Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
102	0.005508	0.1855	b0659	ybeY	-7.73	0.351978	30 -- 54	64 -- 89	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor	_____________29_________________________55\n_____________\|__________________________\|\n5'-ACU...AUCGA__________________AA______AGCUU...CGC-3'\n______________AGUGCUG_GCCGAUGUCG__GAGAUC\n______________\|:\|:\|\|\|_\|\|\|:\|:::\|:__\|\|:\|\|\|\n______________UUAUGAC_CGGUUGUGGU__CUUUAG\n3'-UUU...CGCGC_______G__________CC______AACCG...GUG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	30 -- 36	83 -- 89	-23.8058 kcal/mol	8.19456 kcal/mol	7.88317 kcal/mol	29 55@LB@ \| \|@LB@5'-ACU...AUCGA AA AGCUU...CGC-3'@LB@ AGUGCUG GCCGAUGUCG GAGAUC@LB@ \|:\|:\|\|\| \|\|\|:\|:::\|: \|\|:\|\|\|@LB@ UUAUGAC CGGUUGUGGU CUUUAG@LB@3'-UUU...CGCGC G CC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -7.73 kcal/mol@LB@Hybridization Energy -23.8058 kcal/mol@LB@Unfolding Energy - mRNA 8.19456 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 30 -- 54@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 83 -- 89@LB@
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase	_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
44	0.002208	0.1727	b1859	znuB	-7.63	0.365449	19 -- 38	72 -- 88	zinc ABC transporter permease	_____________18___________________39\n_____________\|____________________\|\n5'-AUG...AUGAA__________UGAAU_____CAUUU...AUU-3'\n______________GUGCUGUGCC_____CACCA\n______________:\|:\|\|\|:\|\|\|_____\|\|\|\|\|\n______________UAUGACGCGG_____GUGGU\n3'-UUU...GCGCU__________UU________CCCUU...GUG-5'\n_____________\|____________________\|\n_____________89___________________71\n	22 -- 28	79 -- 85	-22.3137 kcal/mol	7.44481 kcal/mol	7.24148 kcal/mol	18 39@LB@ \| \|@LB@5'-AUG...AUGAA UGAAU CAUUU...AUU-3'@LB@ GUGCUGUGCC CACCA@LB@ :\|:\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAUGACGCGG GUGGU@LB@3'-UUU...GCGCU UU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -22.3137 kcal/mol@LB@Unfolding Energy - mRNA 7.44481 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 19 -- 38@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 79 -- 85@LB@
159	0.009346	0.2062	b3661	nlpA	-7.63	0.365650	232 -- 240	1 -- 9	cytoplasmic membrane lipoprotein-28	_____________231_______241\n_____________\|_________\|\n5'-UGU...GACAG_________UAUUG...ACA-3'\n______________GGGCCGCAU\n______________:\|\|\|\|\|\|\|:\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	234 -- 240	1 -- 7	-16.6231 kcal/mol	3.46198 kcal/mol	5.10726 kcal/mol	231 241@LB@ \| \|@LB@5'-UGU...GACAG UAUUG...ACA-3'@LB@ GGGCCGCAU@LB@ :\|\|\|\|\|\|\|:@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -16.6231 kcal/mol@LB@Unfolding Energy - mRNA 3.46198 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 232 -- 240@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
145	0.008374	0.2033	b0068	thiB	-7.61	0.367750	229 -- 244	73 -- 87	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein	_____________228______________245\n_____________\|________________\|\n5'-UUU...GCUGU________A_______CGUUU...ACU-3'\n______________UGCUGUGC_CAGCGCC\n______________\|:\|\|\|:\|\|_\|\|:\|:\|\|\n______________AUGACGCG_GUUGUGG\n3'-UUU...CGCUU________________UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	230 -- 236	80 -- 86	-23.483 kcal/mol	8.91653 kcal/mol	6.95602 kcal/mol	228 245@LB@ \| \|@LB@5'-UUU...GCUGU A CGUUU...ACU-3'@LB@ UGCUGUGC CAGCGCC@LB@ \|:\|\|\|:\|\| \|\|:\|:\|\|@LB@ AUGACGCG GUUGUGG@LB@3'-UUU...CGCUU UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -23.483 kcal/mol@LB@Unfolding Energy - mRNA 8.91653 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 229 -- 244@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 80 -- 86@LB@
197	0.01211	0.2164	b0495	ybbA	-7.53	0.379415	88 -- 97	1 -- 10	putative ABC transporter ATPase	_____________87_________98\n_____________\|__________\|\n5'-GCC...CAGGC__________UGGCA...UCA-3'\n______________CAGGCCGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUCCGGCGUG\n3'-UUU...AAAAA__________-5'\n_____________\|_________\|\n_____________11________1\n	91 -- 97	1 -- 7	-21.6304 kcal/mol	8.71663 kcal/mol	5.44172 kcal/mol	87 98@LB@ \| \|@LB@5'-GCC...CAGGC UGGCA...UCA-3'@LB@ CAGGCCGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUCCGGCGUG@LB@3'-UUU...AAAAA -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -21.6304 kcal/mol@LB@Unfolding Energy - mRNA 8.71663 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 1 -- 7@LB@
