Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
187	0.02188	0.3768	b3065	rpsU	-8.54	0.042773	188 -- 200	37 -- 49	30S ribosomal subunit protein S21	_____________187___________201\n_____________\|_____________\|\n5'-GAC...AUCAA_____________AUGCC...GUC-3'\n______________AGGUGAGAGGCAC\n______________\|:\|::\|\|\|:\|\|\|\|\n______________UUCGUUCUUCGUG\n3'-UUU...ACGAA_____________AAUUU...CAA-5'\n_____________\|_____________\|\n_____________50____________36\n	194 -- 200	37 -- 43	-18.635 kcal/mol	4.05763 kcal/mol	6.03369 kcal/mol	187 201@LB@ \| \|@LB@5'-GAC...AUCAA AUGCC...GUC-3'@LB@ AGGUGAGAGGCAC@LB@ \|:\|::\|\|\|:\|\|\|\|@LB@ UUCGUUCUUCGUG@LB@3'-UUU...ACGAA AAUUU...CAA-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -18.635 kcal/mol@LB@Unfolding Energy - mRNA 4.05763 kcal/mol@LB@Unfolding Energy - sRNA 6.03369 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 37 -- 43@LB@
8	5.642e-05	0.02272	b2282	nuoH	-5.33	0.272754	189 -- 221	13 -- 44	NADH:ubiquinone oxidoreductase membrane subunit H	_____________188________________________________222\n_____________\|__________________________________\|\n5'-CUC...CUCAA________AACAAU_____G_A__U_________CUGAU...GCU-3'\n______________GGAGGCAC______GAGUU_G_UA_CACC_GGAA\n______________:\|\|:\|\|\|\|______:\|:\|\|_\|_\|\|_\|\|\|\|_\|\|\|\|\n______________UCUUCGUG______UUUAA_C_AU_GUGG_CCUU\n3'-UUU...UUCGU________AAUUU______G_A_______U____UAGAC...CAA-5'\n_____________\|__________________________________\|\n_____________45_________________________________12\n	190 -- 196	37 -- 43	-24.1154 kcal/mol	6.60325 kcal/mol	12.1776 kcal/mol	188 222@LB@ \| \|@LB@5'-CUC...CUCAA AACAAU G A U CUGAU...GCU-3'@LB@ GGAGGCAC GAGUU G UA CACC GGAA@LB@ :\|\|:\|\|\|\| :\|:\|\| \| \|\| \|\|\|\| \|\|\|\|@LB@ UCUUCGUG UUUAA C AU GUGG CCUU@LB@3'-UUU...UUCGU AAUUU G A U UAGAC...CAA-5'@LB@ \| \|@LB@ 45 12@LB@@LB@@LB@Energy -5.33 kcal/mol@LB@Hybridization Energy -24.1154 kcal/mol@LB@Unfolding Energy - mRNA 6.60325 kcal/mol@LB@Unfolding Energy - sRNA 12.1776 kcal/mol@LB@@LB@Position - mRNA 189 -- 221@LB@Position - sRNA 13 -- 44@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 37 -- 43@LB@
62	0.00332	0.1645	b1305	pspB	-5.29	0.278747	189 -- 201	34 -- 46	psp operon transcription co-activator	_____________188___________202\n_____________\|_____________\|\n5'-AUU...UCGUC_____________UGAGC...GUG-3'\n______________UAAGGAGUACUUA\n______________:\|\|\|:\|\|:\|\|\|\|\|\n______________GUUCUUCGUGAAU\n3'-UUU...AAUUC_____________UUUUU...CAA-5'\n_____________\|_____________\|\n_____________47____________33\n	195 -- 201	34 -- 40	-14.7021 kcal/mol	3.41245 kcal/mol	5.99897 kcal/mol	188 202@LB@ \| \|@LB@5'-AUU...UCGUC UGAGC...GUG-3'@LB@ UAAGGAGUACUUA@LB@ :\|\|\|:\|\|:\|\|\|\|\|@LB@ GUUCUUCGUGAAU@LB@3'-UUU...AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -5.29 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 3.41245 kcal/mol@LB@Unfolding Energy - sRNA 5.99897 kcal/mol@LB@@LB@Position - mRNA 189 -- 201@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@LB@
