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
100	0.009417	0.3118	b4363	yjjB	-11.70	0.052026	267 -- 280	41 -- 54	DUF3815 family inner membrane protein	_____________266____________281\n_____________\|______________\|\n5'-ACU...CGGUC___UU_________GUUCA...GGG-3'\n______________GGC__UGCGAUGGU\n______________\|\|\|__\|\|\|:\|\|\|\|:\n______________CCG__ACGUUACCG\n3'-UUU...AGUCA___UU_________GGUUG...UUG-5'\n_____________\|______________\|\n_____________55_____________40\n	274 -- 280	41 -- 47	-20.909 kcal/mol	5.32115 kcal/mol	3.89026 kcal/mol	266 281@LB@ \| \|@LB@5'-ACU...CGGUC UU GUUCA...GGG-3'@LB@ GGC UGCGAUGGU@LB@ \|\|\| \|\|\|:\|\|\|\|:@LB@ CCG ACGUUACCG@LB@3'-UUU...AGUCA UU GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -20.909 kcal/mol@LB@Unfolding Energy - mRNA 5.32115 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 267 -- 280@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@LB@
104	0.009649	0.3118	b0910	cmk	-9.70	0.140357	282 -- 294	41 -- 53	cytidylate kinase	_____________281___________295\n_____________\|_____________\|\n5'-CCG...CGGAA___U_________AUCUGC-3'\n______________GCG_UGCAAUGGC\n______________\|\|:_\|\|\|\|\|\|\|\|\|\n______________CGU_ACGUUACCG\n3'-UUU...GUCAC___U_________GGUUG...UUG-5'\n_____________\|_____________\|\n_____________54____________40\n	288 -- 294	41 -- 47	-19.191 kcal/mol	5.61932 kcal/mol	3.8759 kcal/mol	281 295@LB@ \| \|@LB@5'-CCG...CGGAA U AUCUGC-3'@LB@ GCG UGCAAUGGC@LB@ \|\|: \|\|\|\|\|\|\|\|\|@LB@ CGU ACGUUACCG@LB@3'-UUU...GUCAC U GGUUG...UUG-5'@LB@ \| \|@LB@ 54 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -19.191 kcal/mol@LB@Unfolding Energy - mRNA 5.61932 kcal/mol@LB@Unfolding Energy - sRNA 3.8759 kcal/mol@LB@@LB@Position - mRNA 282 -- 294@LB@Position - sRNA 41 -- 53@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 41 -- 47@LB@
124	0.01277	0.3462	b2812	tcdA	-10.63	0.089790	208 -- 228	41 -- 66	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________207________________________229\n_____________\|__________________________\|\n5'-GUG...GUCUG___U______________________GUCAG...UUU-3'\n______________UGG__AAUUAGUG___AUGC_AUGGC\n______________\|\|\|__\|\|\|:\|\|\|\|___\|\|\|\|_\|\|\|\|\|\n______________ACC__UUAGUCAC___UACG_UACCG\n3'-UUU...AUACA___UU________CGU____U_____GGUUG...UUG-5'\n_____________\|__________________________\|\n_____________67_________________________40\n	213 -- 219	54 -- 60	-21.2123 kcal/mol	4.76037 kcal/mol	5.82355 kcal/mol	207 229@LB@ \| \|@LB@5'-GUG...GUCUG U GUCAG...UUU-3'@LB@ UGG AAUUAGUG AUGC AUGGC@LB@ \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ ACC UUAGUCAC UACG UACCG@LB@3'-UUU...AUACA UU CGU U GGUUG...UUG-5'@LB@ \| \|@LB@ 67 40@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -21.2123 kcal/mol@LB@Unfolding Energy - mRNA 4.76037 kcal/mol@LB@Unfolding Energy - sRNA 5.82355 kcal/mol@LB@@LB@Position - mRNA 208 -- 228@LB@Position - sRNA 41 -- 66@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 54 -- 60@LB@
138	0.01562	0.3807	b1735	chbR	-9.56	0.149643	62 -- 73	41 -- 54	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________61_____________74\n_____________\|______________\|\n5'-GAU...UUGAA______________GAAGG...CUG-3'\n______________GGCGAUGCG__GGC\n______________\|\|\|:\|\|\|\|:__\|\|\|\n______________CCGUUACGU__CCG\n3'-UUU...AGUCA_________UA___GGUUG...UUG-5'\n_____________\|______________\|\n_____________55_____________40\n	64 -- 70	46 -- 52	-18.6965 kcal/mol	5.24959 kcal/mol	3.89026 kcal/mol	61 74@LB@ \| \|@LB@5'-GAU...UUGAA GAAGG...CUG-3'@LB@ GGCGAUGCG GGC@LB@ \|\|\|:\|\|\|\|: \|\|\|@LB@ CCGUUACGU CCG@LB@3'-UUU...AGUCA UA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -18.6965 kcal/mol@LB@Unfolding Energy - mRNA 5.24959 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 62 -- 73@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 46 -- 52@LB@
