Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
180	0.009034	0.1747	b3146	rsmI	-12.76	0.071583	191 -- 238	34 -- 76	16S rRNA C1402 2'-O-ribose methyltransferase SAM-dependent	_____________190____________________________________________________239\n_____________\|______________________________________________________\|\n5'-CAG...AAUAC____G____AAUGAAACA___C_______GC_GAUAAUU_______________GCUUU...AGG-3'\n______________GGAC_ACAC_________ACA_CAA_UCG__G_______CUCAGGG_____CCA\n______________:\|\|\|_\|\|\|\|_________\|\|\|_\|\|\|_\|\|\|__\|_______\|\|\|\|\|\|\|_____\|\|\|\n______________UCUG_UGUG_________UGU_GUU_AGC__C_______GAGUCCC_____GGU\n3'-UUU...CCGUU____A________________C___A___AA_AAAGU_________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________________________\|\n_____________77_____________________________________________________33\n	229 -- 235	42 -- 48	-25.3144 kcal/mol	7.73901 kcal/mol	4.816 kcal/mol	190 239@LB@ \| \|@LB@5'-CAG...AAUAC G AAUGAAACA C GC GAUAAUU GCUUU...AGG-3'@LB@ GGAC ACAC ACA CAA UCG G CUCAGGG CCA@LB@ :\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\| \| \|\|\|\|\|\|\| \|\|\|@LB@ UCUG UGUG UGU GUU AGC C GAGUCCC GGU@LB@3'-UUU...CCGUU A C A AA AAAGU CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -25.3144 kcal/mol@LB@Unfolding Energy - mRNA 7.73901 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 191 -- 238@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 42 -- 48@LB@
90	0.004009	0.1538	b3152	yraR	-13.99	0.037452	47 -- 72	45 -- 75	putative nucleoside-diphosphate-sugar epimerase	_____________46______________________________73\n_____________\|_______________________________\|\n5'-ACU...UCAGU_____AA___________UC___________UGCUU...CGA-3'\n______________GAUUA___ACGGCAAUUU______UUACUCA\n______________\|\|:\|\|___\|\|:\|\|\|\|\|\|:______\|:\|\|\|\|\|\n______________CUGAU___UGUCGUUAAG______AGUGAGU\n3'-UUU...CGUUU_____GUG__________CAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	66 -- 72	45 -- 51	-19.6514 kcal/mol	1.92306 kcal/mol	3.74078 kcal/mol	46 73@LB@ \| \|@LB@5'-ACU...UCAGU AA UC UGCUU...CGA-3'@LB@ GAUUA ACGGCAAUUU UUACUCA@LB@ \|\|:\|\| \|\|:\|\|\|\|\|\|: \|:\|\|\|\|\|@LB@ CUGAU UGUCGUUAAG AGUGAGU@LB@3'-UUU...CGUUU GUG CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -19.6514 kcal/mol@LB@Unfolding Energy - mRNA 1.92306 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 47 -- 72@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 45 -- 51@LB@
157	0.007641	0.1668	b3154	yhbP	-10.32	0.216043	188 -- 213	45 -- 78	UPF0306 family protein	_____________187________________________________214\n_____________\|__________________________________\|\n5'-AAA...GUAUA_____GA____________GGAAA__________UCGCC...UUU-3'\n______________AAAGA______ACAGCAAU_________CACUCA\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|_________\|\|\|\|\|\|\n______________UUUCU______UGUCGUUA_________GUGAGU\n3'-UUU...ACCCG_____GAUGUG________AGCAACAAA______CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________44\n	196 -- 202	60 -- 66	-17.2265 kcal/mol	3.1682 kcal/mol	3.741 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...GUAUA GA GGAAA UCGCC...UUU-3'@LB@ AAAGA ACAGCAAU CACUCA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUCU UGUCGUUA GUGAGU@LB@3'-UUU...ACCCG GAUGUG AGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.2265 kcal/mol@LB@Unfolding Energy - mRNA 3.1682 kcal/mol@LB@Unfolding Energy - sRNA 3.741 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 60 -- 66@LB@
