Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
53	0.003903	0.237	b0946	zapC	-7.74	0.322468	177 -- 206	45 -- 76	FtsZ stabilizer	_____________176_________________________________207\n_____________\|___________________________________\|\n5'-AUU...UGCGG_______GG__AG______________A_______AUUAA...GUU-3'\n______________UUUUAUA__GU__GGGAGA_____GGC_GAUGCGA\n______________\|\|\|\|\|\|\|__\|\|__\|\|:\|:\|_____\|\|\|_:\|\|\|\|:\|\n______________AAAAUAU__CA__CCUUUU_____CCG_UUACGUU\n3'-UUU...ACAGA_______A___A_______AGUCA___________ACCGG...UUG-5'\n_____________\|___________________________________\|\n_____________77__________________________________44\n	200 -- 206	45 -- 51	-19.1898 kcal/mol	6.23804 kcal/mol	5.21532 kcal/mol	176 207@LB@ \| \|@LB@5'-AUU...UGCGG GG AG A AUUAA...GUU-3'@LB@ UUUUAUA GU GGGAGA GGC GAUGCGA@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|:\| \|\|\| :\|\|\|\|:\|@LB@ AAAAUAU CA CCUUUU CCG UUACGUU@LB@3'-UUU...ACAGA A A AGUCA ACCGG...UUG-5'@LB@ \| \|@LB@ 77 44@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -19.1898 kcal/mol@LB@Unfolding Energy - mRNA 6.23804 kcal/mol@LB@Unfolding Energy - sRNA 5.21532 kcal/mol@LB@@LB@Position - mRNA 177 -- 206@LB@Position - sRNA 45 -- 76@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 45 -- 51@LB@
42	0.002679	0.2088	b1427	rimL	-12.89	0.027177	178 -- 217	11 -- 49	ribosomal-protein-L7/L12-serine acetyltransferase	_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-GAU...ACAAC________AU____U___________GA___AA________AGUAA...CCU-3'\n______________UGC_AUGG__UGAC_GGAGAUAAGAU__CUG__ACGAUAAA\n______________\|\|\|_\|\|\|\|__::\|\|_\|:\|:\|\|\|\|:\|\|__\|\|\|__\|\|:\|\|\|\|\|\n______________ACG_UACC__GUUG_CUUUUAUUUUA__GAC__UGUUAUUU\n3'-UUU...CCGUU___U____GG____U________________AC________CCGUA...UUG-5'\n_____________\|_________________________________________\|\n_____________50________________________________________10\n	211 -- 217	11 -- 17	-27.9575 kcal/mol	3.9779 kcal/mol	11.0867 kcal/mol	177 218@LB@ \| \|@LB@5'-GAU...ACAAC AU U GA AA AGUAA...CCU-3'@LB@ UGC AUGG UGAC GGAGAUAAGAU CUG ACGAUAAA@LB@ \|\|\| \|\|\|\| ::\|\| \|:\|:\|\|\|\|:\|\| \|\|\| \|\|:\|\|\|\|\|@LB@ ACG UACC GUUG CUUUUAUUUUA GAC UGUUAUUU@LB@3'-UUU...CCGUU U GG U AC CCGUA...UUG-5'@LB@ \| \|@LB@ 50 10@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -27.9575 kcal/mol@LB@Unfolding Energy - mRNA 3.9779 kcal/mol@LB@Unfolding Energy - sRNA 11.0867 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 11 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
111	0.01033	0.313	b1120	cobB	-14.51	0.010573	178 -- 236	7 -- 64	deacetylase of acs and cheY chemotaxis regulator	_____________177______________________________________________________________237\n_____________\|________________________________________________________________\|\n5'-CGC...UUUCA____UAA______GCCG__A_______AAA___CA______C____GUAC______________GGAAU...AUC-3'\n______________GAGA___AGUGGU____GA_GCAAUGG___AAC__AGAGUA___UC____UGACAG___GGGCA\n______________\|\|:\|___\|\|\|\|\|:____:\|_\|\|\|\|\|\|\|___\|\|\|__\|:\|:\|\|___\|\|____\|\|\|\|\|:___:\|\|\|\|\n______________CUUU___UCACCG____UU_CGUUACC___UUG__UUUUAU___AG____ACUGUU___UCCGU\n3'-UUU...ACAAC____UAG____________A_______GGG___UC______UUU__AC________AUU_____AUAUUG-5'\n_____________\|________________________________________________________________\|\n_____________65_______________________________________________________________6\n	198 -- 204	42 -- 48	-37.7371 kcal/mol	11.0723 kcal/mol	12.1536 kcal/mol	177 237@LB@ \| \|@LB@5'-CGC...UUUCA UAA GCCG A AAA CA C GUAC GGAAU...AUC-3'@LB@ GAGA AGUGGU GA GCAAUGG AAC AGAGUA UC UGACAG GGGCA@LB@ \|\|:\| \|\|\|\|\|: :\| \|\|\|\|\|\|\| \|\|\| \|:\|:\|\| \|\| \|\|\|\|\|: :\|\|\|\|@LB@ CUUU UCACCG UU CGUUACC UUG UUUUAU AG ACUGUU UCCGU@LB@3'-UUU...ACAAC UAG A GGG UC UUU AC AUU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -37.7371 kcal/mol@LB@Unfolding Energy - mRNA 11.0723 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 178 -- 236@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
