Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
173	0.02087	0.4033	b2239	glpQ	-12.95	0.026326	256 -- 274	41 -- 66	periplasmic glycerophosphodiester phosphodiesterase	_____________255________________________275\n_____________\|__________________________\|\n5'-CGG...AGUCA__________________________GGCGG...UCA-3'\n______________UGGGAA_______GCAGUGCAAUGGC\n______________\|\|\|:\|\|_______\|\|\|:\|\|\|\|\|\|\|\|\|\n______________ACCUUU_______CGUUACGUUACCG\n3'-UUU...AUACA______UAGUCAC_____________GGUUG...UUG-5'\n_____________\|__________________________\|\n_____________67_________________________40\n	268 -- 274	41 -- 47	-26.6029 kcal/mol	7.82977 kcal/mol	5.82355 kcal/mol	255 275@LB@ \| \|@LB@5'-CGG...AGUCA GGCGG...UCA-3'@LB@ UGGGAA GCAGUGCAAUGGC@LB@ \|\|\|:\|\| \|\|\|:\|\|\|\|\|\|\|\|\|@LB@ ACCUUU CGUUACGUUACCG@LB@3'-UUU...AUACA UAGUCAC GGUUG...UUG-5'@LB@ \| \|@LB@ 67 40@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -26.6029 kcal/mol@LB@Unfolding Energy - mRNA 7.82977 kcal/mol@LB@Unfolding Energy - sRNA 5.82355 kcal/mol@LB@@LB@Position - mRNA 256 -- 274@LB@Position - sRNA 41 -- 66@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 41 -- 47@LB@
15	0.0005657	0.1268	b3715	yieH	-7.91	0.301098	195 -- 204	4 -- 13	phosphoenolpyruvate and 6-phosphogluconate phosphatase	_____________194________205\n_____________\|__________\|\n5'-CUG...AAAGG__________CCCGG...UUG-3'\n______________AAAGGCAUGU\n______________\|\|\|\|\|\|\|\|:\|\n______________UUUCCGUAUA\n3'-UUU...UGUUA__________UUG-5'\n_____________\|__________\|\n_____________14_________3\n	198 -- 204	4 -- 10	-12.382 kcal/mol	1.66065 kcal/mol	2.80714 kcal/mol	194 205@LB@ \| \|@LB@5'-CUG...AAAGG CCCGG...UUG-3'@LB@ AAAGGCAUGU@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UUUCCGUAUA@LB@3'-UUU...UGUUA UUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -7.91 kcal/mol@LB@Hybridization Energy -12.382 kcal/mol@LB@Unfolding Energy - mRNA 1.66065 kcal/mol@LB@Unfolding Energy - sRNA 2.80714 kcal/mol@LB@@LB@Position - mRNA 195 -- 204@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 4 -- 10@LB@
91	0.007817	0.2889	b3380	yhfW	-10.82	0.081759	179 -- 205	41 -- 67	phosphopentomutase-related metalloenzyme superfamily protein	_____________178_________________________206\n_____________\|___________________________\|\n5'-CUC...CAGUC_______C__UC___G__C________GCGAU...GUG-3'\n______________UUGGAAA_UC__UGG_GG_GUAAUGGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_::_\|:\|\|\|\|\|\|\n______________AACCUUU_AG__ACC_UU_CGUUACCG\n3'-UUU...UAUAC_______U__UC___G__A________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________68__________________________40\n	199 -- 205	41 -- 47	-26.7792 kcal/mol	10.1319 kcal/mol	5.83043 kcal/mol	178 206@LB@ \| \|@LB@5'-CUC...CAGUC C UC G C GCGAU...GUG-3'@LB@ UUGGAAA UC UGG GG GUAAUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| :: \|:\|\|\|\|\|\|@LB@ AACCUUU AG ACC UU CGUUACCG@LB@3'-UUU...UAUAC U UC G A GGUUG...UUG-5'@LB@ \| \|@LB@ 68 40@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -26.7792 kcal/mol@LB@Unfolding Energy - mRNA 10.1319 kcal/mol@LB@Unfolding Energy - sRNA 5.83043 kcal/mol@LB@@LB@Position - mRNA 179 -- 205@LB@Position - sRNA 41 -- 67@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
