Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
175	0.007208	0.145	b1444	patD	-10.32	0.092173	197 -- 205	69 -- 77	gamma-aminobutyraldehyde dehydrogenase	_____________196_______206\n_____________\|_________\|\n5'-UCG...GAAUA_________ACAUA...UUG-3'\n______________UGCUAUGCA\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAUACGU\n3'-UUU...UUAAC_________CAUUA...ACG-5'\n_____________\|_________\|\n_____________78________68\n	199 -- 205	69 -- 75	-13.9965 kcal/mol	1.91367 kcal/mol	1.75858 kcal/mol	196 206@LB@ \| \|@LB@5'-UCG...GAAUA ACAUA...UUG-3'@LB@ UGCUAUGCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAUACGU@LB@3'-UUU...UUAAC CAUUA...ACG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -13.9965 kcal/mol@LB@Unfolding Energy - mRNA 1.91367 kcal/mol@LB@Unfolding Energy - sRNA 1.75858 kcal/mol@LB@@LB@Position - mRNA 197 -- 205@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
117	0.00395	0.1189	b3447	ggt	-7.92	0.307079	7 -- 34	69 -- 94	gamma-glutamyltranspeptidase	_____________6____________________________35\n_____________\|____________________________\|\n_____5'-GUUAGG_____UCA____AUUAA__G________AAGCC...CGU-3'\n______________GUUGU___GAGU_____UG_GCUGUGCA\n______________\|\|:\|\|___\|\|:\|_____\|\|_\|\|\|:\|\|\|\|\n______________CAGCA___CUUA_____AC_CGAUACGU\n3'-UUU...AGCCG_____UG_____GUUA___A________CAUUA...ACG-5'\n_____________\|____________________________\|\n_____________95___________________________68\n	28 -- 34	69 -- 75	-19.4914 kcal/mol	6.89072 kcal/mol	4.68367 kcal/mol	6 35@LB@ \| \|@LB@ 5'-GUUAGG UCA AUUAA G AAGCC...CGU-3'@LB@ GUUGU GAGU UG GCUGUGCA@LB@ \|\|:\|\| \|\|:\| \|\| \|\|\|:\|\|\|\|@LB@ CAGCA CUUA AC CGAUACGU@LB@3'-UUU...AGCCG UG GUUA A CAUUA...ACG-5'@LB@ \| \|@LB@ 95 68@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -19.4914 kcal/mol@LB@Unfolding Energy - mRNA 6.89072 kcal/mol@LB@Unfolding Energy - sRNA 4.68367 kcal/mol@LB@@LB@Position - mRNA 7 -- 34@LB@Position - sRNA 69 -- 94@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 69 -- 75@LB@
168	0.006702	0.1406	b2051	wcaH	-7.67	0.342256	86 -- 123	5 -- 40	GDP-mannose mannosyl hydrolase	_____________85_______________________________________124\n_____________\|________________________________________\|\n5'-GCG...ACUGC____U___AC_____UG____A_______UG_________GAAAU...UUG-3'\n______________UGGA_GUG__GCGCC__CAUC_GCUUGGC___GUA_UCAC\n______________\|\|\|\|_\|:\|__:\|\|\|\|__\|\|\|\|_\|\|\|\|\|:\|___\|:\|_\|\|\|\|\n______________ACCU_CGC__UGCGG__GUAG_CGAACUG___CGU_AGUG\n3'-UUU...GUUAU________GU___________________CAA___A____GACG-5'\n_____________\|________________________________________\|\n_____________41_______________________________________4\n	108 -- 114	16 -- 22	-36.6804 kcal/mol	13.756 kcal/mol	15.262 kcal/mol	85 124@LB@ \| \|@LB@5'-GCG...ACUGC U AC UG A UG GAAAU...UUG-3'@LB@ UGGA GUG GCGCC CAUC GCUUGGC GUA UCAC@LB@ \|\|\|\| \|:\| :\|\|\|\| \|\|\|\| \|\|\|\|\|:\| \|:\| \|\|\|\|@LB@ ACCU CGC UGCGG GUAG CGAACUG CGU AGUG@LB@3'-UUU...GUUAU GU CAA A GACG-5'@LB@ \| \|@LB@ 41 4@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -36.6804 kcal/mol@LB@Unfolding Energy - mRNA 13.756 kcal/mol@LB@Unfolding Energy - sRNA 15.262 kcal/mol@LB@@LB@Position - mRNA 86 -- 123@LB@Position - sRNA 5 -- 40@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 16 -- 22@LB@