91	0.007817	0.2889	b3380	yhfW	-10.82	0.081759	179 -- 205	41 -- 67	phosphopentomutase-related metalloenzyme superfamily protein	_____________178_________________________206\n_____________\|___________________________\|\n5'-CUC...CAGUC_______C__UC___G__C________GCGAU...GUG-3'\n______________UUGGAAA_UC__UGG_GG_GUAAUGGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_::_\|:\|\|\|\|\|\|\n______________AACCUUU_AG__ACC_UU_CGUUACCG\n3'-UUU...UAUAC_______U__UC___G__A________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________68__________________________40\n	199 -- 205	41 -- 47	-26.7792 kcal/mol	10.1319 kcal/mol	5.83043 kcal/mol	178 206@LB@ \| \|@LB@5'-CUC...CAGUC C UC G C GCGAU...GUG-3'@LB@ UUGGAAA UC UGG GG GUAAUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| :: \|:\|\|\|\|\|\|@LB@ AACCUUU AG ACC UU CGUUACCG@LB@3'-UUU...UAUAC U UC G A GGUUG...UUG-5'@LB@ \| \|@LB@ 68 40@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -26.7792 kcal/mol@LB@Unfolding Energy - mRNA 10.1319 kcal/mol@LB@Unfolding Energy - sRNA 5.83043 kcal/mol@LB@@LB@Position - mRNA 179 -- 205@LB@Position - sRNA 41 -- 67@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
121	0.01216	0.338	b3416	malQ	-13.35	0.020947	179 -- 225	13 -- 54	4-alpha-glucanotransferase (amylomaltase)	_____________178______________________________________________226\n_____________\|________________________________________________\|\n5'-GCG...UGGCA_____AAC__U__GGAA_____________C___C_____________CCGCG...CCA-3'\n______________GGCAA___GC_AA____GCUCGAUGGAAAG_AAA_GUCUG_GAUAAUG\n______________\|\|\|\|\|___\|\|_\|\|____\|\|:\|:\|::\|\|\|\|:_\|\|\|_:\|\|\|\|_\|\|:\|\|\|:\n______________CCGUU___CG_UU____CGGGUUGUCUUUU_UUU_UAGAC_CUGUUAU\n3'-UUU...AGUCA_____A_______AC_______________A_________A_______UUCCG...UUG-5'\n_____________\|________________________________________________\|\n_____________55_______________________________________________12\n	219 -- 225	13 -- 19	-33.3316 kcal/mol	8.88616 kcal/mol	11.0933 kcal/mol	178 226@LB@ \| \|@LB@5'-GCG...UGGCA AAC U GGAA C C CCGCG...CCA-3'@LB@ GGCAA GC AA GCUCGAUGGAAAG AAA GUCUG GAUAAUG@LB@ \|\|\|\|\| \|\| \|\| \|\|:\|:\|::\|\|\|\|: \|\|\| :\|\|\|\| \|\|:\|\|\|:@LB@ CCGUU CG UU CGGGUUGUCUUUU UUU UAGAC CUGUUAU@LB@3'-UUU...AGUCA A AC A A UUCCG...UUG-5'@LB@ \| \|@LB@ 55 12@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -33.3316 kcal/mol@LB@Unfolding Energy - mRNA 8.88616 kcal/mol@LB@Unfolding Energy - sRNA 11.0933 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 13 -- 54@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 13 -- 19@LB@
25	0.001369	0.1841	b2599	pheA	-10.09	0.116571	180 -- 205	1 -- 20	chorismate mutase and prephenate dehydratase P-protein	_____________179________________________206\n_____________\|__________________________\|\n5'-UGA...UUUAU______CAA_______ACAC______AUCGG...UCG-3'\n______________UGAUAA___AAAGGCA____UAUGAC\n______________\|\|\|:\|\|___\|\|\|\|\|\|\|____\|\|\|:\|\|\n______________ACUGUU___UUUCCGU____AUAUUG\n3'-UUU...UAGAC______A___________________-5'\n_____________\|_________________________\|\n_____________21________________________1\n	189 -- 195	7 -- 13	-16.49 kcal/mol	2.17136 kcal/mol	4.22784 kcal/mol	179 206@LB@ \| \|@LB@5'-UGA...UUUAU CAA ACAC AUCGG...UCG-3'@LB@ UGAUAA AAAGGCA UAUGAC@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:\|\|@LB@ ACUGUU UUUCCGU AUAUUG@LB@3'-UUU...UAGAC A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -16.49 kcal/mol@LB@Unfolding Energy - mRNA 2.17136 kcal/mol@LB@Unfolding Energy - sRNA 4.22784 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 7 -- 13@LB@
