Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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	Additional homologs
111	0.004429	0.1334	b0141	yadN	-9.15	0.234499	216 -- 249	16 -- 43	putative fimbrial-like adhesin protein		_____________215____________________________________250\n_____________\|______________________________________\|\n5'-UUA...AAUUA_____UGCCCUGU_____CUUAU_______________UUGCA...GUG-3'\n______________GGUUU________CUGGU_____GCUGGCG____AUGG\n______________\|\|\|\|:________\|\|\|\|\|_____\|\|\|:\|\|:____\|\|\|\|\n______________CCAAG________GACCA_____CGAUCGU____UACC\n3'-UUU...CUCCA__________________UGU_________AAAA____CAAUA...UCG-5'\n_____________\|______________________________________\|\n_____________44_____________________________________15\n	239 -- 245	24 -- 30	-21.9877 kcal/mol	8.2619 kcal/mol	4.57091 kcal/mol	215 250@LB@ \| \|@LB@5'-UUA...AAUUA UGCCCUGU CUUAU UUGCA...GUG-3'@LB@ GGUUU CUGGU GCUGGCG AUGG@LB@ \|\|\|\|: \|\|\|\|\| \|\|\|:\|\|: \|\|\|\|@LB@ CCAAG GACCA CGAUCGU UACC@LB@3'-UUU...CUCCA UGU AAAA CAAUA...UCG-5'@LB@ \| \|@LB@ 44 15@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -21.9877 kcal/mol@LB@Unfolding Energy - mRNA 8.2619 kcal/mol@LB@Unfolding Energy - sRNA 4.57091 kcal/mol@LB@@LB@Position - mRNA 216 -- 249@LB@Position - sRNA 16 -- 43@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 24 -- 30@LB@
112	0.004445	0.1334	b0132	yadD	-7.85	0.370183	131 -- 161	16 -- 48	transposase_31 family protein	b3411 b2244 b2305	_____________130________________________________162\n_____________\|__________________________________\|\n5'-CCC...AUAAA_____________ACG_____GC__C__GAC___AUACU...UGG-3'\n______________GAGGUGG___CUG___AUAGC__GC_UU___UGG\n______________\|\|\|\|\|\|\|___\|\|\|___\|:\|\|\|__\|\|_\|\|___\|\|\|\n______________CUCCACC___GAC___UGUCG__CG_AA___ACC\n3'-UUU...GAUUC_______AAG___CA______AU__U__AAU___CAAUA...UCG-5'\n_____________\|__________________________________\|\n_____________49_________________________________15\n	131 -- 137	42 -- 48	-24.9925 kcal/mol	12.5665 kcal/mol	4.57255 kcal/mol	130 162@LB@ \| \|@LB@5'-CCC...AUAAA ACG GC C GAC AUACU...UGG-3'@LB@ GAGGUGG CUG AUAGC GC UU UGG@LB@ \|\|\|\|\|\|\| \|\|\| \|:\|\|\| \|\| \|\| \|\|\|@LB@ CUCCACC GAC UGUCG CG AA ACC@LB@3'-UUU...GAUUC AAG CA AU U AAU CAAUA...UCG-5'@LB@ \| \|@LB@ 49 15@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -24.9925 kcal/mol@LB@Unfolding Energy - mRNA 12.5665 kcal/mol@LB@Unfolding Energy - sRNA 4.57255 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 16 -- 48@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 42 -- 48@LB@
113	0.004738	0.1404	b3197	kdsD	-14.34	0.017174	210 -- 240	1 -- 35	D-arabinose 5-phosphate isomerase		_____________209_________________________________241\n_____________\|___________________________________\|\n5'-AGG...CGCAC___G________ACC________U__AC_______AAGCA...ACA-3'\n______________GUA_AGUUA_CA______GGGUU_UG__UUUCAGC\n______________\|\|\|_\|\|:\|\|_\|\|______\|\|\|\|\|_\|\|__\|\|\|\|\|\|\|\n______________CAU_UCGAU_GU______CCCAA_AC__AAAGUCG\n3'-UUU...AGGAC___G_____C__AAAAUA_____U__AA_______-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	234 -- 240	1 -- 7	-24.924 kcal/mol	9.08416 kcal/mol	1.49508 kcal/mol	209 241@LB@ \| \|@LB@5'-AGG...CGCAC G ACC U AC AAGCA...ACA-3'@LB@ GUA AGUUA CA GGGUU UG UUUCAGC@LB@ \|\|\| \|\|:\|\| \|\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CAU UCGAU GU CCCAA AC AAAGUCG@LB@3'-UUU...AGGAC G C AAAAUA U AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.924 kcal/mol@LB@Unfolding Energy - mRNA 9.08416 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 210 -- 240@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