148	0.01496	0.3255	b2202	napC	-5.47	0.254772	189 -- 211	26 -- 46	quinol dehydrogenase electron source for NapAB	_____________188_____________________212\n_____________\|_______________________\|\n5'-ACG...GGAAA_______U____A__________UGACC...GUU-3'\n______________UAAGAGG_UAUU_UGGGAAAUUC\n______________:\|\|\|\|:\|_:\|:\|_\|:::\|\|\|\|\|\|\n______________GUUCUUC_GUGA_AUUUUUUAAG\n3'-UUU...AAUUC_______________________CAAUG...CAA-5'\n_____________\|_______________________\|\n_____________47______________________25\n	205 -- 211	26 -- 32	-14.2639 kcal/mol	2.66276 kcal/mol	6.13041 kcal/mol	188 212@LB@ \| \|@LB@5'-ACG...GGAAA U A UGACC...GUU-3'@LB@ UAAGAGG UAUU UGGGAAAUUC@LB@ :\|\|\|\|:\| :\|:\| \|:::\|\|\|\|\|\|@LB@ GUUCUUC GUGA AUUUUUUAAG@LB@3'-UUU...AAUUC CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -14.2639 kcal/mol@LB@Unfolding Energy - mRNA 2.66276 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 26 -- 32@LB@
151	0.0157	0.3349	b0586	entF	-8.26	0.051334	189 -- 199	37 -- 47	enterobactin synthase multienzyme complex component ATP-dependent	_____________188_________200\n_____________\|___________\|\n5'-CCC...CAGUU___________AAUGA...UUG-3'\n______________GCAGGAGGCAC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	193 -- 199	37 -- 43	-17.6877 kcal/mol	4.1913 kcal/mol	5.23944 kcal/mol	188 200@LB@ \| \|@LB@5'-CCC...CAGUU AAUGA...UUG-3'@LB@ GCAGGAGGCAC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -17.6877 kcal/mol@LB@Unfolding Energy - mRNA 4.1913 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
157	0.01701	0.3489	b3856	mobB	-4.94	0.329991	189 -- 197	52 -- 60	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________188_______198\n_____________\|_________\|\n5'-GUG...CCAGA_________CCGAU...CCA-3'\n______________GGAGCUUGC\n______________\|:\|:\|\|\|\|\|\n______________CUUUGAACG\n3'-UUU...CCCUA_________AAUUC...CAA-5'\n_____________\|_________\|\n_____________61________51\n	191 -- 197	52 -- 58	-10.6989 kcal/mol	2.59286 kcal/mol	3.16562 kcal/mol	188 198@LB@ \| \|@LB@5'-GUG...CCAGA CCGAU...CCA-3'@LB@ GGAGCUUGC@LB@ \|:\|:\|\|\|\|\|@LB@ CUUUGAACG@LB@3'-UUU...CCCUA AAUUC...CAA-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -4.94 kcal/mol@LB@Hybridization Energy -10.6989 kcal/mol@LB@Unfolding Energy - mRNA 2.59286 kcal/mol@LB@Unfolding Energy - sRNA 3.16562 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
70	0.003574	0.1645	b0145	dksA	-6.64	0.135564	191 -- 197	39 -- 45	transcriptional regulator of rRNA transcription; DnaK suppressor protein	_____________190_____198\n_____________\|_______\|\n5'-AAU...UUAAG_______AACAU...AUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	191 -- 197	39 -- 45	-7.63285 kcal/mol	0.475666 kcal/mol	0.514773 kcal/mol	190 198@LB@ \| \|@LB@5'-AAU...UUAAG AACAU...AUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -7.63285 kcal/mol@LB@Unfolding Energy - mRNA 0.475666 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 191 -- 197@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