96	0.004462	0.1538	b3260	dusB	-10.19	0.227205	72 -- 117	38 -- 74	tRNA-dihydrouridine synthase B	_____________71_____________________________________________118\n_____________\|______________________________________________\|\n5'-ACU...AUCGC__C____U__UUUUAAAU_______U___AUC__U_____A_____GGUCA...GAG-3'\n______________AC_ACGC_CA________GCAAUUC_UUG___CA_CUCAG_GGAUU\n______________\|\|_\|\|:\|_\|\|________\|\|\|\|\|\|\|_\|\|\|___\|\|_\|\|\|\|\|_\|\|\|\|\|\n______________UG_UGUG_GU________CGUUAAG_AAC___GU_GAGUC_CCUAA\n3'-UUU...GUUUC__A____U_________________C___AAA________C_____AGGUA...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________37\n	90 -- 96	58 -- 64	-26.7161 kcal/mol	11.7467 kcal/mol	4.77867 kcal/mol	71 118@LB@ \| \|@LB@5'-ACU...AUCGC C U UUUUAAAU U AUC U A GGUCA...GAG-3'@LB@ AC ACGC CA GCAAUUC UUG CA CUCAG GGAUU@LB@ \|\| \|\|:\| \|\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\| \|\|\|\|\|@LB@ UG UGUG GU CGUUAAG AAC GU GAGUC CCUAA@LB@3'-UUU...GUUUC A U C AAA C AGGUA...GCA-5'@LB@ \| \|@LB@ 75 37@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -26.7161 kcal/mol@LB@Unfolding Energy - mRNA 11.7467 kcal/mol@LB@Unfolding Energy - sRNA 4.77867 kcal/mol@LB@@LB@Position - mRNA 72 -- 117@LB@Position - sRNA 38 -- 74@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 58 -- 64@LB@
4	8.9e-06	0.006694	b3281	aroE	-13.87	0.039990	230 -- 259	45 -- 75	dehydroshikimate reductase NAD(P)-binding	_____________229_____________________________260\n_____________\|_______________________________\|\n5'-UUU...AAUCC___A__C________A___CCA_________UCAGC...AUG-3'\n______________GAU_GC_CACAGCAA_UCG____UUCAUUCA\n______________\|\|:_:\|_\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|\|:\|\|\|\n______________CUG_UG_GUGUCGUU_AGC____AAGUGAGU\n3'-UUU...CGUUU___A__U________A___AACA________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	253 -- 259	45 -- 51	-26.2723 kcal/mol	8.66309 kcal/mol	3.74078 kcal/mol	229 260@LB@ \| \|@LB@5'-UUU...AAUCC A C A CCA UCAGC...AUG-3'@LB@ GAU GC CACAGCAA UCG UUCAUUCA@LB@ \|\|: :\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ CUG UG GUGUCGUU AGC AAGUGAGU@LB@3'-UUU...CGUUU A U A AACA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -26.2723 kcal/mol@LB@Unfolding Energy - mRNA 8.66309 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
170	0.008354	0.1723	b3294	rplQ	-12.86	0.068031	178 -- 204	31 -- 54	50S ribosomal subunit protein L17	_____________177_________________________205\n_____________\|___________________________\|\n5'-UAU...UUAAG________G__AA____AAGG______GCCAU...UCA-3'\n______________GUUUUACU_AG__GGAU____UCAUGC\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|____:\|\|\|\|\|\n______________CAAAGUGA_UC__CCUA____GGUACG\n3'-UUU...AGCAA________G__C_____AA________AAUAU...GCA-5'\n_____________\|___________________________\|\n_____________55__________________________30\n	179 -- 185	47 -- 53	-21.6424 kcal/mol	4.376 kcal/mol	4.40484 kcal/mol	177 205@LB@ \| \|@LB@5'-UAU...UUAAG G AA AAGG GCCAU...UCA-3'@LB@ GUUUUACU AG GGAU UCAUGC@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\| :\|\|\|\|\|@LB@ CAAAGUGA UC CCUA GGUACG@LB@3'-UUU...AGCAA G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 55 30@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -21.6424 kcal/mol@LB@Unfolding Energy - mRNA 4.376 kcal/mol@LB@Unfolding Energy - sRNA 4.40484 kcal/mol@LB@@LB@Position - mRNA 178 -- 204@LB@Position - sRNA 31 -- 54@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 47 -- 53@LB@
145	0.006641	0.1605	b3316	rpsS	-10.41	0.208024	125 -- 141	61 -- 77	30S ribosomal subunit protein S19	_____________124_______________142\n_____________\|_________________\|\n5'-GCG...AAGGU____AG__C________CAAGC...CUU-3'\n______________AAGA__AC_CGCAGCAA\n______________\|\|\|\|__\|\|_\|:\|\|\|\|\|\|\n______________UUCU__UG_GUGUCGUU\n3'-UUU...CCCGU____GA__U________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________78________________60\n	135 -- 141	61 -- 67	-16.0034 kcal/mol	2.33428 kcal/mol	3.25748 kcal/mol	124 142@LB@ \| \|@LB@5'-GCG...AAGGU AG C CAAGC...CUU-3'@LB@ AAGA AC CGCAGCAA@LB@ \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ UUCU UG GUGUCGUU@LB@3'-UUU...CCCGU GA U AAGCA...GCA-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -16.0034 kcal/mol@LB@Unfolding Energy - mRNA 2.33428 kcal/mol@LB@Unfolding Energy - sRNA 3.25748 kcal/mol@LB@@LB@Position - mRNA 125 -- 141@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 61 -- 67@LB@
