Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
109	0.02227	0.6177	b4040	ubiA	-8.97	0.066674	182 -- 194	44 -- 55	p-hydroxybenzoate octaprenyltransferase	_____________181___________195\n_____________\|_____________\|\n5'-AGC...CCGUU__A_U________AAAAA...UAU-3'\n______________GU_C_AAGAGGAA\n______________\|\|_\|_\|\|\|\|\|\|\|\|\n______________CA_G_UUCUCCUU\n3'-UUU...CCGGG____U________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	188 -- 194	44 -- 50	-10.7786 kcal/mol	0.870226 kcal/mol	0.941432 kcal/mol	181 195@LB@ \| \|@LB@5'-AGC...CCGUU A U AAAAA...UAU-3'@LB@ GU C AAGAGGAA@LB@ \|\| \| \|\|\|\|\|\|\|\|@LB@ CA G UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -10.7786 kcal/mol@LB@Unfolding Energy - mRNA 0.870226 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein	_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@LB@
199	0.0417	0.6177	b4070	nrfA	-7.95	0.106497	2 -- 16	44 -- 55	nitrite reductase formate-dependent cytochrome	_____________1_______________17\n_____________\|_______________\|\n__________5'-U___GAA_________GAUAC...CAA-3'\n______________GUU___AAAGAGGAA\n______________\|\|:___\|\|\|\|\|\|\|\|\|\n______________CAG___UUUCUCCUU\n3'-UUU...CCGGG_______________AAAGU...ACA-5'\n_____________\|_______________\|\n_____________56______________43\n	10 -- 16	44 -- 50	-11.2989 kcal/mol	2.40804 kcal/mol	0.941432 kcal/mol	1 17@LB@ \| \|@LB@ 5'-U GAA GAUAC...CAA-3'@LB@ GUU AAAGAGGAA@LB@ \|\|: \|\|\|\|\|\|\|\|\|@LB@ CAG UUUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -11.2989 kcal/mol@LB@Unfolding Energy - mRNA 2.40804 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 2 -- 16@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 44 -- 50@LB@
114	0.02277	0.6177	b4077	gltP	-4.92	0.386213	48 -- 56	47 -- 55	glutamate/aspartate:proton symporter	_____________47________57\n_____________\|_________\|\n5'-GCC...CUGUU_________UUGCG...GCG-3'\n______________GUUAAAGGG\n______________\|\|:\|\|\|\|:\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	50 -- 56	47 -- 53	-9.45392 kcal/mol	3.63887 kcal/mol	0.899516 kcal/mol	47 57@LB@ \| \|@LB@5'-GCC...CUGUU UUGCG...GCG-3'@LB@ GUUAAAGGG@LB@ \|\|:\|\|\|\|:\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -9.45392 kcal/mol@LB@Unfolding Energy - mRNA 3.63887 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 48 -- 56@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 47 -- 53@LB@
157	0.03134	0.6177	b4086	alsC	-8.98	0.066369	183 -- 191	45 -- 53	D-allose ABC transporter permease	_____________182_______192\n_____________\|_________\|\n5'-CGC...AUGAG_________GAUUA...CGA-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	185 -- 191	45 -- 51	-13.528 kcal/mol	3.63363 kcal/mol	0.917553 kcal/mol	182 192@LB@ \| \|@LB@5'-CGC...AUGAG GAUUA...CGA-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.528 kcal/mol@LB@Unfolding Energy - mRNA 3.63363 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 45 -- 51@LB@
60	0.01286	0.6177	b4113	basR	-8.68	0.076010	6 -- 31	48 -- 75	response regulator in two-component regulatory system with BasS	_____________5____________________________32\n_____________\|____________________________\|\n______5'-CAGGU_______C____________________AUUAU...CGC-3'\n______________GCCGAUG_UGCUG_UGG_CUGUCGGAGG\n______________\|\|\|:\|\|:_:\|\|\|:_\|\|\|_\|:\|\|\|::\|\|:\n______________CGGUUAU_GCGAU_ACC_GGCAGUUUCU\n3'-UUU...UUUAC_______A_____A___G__________CCUUA...ACA-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	25 -- 31	48 -- 54	-31.4034 kcal/mol	11.3837 kcal/mol	11.3355 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAGGU C AUUAU...CGC-3'@LB@ GCCGAUG UGCUG UGG CUGUCGGAGG@LB@ \|\|\|:\|\|: :\|\|\|: \|\|\| \|:\|\|\|::\|\|:@LB@ CGGUUAU GCGAU ACC GGCAGUUUCU@LB@3'-UUU...UUUAC A A G CCUUA...ACA-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -8.68 kcal/mol@LB@Hybridization Energy -31.4034 kcal/mol@LB@Unfolding Energy - mRNA 11.3837 kcal/mol@LB@Unfolding Energy - sRNA 11.3355 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 48 -- 54@LB@
