chaperone putative ProP translation regulator	_____________158_____________________________________________203\n_____________\|_______________________________________________\|\n5'-UUA...UUCAU___UG______U________A____CGUUGU__UC___A________GGAAA...CGC-3'\n______________GCC_____CGC_UGUUGGCU_CGUC______AA__AGG_AAUUUCAU\n______________\|\|\|_____\|\|\|_\|:\|\|\|\|\|:_\|\|\|\|______\|\|__\|\|\|_\|\|\|\|\|\|\|\|\n______________CGG_____GCG_AUAACCGG_GCAG______UU__UCC_UUAAAGUA\n3'-UUU...UUUAC___UUAUA_________________________UC____________AAAAA...ACA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________37\n	196 -- 202	38 -- 44	-31.8607 kcal/mol	10.974 kcal/mol	13.6034 kcal/mol	158 203@LB@ \| \|@LB@5'-UUA...UUCAU UG U A CGUUGU UC A GGAAA...CGC-3'@LB@ GCC CGC UGUUGGCU CGUC AA AGG AAUUUCAU@LB@ \|\|\| \|\|\| \|:\|\|\|\|\|: \|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CGG GCG AUAACCGG GCAG UU UCC UUAAAGUA@LB@3'-UUU...UUUAC UUAUA UC AAAAA...ACA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -31.8607 kcal/mol@LB@Unfolding Energy - mRNA 10.974 kcal/mol@LB@Unfolding Energy - sRNA 13.6034 kcal/mol@LB@@LB@Position - mRNA 159 -- 202@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
107	0.02168	0.6177	b1738	chbB	-9.32	0.056668	26 -- 34	47 -- 55	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________25________35\n_____________\|_________\|\n5'-AAU...CACAG_________AAACA...CGG-3'\n______________GUCAAGGAG\n______________\|\|\|\|\|:\|\|\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	28 -- 34	47 -- 53	-13.6925 kcal/mol	3.47679 kcal/mol	0.899516 kcal/mol	25 35@LB@ \| \|@LB@5'-AAU...CACAG AAACA...CGG-3'@LB@ GUCAAGGAG@LB@ \|\|\|\|\|:\|\|\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -13.6925 kcal/mol@LB@Unfolding Energy - mRNA 3.47679 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 26 -- 34@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 47 -- 53@LB@
108	0.0217	0.6177	b0243	proA	-8.76	0.073409	183 -- 193	47 -- 57	gamma-glutamylphosphate reductase	_____________182_________194\n_____________\|___________\|\n5'-AAU...AUUAC___________CAGGC...AUG-3'\n______________CCGUUAAGGAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	187 -- 193	47 -- 53	-14.7866 kcal/mol	3.29159 kcal/mol	2.73556 kcal/mol	182 194@LB@ \| \|@LB@5'-AAU...AUUAC CAGGC...AUG-3'@LB@ CCGUUAAGGAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -14.7866 kcal/mol@LB@Unfolding Energy - mRNA 3.29159 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
109	0.02227	0.6177	b4040	ubiA	-8.97	0.066674	182 -- 194	44 -- 55	p-hydroxybenzoate octaprenyltransferase	_____________181___________195\n_____________\|_____________\|\n5'-AGC...CCGUU__A_U________AAAAA...UAU-3'\n______________GU_C_AAGAGGAA\n______________\|\|_\|_\|\|\|\|\|\|\|\|\n______________CA_G_UUCUCCUU\n3'-UUU...CCGGG____U________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	188 -- 194	44 -- 50	-10.7786 kcal/mol	0.870226 kcal/mol	0.941432 kcal/mol	181 195@LB@ \| \|@LB@5'-AGC...CCGUU A U AAAAA...UAU-3'@LB@ GU C AAGAGGAA@LB@ \|\| \| \|\|\|\|\|\|\|\|@LB@ CA G UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -10.7786 kcal/mol@LB@Unfolding Energy - mRNA 0.870226 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
110	0.02234	0.6177	b0141	yadN	-8.72	0.074917	179 -- 189	37 -- 47	putative fimbrial-like adhesin protein	_____________178_________190\n_____________\|___________\|\n5'-UUA...CUAAU___________AAAGG...GUG-3'\n______________GGAAUUUUAUU\n______________\|\|\|\|\|\|\|:\|\|\|\n______________CCUUAAAGUAA\n3'-UUU...UUUCU___________AAAAA...ACA-5'\n_____________\|___________\|\n_____________48__________36\n	183 -- 189	37 -- 43	-11.1734 kcal/mol	1.41261 kcal/mol	1.04525 kcal/mol	178 190@LB@ \| \|@LB@5'-UUA...CUAAU AAAGG...GUG-3'@LB@ GGAAUUUUAUU@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ CCUUAAAGUAA@LB@3'-UUU...UUUCU AAAAA...ACA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1734 kcal/mol@LB@Unfolding Energy - mRNA 1.41261 kcal/mol@LB@Unfolding Energy - sRNA 1.04525 kcal/mol@LB@@LB@Position - mRNA 179 -- 189@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 37 -- 43@LB@
