Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
123	0.004425	0.1258	b2535	csiE	-7.63	0.347411	1 -- 40	5 -- 36	stationary phase inducible protein		______________1_______________________________________41\n______________\|_______________________________________\|\n___________5'-__AG___UAA____UGA_____A_C___AUAAU_______AAAAC...UGG-3'\n______________GC__AAC___CCCA___UCGCU_G_ACG_____CAUUCAC\n______________\|\|__\|\|\|___\|\|\|\|___\|\|\|\|\|_\|_\|\|\|_____\|\|\|\|\|\|\|\n______________CG__UUG___GGGU___AGCGA_C_UGC_____GUAAGUG\n3'-UUU...UACCU__CG___C______________A_____AAC_________GACG-5'\n_____________\|________________________________________\|\n_____________37_______________________________________4\n	34 -- 40	5 -- 11	-25.9316 kcal/mol	3.04784 kcal/mol	15.2569 kcal/mol	1 41@LB@ \| \|@LB@ 5'- AG UAA UGA A C AUAAU AAAAC...UGG-3'@LB@ GC AAC CCCA UCGCU G ACG CAUUCAC@LB@ \|\| \|\|\| \|\|\|\| \|\|\|\|\| \| \|\|\| \|\|\|\|\|\|\|@LB@ CG UUG GGGU AGCGA C UGC GUAAGUG@LB@3'-UUU...UACCU CG C A AAC GACG-5'@LB@ \| \|@LB@ 37 4@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -25.9316 kcal/mol@LB@Unfolding Energy - mRNA 3.04784 kcal/mol@LB@Unfolding Energy - sRNA 15.2569 kcal/mol@LB@@LB@Position - mRNA 1 -- 40@LB@Position - sRNA 5 -- 36@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 5 -- 11@LB@
151	0.005924	0.1368	b3248	yhdE	-13.35	0.014399	2 -- 41	1 -- 42	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase		_____________1___________________________________________42\n_____________\|___________________________________________\|\n__________5'-U_____C___A_______G_____C_________U______G__GGUGG...AGC-3'\n______________UAUGG_AGC__GGCGCU_GUCGU___AUGUUGC_UUCGCU_GU\n______________\|\|\|\|\|_\|\|\|__::\|\|\|:_:\|\|\|:___\|:\|\|\|\|\|_\|\|\|:\|:_\|:\n______________AUACC_UCG__UUGCGG_UAGCG___UGCAACG_AAGUGG_CG\n3'-UUU...CUGUU_________CG______G_____AAC_______U______A__-5'\n_____________\|__________________________________________\|\n_____________43_________________________________________1\n	25 -- 31	11 -- 17	-43.9582 kcal/mol	15.3205 kcal/mol	15.293 kcal/mol	1 42@LB@ \| \|@LB@ 5'-U C A G C U G GGUGG...AGC-3'@LB@ UAUGG AGC GGCGCU GUCGU AUGUUGC UUCGCU GU@LB@ \|\|\|\|\| \|\|\| ::\|\|\|: :\|\|\|: \|:\|\|\|\|\| \|\|\|:\|: \|:@LB@ AUACC UCG UUGCGG UAGCG UGCAACG AAGUGG CG@LB@3'-UUU...CUGUU CG G AAC U A -5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -43.9582 kcal/mol@LB@Unfolding Energy - mRNA 15.3205 kcal/mol@LB@Unfolding Energy - sRNA 15.293 kcal/mol@LB@@LB@Position - mRNA 2 -- 41@LB@Position - sRNA 1 -- 42@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