153	0.016	0.3359	b2167	fruA	-4.10	0.476180	191 -- 199	37 -- 45	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________190_______200\n_____________\|_________\|\n5'-CGC...AGCAG_________AAUGA...AAA-3'\n______________GAGAGGCAU\n______________:\|\|\|:\|\|\|:\n______________UUCUUCGUG\n3'-UUU...AUUCG_________AAUUU...CAA-5'\n_____________\|_________\|\n_____________46________36\n	193 -- 199	37 -- 43	-10.9543 kcal/mol	1.97714 kcal/mol	4.8783 kcal/mol	190 200@LB@ \| \|@LB@5'-CGC...AGCAG AAUGA...AAA-3'@LB@ GAGAGGCAU@LB@ :\|\|\|:\|\|\|:@LB@ UUCUUCGUG@LB@3'-UUU...AUUCG AAUUU...CAA-5'@LB@ \| \|@LB@ 46 36@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -10.9543 kcal/mol@LB@Unfolding Energy - mRNA 1.97714 kcal/mol@LB@Unfolding Energy - sRNA 4.8783 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 37 -- 45@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
41	0.001644	0.1292	b1918	yecS	-7.37	0.088723	192 -- 214	37 -- 60	ABC family putative inner membrane permease	_____________191_______________________215\n_____________\|_________________________\|\n5'-GGC...CUCCG__________CAU_______A____ACAAC...GCU-3'\n______________GAAAC__GCU___GCAAGAA_GUAU\n______________\|\|\|\|\|__\|\|\|___\|\|\|\|\|\|\|_\|:\|:\n______________CUUUG__CGA___CGUUCUU_CGUG\n3'-UUU...CCCUA_____AA___AUU____________AAUUU...CAA-5'\n_____________\|_________________________\|\n_____________61________________________36\n	203 -- 209	41 -- 47	-18.5053 kcal/mol	4.89056 kcal/mol	6.24651 kcal/mol	191 215@LB@ \| \|@LB@5'-GGC...CUCCG CAU A ACAAC...GCU-3'@LB@ GAAAC GCU GCAAGAA GUAU@LB@ \|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|:\|:@LB@ CUUUG CGA CGUUCUU CGUG@LB@3'-UUU...CCCUA AA AUU AAUUU...CAA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -18.5053 kcal/mol@LB@Unfolding Energy - mRNA 4.89056 kcal/mol@LB@Unfolding Energy - sRNA 6.24651 kcal/mol@LB@@LB@Position - mRNA 192 -- 214@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 41 -- 47@LB@
128	0.01225	0.3033	b3299	rpmJ	-5.94	0.199813	193 -- 212	24 -- 42	50S ribosomal subunit protein L36	_____________192__________________213\n_____________\|____________________\|\n5'-GGA...ACGGA_____AAAAU__________GCUUC...AUA-3'\n______________GAGUA_____GAAAGUUCGU\n______________:\|\|:\|_____:\|\|\|:\|\|\|\|\|\n______________UUCGU_____UUUUUAAGCA\n3'-UUU...CGUUC_____GAAU___________AUGUG...CAA-5'\n_____________\|____________________\|\n_____________43___________________23\n	206 -- 212	24 -- 30	-12.4383 kcal/mol	4.85088 kcal/mol	1.64896 kcal/mol	192 213@LB@ \| \|@LB@5'-GGA...ACGGA AAAAU GCUUC...AUA-3'@LB@ GAGUA GAAAGUUCGU@LB@ :\|\|:\| :\|\|\|:\|\|\|\|\|@LB@ UUCGU UUUUUAAGCA@LB@3'-UUU...CGUUC GAAU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -12.4383 kcal/mol@LB@Unfolding Energy - mRNA 4.85088 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 24 -- 30@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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