43	0.002187	0.1727	b2222	atoA	-7.38	0.400797	260 -- 273	68 -- 82	acetyl-CoA:acetoacetyl-CoA transferase beta subunit	_____________259_____________274\n_____________\|_______________\|\n5'-CGC...GACAU_______________UCGGU...AUU-3'\n______________CGUUAAC_UUAGGGA\n______________\|\|::\|\|\|_::\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	267 -- 273	68 -- 74	-16.5153 kcal/mol	2.15948 kcal/mol	6.98098 kcal/mol	259 274@LB@ \| \|@LB@5'-CGC...GACAU UCGGU...AUU-3'@LB@ CGUUAAC UUAGGGA@LB@ \|\|::\|\|\| ::\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -16.5153 kcal/mol@LB@Unfolding Energy - mRNA 2.15948 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 260 -- 273@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 68 -- 74@LB@
94	0.005015	0.1855	b2703	srlE	-7.35	0.404948	254 -- 271	70 -- 86	glucitol/sorbitol-specific enzyme IIB component of PTS	_____________253_________________272\n_____________\|___________________\|\n5'-GAA...CUUGA____AAA____________AAAAA...GUA-3'\n______________GCUG___GCC_ACGCCGGG\n______________:\|\|\|___\|\|\|_\|\|:\|\|:\|\|\n______________UGAC___CGG_UGUGGUCC\n3'-UUU...GCUUA____G_____U________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	265 -- 271	70 -- 76	-23.089 kcal/mol	8.46506 kcal/mol	7.27772 kcal/mol	253 272@LB@ \| \|@LB@5'-GAA...CUUGA AAA AAAAA...GUA-3'@LB@ GCUG GCC ACGCCGGG@LB@ :\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ UGAC CGG UGUGGUCC@LB@3'-UUU...GCUUA G U CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -23.089 kcal/mol@LB@Unfolding Energy - mRNA 8.46506 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 254 -- 271@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 70 -- 76@LB@
90	0.004828	0.1855	b2149	mglA	-7.32	0.409352	216 -- 239	61 -- 86	methyl-galactoside ABC transporter ATPase	_____________215________________________240\n_____________\|__________________________\|\n5'-CGA...CAACG___C____CU__________UA____UUGGA...AUU-3'\n______________ACU_CGUC____CCGGGGAA__CUUG\n______________\|\|\|_\|\|:\|____\|\|:\|\|\|\|\|__\|\|\|\|\n______________UGA_GCGG____GGUCCCUU__GAAC\n3'-UUU...GCUUA___C____UUGU________UA____CGACG...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	227 -- 233	67 -- 73	-23.5814 kcal/mol	8.829 kcal/mol	7.43637 kcal/mol	215 240@LB@ \| \|@LB@5'-CGA...CAACG C CU UA UUGGA...AUU-3'@LB@ ACU CGUC CCGGGGAA CUUG@LB@ \|\|\| \|\|:\| \|\|:\|\|\|\|\| \|\|\|\|@LB@ UGA GCGG GGUCCCUU GAAC@LB@3'-UUU...GCUUA C UUGU UA CGACG...GUG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -7.32 kcal/mol@LB@Hybridization Energy -23.5814 kcal/mol@LB@Unfolding Energy - mRNA 8.829 kcal/mol@LB@Unfolding Energy - sRNA 7.43637 kcal/mol@LB@@LB@Position - mRNA 216 -- 239@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 67 -- 73@LB@
112	0.005982	0.1855	b1820	yobD	-7.30	0.411799	229 -- 243	1 -- 14	UPF0266 family inner membrane protein	_____________228_____________244\n_____________\|_______________\|\n5'-ACC...GAUUC______UC_______UCCUG...CCC-3'\n______________UUUUCA__GCCGCAC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________AAAAGU__CGGCGUG\n3'-UUU...UGACA______C________-5'\n_____________\|______________\|\n_____________15_____________1\n	237 -- 243	1 -- 7	-17.9899 kcal/mol	4.95197 kcal/mol	5.72803 kcal/mol	228 244@LB@ \| \|@LB@5'-ACC...GAUUC UC UCCUG...CCC-3'@LB@ UUUUCA GCCGCAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAAAGU CGGCGUG@LB@3'-UUU...UGACA C -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -17.9899 kcal/mol@LB@Unfolding Energy - mRNA 4.95197 kcal/mol@LB@Unfolding Energy - sRNA 5.72803 kcal/mol@LB@@LB@Position - mRNA 229 -- 243@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 237 -- 243@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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usability assessment

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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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