Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
26	0.001009	0.1361	b3731	atpC	-14.21	0.042680	144 -- 160	2 -- 20	F1 sector of membrane-bound ATP synthase epsilon subunit	_____________143_________________161\n_____________\|___________________\|\n5'-UCC...GGUUC______________U____AAAAA...UGG-3'\n______________CAUCGAAGA__AGC_GUGG\n______________\|\|\|\|:\|\|\|\|__\|\|\|_\|\|\|\|\n______________GUAGUUUCU__UCG_CACC\n3'-UUU...CCCCU_________UU___U____G-5'\n_____________\|___________________\|\n_____________21__________________1\n	146 -- 152	12 -- 18	-19.7705 kcal/mol	4.1055 kcal/mol	1.45839 kcal/mol	143 161@LB@ \| \|@LB@5'-UCC...GGUUC U AAAAA...UGG-3'@LB@ CAUCGAAGA AGC GUGG@LB@ \|\|\|\|:\|\|\|\| \|\|\| \|\|\|\|@LB@ GUAGUUUCU UCG CACC@LB@3'-UUU...CCCCU UU U G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -19.7705 kcal/mol@LB@Unfolding Energy - mRNA 4.1055 kcal/mol@LB@Unfolding Energy - sRNA 1.45839 kcal/mol@LB@@LB@Position - mRNA 144 -- 160@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 12 -- 18@LB@
25	0.0009834	0.1361	b3733	atpG	-13.27	0.068654	183 -- 205	1 -- 22	F1 sector of membrane-bound ATP synthase gamma subunit	_____________182_____________________206\n_____________\|_______________________\|\n5'-GGC...CGCAA________________UCA____CGGCG...GUA-3'\n______________GGCAUUGAGGAGAAGC___UGGC\n______________\|:\|\|\|::\|:\|\|:\|\|\|\|___\|\|\|\|\n______________CUGUAGUUUCUUUUCG___ACCG\n3'-UUU...UACCC________________UC_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	192 -- 198	7 -- 13	-25.5897 kcal/mol	10.7799 kcal/mol	1.54023 kcal/mol	182 206@LB@ \| \|@LB@5'-GGC...CGCAA UCA CGGCG...GUA-3'@LB@ GGCAUUGAGGAGAAGC UGGC@LB@ \|:\|\|\|::\|:\|\|:\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUUUUCG ACCG@LB@3'-UUU...UACCC UC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -25.5897 kcal/mol@LB@Unfolding Energy - mRNA 10.7799 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
175	0.01275	0.2504	b3057	bacA	-10.43	0.234919	238 -- 261	5 -- 26	undecaprenyl pyrophosphate phosphatase	_____________237______________________262\n_____________\|________________________\|\n5'-UUC...AAUAU____U_UG_________UU_A___AAUUU...UUG-3'\n______________UGGG_G__GUCGAAGGA__G_CAG\n______________\|\|\|\|_\|__:\|\|:\|\|\|:\|__\|_\|\|\|\n______________ACCC_C__UAGUUUCUU__C_GUC\n3'-UUU...GUUUU______UG_________UU_____ACCG-5'\n_____________\|________________________\|\n_____________27_______________________4\n	248 -- 254	11 -- 17	-20.3624 kcal/mol	7.43347 kcal/mol	2.50108 kcal/mol	237 262@LB@ \| \|@LB@5'-UUC...AAUAU U UG UU A AAUUU...UUG-3'@LB@ UGGG G GUCGAAGGA G CAG@LB@ \|\|\|\| \| :\|\|:\|\|\|:\| \| \|\|\|@LB@ ACCC C UAGUUUCUU C GUC@LB@3'-UUU...GUUUU UG UU ACCG-5'@LB@ \| \|@LB@ 27 4@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -20.3624 kcal/mol@LB@Unfolding Energy - mRNA 7.43347 kcal/mol@LB@Unfolding Energy - sRNA 2.50108 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 5 -- 26@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 11 -- 17@LB@