31	0.0001757	0.01997	b4222	ytfP	-8.86	0.198985	202 -- 224	67 -- 90	GGCT-like protein	_____________201_______________________225\n_____________\|_________________________\|\n5'-ACC...AGCAA_______AU_________CG_____UUACG...ACC-3'\n______________UGCGAAU___UUGU_CUA__GCAGU\n______________\|:\|\|\|\|\|___\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________AUGCUUA___AACA_GAU__CGUCA\n3'-UUU...GCAGC_______GUU____C___A______UUAAG...ACG-5'\n_____________\|_________________________\|\n_____________91________________________66\n	202 -- 208	84 -- 90	-18.173 kcal/mol	4.78992 kcal/mol	4.5307 kcal/mol	201 225@LB@ \| \|@LB@5'-ACC...AGCAA AU CG UUACG...ACC-3'@LB@ UGCGAAU UUGU CUA GCAGU@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ AUGCUUA AACA GAU CGUCA@LB@3'-UUU...GCAGC GUU C A UUAAG...ACG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -18.173 kcal/mol@LB@Unfolding Energy - mRNA 4.78992 kcal/mol@LB@Unfolding Energy - sRNA 4.5307 kcal/mol@LB@@LB@Position - mRNA 202 -- 224@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 84 -- 90@LB@
66	0.001137	0.05992	b0076	leuO	-9.90	0.116504	167 -- 195	35 -- 60	global transcription factor	_____________166_____________________________196\n_____________\|_______________________________\|\n5'-UAU...AUAAG___________UAAGUGU_____________UAAGU...UGA-3'\n______________GGAAAGGGAGU_______GACA__GUGGAGU\n______________::\|\|\|\|\|:\|\|\|_______\|\|\|\|__:\|\|\|\|\|:\n______________UUUUUCCUUCA_______CUGU__UACCUCG\n3'-UUU...UAAGU___________UU_________UA_______CGUUG...ACG-5'\n_____________\|_______________________________\|\n_____________61______________________________34\n	189 -- 195	35 -- 41	-23.1584 kcal/mol	8.98888 kcal/mol	4.23745 kcal/mol	166 196@LB@ \| \|@LB@5'-UAU...AUAAG UAAGUGU UAAGU...UGA-3'@LB@ GGAAAGGGAGU GACA GUGGAGU@LB@ ::\|\|\|\|\|:\|\|\| \|\|\|\| :\|\|\|\|\|:@LB@ UUUUUCCUUCA CUGU UACCUCG@LB@3'-UUU...UAAGU UU UA CGUUG...ACG-5'@LB@ \| \|@LB@ 61 34@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.1584 kcal/mol@LB@Unfolding Energy - mRNA 8.98888 kcal/mol@LB@Unfolding Energy - sRNA 4.23745 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 35 -- 60@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 35 -- 41@LB@
172	0.007014	0.1437	b3430	glgC	-13.14	0.016567	21 -- 80	1 -- 39	glucose-1-phosphate adenylyltransferase	_____________20______________________________________________________________81\n_____________\|_______________________________________________________________\|\n5'-CAG...CUCUC___U___UUUUUGAUCGCAAUU______A_________G__AACAGAGAU_____________UGGGG...UGA-3'\n______________GGA_CGC_______________AACGCC___CGCUUGA_GU_________UGU_UUUACCUGC\n______________\|\|\|_\|\|\|_______________\|\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|_________\|\|:_\|\|:\|\|\|\|\|\|\n______________CCU_GCG_______________UUGCGG___GCGAACU_CA_________ACG_AAGUGGACG\n3'-UUU...UUAUA___C________________________GUA_______G______________U_________-5'\n_____________\|______________________________________________________________\|\n_____________40_____________________________________________________________1\n	74 -- 80	1 -- 7	-41.5646 kcal/mol	13.1395 kcal/mol	15.291 kcal/mol	20 81@LB@ \| \|@LB@5'-CAG...CUCUC U UUUUUGAUCGCAAUU A G AACAGAGAU UGGGG...UGA-3'@LB@ GGA CGC AACGCC CGCUUGA GU UGU UUUACCUGC@LB@ \|\|\| \|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\| \|\|: \|\|:\|\|\|\|\|\|@LB@ CCU GCG UUGCGG GCGAACU CA ACG AAGUGGACG@LB@3'-UUU...UUAUA C GUA G U -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -41.5646 kcal/mol@LB@Unfolding Energy - mRNA 13.1395 kcal/mol@LB@Unfolding Energy - sRNA 15.291 kcal/mol@LB@@LB@Position - mRNA 21 -- 80@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 1 -- 7@LB@