102	0.003332	0.1114	b1279	yciS	-9.50	0.143375	3 -- 9	1 -- 7	DUF1049 family inner membrane protein function unknown		_____________2_______10\n_____________\|_______\|\n_________5'-AC_______GGAAG...UGU-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	3 -- 9	1 -- 7	-13.2462 kcal/mol	1.40693 kcal/mol	2.34039 kcal/mol	2 10@LB@ \| \|@LB@ 5'-AC GGAAG...UGU-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -13.2462 kcal/mol@LB@Unfolding Energy - mRNA 1.40693 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 3 -- 9@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 1 -- 7@LB@
187	0.008226	0.1545	b1446	ydcY	-8.50	0.236240	3 -- 9	2 -- 8	DUF2526 family protein		_____________2_______10\n_____________\|_______\|\n_________5'-UA_______GUUUC...ACG-3'\n______________UCACCUG\n______________\|\|\|\|\|\|\|\n______________AGUGGAC\n3'-UUU...ACGUA_______G-5'\n_____________\|_______\|\n_____________9_______1\n	3 -- 9	2 -- 8	-11.529 kcal/mol	0.673638 kcal/mol	2.36182 kcal/mol	2 10@LB@ \| \|@LB@ 5'-UA GUUUC...ACG-3'@LB@ UCACCUG@LB@ \|\|\|\|\|\|\|@LB@ AGUGGAC@LB@3'-UUU...ACGUA G-5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -11.529 kcal/mol@LB@Unfolding Energy - mRNA 0.673638 kcal/mol@LB@Unfolding Energy - sRNA 2.36182 kcal/mol@LB@@LB@Position - mRNA 3 -- 9@LB@Position - sRNA 2 -- 8@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 2 -- 8@LB@
79	0.001882	0.08273	b2219	atoS	-12.26	0.029240	6 -- 44	51 -- 94	sensory histidine kinase in two-component regulatory system with AtoC		_____________5_____________________________________________45\n_____________\|_____________________________________________\|\n______5'-UCAGG__________AA__A_____AA_______U__________C____CUCCG...AUA-3'\n______________GUUGUACGAA__GA____GC_____GGUA_UUCAAAGGGG_GAAG\n______________\|\|:\|\|\|\|\|\|\|__:\|____\|\|_____:\|\|\|_\|\|\|\|\|\|:::\|_\|\|\|\|\n______________CAGCAUGCUU__UU____CG_____UCAU_AAGUUUUUUC_CUUC\n3'-UUU...AGCCG__________AG__AACA__AUACG____U_______________AUUCU...ACG-5'\n_____________\|_____________________________________________\|\n_____________95____________________________________________50\n	9 -- 15	85 -- 91	-28.4119 kcal/mol	11.2894 kcal/mol	4.86774 kcal/mol	5 45@LB@ \| \|@LB@ 5'-UCAGG AA A AA U C CUCCG...AUA-3'@LB@ GUUGUACGAA GA GC GGUA UUCAAAGGGG GAAG@LB@ \|\|:\|\|\|\|\|\|\| :\| \|\| :\|\|\| \|\|\|\|\|\|:::\| \|\|\|\|@LB@ CAGCAUGCUU UU CG UCAU AAGUUUUUUC CUUC@LB@3'-UUU...AGCCG AG AACA AUACG U AUUCU...ACG-5'@LB@ \| \|@LB@ 95 50@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -28.4119 kcal/mol@LB@Unfolding Energy - mRNA 11.2894 kcal/mol@LB@Unfolding Energy - sRNA 4.86774 kcal/mol@LB@@LB@Position - mRNA 6 -- 44@LB@Position - sRNA 51 -- 94@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 85 -- 91@LB@
