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
176	0.03596	0.6177	b1747	astA	-4.82	0.399998	129 -- 139	46 -- 56	arginine succinyltransferase	_____________128_________140\n_____________\|___________\|\n5'-GGC...GUCAG__AA_______UGACG...AAG-3'\n______________CG__GAAGAGG\n______________\|\|__:\|\|\|\|\|\|\n______________GC__UUUCUCC\n3'-UUU...ACCGG__AG_______UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	133 -- 139	46 -- 52	-9.86744 kcal/mol	4.11365 kcal/mol	0.93204 kcal/mol	128 140@LB@ \| \|@LB@5'-GGC...GUCAG AA UGACG...AAG-3'@LB@ CG GAAGAGG@LB@ \|\| :\|\|\|\|\|\|@LB@ GC UUUCUCC@LB@3'-UUU...ACCGG AG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -4.82 kcal/mol@LB@Hybridization Energy -9.86744 kcal/mol@LB@Unfolding Energy - mRNA 4.11365 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 129 -- 139@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 46 -- 52@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@
47	0.009275	0.6129	b3412	bioH	-9.55	0.050822	229 -- 245	38 -- 55	pimeloyl-ACP methyl ester carboxylesterase	_____________228_________________246\n_____________\|___________________\|\n5'-GGC...CAAAG_____________G_____CUUGU...ACG-3'\n______________GUC__AGGGGAAU_UUCAU\n______________\|\|\|__\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________CAG__UCUCCUUA_AAGUA\n3'-UUU...CCGGG___UU______________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	233 -- 239	43 -- 49	-15.7204 kcal/mol	5.00086 kcal/mol	1.17036 kcal/mol	228 246@LB@ \| \|@LB@5'-GGC...CAAAG G CUUGU...ACG-3'@LB@ GUC AGGGGAAU UUCAU@LB@ \|\|\| \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ CAG UCUCCUUA AAGUA@LB@3'-UUU...CCGGG UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -15.7204 kcal/mol@LB@Unfolding Energy - mRNA 5.00086 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 229 -- 245@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 43 -- 49@LB@
79	0.01695	0.6177	b0435	bolA	-9.02	0.064980	184 -- 202	38 -- 55	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________183_________________203\n_____________\|___________________\|\n5'-UGA...GCGUU___G______AU_______GAUGA...CCG-3'\n______________GUC_GAGGAG__AUUUCAU\n______________\|\|\|_:\|:\|\|\|__\|\|\|\|\|\|\|\n______________CAG_UUUCUC__UAAAGUA\n3'-UUU...CCGGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	196 -- 202	38 -- 44	-15.2358 kcal/mol	5.04311 kcal/mol	1.17036 kcal/mol	183 203@LB@ \| \|@LB@5'-UGA...GCGUU G AU GAUGA...CCG-3'@LB@ GUC GAGGAG AUUUCAU@LB@ \|\|\| :\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAG UUUCUC UAAAGUA@LB@3'-UUU...CCGGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.2358 kcal/mol@LB@Unfolding Energy - mRNA 5.04311 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
56	0.01199	0.6177	b0836	bssR	-10.68	0.029916	18 -- 32	42 -- 55	repressor of biofilm formation by indole transport regulation	_____________17______________33\n_____________\|_______________\|\n5'-AUU...GAAAG_______C_______CUACA...ACA-3'\n______________GUCAGGG_AGGGAUU\n______________\|\|\|\|::\|_\|\|\|:\|\|\|\n______________CAGUUUC_UCCUUAA\n3'-UUU...CCGGG_______________AGUAA...ACA-5'\n_____________\|_______________\|\n_____________56______________41\n	26 -- 32	42 -- 48	-16.3055 kcal/mol	4.68166 kcal/mol	0.947316 kcal/mol	17 33@LB@ \| \|@LB@5'-AUU...GAAAG C CUACA...ACA-3'@LB@ GUCAGGG AGGGAUU@LB@ \|\|\|\|::\| \|\|\|:\|\|\|@LB@ CAGUUUC UCCUUAA@LB@3'-UUU...CCGGG AGUAA...ACA-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -16.3055 kcal/mol@LB@Unfolding Energy - mRNA 4.68166 kcal/mol@LB@Unfolding Energy - sRNA 0.947316 kcal/mol@LB@@LB@Position - mRNA 18 -- 32@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 42 -- 48@LB@