114	0.004808	0.1404	b2372	yfdV	-9.14	0.236047	240 -- 266	1 -- 35	putative transporter		_____________239____________________________________267\n_____________\|______________________________________\|\n5'-UUC...UUAUC___AU__U______________________________GGCAG...CUC-3'\n______________GUA__CA_GCU_GU______UGGGUUAU____UUUAGC\n______________\|\|\|__\|\|_\|\|\|_\|:______\|\|\|\|\|\|\|\|____\|\|:\|\|\|\n______________CAU__GU_CGA_CG______ACCCAAUA____AAGUCG\n3'-UUU...AGGAC___________U__UAAAAU________CAAA______-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	254 -- 260	11 -- 17	-17.7969 kcal/mol	7.16419 kcal/mol	1.49508 kcal/mol	239 267@LB@ \| \|@LB@5'-UUC...UUAUC AU U GGCAG...CUC-3'@LB@ GUA CA GCU GU UGGGUUAU UUUAGC@LB@ \|\|\| \|\| \|\|\| \|: \|\|\|\|\|\|\|\| \|\|:\|\|\|@LB@ CAU GU CGA CG ACCCAAUA AAGUCG@LB@3'-UUU...AGGAC U UAAAAU CAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -17.7969 kcal/mol@LB@Unfolding Energy - mRNA 7.16419 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 240 -- 266@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
115	0.004814	0.1404	b2743	pcm	-10.63	0.126788	157 -- 183	29 -- 48	L-isoaspartate protein carboxylmethyltransferase type II		_____________156_________________________184\n_____________\|___________________________\|\n5'-AUC...CGCAA__U_______CAGA_____UAA_____GUGGG...AAA-3'\n______________GA_GUGGUUU____CUGGU___ACAGC\n______________\|\|_\|\|\|\|\|\|:____\|\|\|\|\|___\|\|\|\|\|\n______________CU_CACCAAG____GACCA___UGUCG\n3'-UUU...GAUUC__C________________________AUCGU...UCG-5'\n_____________\|___________________________\|\n_____________49__________________________28\n	160 -- 166	39 -- 45	-22.1612 kcal/mol	7.2267 kcal/mol	4.30129 kcal/mol	156 184@LB@ \| \|@LB@5'-AUC...CGCAA U CAGA UAA GUGGG...AAA-3'@LB@ GA GUGGUUU CUGGU ACAGC@LB@ \|\| \|\|\|\|\|\|: \|\|\|\|\| \|\|\|\|\|@LB@ CU CACCAAG GACCA UGUCG@LB@3'-UUU...GAUUC C AUCGU...UCG-5'@LB@ \| \|@LB@ 49 28@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -22.1612 kcal/mol@LB@Unfolding Energy - mRNA 7.2267 kcal/mol@LB@Unfolding Energy - sRNA 4.30129 kcal/mol@LB@@LB@Position - mRNA 157 -- 183@LB@Position - sRNA 29 -- 48@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 39 -- 45@LB@
116	0.004845	0.1404	b2277	nuoM	-9.49	0.205960	1 -- 40	8 -- 43	NADH:ubiquinone oxidoreductase membrane subunit M		______________1___________________________________________41\n______________\|___________________________________________\|\n___________5'-_____G______________CUGUUG____UACUGC____A___AAGGA...UGA-3'\n______________GG_UC_UGGU___GCUGGCA______AUGG______GUUG_GUU\n______________\|\|_\|\|_\|\|\|\|___\|\|\|:\|\|\|______\|\|\|\|______\|\|\|:_\|\|\|\n______________CC_AG_ACCA___CGAUCGU______UACC______CAAU_CAA\n3'-UUU...CUCCA__A__G____UGU_______AAAA________________A___AAAGUCG-5'\n_____________\|____________________________________________\|\n_____________44___________________________________________7\n	