162	0.012	0.2504	b2079	baeR	-15.58	0.019969	182 -- 201	6 -- 24	response regulator in two-component regulatory system with BaeS	_____________181__________________202\n_____________\|____________________\|\n5'-CAG...GGAAC_____UUA____________UGACC...CGA-3'\n______________GGGAU___CAGAGAGAAGUA\n______________\|\|\|\|:___\|\|:\|\|\|:\|\|\|:\|\n______________CCCUG___GUUUCUUUUCGU\n3'-UUU...UUUAC_____UA_____________CACCG-5'\n_____________\|____________________\|\n_____________25___________________5\n	195 -- 201	6 -- 12	-20.602 kcal/mol	4.32458 kcal/mol	0.702143 kcal/mol	181 202@LB@ \| \|@LB@5'-CAG...GGAAC UUA UGACC...CGA-3'@LB@ GGGAU CAGAGAGAAGUA@LB@ \|\|\|\|: \|\|:\|\|\|:\|\|\|:\|@LB@ CCCUG GUUUCUUUUCGU@LB@3'-UUU...UUUAC UA CACCG-5'@LB@ \| \|@LB@ 25 5@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -20.602 kcal/mol@LB@Unfolding Energy - mRNA 4.32458 kcal/mol@LB@Unfolding Energy - sRNA 0.702143 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 6 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
191	0.01405	0.2529	b3532	bcsB	-12.45	0.101006	205 -- 235	1 -- 16	regulator of cellulose synthase cyclic di-GMP binding	_____________204_____________________________236\n_____________\|_______________________________\|\n5'-AAG...GAUGA________CUAUUCUGGAUUUGU________UAUGG...UCA-3'\n______________AAAGAAAA_______________GCAGUGGC\n______________\|\|\|\|\|\|\|\|_______________\|\|\|\|\|\|\|\|\n______________UUUCUUUU_______________CGUCACCG\n3'-UUU...UGUAG_______________________________-5'\n_____________\|______________________________\|\n_____________17_____________________________1\n	229 -- 235	1 -- 7	-19.2133 kcal/mol	5.41496 kcal/mol	1.34555 kcal/mol	204 236@LB@ \| \|@LB@5'-AAG...GAUGA CUAUUCUGGAUUUGU UAUGG...UCA-3'@LB@ AAAGAAAA GCAGUGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUCUUUU CGUCACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.2133 kcal/mol@LB@Unfolding Energy - mRNA 5.41496 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 205 -- 235@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
122	0.008886	0.2491	b4366	bglJ	-14.76	0.031763	19 -- 32	15 -- 29	bgl operon transcriptional activator	_____________18______________33\n_____________\|_______________\|\n5'-CUG...GUAAA_______________CCAGA...GUA-3'\n______________GGAUGGGG_CAUCAA\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUUACCCC_GUAGUU\n3'-UUU...GGUGU________U______UCUUU...CCG-5'\n_____________\|_______________\|\n_____________30______________14\n	20 -- 26	22 -- 28	-19.2746 kcal/mol	3.84044 kcal/mol	0.677927 kcal/mol	18 33@LB@ \| \|@LB@5'-CUG...GUAAA CCAGA...GUA-3'@LB@ GGAUGGGG CAUCAA@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUACCCC GUAGUU@LB@3'-UUU...GGUGU U UCUUU...CCG-5'@LB@ \| \|@LB@ 30 14@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -19.2746 kcal/mol@LB@Unfolding Energy - mRNA 3.84044 kcal/mol@LB@Unfolding Energy - sRNA 0.677927 kcal/mol@LB@@LB@Position - mRNA 19 -- 32@LB@Position - sRNA 15 -- 29@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 22 -- 28@LB@
154	0.01125	0.2504	b3412	bioH	-12.84	0.084220	262 -- 288	1 -- 28	pimeloyl-ACP methyl ester carboxylesterase	_____________261__________________________289\n_____________\|____________________________\|\n5'-GGC...GCACG_________UGAAUGCC___________GUUGC...ACG-3'\n______________GAUGGGGAC________GAAGU_GUGGC\n______________:\|\|\|\|\|\|\|\|________:\|\|\|:_\|\|\|\|\|\n______________UUACCCCUG________UUUCG_CACCG\n3'-UUU...GUGUU_________UAGUUUCU_____U_____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	264 -- 270	20 -- 26	-27.647 kcal/mol	12.2839 kcal/mol	2.519 kcal/mol	261 289@LB@ \| \|@LB@5'-GGC...GCACG UGAAUGCC GUUGC...ACG-3'@LB@ GAUGGGGAC GAAGU GUGGC@LB@ :\|\|\|\|\|\|\|\| :\|\|\|: \|\|\|\|\|@LB@ UUACCCCUG UUUCG CACCG@LB@3'-UUU...GUGUU UAGUUUCU U -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -27.647 kcal/mol@LB@Unfolding Energy - mRNA 12.2839 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 262 -- 288@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 20 -- 26@LB@