87	0.002406	0.09689	b3317	rplB	-11.53	0.045926	6 -- 24	68 -- 86	50S ribosomal subunit protein L2		_____________5___________________25\n_____________\|___________________\|\n______5'-GCAGA______AGC__________AAACU...UGC-3'\n______________AAUCAA___UGCUGUGCAG\n______________\|\|\|\|\|\|___\|\|\|\|:\|\|\|\|\|\n______________UUAGUU___ACGAUACGUC\n3'-UUU...CAUGC______AAC__________AUUAA...ACG-5'\n_____________\|___________________\|\n_____________87__________________67\n	18 -- 24	68 -- 74	-20.8348 kcal/mol	5.62876 kcal/mol	3.67996 kcal/mol	5 25@LB@ \| \|@LB@ 5'-GCAGA AGC AAACU...UGC-3'@LB@ AAUCAA UGCUGUGCAG@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UUAGUU ACGAUACGUC@LB@3'-UUU...CAUGC AAC AUUAA...ACG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -20.8348 kcal/mol@LB@Unfolding Energy - mRNA 5.62876 kcal/mol@LB@Unfolding Energy - sRNA 3.67996 kcal/mol@LB@@LB@Position - mRNA 6 -- 24@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
170	0.006792	0.1407	b1884	cheR	-8.41	0.246459	6 -- 26	68 -- 89	chemotaxis regulator protein-glutamate methyltransferase		_____________5_______________________27\n_____________\|_______________________\|\n______5'-GCCAG______________A__CA____AACGC...UGA-3'\n______________AUGGAUCAG__GUG_CU__GCAG\n______________\|:\|:\|\|\|\|:__\|\|\|_\|\|__\|\|\|\|\n______________UGCUUAGUU__CAC_GA__CGUC\n3'-UUU...CAGCA_________AA______UA____AUUAA...ACG-5'\n_____________\|_______________________\|\n_____________90______________________67\n	8 -- 14	81 -- 87	-16.9281 kcal/mol	4.01768 kcal/mol	4.506 kcal/mol	5 27@LB@ \| \|@LB@ 5'-GCCAG A CA AACGC...UGA-3'@LB@ AUGGAUCAG GUG CU GCAG@LB@ \|:\|:\|\|\|\|: \|\|\| \|\| \|\|\|\|@LB@ UGCUUAGUU CAC GA CGUC@LB@3'-UUU...CAGCA AA UA AUUAA...ACG-5'@LB@ \| \|@LB@ 90 67@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -16.9281 kcal/mol@LB@Unfolding Energy - mRNA 4.01768 kcal/mol@LB@Unfolding Energy - sRNA 4.506 kcal/mol@LB@@LB@Position - mRNA 6 -- 26@LB@Position - sRNA 68 -- 89@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 81 -- 87@LB@
117	0.00395	0.1189	b3447	ggt	-7.92	0.307079	7 -- 34	69 -- 94	gamma-glutamyltranspeptidase		_____________6____________________________35\n_____________\|____________________________\|\n_____5'-GUUAGG_____UCA____AUUAA__G________AAGCC...CGU-3'\n______________GUUGU___GAGU_____UG_GCUGUGCA\n______________\|\|:\|\|___\|\|:\|_____\|\|_\|\|\|:\|\|\|\|\n______________CAGCA___CUUA_____AC_CGAUACGU\n3'-UUU...AGCCG_____UG_____GUUA___A________CAUUA...ACG-5'\n_____________\|____________________________\|\n_____________95___________________________68\n	28 -- 34	69 -- 75	-19.4914 kcal/mol	6.89072 kcal/mol	4.68367 kcal/mol	6 35@LB@ \| \|@LB@ 5'-GUUAGG UCA AUUAA G AAGCC...CGU-3'@LB@ GUUGU GAGU UG GCUGUGCA@LB@ \|\|:\|\| \|\|:\| \|\| \|\|\|:\|\|\|\|@LB@ CAGCA CUUA AC CGAUACGU@LB@3'-UUU...AGCCG UG GUUA A CAUUA...ACG-5'@LB@ \| \|@LB@ 95 68@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -19.4914 kcal/mol@LB@Unfolding Energy - mRNA 6.89072 kcal/mol@LB@Unfolding Energy - sRNA 4.68367 kcal/mol@LB@@LB@Position - mRNA 7 -- 34@LB@Position - sRNA 69 -- 94@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 69 -- 75@LB@