151	0.01786	0.3828	b0412	yajI	-11.20	0.067280	41 -- 55	41 -- 54	putative lipoprotein	_____________40______________56\n_____________\|_______________\|\n5'-CGA...GAAUG_________UAC___GUCCU...UCA-3'\n______________GGCAAUGCA___GGC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\n______________CCGUUACGU___CCG\n3'-UUU...AGUCA_________UA____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	43 -- 49	46 -- 52	-19.8433 kcal/mol	4.75092 kcal/mol	3.89026 kcal/mol	40 56@LB@ \| \|@LB@5'-CGA...GAAUG UAC GUCCU...UCA-3'@LB@ GGCAAUGCA GGC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUUACGU CCG@LB@3'-UUU...AGUCA UA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.8433 kcal/mol@LB@Unfolding Energy - mRNA 4.75092 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 41 -- 55@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 46 -- 52@LB@
152	0.01787	0.3828	b1659	ydhB	-7.85	0.308650	225 -- 251	41 -- 68	LysR family putative transcriptional regulator	_____________224__________________________252\n_____________\|____________________________\|\n5'-CGA...UCGAA____UU__UG____A___C_________AGUUU...UCA-3'\n______________GUUG__GA__CGGU_GCG__GUAAUGGU\n______________\|\|\|\|__:\|__\|:\|\|_\|\|:__\|:\|\|\|\|\|:\n______________CAAC__UU__GUCA_CGU__CGUUACCG\n3'-UUU...AUAUA____CU__UA____C___UA________GGUUG...UUG-5'\n_____________\|____________________________\|\n_____________69___________________________40\n	245 -- 251	41 -- 47	-21.9924 kcal/mol	7.69552 kcal/mol	6.44645 kcal/mol	224 252@LB@ \| \|@LB@5'-CGA...UCGAA UU UG A C AGUUU...UCA-3'@LB@ GUUG GA CGGU GCG GUAAUGGU@LB@ \|\|\|\| :\| \|:\|\| \|\|: \|:\|\|\|\|\|:@LB@ CAAC UU GUCA CGU CGUUACCG@LB@3'-UUU...AUAUA CU UA C UA GGUUG...UUG-5'@LB@ \| \|@LB@ 69 40@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -21.9924 kcal/mol@LB@Unfolding Energy - mRNA 7.69552 kcal/mol@LB@Unfolding Energy - sRNA 6.44645 kcal/mol@LB@@LB@Position - mRNA 225 -- 251@LB@Position - sRNA 41 -- 68@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 41 -- 47@LB@
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@
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@
195	0.02483	0.4256	b2905	gcvT	-11.07	0.071827	75 -- 92	41 -- 59	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________74__________________93\n_____________\|___________________\|\n5'-CUG...CUGUU_____________UCA___AAAAG...AAA-3'\n______________UCGGUGGUAA_GU___GGC\n______________\|\|:\|\|\|\|:\|\|_\|:___\|\|\|\n______________AGUCACCGUU_CG___CCG\n3'-UUU...CUUUU__________A__UUA___GGUUG...UUG-5'\n_____________\|___________________\|\n_____________60__________________40\n	78 -- 84	50 -- 56	-19.3336 kcal/mol	3.99003 kcal/mol	4.26967 kcal/mol	74 93@LB@ \| \|@LB@5'-CUG...CUGUU UCA AAAAG...AAA-3'@LB@ UCGGUGGUAA GU GGC@LB@ \|\|:\|\|\|\|:\|\| \|: \|\|\|@LB@ AGUCACCGUU CG CCG@LB@3'-UUU...CUUUU A UUA GGUUG...UUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -19.3336 kcal/mol@LB@Unfolding Energy - mRNA 3.99003 kcal/mol@LB@Unfolding Energy - sRNA 4.26967 kcal/mol@LB@@LB@Position - mRNA 75 -- 92@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 50 -- 56@LB@
197	0.02537	0.4256	b3317	rplB	-11.01	0.074049	182 -- 205	41 -- 62	50S ribosomal subunit protein L2	_____________181______________________206\n_____________\|________________________\|\n5'-GCA...UGAGU_______AG_A_____A_______AGUUG...UGC-3'\n______________AAGUCGG__G_GUAAU_CAAUGGC\n______________\|\|:\|\|:\|__\|_\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUUAGUC__C_CGUUA_GUUACCG\n3'-UUU...AACCU_______A________C_______GGUUG...UUG-5'\n_____________\|________________________\|\n_____________63_______________________40\n	199 -- 205	41 -- 47	-19.8959 kcal/mol	4.6063 kcal/mol	4.27585 kcal/mol	181 206@LB@ \| \|@LB@5'-GCA...UGAGU AG A A AGUUG...UGC-3'@LB@ AAGUCGG G GUAAU CAAUGGC@LB@ \|\|:\|\|:\| \| \|:\|\|\| \|\|\|\|\|\|\|@LB@ UUUAGUC C CGUUA GUUACCG@LB@3'-UUU...AACCU A C GGUUG...UUG-5'@LB@ \| \|@LB@ 63 40@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -19.8959 kcal/mol@LB@Unfolding Energy - mRNA 4.6063 kcal/mol@LB@Unfolding Energy - sRNA 4.27585 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 41 -- 62@LB@Position Seed - mRNA 199 -- 205@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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