59	0.003042	0.1789	b4132	cadB	-12.03	0.121895	256 -- 272	4 -- 32	putative lysine/cadaverine transporter	_____________255___________________________273\n_____________\|_____________________________\|\n5'-UCA...CGGUA___U_________________________AUUGC...CAA-3'\n______________AUA_GAUGGGGA____________GCGGU\n______________\|:\|_:\|\|\|\|\|\|\|____________\|\|:\|\|\n______________UGU_UUACCCCU____________CGUCA\n3'-UUU...CGAGG___U________GUAGUUUCUUUU_____CCG-5'\n_____________\|_____________________________\|\n_____________33____________________________3\n	261 -- 267	21 -- 27	-16.7324 kcal/mol	2.16267 kcal/mol	2.53583 kcal/mol	255 273@LB@ \| \|@LB@5'-UCA...CGGUA U AUUGC...CAA-3'@LB@ AUA GAUGGGGA GCGGU@LB@ \|:\| :\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGU UUACCCCU CGUCA@LB@3'-UUU...CGAGG U GUAGUUUCUUUU CCG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -16.7324 kcal/mol@LB@Unfolding Energy - mRNA 2.16267 kcal/mol@LB@Unfolding Energy - sRNA 2.53583 kcal/mol@LB@@LB@Position - mRNA 256 -- 272@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 21 -- 27@LB@
34	0.001647	0.1648	b1218	chaC	-13.74	0.054411	171 -- 189	1 -- 17	cation transport regulator	_____________170_________________190\n_____________\|___________________\|\n5'-AUA...UGUCG________UAU________GGAAG...CGC-3'\n______________CAGGGAAG___GCAGUGGC\n______________\|\|::\|\|\|:___\|\|\|\|\|\|\|\|\n______________GUUUCUUU___CGUCACCG\n3'-UUU...CUGUA________U__________-5'\n_____________\|__________________\|\n_____________18_________________1\n	183 -- 189	1 -- 7	-23.3292 kcal/mol	8.15416 kcal/mol	1.43853 kcal/mol	170 190@LB@ \| \|@LB@5'-AUA...UGUCG UAU GGAAG...CGC-3'@LB@ CAGGGAAG GCAGUGGC@LB@ \|\|::\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.74 kcal/mol@LB@Hybridization Energy -23.3292 kcal/mol@LB@Unfolding Energy - mRNA 8.15416 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 171 -- 189@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.004177	0.1979	b2155	cirA	-15.75	0.017995	130 -- 157	1 -- 33	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter	_____________129________________________________158\n_____________\|__________________________________\|\n5'-GGA...CCGUA_________________________U_____A__GAUAA...UGG-3'\n______________CGCAA___GGGGACGU_GAAGAAGA___GUG_GC\n______________\|:\|\|\|___\|\|\|\|\|\|:\|_:\|\|\|\|\|:\|___\|\|\|_\|\|\n______________GUGUU___CCCCUGUA_UUUCUUUU___CAC_CG\n3'-UUU...CCGAG_____UUA________G________CGU______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	144 -- 150	9 -- 15	-28.6012 kcal/mol	9.77062 kcal/mol	3.07861 kcal/mol	129 158@LB@ \| \|@LB@5'-GGA...CCGUA U A GAUAA...UGG-3'@LB@ CGCAA GGGGACGU GAAGAAGA GUG GC@LB@ \|:\|\|\| \|\|\|\|\|\|:\| :\|\|\|\|\|:\| \|\|\| \|\|@LB@ GUGUU CCCCUGUA UUUCUUUU CAC CG@LB@3'-UUU...CCGAG UUA G CGU -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -28.6012 kcal/mol@LB@Unfolding Energy - mRNA 9.77062 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 130 -- 157@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 9 -- 15@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)

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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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