Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
151	0.01843	0.4072	b4028	yjbG	-13.08	0.058794	282 -- 297	40 -- 55	extracellular polysaccharide export OMA protein	_____________281______________298\n_____________\|________________\|\n5'-AAA...UGUUC_______GC_______AGG-3'\n______________AGCAAUG__AGCAGUG\n______________\|\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________UCGUUAC__UCGUUAC\n3'-UUU...GACCU_______AC_______AGCAC...GCG-5'\n_____________\|________________\|\n_____________56_______________39\n	291 -- 297	40 -- 46	-18.8155 kcal/mol	2.52344 kcal/mol	3.20849 kcal/mol	281 298@LB@ \| \|@LB@5'-AAA...UGUUC GC AGG-3'@LB@ AGCAAUG AGCAGUG@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\|@LB@ UCGUUAC UCGUUAC@LB@3'-UUU...GACCU AC AGCAC...GCG-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -18.8155 kcal/mol@LB@Unfolding Energy - mRNA 2.52344 kcal/mol@LB@Unfolding Energy - sRNA 3.20849 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 40 -- 46@LB@
154	0.01903	0.4072	b2823	ppdC	-17.47	0.010387	242 -- 260	40 -- 58	putative prepilin peptidase-dependent protein	_____________241_________________261\n_____________\|___________________\|\n5'-ACG...CUGCC___________U_______GUGUU...UCC-3'\n______________GGAGGUAAUGU_GGCGAUG\n______________\|\|\|:\|:\|\|\|\|\|_:\|\|:\|\|\|\n______________CCUUCGUUACA_UCGUUAC\n3'-UUU...UAUGA___________C_______AGCAC...GCG-5'\n_____________\|___________________\|\n_____________59__________________39\n	254 -- 260	40 -- 46	-26.2879 kcal/mol	5.60197 kcal/mol	3.21578 kcal/mol	241 261@LB@ \| \|@LB@5'-ACG...CUGCC U GUGUU...UCC-3'@LB@ GGAGGUAAUGU GGCGAUG@LB@ \|\|\|:\|:\|\|\|\|\| :\|\|:\|\|\|@LB@ CCUUCGUUACA UCGUUAC@LB@3'-UUU...UAUGA C AGCAC...GCG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -17.47 kcal/mol@LB@Hybridization Energy -26.2879 kcal/mol@LB@Unfolding Energy - mRNA 5.60197 kcal/mol@LB@Unfolding Energy - sRNA 3.21578 kcal/mol@LB@@LB@Position - mRNA 242 -- 260@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
186	0.02299	0.4113	b3996	nudC	-11.58	0.104830	175 -- 203	40 -- 67	NADH pyrophosphatase	_____________174____________________________204\n_____________\|______________________________\|\n5'-GAU...AUGCC________AA_________CAA____U___GAUCG...CGG-3'\n______________AGUGAUGC___AGGUAGUG___GAGC_AUG\n______________\|\|\|:\|\|:\|___\|:\|:\|:\|\|___\|\|\|\|_\|\|\|\n______________UCAUUAUG___UUCGUUAC___CUCG_UAC\n3'-UUU...CCGAU________ACC________A______U___AGCAC...GCG-5'\n_____________\|______________________________\|\n_____________68_____________________________39\n	186 -- 192	49 -- 55	-21.6638 kcal/mol	6.77954 kcal/mol	3.30504 kcal/mol	174 204@LB@ \| \|@LB@5'-GAU...AUGCC AA CAA U GAUCG...CGG-3'@LB@ AGUGAUGC AGGUAGUG GAGC AUG@LB@ \|\|\|:\|\|:\| \|:\|:\|:\|\| \|\|\|\| \|\|\|@LB@ UCAUUAUG UUCGUUAC CUCG UAC@LB@3'-UUU...CCGAU ACC A U AGCAC...GCG-5'@LB@ \| \|@LB@ 68 39@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -21.6638 kcal/mol@LB@Unfolding Energy - mRNA 6.77954 kcal/mol@LB@Unfolding Energy - sRNA 3.30504 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 67@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 49 -- 55@LB@
