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
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@
62	0.005646	0.3084	b1242	ychE	-13.92	0.024785	141 -- 151	1 -- 11	UPF0056 family inner membrane protein		_____________140_________152\n_____________\|___________\|\n5'-CAU...UGUCA___________CAACC...GCA-3'\n______________GCGCGUCUUUU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________CGCGCAGAAAG\n3'-UUU...GUUUA___________-5'\n_____________\|__________\|\n_____________12_________1\n	145 -- 151	1 -- 7	-17.9236 kcal/mol	2.83374 kcal/mol	1.17076 kcal/mol	140 152@LB@ \| \|@LB@5'-CAU...UGUCA CAACC...GCA-3'@LB@ GCGCGUCUUUU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ CGCGCAGAAAG@LB@3'-UUU...GUUUA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.9236 kcal/mol@LB@Unfolding Energy - mRNA 2.83374 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 141 -- 151@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein		_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
64	0.005939	0.3087	b3237	argR	-9.39	0.153279	85 -- 104	1 -- 19	l-arginine-responsive arginine metabolism regulon transcriptional regulator		_____________84____________________105\n_____________\|_____________________\|\n5'-ACA...AAAUU_______AUCC__________AUAAC...UGC-3'\n______________UGAUAAA____CGC_UCUUUC\n______________\|:\|:\|\|\|____\|\|\|_\|\|\|\|\|\|\n______________AUUGUUU____GCG_AGAAAG\n3'-UUU...CUACU_______AC_____C______-5'\n_____________\|____________________\|\n_____________20___________________1\n	85 -- 91	13 -- 19	-12.1021 kcal/mol	1.46458 kcal/mol	1.25156 kcal/mol	84 105@LB@ \| \|@LB@5'-ACA...AAAUU AUCC AUAAC...UGC-3'@LB@ UGAUAAA CGC UCUUUC@LB@ \|:\|:\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AUUGUUU GCG AGAAAG@LB@3'-UUU...CUACU AC C -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.46458 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 85 -- 104@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 13 -- 19@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@
66	0.006019	0.3087	b0223	yafJ	-7.05	0.351504	68 -- 78	1 -- 10	type 2 glutamine amidotransferase family protein		_____________67__________79\n_____________\|___________\|\n5'-GCG...GCUGA________A__AUGCC...AAG-3'\n______________CGCGUCUU_UC\n______________\|\|\|\|\|\|\|\|_\|\|\n______________GCGCAGAA_AG\n3'-UUU...UUUAC___________-5'\n_____________\|__________\|\n_____________11_________1\n	69 -- 75	3 -- 9	-12.9748 kcal/mol	4.76165 kcal/mol	1.16635 kcal/mol	67 79@LB@ \| \|@LB@5'-GCG...GCUGA A AUGCC...AAG-3'@LB@ CGCGUCUU UC@LB@ \|\|\|\|\|\|\|\| \|\|@LB@ GCGCAGAA AG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.05 kcal/mol@LB@Hybridization Energy -12.9748 kcal/mol@LB@Unfolding Energy - mRNA 4.76165 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 68 -- 78@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 3 -- 9@LB@
67	0.006163	0.3087	b0773	ybhB	-10.36	0.105479	214 -- 228	7 -- 20	kinase inhibitor homolog UPF0098 family	b0545	_____________213_____________229\n_____________\|_______________\|\n5'-UGU...CAUCA_______UC______AUGGC...AUC-3'\n______________GUAACGA__UGCGCG\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\n______________UAUUGUU__ACGCGC\n3'-UUU...ACUAC_______U_______AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	214 -- 220	14 -- 20	-16.0436 kcal/mol	4.44842 kcal/mol	1.23906 kcal/mol	213 229@LB@ \| \|@LB@5'-UGU...CAUCA UC AUGGC...AUC-3'@LB@ GUAACGA UGCGCG@LB@ :\|\|\|\|:\| \|\|\|\|\|\|@LB@ UAUUGUU ACGCGC@LB@3'-UUU...ACUAC U AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.0436 kcal/mol@LB@Unfolding Energy - mRNA 4.44842 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 214 -- 228@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@LB@
68	0.006348	0.3087	b1202	ycgV	-6.40	0.429936	233 -- 244	4 -- 18	putative adhesin	b2647	_____________232_____________245\n_____________\|_______________\|\n5'-ACU...ACCAA_______________CGCUG...UUG-3'\n______________AGCAGAU___CGUCU\n______________\|:\|\|:\|\|___\|\|\|\|\|\n______________UUGUUUA___GCAGA\n3'-UUU...UACUA_______CGC_____AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	233 -- 239	12 -- 18	-9.8712 kcal/mol	2.23703 kcal/mol	1.22995 kcal/mol	232 245@LB@ \| \|@LB@5'-ACU...ACCAA CGCUG...UUG-3'@LB@ AGCAGAU CGUCU@LB@ \|:\|\|:\|\| \|\|\|\|\|@LB@ UUGUUUA GCAGA@LB@3'-UUU...UACUA CGC AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -9.8712 kcal/mol@LB@Unfolding Energy - mRNA 2.23703 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 233 -- 244@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 12 -- 18@LB@
69	0.006491	0.3087	b3347	fkpA	-11.66	0.062814	96 -- 113	4 -- 22	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)		_____________95__________________114\n_____________\|___________________\|\n5'-UGG...AUAGA___________________GUAUG...CAG-3'\n______________UGAUAAUAGG_GCGUGUCU\n______________\|\|\|\|\|\|:\|::_\|\|\|:\|\|\|\|\n______________ACUAUUGUUU_CGCGCAGA\n3'-UUU...CUACU__________A________AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	107 -- 113	4 -- 10	-21.7718 kcal/mol	8.85627 kcal/mol	1.2572 kcal/mol	95 114@LB@ \| \|@LB@5'-UGG...AUAGA GUAUG...CAG-3'@LB@ UGAUAAUAGG GCGUGUCU@LB@ \|\|\|\|\|\|:\|:: \|\|\|:\|\|\|\|@LB@ ACUAUUGUUU CGCGCAGA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -21.7718 kcal/mol@LB@Unfolding Energy - mRNA 8.85627 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 96 -- 113@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 4 -- 10@LB@
70	0.006501	0.3087	b3301	rplO	-9.96	0.122936	194 -- 206	8 -- 20	50S ribosomal subunit protein L15		_____________193___________207\n_____________\|_____________\|\n5'-UUC...GAGGA____G________UUAAA...GUG-3'\n______________GUAA_AGAUGCGU\n______________:\|\|\|_\|:\|\|\|\|\|:\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	200 -- 206	8 -- 14	-13.6668 kcal/mol	2.47062 kcal/mol	1.23367 kcal/mol	193 207@LB@ \| \|@LB@5'-UUC...GAGGA G UUAAA...GUG-3'@LB@ GUAA AGAUGCGU@LB@ :\|\|\| \|:\|\|\|\|\|:@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -13.6668 kcal/mol@LB@Unfolding Energy - mRNA 2.47062 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 194 -- 206@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@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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