11	9.086e-05	0.0245	b3337	bfd	-12.11	0.098410	247 -- 280	34 -- 76	bacterioferritin-associated ferredoxin	_____________246_________________________________________281\n_____________\|___________________________________________\|\n5'-GCG...UCGUC___________________UCCCC___________________GCAAU...UUC-3'\n______________AGGCUGUGCGC__CAGUUU______UCACUCG______UUCCA\n______________\|\|:\|\|:::\|:\|__\|\|:\|\|:______\|\|\|\|\|\|:______\|\|\|\|\|\n______________UCUGAUGUGUG__GUUAAG______AGUGAGU______AAGGU\n3'-UUU...CCGUU___________UC______CAACAA_______CCCCUA_____ACGAA...GCA-5'\n_____________\|___________________________________________\|\n_____________77__________________________________________33\n	269 -- 275	45 -- 51	-24.9474 kcal/mol	8.02269 kcal/mol	4.816 kcal/mol	246 281@LB@ \| \|@LB@5'-GCG...UCGUC UCCCC GCAAU...UUC-3'@LB@ AGGCUGUGCGC CAGUUU UCACUCG UUCCA@LB@ \|\|:\|\|:::\|:\| \|\|:\|\|: \|\|\|\|\|\|: \|\|\|\|\|@LB@ UCUGAUGUGUG GUUAAG AGUGAGU AAGGU@LB@3'-UUU...CCGUU UC CAACAA CCCCUA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -24.9474 kcal/mol@LB@Unfolding Energy - mRNA 8.02269 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 247 -- 280@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 45 -- 51@LB@
105	0.004683	0.1538	b3349	slyD	-10.61	0.192215	166 -- 197	39 -- 73	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________165_________________________________198\n_____________\|___________________________________\|\n5'-UGU...ACAAU___________U____UUCCCAU________A___AUCAU...ACU-3'\n______________CUGCGC_CA_C_AUUC________GCUCAGG_GAU\n______________\|\|:\|:\|_\|\|_\|_\|\|\|\|________:\|\|\|\|\|\|_\|\|\|\n______________GAUGUG_GU_G_UAAG________UGAGUCC_CUA\n3'-UUU...UUUCU______U__C_U____CAACAAAG_______C___AAGGU...GCA-5'\n_____________\|___________________________________\|\n_____________74__________________________________38\n	187 -- 193	43 -- 49	-23.2642 kcal/mol	7.88699 kcal/mol	4.77295 kcal/mol	165 198@LB@ \| \|@LB@5'-UGU...ACAAU U UUCCCAU A AUCAU...ACU-3'@LB@ CUGCGC CA C AUUC GCUCAGG GAU@LB@ \|\|:\|:\| \|\| \| \|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ GAUGUG GU G UAAG UGAGUCC CUA@LB@3'-UUU...UUUCU U C U CAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 74 38@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -23.2642 kcal/mol@LB@Unfolding Energy - mRNA 7.88699 kcal/mol@LB@Unfolding Energy - sRNA 4.77295 kcal/mol@LB@@LB@Position - mRNA 166 -- 197@LB@Position - sRNA 39 -- 73@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
165	0.007934	0.1692	b3355	prkB	-7.13	0.603515	287 -- 294	63 -- 70	putative phosphoribulokinase	_____________286______295\n_____________\|________\|\n5'-GGC...AUAUU________UAAAUC-3'\n______________CGCGCAGU\n______________\|:\|:\|\|\|:\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	288 -- 294	63 -- 69	-11.0055 kcal/mol	0.741841 kcal/mol	3.13161 kcal/mol	286 295@LB@ \| \|@LB@5'-GGC...AUAUU UAAAUC-3'@LB@ CGCGCAGU@LB@ \|:\|:\|\|\|:@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.13 kcal/mol@LB@Hybridization Energy -11.0055 kcal/mol@LB@Unfolding Energy - mRNA 0.741841 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 287 -- 294@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 63 -- 69@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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