37	0.007616	0.6129	b4141	yjeH	-11.12	0.024259	30 -- 40	44 -- 54	putative transporter	_____________29__________41\n_____________\|___________\|\n5'-CAG...CCCCU___________AAAGA...CUG-3'\n______________UCAAGGGGGAA\n______________\|\|\|\|:\|:\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	34 -- 40	44 -- 50	-14.4219 kcal/mol	2.36204 kcal/mol	0.939671 kcal/mol	29 41@LB@ \| \|@LB@5'-CAG...CCCCU AAAGA...CUG-3'@LB@ UCAAGGGGGAA@LB@ \|\|\|\|:\|:\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.4219 kcal/mol@LB@Unfolding Energy - mRNA 2.36204 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 30 -- 40@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 44 -- 50@LB@
61	0.01292	0.6177	b4154	frdA	-9.46	0.053105	187 -- 202	38 -- 54	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit	_____________186_______________203\n_____________\|_________________\|\n5'-UAA...AACAA__U_________G____GCAAA...UCG-3'\n______________UC__GGAGGAAU_UCGU\n______________\|\|__:\|\|\|\|\|\|\|_\|\|:\|\n______________AG__UCUCCUUA_AGUA\n3'-UUU...CGGGC__UU________A____AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	191 -- 197	43 -- 49	-14.1575 kcal/mol	3.5319 kcal/mol	1.17036 kcal/mol	186 203@LB@ \| \|@LB@5'-UAA...AACAA U G GCAAA...UCG-3'@LB@ UC GGAGGAAU UCGU@LB@ \|\| :\|\|\|\|\|\|\| \|\|:\|@LB@ AG UCUCCUUA AGUA@LB@3'-UUU...CGGGC UU A AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -14.1575 kcal/mol@LB@Unfolding Energy - mRNA 3.5319 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 187 -- 202@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
20	0.00399	0.5992	b4175	hflC	-10.54	0.031960	184 -- 196	43 -- 56	HflB protease modulator specific for phage lambda cII repressor	_____________183____________197\n_____________\|______________\|\n5'-UUA...ACCAG______________AACGA...GUU-3'\n______________CGUCAGGG_GGAAU\n______________\|\|\|\|\|::\|_\|\|\|\|\|\n______________GCAGUUUC_CCUUA\n3'-UUU...ACCGG________U_____AAGUA...ACA-5'\n_____________\|______________\|\n_____________57_____________42\n	185 -- 191	49 -- 55	-15.8123 kcal/mol	4.32193 kcal/mol	0.953958 kcal/mol	183 197@LB@ \| \|@LB@5'-UUA...ACCAG AACGA...GUU-3'@LB@ CGUCAGGG GGAAU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ GCAGUUUC CCUUA@LB@3'-UUU...ACCGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.8123 kcal/mol@LB@Unfolding Energy - mRNA 4.32193 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 49 -- 55@LB@
34	0.007003	0.6129	b4199	yjfY	-12.43	0.013073	184 -- 195	46 -- 57	YhcN family protein periplasmic	_____________183__________196\n_____________\|____________\|\n5'-AGG...GUCAG____________UAUCU...ACG-3'\n______________CCGUCGAGGAGG\n______________\|\|\|\|\|:\|:\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	189 -- 195	46 -- 52	-19.9606 kcal/mol	4.79886 kcal/mol	2.7365 kcal/mol	183 196@LB@ \| \|@LB@5'-AGG...GUCAG UAUCU...ACG-3'@LB@ CCGUCGAGGAGG@LB@ \|\|\|\|\|:\|:\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -19.9606 kcal/mol@LB@Unfolding Energy - mRNA 4.79886 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@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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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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