188	0.02326	0.4145	b2501	ppk	-10.84	0.080977	186 -- 203	48 -- 65	polyphosphate kinase component of RNA degradosome	_____________185________________204\n_____________\|__________________\|\n5'-CGC...AAAAC____UAAA__________GGUCA...UUG-3'\n______________GGAG____AGUGGUAAUG\n______________\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________CCUU____UCACCGUUAC\n3'-UUU...UACAA____UUAG__________GUUAC...UUG-5'\n_____________\|__________________\|\n_____________66_________________47\n	197 -- 203	48 -- 54	-18.775 kcal/mol	3.93073 kcal/mol	4.00814 kcal/mol	185 204@LB@ \| \|@LB@5'-CGC...AAAAC UAAA GGUCA...UUG-3'@LB@ GGAG AGUGGUAAUG@LB@ \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ CCUU UCACCGUUAC@LB@3'-UUU...UACAA UUAG GUUAC...UUG-5'@LB@ \| \|@LB@ 66 47@LB@@LB@@LB@Energy -10.84 kcal/mol@LB@Hybridization Energy -18.775 kcal/mol@LB@Unfolding Energy - mRNA 3.93073 kcal/mol@LB@Unfolding Energy - sRNA 4.00814 kcal/mol@LB@@LB@Position - mRNA 186 -- 203@LB@Position - sRNA 48 -- 65@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@LB@
96	0.009004	0.3118	b3981	secE	-8.82	0.207803	253 -- 270	42 -- 57	preprotein translocase membrane subunit	_____________252________________271\n_____________\|__________________\|\n5'-UAA...GAUGA_____GUCGU________CAUUG...ACU-3'\n______________AGUGG_____UGUGGUGG\n______________\|\|\|\|\|_____\|\|:::\|\|\|\n______________UCACC_____ACGUUACC\n3'-UUU...UUUAG_____GUU__________GGGUU...UUG-5'\n_____________\|__________________\|\n_____________58_________________41\n	264 -- 270	42 -- 48	-15.0916 kcal/mol	2.64473 kcal/mol	3.62906 kcal/mol	252 271@LB@ \| \|@LB@5'-UAA...GAUGA GUCGU CAUUG...ACU-3'@LB@ AGUGG UGUGGUGG@LB@ \|\|\|\|\| \|\|:::\|\|\|@LB@ UCACC ACGUUACC@LB@3'-UUU...UUUAG GUU GGGUU...UUG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -15.0916 kcal/mol@LB@Unfolding Energy - mRNA 2.64473 kcal/mol@LB@Unfolding Energy - sRNA 3.62906 kcal/mol@LB@@LB@Position - mRNA 253 -- 270@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 42 -- 48@LB@
11	0.000438	0.1262	b0467	priC	-14.72	0.009297	1 -- 37	32 -- 65	primosomal replication protein N''	______________1____________________________________38\n______________\|____________________________________\|\n___________5'-______GAACG_____A___CCA___CG_________UAAAC...GUU-3'\n______________GGGGAA_____GGCAA_GCA___GGC__CCAGCAGGA\n______________\|\|::\|\|_____\|\|\|\|\|_\|\|\|___\|\|\|__\|\|\|:\|\|\|:\|\n______________CCUUUU_____CCGUU_CGU___CCG__GGUUGUCUU\n3'-UUU...UACAA______AGUCA_____A___UA_______________UUAUU...UUG-5'\n_____________\|_____________________________________\|\n_____________66____________________________________31\n	30 -- 36	33 -- 39	-34.0772 kcal/mol	8.3902 kcal/mol	10.9649 kcal/mol	1 38@LB@ \| \|@LB@ 5'- GAACG A CCA CG UAAAC...GUU-3'@LB@ GGGGAA GGCAA GCA GGC CCAGCAGGA@LB@ \|\|::\|\| \|\|\|\|\| \|\|\| \|\|\| \|\|\|:\|\|\|:\|@LB@ CCUUUU CCGUU CGU CCG GGUUGUCUU@LB@3'-UUU...UACAA AGUCA A UA UUAUU...UUG-5'@LB@ \| \|@LB@ 66 31@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -34.0772 kcal/mol@LB@Unfolding Energy - mRNA 8.3902 kcal/mol@LB@Unfolding Energy - sRNA 10.9649 kcal/mol@LB@@LB@Position - mRNA 1 -- 37@LB@Position - sRNA 32 -- 65@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 33 -- 39@LB@
172	0.02065	0.4033	b1015	putP	-10.70	0.086688	188 -- 205	52 -- 67	proline:sodium symporter	_____________187________________206\n_____________\|__________________\|\n5'-AGA...AUUUU_______CU____A____UAUUA...ACG-3'\n______________UUGGAGA__UUAG_UGGC\n______________\|\|\|\|\|:\|__\|:\|\|_\|\|\|\|\n______________AACCUUU__AGUC_ACCG\n3'-UUU...UAUAC_______U__________UUACG...UUG-5'\n_____________\|__________________\|\n_____________68_________________51\n	188 -- 194	61 -- 67	-15.9795 kcal/mol	2.37428 kcal/mol	2.90583 kcal/mol	187 206@LB@ \| \|@LB@5'-AGA...AUUUU CU A UAUUA...ACG-3'@LB@ UUGGAGA UUAG UGGC@LB@ \|\|\|\|\|:\| \|:\|\| \|\|\|\|@LB@ AACCUUU AGUC ACCG@LB@3'-UUU...UAUAC U UUACG...UUG-5'@LB@ \| \|@LB@ 68 51@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -15.9795 kcal/mol@LB@Unfolding Energy - mRNA 2.37428 kcal/mol@LB@Unfolding Energy - sRNA 2.90583 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 52 -- 67@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 61 -- 67@LB@