51	0.009714	0.6129	b1736	chbA	-9.09	0.063099	186 -- 194	44 -- 52	N N'-diacetylchitobiose-specific enzyme IIA component of PTS	_____________185_______195\n_____________\|_________\|\n5'-GGU...AGAAA_________CGAUG...GCC-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	188 -- 194	44 -- 50	-11.469 kcal/mol	1.52278 kcal/mol	0.860683 kcal/mol	185 195@LB@ \| \|@LB@5'-GGU...AGAAA CGAUG...GCC-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -11.469 kcal/mol@LB@Unfolding Energy - mRNA 1.52278 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
107	0.02168	0.6177	b1738	chbB	-9.32	0.056668	26 -- 34	47 -- 55	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________25________35\n_____________\|_________\|\n5'-AAU...CACAG_________AAACA...CGG-3'\n______________GUCAAGGAG\n______________\|\|\|\|\|:\|\|\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	28 -- 34	47 -- 53	-13.6925 kcal/mol	3.47679 kcal/mol	0.899516 kcal/mol	25 35@LB@ \| \|@LB@5'-AAU...CACAG AAACA...CGG-3'@LB@ GUCAAGGAG@LB@ \|\|\|\|\|:\|\|\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -13.6925 kcal/mol@LB@Unfolding Energy - mRNA 3.47679 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 26 -- 34@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 47 -- 53@LB@
2	6.241e-06	0.01004	b1737	chbC	-18.35	0.000789	134 -- 152	38 -- 56	N N'-diacetylchitobiose-specific enzyme IIC component of PTS	_____________133_________________153\n_____________\|___________________\|\n5'-GUU...UUUCC__________UU_______AAAUC...UUC-3'\n______________CGUCAAAGAG__AUUUCAU\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________GCAGUUUCUC__UAAAGUA\n3'-UUU...ACCGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	146 -- 152	38 -- 44	-21.3647 kcal/mol	1.83077 kcal/mol	1.17918 kcal/mol	133 153@LB@ \| \|@LB@5'-GUU...UUUCC UU AAAUC...UUC-3'@LB@ CGUCAAAGAG AUUUCAU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCAGUUUCUC UAAAGUA@LB@3'-UUU...ACCGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -21.3647 kcal/mol@LB@Unfolding Energy - mRNA 1.83077 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 134 -- 152@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 38 -- 44@LB@
3	9.453e-06	0.01014	b0681	chiP	-16.40	0.001982	182 -- 193	45 -- 56	chitoporin uptake of chitosugars	_____________181__________194\n_____________\|____________\|\n5'-CUU...UUAUA____________UUAAC...AAG-3'\n______________CGUCAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCCU\n3'-UUU...ACCGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	187 -- 193	45 -- 51	-19.4659 kcal/mol	2.1233 kcal/mol	0.938337 kcal/mol	181 194@LB@ \| \|@LB@5'-CUU...UUAUA UUAAC...AAG-3'@LB@ CGUCAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCCU@LB@3'-UUU...ACCGG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -19.4659 kcal/mol@LB@Unfolding Energy - mRNA 2.1233 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
144	0.02798	0.6177	b0682	chiQ	-9.70	0.047426	184 -- 197	41 -- 56	chitosugar-induced verified lipoprotein	_____________183______________198\n_____________\|________________\|\n5'-CGG...CCGCA____U___________GCUAU...ACA-3'\n______________CGUU___GAGGAAUUU\n______________\|\|\|:___\|\|\|\|\|\|\|\|\|\n______________GCAG___CUCCUUAAA\n3'-UUU...ACCGG____UUU_________GUAAA...ACA-5'\n_____________\|________________\|\n_____________57_______________40\n	191 -- 197	41 -- 47	-13.1137 kcal/mol	2.46147 kcal/mol	0.955312 kcal/mol	183 198@LB@ \| \|@LB@5'-CGG...CCGCA U GCUAU...ACA-3'@LB@ CGUU GAGGAAUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GCAG CUCCUUAAA@LB@3'-UUU...ACCGG UUU GUAAA...ACA-5'@LB@ \| \|@LB@ 57 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.1137 kcal/mol@LB@Unfolding Energy - mRNA 2.46147 kcal/mol@LB@Unfolding Energy - sRNA 0.955312 kcal/mol@LB@@LB@Position - mRNA 184 -- 197@LB@Position - sRNA 41 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@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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