123	0.01273	0.3462	b1817	manX	-9.41	0.160028	181 -- 191	9 -- 19	fused mannose-specific PTS enzymes: IIA component/IIB component	_____________180_________192\n_____________\|___________\|\n5'-UUA...UUAAC___________AGGUA...GGA-3'\n______________GAUAAUAAAGG\n______________\|\|:\|\|\|\|\|\|\|\|\n______________CUGUUAUUUCC\n3'-UUU...AGACA___________GUAUAUUG-5'\n_____________\|___________\|\n_____________20__________8\n	185 -- 191	9 -- 15	-11.4394 kcal/mol	1.08042 kcal/mol	0.949641 kcal/mol	180 192@LB@ \| \|@LB@5'-UUA...UUAAC AGGUA...GGA-3'@LB@ GAUAAUAAAGG@LB@ \|\|:\|\|\|\|\|\|\|\|@LB@ CUGUUAUUUCC@LB@3'-UUU...AGACA GUAUAUUG-5'@LB@ \| \|@LB@ 20 8@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -11.4394 kcal/mol@LB@Unfolding Energy - mRNA 1.08042 kcal/mol@LB@Unfolding Energy - sRNA 0.949641 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 9 -- 19@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 9 -- 15@LB@
197	0.02537	0.4256	b3317	rplB	-11.01	0.074049	182 -- 205	41 -- 62	50S ribosomal subunit protein L2	_____________181______________________206\n_____________\|________________________\|\n5'-GCA...UGAGU_______AG_A_____A_______AGUUG...UGC-3'\n______________AAGUCGG__G_GUAAU_CAAUGGC\n______________\|\|:\|\|:\|__\|_\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUUAGUC__C_CGUUA_GUUACCG\n3'-UUU...AACCU_______A________C_______GGUUG...UUG-5'\n_____________\|________________________\|\n_____________63_______________________40\n	199 -- 205	41 -- 47	-19.8959 kcal/mol	4.6063 kcal/mol	4.27585 kcal/mol	181 206@LB@ \| \|@LB@5'-GCA...UGAGU AG A A AGUUG...UGC-3'@LB@ AAGUCGG G GUAAU CAAUGGC@LB@ \|\|:\|\|:\| \| \|:\|\|\| \|\|\|\|\|\|\|@LB@ UUUAGUC C CGUUA GUUACCG@LB@3'-UUU...AACCU A C GGUUG...UUG-5'@LB@ \| \|@LB@ 63 40@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -19.8959 kcal/mol@LB@Unfolding Energy - mRNA 4.6063 kcal/mol@LB@Unfolding Energy - sRNA 4.27585 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 41 -- 62@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
35	0.002227	0.2088	b1482	osmC	-7.15	0.399399	183 -- 208	14 -- 42	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin	_____________182___________________________209\n_____________\|_____________________________\|\n5'-UAG...UUUAA_____________GCAACAA_________CCAUA...CGU-3'\n______________GCCC_ACAGGAGA_________UGACAAU\n______________\|\|\|\|_\|\|\|\|:\|:\|_________\|\|\|\|\|\|\|\n______________CGGG_UGUCUUUU_________ACUGUUA\n3'-UUU...GUUAC____U________AUUUUAGAC_______UUUCC...UUG-5'\n_____________\|_____________________________\|\n_____________43____________________________13\n	202 -- 208	14 -- 20	-22.1887 kcal/mol	4.46968 kcal/mol	10.5676 kcal/mol	182 209@LB@ \| \|@LB@5'-UAG...UUUAA GCAACAA CCAUA...CGU-3'@LB@ GCCC ACAGGAGA UGACAAU@LB@ \|\|\|\| \|\|\|\|:\|:\| \|\|\|\|\|\|\|@LB@ CGGG UGUCUUUU ACUGUUA@LB@3'-UUU...GUUAC U AUUUUAGAC UUUCC...UUG-5'@LB@ \| \|@LB@ 43 13@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -22.1887 kcal/mol@LB@Unfolding Energy - mRNA 4.46968 kcal/mol@LB@Unfolding Energy - sRNA 10.5676 kcal/mol@LB@@LB@Position - mRNA 183 -- 208@LB@Position - sRNA 14 -- 42@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 14 -- 20@LB@
6	0.0002023	0.1081	b1884	cheR	-8.31	0.257615	184 -- 205	1 -- 21	chemotaxis regulator protein-glutamate methyltransferase	_____________183____________________206\n_____________\|______________________\|\n5'-GCC...CUGAA_____UGA_______C______UUCAU...UGA-3'\n______________GUGAU___GAAGGCG_UAUGAC\n______________\|\|\|\|:___:\|\|\|\|\|:_\|\|\|:\|\|\n______________CACUG___UUUCCGU_AUAUUG\n3'-UUU...UUAGA_____UUA______________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	192 -- 198	7 -- 13	-19.9838 kcal/mol	7.26541 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-GCC...CUGAA UGA C UUCAU...UGA-3'@LB@ GUGAU GAAGGCG UAUGAC@LB@ \|\|\|\|: :\|\|\|\|\|: \|\|\|:\|\|@LB@ CACUG UUUCCGU AUAUUG@LB@3'-UUU...UUAGA UUA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -19.9838 kcal/mol@LB@Unfolding Energy - mRNA 7.26541 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@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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