188	0.02302	0.4113	b3105	yhaJ	-12.66	0.069284	224 -- 245	40 -- 61	LysR family putative transcriptional regulator	_____________223____________________246\n_____________\|______________________\|\n5'-CGG...UUAAC__________CUAC____U___GAUGC...GCG-3'\n______________GCUGGAAGCA____GGGU_AUG\n______________:\|\|\|\|\|\|\|\|\|____\|:\|:_\|\|\|\n______________UGACCUUCGU____CUCG_UAC\n3'-UUU...CAUUA__________UACA____U___AGCAC...GCG-5'\n_____________\|______________________\|\n_____________62_____________________39\n	227 -- 233	52 -- 58	-21.8067 kcal/mol	5.84576 kcal/mol	3.30075 kcal/mol	223 246@LB@ \| \|@LB@5'-CGG...UUAAC CUAC U GAUGC...GCG-3'@LB@ GCUGGAAGCA GGGU AUG@LB@ :\|\|\|\|\|\|\|\|\| \|:\|: \|\|\|@LB@ UGACCUUCGU CUCG UAC@LB@3'-UUU...CAUUA UACA U AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -12.66 kcal/mol@LB@Hybridization Energy -21.8067 kcal/mol@LB@Unfolding Energy - mRNA 5.84576 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 224 -- 245@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 52 -- 58@LB@
60	0.005592	0.2905	b3577	yiaM	-14.71	0.031138	209 -- 232	41 -- 64	2 3-diketo-L-gulonate TRAP transporter small permease protein	_____________208______________________233\n_____________\|________________________\|\n5'-UUC...AAAAA______C________ACU______UAAUC...GCA-3'\n______________AAUACU_GAAGCAAU___GGCGAU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|___:\|\|:\|\|\n______________UUAUGA_CUUCGUUA___UCGUUA\n3'-UUU...AUUCA______C________CAC______CAGCA...GCG-5'\n_____________\|________________________\|\n_____________65_______________________40\n	217 -- 223	50 -- 56	-21.6131 kcal/mol	3.60615 kcal/mol	3.30185 kcal/mol	208 233@LB@ \| \|@LB@5'-UUC...AAAAA C ACU UAAUC...GCA-3'@LB@ AAUACU GAAGCAAU GGCGAU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\| :\|\|:\|\|@LB@ UUAUGA CUUCGUUA UCGUUA@LB@3'-UUU...AUUCA C CAC CAGCA...GCG-5'@LB@ \| \|@LB@ 65 40@LB@@LB@@LB@Energy -14.71 kcal/mol@LB@Hybridization Energy -21.6131 kcal/mol@LB@Unfolding Energy - mRNA 3.60615 kcal/mol@LB@Unfolding Energy - sRNA 3.30185 kcal/mol@LB@@LB@Position - mRNA 209 -- 232@LB@Position - sRNA 41 -- 64@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 50 -- 56@LB@
106	0.01088	0.3447	b3543	dppB	-11.69	0.100651	144 -- 153	41 -- 50	dipeptide/heme ABC transporter permease	_____________143________154\n_____________\|__________\|\n5'-CGG...UGAUU__________ACAGA...AUC-3'\n______________UGUGAGCAAU\n______________\|\|\|\|\|\|\|\|\|\|\n______________ACACUCGUUA\n3'-UUU...UCGUU__________CAGCA...GCG-5'\n_____________\|__________\|\n_____________51_________40\n	147 -- 153	41 -- 47	-14.8509 kcal/mol	2.00067 kcal/mol	1.16388 kcal/mol	143 154@LB@ \| \|@LB@5'-CGG...UGAUU ACAGA...AUC-3'@LB@ UGUGAGCAAU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ ACACUCGUUA@LB@3'-UUU...UCGUU CAGCA...GCG-5'@LB@ \| \|@LB@ 51 40@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -14.8509 kcal/mol@LB@Unfolding Energy - mRNA 2.00067 kcal/mol@LB@Unfolding Energy - sRNA 1.16388 kcal/mol@LB@@LB@Position - mRNA 144 -- 153@LB@Position - sRNA 41 -- 50@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 41 -- 47@LB@
120	0.0128	0.3585	b0445	ybaE	-11.02	0.129416	154 -- 176	41 -- 63	putative ABC transporter periplasmic binding protein	_____________153______________________177\n_____________\|________________________\|\n5'-CGU...GAUAU______________A____A____UAAAU...GUU-3'\n______________AUAC_GGAAGUAAU_GUGA_UAGU\n______________\|\|\|\|_\|\|\|\|\|:\|\|\|_\|\|\|\|_:\|:\|\n______________UAUG_CCUUCGUUA_CACU_GUUA\n3'-UUU...UUCAU____A______________C____CAGCA...GCG-5'\n_____________\|________________________\|\n_____________64_______________________40\n	159 -- 165	51 -- 57	-19.1991 kcal/mol	4.87781 kcal/mol	3.30177 kcal/mol	153 177@LB@ \| \|@LB@5'-CGU...GAUAU A A UAAAU...GUU-3'@LB@ AUAC GGAAGUAAU GUGA UAGU@LB@ \|\|\|\| \|\|\|\|\|:\|\|\| \|\|\|\| :\|:\|@LB@ UAUG CCUUCGUUA CACU GUUA@LB@3'-UUU...UUCAU A C CAGCA...GCG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -11.02 kcal/mol@LB@Hybridization Energy -19.1991 kcal/mol@LB@Unfolding Energy - mRNA 4.87781 kcal/mol@LB@Unfolding Energy - sRNA 3.30177 kcal/mol@LB@@LB@Position - mRNA 154 -- 176@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 51 -- 57@LB@