186	0.02292	0.4143	b2717	hycI	-8.63	0.225035	220 -- 254	38 -- 70	protease involved in processing C-terminal end of HycE	_____________219___________________________________255\n_____________\|_____________________________________\|\n5'-AGC...ACUCU_______C__UAG__UGAUG______________G__GGUCC...ACU-3'\n______________GUGUUGG_AA___CA_____GGCGAUG__AUGGC_CA\n______________:\|\|\|\|\|\|_\|\|___\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|_\|\|\n______________UACAACC_UU___GU_____CCGUUAC__UACCG_GU\n3'-UUU...AAAUA__________UUA__CA__________GU_____G__UGUCU...UUG-5'\n_____________\|_____________________________________\|\n_____________71____________________________________37\n	240 -- 246	48 -- 54	-27.127 kcal/mol	11.1995 kcal/mol	7.29667 kcal/mol	219 255@LB@ \| \|@LB@5'-AGC...ACUCU C UAG UGAUG G GGUCC...ACU-3'@LB@ GUGUUGG AA CA GGCGAUG AUGGC CA@LB@ :\|\|\|\|\|\| \|\| \|\| \|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UACAACC UU GU CCGUUAC UACCG GU@LB@3'-UUU...AAAUA UUA CA GU G UGUCU...UUG-5'@LB@ \| \|@LB@ 71 37@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -27.127 kcal/mol@LB@Unfolding Energy - mRNA 11.1995 kcal/mol@LB@Unfolding Energy - sRNA 7.29667 kcal/mol@LB@@LB@Position - mRNA 220 -- 254@LB@Position - sRNA 38 -- 70@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 48 -- 54@LB@
3	3.498e-05	0.03921	b4255	rraB	-13.36	0.020838	142 -- 156	41 -- 54	protein inhibitor of RNase E	_____________141_____________157\n_____________\|_______________\|\n5'-GAG...GUGGA_______U_______GUGUG...CCA-3'\n______________GGCAAUG_CAGUGGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|:\n______________CCGUUAC_GUUACCG\n3'-UUU...AGUCA_______________GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	150 -- 156	41 -- 47	-21.65 kcal/mol	4.39843 kcal/mol	3.89026 kcal/mol	141 157@LB@ \| \|@LB@5'-GAG...GUGGA U GUGUG...CCA-3'@LB@ GGCAAUG CAGUGGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ CCGUUAC GUUACCG@LB@3'-UUU...AGUCA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -13.36 kcal/mol@LB@Hybridization Energy -21.65 kcal/mol@LB@Unfolding Energy - mRNA 4.39843 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 142 -- 156@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 41 -- 47@LB@
190	0.0237	0.4194	b0428	cyoE	-16.93	0.002220	1 -- 26	41 -- 65	protoheme IX farnesyltransferase	______________1__________________________27\n______________\|__________________________\|\n___________5'-____C____C________G________ACAGG...GCA-3'\n______________GGAA_AAUC__UGGCAAU_GCAGUGGU\n______________\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|:\|\|\|:\n______________CCUU_UUAG__ACCGUUA_CGUUACCG\n3'-UUU...UACAA_________UC________________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________66__________________________40\n	20 -- 26	41 -- 47	-29.3415 kcal/mol	6.59984 kcal/mol	5.80973 kcal/mol	1 27@LB@ \| \|@LB@ 5'- C C G ACAGG...GCA-3'@LB@ GGAA AAUC UGGCAAU GCAGUGGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|\|\|:@LB@ CCUU UUAG ACCGUUA CGUUACCG@LB@3'-UUU...UACAA UC GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -29.3415 kcal/mol@LB@Unfolding Energy - mRNA 6.59984 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 1 -- 26@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 20 -- 26@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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