Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
160	0.015	0.3104	b2022	hisB	-11.12	0.077869	165 -- 171	5 -- 11	histidinol-phosphatase and imidazoleglycerol-phosphate dehydratase		_____________164_____172\n_____________\|_______\|\n5'-CAG...AGCCA_______AUUGA...AAC-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	165 -- 171	5 -- 11	-14.7431 kcal/mol	2.50821 kcal/mol	1.11145 kcal/mol	164 172@LB@ \| \|@LB@5'-CAG...AGCCA AUUGA...AAC-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.7431 kcal/mol@LB@Unfolding Energy - mRNA 2.50821 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 165 -- 171@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 5 -- 11@LB@
48	0.00405	0.2857	b0409	secF	-13.37	0.031213	166 -- 172	5 -- 11	SecYEG protein translocase auxillary subunit		_____________165_____173\n_____________\|_______\|\n5'-CUU...GGCAA_______AAGAA...UGU-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	166 -- 172	5 -- 11	-14.9857 kcal/mol	0.509172 kcal/mol	1.11145 kcal/mol	165 173@LB@ \| \|@LB@5'-CUU...GGCAA AAGAA...UGU-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -13.37 kcal/mol@LB@Hybridization Energy -14.9857 kcal/mol@LB@Unfolding Energy - mRNA 0.509172 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 166 -- 172@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 5 -- 11@LB@
163	0.0151	0.3104	b1517	lsrF	-8.60	0.205199	166 -- 179	8 -- 21	putative autoinducer-2 (AI-2) aldolase		_____________165____________180\n_____________\|______________\|\n5'-AAA...AAUAC___UU_U_______AUUAC...AUU-3'\n______________GAU__C_GAUGUGC\n______________\|\|\|__\|_:\|\|\|:\|\|\n______________CUA__G_UUACGCG\n3'-UUU...UACUA___UU_U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	173 -- 179	8 -- 14	-12.6785 kcal/mol	2.84069 kcal/mol	1.23638 kcal/mol	165 180@LB@ \| \|@LB@5'-AAA...AAUAC UU U AUUAC...AUU-3'@LB@ GAU C GAUGUGC@LB@ \|\|\| \| :\|\|\|:\|\|@LB@ CUA G UUACGCG@LB@3'-UUU...UACUA UU U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6785 kcal/mol@LB@Unfolding Energy - mRNA 2.84069 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 166 -- 179@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 8 -- 14@LB@
65	0.005951	0.3087	b0064	araC	-16.15	0.009664	167 -- 213	8 -- 48	ara regulon transcriptional activator; autorepressor		_____________166_____________________________________________214\n_____________\|_______________________________________________\|\n5'-GGA...CAAUU______U_________GGU____GU____AAAGUA____U__A____AAAAU...AUU-3'\n______________GGUUUC_UCUCUGAAU___GGGA__AUGA______UGGC_GA_GCGC\n______________::\|\|\|\|_\|\|\|\|\|\|\|\|\|___\|\|\|\|__\|\|\|\|______\|::\|_:\|_\|\|\|\|\n______________UUAAAG_AGAGACUUA___CCCU__UACU______AUUG_UU_CGCG\n3'-UUU...CGGUU______U_________AGU____AC______________U__A____CAGAAAG-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________7\n	174 -- 180	35 -- 41	-36.5778 kcal/mol	10.9694 kcal/mol	9.45905 kcal/mol	166 214@LB@ \| \|@LB@5'-GGA...CAAUU U GGU GU AAAGUA U A AAAAU...AUU-3'@LB@ GGUUUC UCUCUGAAU GGGA AUGA UGGC GA GCGC@LB@ ::\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|::\| :\| \|\|\|\|@LB@ UUAAAG AGAGACUUA CCCU UACU AUUG UU CGCG@LB@3'-UUU...CGGUU U AGU AC U A CAGAAAG-5'@LB@ \| \|@LB@ 49 7@LB@@LB@@LB@Energy -16.15 kcal/mol@LB@Hybridization Energy -36.5778 kcal/mol@LB@Unfolding Energy - mRNA 10.9694 kcal/mol@LB@Unfolding Energy - sRNA 9.45905 kcal/mol@LB@@LB@Position - mRNA 167 -- 213@LB@Position - sRNA 8 -- 48@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 35 -- 41@LB@
107	0.01107	0.3104	b0723	sdhA	-7.08	0.348281	169 -- 200	7 -- 42	succinate dehydrogenase flavoprotein subunit		_____________168__________________________________201\n_____________\|____________________________________\|\n5'-GGU...ACGUG____A________UU_______UG____________AUGAA...GUG-3'\n______________AUUU_UGGAUUCG___GUGGUG_____GGGUGUGUG\n______________\|\|:\|_\|\|:\|\|\|\|:___:\|\|:\|\|_____:::\|\|:\|:\|\n______________UAGA_ACUUAAGU___UACUAC_____UUUACGCGC\n3'-UUU...UAAAG____G________CCC______UAUUG_________AGAAAG-5'\n_____________\|____________________________________\|\n_____________43___________________________________6\n	194 -- 200	7 -- 13	-22.2639 kcal/mol	5.75915 kcal/mol	9.42962 kcal/mol	168 201@LB@ \| \|@LB@5'-GGU...ACGUG A UU UG AUGAA...GUG-3'@LB@ AUUU UGGAUUCG GUGGUG GGGUGUGUG@LB@ \|\|:\| \|\|:\|\|\|\|: :\|\|:\|\| :::\|\|:\|:\|@LB@ UAGA ACUUAAGU UACUAC UUUACGCGC@LB@3'-UUU...UAAAG G CCC UAUUG AGAAAG-5'@LB@ \| \|@LB@ 43 6@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -22.2639 kcal/mol@LB@Unfolding Energy - mRNA 5.75915 kcal/mol@LB@Unfolding Energy - sRNA 9.42962 kcal/mol@LB@@LB@Position - mRNA 169 -- 200@LB@Position - sRNA 7 -- 42@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 7 -- 13@LB@