24	0.0001125	0.01591	b3212	gltB	-12.14	0.031409	27 -- 43	59 -- 75	glutamate synthase large subunit	_____________26________________44\n_____________\|_________________\|\n5'-CUG...CAUAU_____________G___UCCCC...UAC-3'\n______________UUAUGCAGUAAUU_AGA\n______________:\|\|\|\|\|\|\|\|\|\|\|\|_\|:\|\n______________GAUACGUCAUUAA_UUU\n3'-UUU...AACAC_____________G___UUUCC...ACG-5'\n_____________\|_________________\|\n_____________76________________58\n	33 -- 39	63 -- 69	-17.8824 kcal/mol	2.24537 kcal/mol	3.49177 kcal/mol	26 44@LB@ \| \|@LB@5'-CUG...CAUAU G UCCCC...UAC-3'@LB@ UUAUGCAGUAAUU AGA@LB@ :\|\|\|\|\|\|\|\|\|\|\|\| \|:\|@LB@ GAUACGUCAUUAA UUU@LB@3'-UUU...AACAC G UUUCC...ACG-5'@LB@ \| \|@LB@ 76 58@LB@@LB@@LB@Energy -12.14 kcal/mol@LB@Hybridization Energy -17.8824 kcal/mol@LB@Unfolding Energy - mRNA 2.24537 kcal/mol@LB@Unfolding Energy - sRNA 3.49177 kcal/mol@LB@@LB@Position - mRNA 27 -- 43@LB@Position - sRNA 59 -- 75@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 63 -- 69@LB@
86	0.002341	0.09591	b0144	gluQ	-7.21	0.411815	221 -- 264	26 -- 65	glutamyl-Q tRNA(Asp) synthetase	_____________220__________________________________________265\n_____________\|____________________________________________\|\n5'-AGA...UUUUU__________AU__C__ACAC_______AUU__C___UU_____CCUCU...UGA-3'\n______________GUUCAAAGAG__GA_AG____ACAGUAU___GG_CGC__CGCCC\n______________:\|\|\|\|\|\|:\|:__\|\|_\|\|____\|\|\|:\|\|\|___:\|_\|\|\|__\|\|\|\|\|\n______________UAAGUUUUUU__CU_UC____UGUUAUA___UC_GCG__GCGGG\n3'-UUU...GUCAU__________C______AUUC_______CC_______UU_____UAGCG...ACG-5'\n_____________\|____________________________________________\|\n_____________66___________________________________________25\n	242 -- 248	40 -- 46	-28.4973 kcal/mol	7.75098 kcal/mol	13.5387 kcal/mol	220 265@LB@ \| \|@LB@5'-AGA...UUUUU AU C ACAC AUU C UU CCUCU...UGA-3'@LB@ GUUCAAAGAG GA AG ACAGUAU GG CGC CGCCC@LB@ :\|\|\|\|\|\|:\|: \|\| \|\| \|\|\|:\|\|\| :\| \|\|\| \|\|\|\|\|@LB@ UAAGUUUUUU CU UC UGUUAUA UC GCG GCGGG@LB@3'-UUU...GUCAU C AUUC CC UU UAGCG...ACG-5'@LB@ \| \|@LB@ 66 25@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -28.4973 kcal/mol@LB@Unfolding Energy - mRNA 7.75098 kcal/mol@LB@Unfolding Energy - sRNA 13.5387 kcal/mol@LB@@LB@Position - mRNA 221 -- 264@LB@Position - sRNA 26 -- 65@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 40 -- 46@LB@
8	8.903e-06	0.003921	b1654	grxD	-12.06	0.033180	187 -- 203	41 -- 57	glutaredoxin-4	_____________186_____________________204\n_____________\|_______________________\|\n5'-AAA...AGUUU_______C_______________ACCAC...CUG-3'\n______________GAGGAAG_AAGACAAU___GAGC\n______________:\|\|\|\|\|\|_\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCUUC_UUCUGUUA___CUCG\n3'-UUU...GUUUU_______A________UAC____CGUUG...ACG-5'\n_____________\|_______________________\|\n_____________58______________________40\n	196 -- 202	42 -- 48	-22.6133 kcal/mol	5.89741 kcal/mol	4.1846 kcal/mol	186 204@LB@ \| \|@LB@5'-AAA...AGUUU C ACCAC...CUG-3'@LB@ GAGGAAG AAGACAAU GAGC@LB@ :\|\|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCUUC UUCUGUUA CUCG@LB@3'-UUU...GUUUU A UAC CGUUG...ACG-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -12.06 kcal/mol@LB@Hybridization Energy -22.6133 kcal/mol@LB@Unfolding Energy - mRNA 5.89741 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 42 -- 48@LB@
150	0.005897	0.1368	b0887	cydD	-10.72	0.073556	183 -- 190	1 -- 8	glutathione/cysteine ABC transporter export permease/ATPase	_____________182______191\n_____________\|________\|\n5'-AUU...AUAAC________UAAGC...UGA-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	184 -- 190	1 -- 7	-15.001 kcal/mol	1.91816 kcal/mol	2.36381 kcal/mol	182 191@LB@ \| \|@LB@5'-AUU...AUAAC UAAGC...UGA-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.001 kcal/mol@LB@Unfolding Energy - mRNA 1.91816 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@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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