142	0.005444	0.1351	b3950	frwB	-10.99	0.063119	13 -- 50	47 -- 86	putative enzyme IIB component of PTS	b3899	_____________12__________________________________________51\n_____________\|___________________________________________\|\n5'-GCA...GGGGU____U__________C__________________C___C____UUAUA...GGG-3'\n______________GGUC_GAUUGUGCUG__CGGUGGUU____GAAGG_AAG_UGGG\n______________::\|\|_:\|\|\|\|\|\|\|\|:__\|:\|\|::\|\|____:\|\|\|\|_\|\|\|_\|::\|\n______________UUAG_UUAACACGAU__GUCAUUAA____UUUCC_UUC_AUUC\n3'-UUU...CAUGC_______________AC________GUUU______________UGUUA...ACG-5'\n_____________\|___________________________________________\|\n_____________87__________________________________________46\n	30 -- 36	63 -- 69	-27.1662 kcal/mol	11.4404 kcal/mol	4.74035 kcal/mol	12 51@LB@ \| \|@LB@5'-GCA...GGGGU U C C C UUAUA...GGG-3'@LB@ GGUC GAUUGUGCUG CGGUGGUU GAAGG AAG UGGG@LB@ ::\|\| :\|\|\|\|\|\|\|\|: \|:\|\|::\|\| :\|\|\|\| \|\|\| \|::\|@LB@ UUAG UUAACACGAU GUCAUUAA UUUCC UUC AUUC@LB@3'-UUU...CAUGC AC GUUU UGUUA...ACG-5'@LB@ \| \|@LB@ 87 46@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -27.1662 kcal/mol@LB@Unfolding Energy - mRNA 11.4404 kcal/mol@LB@Unfolding Energy - sRNA 4.74035 kcal/mol@LB@@LB@Position - mRNA 13 -- 50@LB@Position - sRNA 47 -- 86@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 63 -- 69@LB@
134	0.004994	0.1313	b1518	lsrG	-14.53	0.006358	14 -- 66	30 -- 79	autoinducer-2 (AI-2) degrading protein LsrG		_____________13_______________________________________________________67\n_____________\|________________________________________________________\|\n5'-GAG...GGAAA____________GCUA____UC____CGCUUCU____UG_________________AUUUU...AAG-3'\n______________UGUGCUG_GCAG____UCGA__AGGG_______GGUG____GAUAUGGGGCGUAAU\n______________\|\|\|\|\|\|:_\|\|\|\|____\|\|:\|__\|:\|\|_______:\|\|:____:\|\|\|\|\|\|:\|\|\|:\|\|:\n______________ACACGAU_CGUC____AGUU__UUCC_______UCAU____UUAUACCUCGCGUUG\n3'-UUU...AGUUA_______A____AUUA____UU____U__________UCUG_______________CGGGU...ACG-5'\n_____________\|________________________________________________________\|\n_____________80_______________________________________________________29\n	58 -- 64	32 -- 38	-43.6874 kcal/mol	15.7058 kcal/mol	13.4555 kcal/mol	13 67@LB@ \| \|@LB@5'-GAG...GGAAA GCUA UC CGCUUCU UG AUUUU...AAG-3'@LB@ UGUGCUG GCAG UCGA AGGG GGUG GAUAUGGGGCGUAAU@LB@ \|\|\|\|\|\|: \|\|\|\| \|\|:\| \|:\|\| :\|\|: :\|\|\|\|\|\|:\|\|\|:\|\|:@LB@ ACACGAU CGUC AGUU UUCC UCAU UUAUACCUCGCGUUG@LB@3'-UUU...AGUUA A AUUA UU U UCUG CGGGU...ACG-5'@LB@ \| \|@LB@ 80 29@LB@@LB@@LB@Energy -14.53 kcal/mol@LB@Hybridization Energy -43.6874 kcal/mol@LB@Unfolding Energy - mRNA 15.7058 kcal/mol@LB@Unfolding Energy - sRNA 13.4555 kcal/mol@LB@@LB@Position - mRNA 14 -- 66@LB@Position - sRNA 30 -- 79@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 32 -- 38@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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