110	0.01118	0.3104	b1726	yniB	-10.98	0.082506	169 -- 185	3 -- 23	putative inner membrane protein		_____________168___________________186\n_____________\|_____________________\|\n5'-AAG...ACUAA_____________________AAUCA...UGA-3'\n______________GUGA_AACGA___CGCGUCUU\n______________:\|\|\|_\|\|\|:\|___\|\|\|\|\|\|\|\|\n______________UACU_UUGUU___GCGCAGAA\n3'-UUU...CCUAC____A_____UAC________AG-5'\n_____________\|_____________________\|\n_____________24____________________2\n	179 -- 185	3 -- 9	-16.6558 kcal/mol	3.14383 kcal/mol	2.53367 kcal/mol	168 186@LB@ \| \|@LB@5'-AAG...ACUAA AAUCA...UGA-3'@LB@ GUGA AACGA CGCGUCUU@LB@ :\|\|\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ UACU UUGUU GCGCAGAA@LB@3'-UUU...CCUAC A UAC AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -16.6558 kcal/mol@LB@Unfolding Energy - mRNA 3.14383 kcal/mol@LB@Unfolding Energy - sRNA 2.53367 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 3 -- 9@LB@
61	0.005608	0.3084	b2174	lpxT	-9.09	0.171357	170 -- 179	1 -- 10	lipid A 1-diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase		_____________169________180\n_____________\|__________\|\n5'-GAA...UUGCC__________AGUAA...CGA-3'\n______________UGCGUUUUUC\n______________:\|\|\|\|:\|\|\|\|\n______________GCGCAGAAAG\n3'-UUU...UUUAC__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-13.1644 kcal/mol	2.90849 kcal/mol	1.16635 kcal/mol	169 180@LB@ \| \|@LB@5'-GAA...UUGCC AGUAA...CGA-3'@LB@ UGCGUUUUUC@LB@ :\|\|\|\|:\|\|\|\|@LB@ GCGCAGAAAG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -13.1644 kcal/mol@LB@Unfolding Energy - mRNA 2.90849 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
21	0.0009524	0.1536	b0241	phoE	-11.39	0.070016	174 -- 180	5 -- 11	outer membrane phosphoporin protein E	b0929 b2215 b1377	_____________173_____181\n_____________\|_______\|\n5'-AGC...UAUUC_______AAUUA...AUG-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	174 -- 180	5 -- 11	-12.879 kcal/mol	0.378776 kcal/mol	1.11145 kcal/mol	173 181@LB@ \| \|@LB@5'-AGC...UAUUC AAUUA...AUG-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -12.879 kcal/mol@LB@Unfolding Energy - mRNA 0.378776 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 174 -- 180@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 5 -- 11@LB@
144	0.01383	0.3104	b1135	rluE	-11.03	0.080673	174 -- 189	5 -- 20	23S rRNA pseudouridine(2457) synthase		_____________173______________190\n_____________\|________________\|\n5'-UGU...CCGUC____A___________AUUAG...AAC-3'\n______________AUGA_AGAUGCGCGUU\n______________\|\|:\|_\|:\|\|\|\|\|\|\|\|:\n______________UAUU_UUUACGCGCAG\n3'-UUU...ACUAC____G___________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	183 -- 189	5 -- 11	-17.9797 kcal/mol	5.69694 kcal/mol	1.24804 kcal/mol	173 190@LB@ \| \|@LB@5'-UGU...CCGUC A AUUAG...AAC-3'@LB@ AUGA AGAUGCGCGUU@LB@ \|\|:\| \|:\|\|\|\|\|\|\|\|:@LB@ UAUU UUUACGCGCAG@LB@3'-UUU...ACUAC G AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -17.9797 kcal/mol@LB@Unfolding Energy - mRNA 5.69694 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 174 -- 189@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 5 -- 11@LB@
173	0.0173	0.3104	b0145	dksA	-10.49	0.099910	175 -- 187	5 -- 21	transcriptional regulator of rRNA transcription; DnaK suppressor protein		_____________174_______________188\n_____________\|_________________\|\n5'-AAU...GGAUC_________________AAGGA...AUG-3'\n______________GAUA____GUGCGUGUU\n______________\|\|\|\|____:\|\|\|\|:\|\|:\n______________CUAU____UACGCGCAG\n3'-UUU...UACUA____UGUU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	181 -- 187	5 -- 11	-14.603 kcal/mol	2.85898 kcal/mol	1.24955 kcal/mol	174 188@LB@ \| \|@LB@5'-AAU...GGAUC AAGGA...AUG-3'@LB@ GAUA GUGCGUGUU@LB@ \|\|\|\| :\|\|\|\|:\|\|:@LB@ CUAU UACGCGCAG@LB@3'-UUU...UACUA UGUU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -14.603 kcal/mol@LB@Unfolding Energy - mRNA 2.85898 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 175 -- 187@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 5 -- 11@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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service.

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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