122	0.01331	0.3627	b0078	ilvH	-10.99	0.130728	66 -- 84	41 -- 61	acetolactate synthase 3 small subunit valine-sensitive	_____________65____________________85\n_____________\|_____________________\|\n5'-GCC...GAGGC_______________C_____AAUCG...UGA-3'\n______________GCUGGAA_CAG_GUG_GCAAU\n______________:\|\|\|\|\|\|_\|\|:_\|\|\|_\|\|\|\|\|\n______________UGACCUU_GUU_CAC_CGUUA\n3'-UUU...CAUUA_______C___A___U_____CAGCA...GCG-5'\n_____________\|_____________________\|\n_____________62____________________40\n	66 -- 72	55 -- 61	-20.2432 kcal/mol	5.95009 kcal/mol	3.30062 kcal/mol	65 85@LB@ \| \|@LB@5'-GCC...GAGGC C AAUCG...UGA-3'@LB@ GCUGGAA CAG GUG GCAAU@LB@ :\|\|\|\|\|\| \|\|: \|\|\| \|\|\|\|\|@LB@ UGACCUU GUU CAC CGUUA@LB@3'-UUU...CAUUA C A U CAGCA...GCG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -20.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.95009 kcal/mol@LB@Unfolding Energy - sRNA 3.30062 kcal/mol@LB@@LB@Position - mRNA 66 -- 84@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 55 -- 61@LB@
193	0.02468	0.4226	b0642	leuS	-10.30	0.169116	191 -- 213	41 -- 61	leucyl-tRNA synthetase	_____________190_____________________214\n_____________\|_______________________\|\n5'-AAU...GGACC_____CU__C___CAA_______ACCGC...AGA-3'\n______________ACUGG__GC_AUG___GAGCAAU\n______________\|\|\|\|\|__\|\|_\|\|\|___\|\|\|\|\|\|\|\n______________UGACC__CG_UAC___CUCGUUA\n3'-UUU...CAUUA_____UU__U___A_________CAGCA...GCG-5'\n_____________\|_______________________\|\n_____________62______________________40\n	207 -- 213	41 -- 47	-20.8037 kcal/mol	7.20782 kcal/mol	3.30062 kcal/mol	190 214@LB@ \| \|@LB@5'-AAU...GGACC CU C CAA ACCGC...AGA-3'@LB@ ACUGG GC AUG GAGCAAU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|@LB@ UGACC CG UAC CUCGUUA@LB@3'-UUU...CAUUA UU U A CAGCA...GCG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -20.8037 kcal/mol@LB@Unfolding Energy - mRNA 7.20782 kcal/mol@LB@Unfolding Energy - sRNA 3.30062 kcal/mol@LB@@LB@Position - mRNA 191 -- 213@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 41 -- 47@LB@
194	0.02479	0.4226	b1260	trpA	-8.29	0.338830	290 -- 297	41 -- 48	tryptophan synthase alpha subunit	_____________289______298\n_____________\|________\|\n5'-GCC...GGCAU________CAU-3'\n______________UGAGCAGU\n______________\|\|\|\|\|\|:\|\n______________ACUCGUUA\n3'-UUU...GUUAC________CAGCA...GCG-5'\n_____________\|________\|\n_____________49_______40\n	291 -- 297	41 -- 47	-10.1831 kcal/mol	0.772851 kcal/mol	1.11967 kcal/mol	289 298@LB@ \| \|@LB@5'-GCC...GGCAU CAU-3'@LB@ UGAGCAGU@LB@ \|\|\|\|\|\|:\|@LB@ ACUCGUUA@LB@3'-UUU...GUUAC CAGCA...GCG-5'@LB@ \| \|@LB@ 49 40@LB@@LB@@LB@Energy -8.29 kcal/mol@LB@Hybridization Energy -10.1831 kcal/mol@LB@Unfolding Energy - mRNA 0.772851 kcal/mol@LB@Unfolding Energy - sRNA 1.11967 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 41 -- 48@LB@Position Seed - mRNA 291 -- 297@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)

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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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