111	0.02245	0.6177	b3413	gntX	-10.38	0.034336	253 -- 267	41 -- 55	DNA catabolic protein	_____________252_____________268\n_____________\|_______________\|\n5'-CCC...GUUAG____UU_________GUUCG...AUA-3'\n______________GUCA__GGGGGAUUU\n______________\|\|\|\|__\|:\|\|:\|\|\|\|\n______________CAGU__CUCCUUAAA\n3'-UUU...CCGGG____UU_________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	261 -- 267	41 -- 47	-16.783 kcal/mol	5.45091 kcal/mol	0.947844 kcal/mol	252 268@LB@ \| \|@LB@5'-CCC...GUUAG UU GUUCG...AUA-3'@LB@ GUCA GGGGGAUUU@LB@ \|\|\|\| \|:\|\|:\|\|\|\|@LB@ CAGU CUCCUUAAA@LB@3'-UUU...CCGGG UU GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.783 kcal/mol@LB@Unfolding Energy - mRNA 5.45091 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 253 -- 267@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 41 -- 47@LB@
112	0.02248	0.6177	b2796	sdaC	-8.62	0.078257	115 -- 131	34 -- 50	putative serine transporter	_____________114_______________132\n_____________\|_________________\|\n5'-AUC...CCGAU___CA____________ACGGU...CAA-3'\n______________AGA__GAUUUCAUUUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|\|\|\n______________UCU__UUAAAGUAAAAA\n3'-UUU...CAGUU___CC____________AAUAA...ACA-5'\n_____________\|_________________\|\n_____________51________________33\n	125 -- 131	34 -- 40	-11.667 kcal/mol	1.97198 kcal/mol	1.0739 kcal/mol	114 132@LB@ \| \|@LB@5'-AUC...CCGAU CA ACGGU...CAA-3'@LB@ AGA GAUUUCAUUUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\|\|\|@LB@ UCU UUAAAGUAAAAA@LB@3'-UUU...CAGUU CC AAUAA...ACA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.667 kcal/mol@LB@Unfolding Energy - mRNA 1.97198 kcal/mol@LB@Unfolding Energy - sRNA 1.0739 kcal/mol@LB@@LB@Position - mRNA 115 -- 131@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 34 -- 40@LB@
113	0.02257	0.6177	b0915	lpxK	-7.55	0.127690	105 -- 116	46 -- 56	lipid A 4'kinase	_____________104__________117\n_____________\|____________\|\n5'-GAA...GUGGU_________U__UGUCA...GCU-3'\n______________CGUCGAGGA_GG\n______________\|\|\|\|:\|:\|\|_\|\|\n______________GCAGUUUCU_CC\n3'-UUU...ACCGG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________57___________45\n	107 -- 113	48 -- 54	-12.734 kcal/mol	4.25329 kcal/mol	0.93204 kcal/mol	104 117@LB@ \| \|@LB@5'-GAA...GUGGU U UGUCA...GCU-3'@LB@ CGUCGAGGA GG@LB@ \|\|\|\|:\|:\|\| \|\|@LB@ GCAGUUUCU CC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -7.55 kcal/mol@LB@Hybridization Energy -12.734 kcal/mol@LB@Unfolding Energy - mRNA 4.25329 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 105 -- 116@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 48 -- 54@LB@
114	0.02277	0.6177	b4077	gltP	-4.92	0.386213	48 -- 56	47 -- 55	glutamate/aspartate:proton symporter	_____________47________57\n_____________\|_________\|\n5'-GCC...CUGUU_________UUGCG...GCG-3'\n______________GUUAAAGGG\n______________\|\|:\|\|\|\|:\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	50 -- 56	47 -- 53	-9.45392 kcal/mol	3.63887 kcal/mol	0.899516 kcal/mol	47 57@LB@ \| \|@LB@5'-GCC...CUGUU UUGCG...GCG-3'@LB@ GUUAAAGGG@LB@ \|\|:\|\|\|\|:\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -9.45392 kcal/mol@LB@Unfolding Energy - mRNA 3.63887 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 48 -- 56@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 47 -- 53@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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