10 -- 16	24 -- 30	-25.9982 kcal/mol	11.9029 kcal/mol	4.60748 kcal/mol	1 41@LB@ \| \|@LB@ 5'- G CUGUUG UACUGC A AAGGA...UGA-3'@LB@ GG UC UGGU GCUGGCA AUGG GUUG GUU@LB@ \|\| \|\| \|\|\|\| \|\|\|:\|\|\| \|\|\|\| \|\|\|: \|\|\|@LB@ CC AG ACCA CGAUCGU UACC CAAU CAA@LB@3'-UUU...CUCCA A G UGU AAAA A AAAGUCG-5'@LB@ \| \|@LB@ 44 7@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -25.9982 kcal/mol@LB@Unfolding Energy - mRNA 11.9029 kcal/mol@LB@Unfolding Energy - sRNA 4.60748 kcal/mol@LB@@LB@Position - mRNA 1 -- 40@LB@Position - sRNA 8 -- 43@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 24 -- 30@LB@
117	0.004938	0.1407	b2560	pgpC	-11.09	0.102961	189 -- 233	4 -- 51	phosphatidylglycerophosphatase C membrane bound		_____________188_________________________________________________234\n_____________\|___________________________________________________\|\n5'-UCG...GUCCA______UA__________CA__UCACG_____CG_________________GACUU...GCC-3'\n______________GAGGAG__UGGUU__UGG__AC_____AGCGU__UGUGG____UGUUUUUU\n______________:\|\|\|\|\|__\|\|\|\|\|__\|\|\|__\|\|_____\|\|\|:\|__\|:\|\|\|____\|\|\|\|\|\|\|:\n______________UUCCUC__ACCAA__ACC__UG_____UCGUA__AUACC____ACAAAAAG\n3'-UUU...UCCGA______C______GG___A___UCGA______AA_____CAAU________UCG-5'\n_____________\|___________________________________________________\|\n_____________52__________________________________________________3\n	227 -- 233	4 -- 10	-30.0966 kcal/mol	14.318 kcal/mol	4.69283 kcal/mol	188 234@LB@ \| \|@LB@5'-UCG...GUCCA UA CA UCACG CG GACUU...GCC-3'@LB@ GAGGAG UGGUU UGG AC AGCGU UGUGG UGUUUUUU@LB@ :\|\|\|\|\| \|\|\|\|\| \|\|\| \|\| \|\|\|:\| \|:\|\|\| \|\|\|\|\|\|\|:@LB@ UUCCUC ACCAA ACC UG UCGUA AUACC ACAAAAAG@LB@3'-UUU...UCCGA C GG A UCGA AA CAAU UCG-5'@LB@ \| \|@LB@ 52 3@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -30.0966 kcal/mol@LB@Unfolding Energy - mRNA 14.318 kcal/mol@LB@Unfolding Energy - sRNA 4.69283 kcal/mol@LB@@LB@Position - mRNA 189 -- 233@LB@Position - sRNA 4 -- 51@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@LB@
118	0.00496	0.1407	b1128	roxA	-15.27	0.009267	80 -- 105	22 -- 49	50S ribosomal protein L16 arginine hydroxylase; 2-oxoglutarate oxygenase		_____________79___________________________106\n_____________\|____________________________\|\n5'-UGG...CGGAU_______A_____________C______CUGCG...ACC-3'\n______________GGAGGUG_UUUUUGGU_C_GC_AGCAUU\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|_\|_\|\|_\|\|\|\|\|\|\n______________CCUCCAC_AAGGACCA_G_CG_UCGUAA\n3'-UUU...CGAUU_______C________U_U__A______AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________50___________________________21\n	80 -- 86	43 -- 49	-30.554 kcal/mol	10.7239 kcal/mol	4.55979 kcal/mol	79 106@LB@ \| \|@LB@5'-UGG...CGGAU A C CUGCG...ACC-3'@LB@ GGAGGUG UUUUUGGU C GC AGCAUU@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\| \| \|\| \|\|\|\|\|\|@LB@ CCUCCAC AAGGACCA G CG UCGUAA@LB@3'-UUU...CGAUU C U U A AAUAC...UCG-5'@LB@ \| \|@LB@ 50 21@LB@@LB@@LB@Energy -15.27 kcal/mol@LB@Hybridization Energy -30.554 kcal/mol@LB@Unfolding Energy - mRNA 10.7239 kcal/mol@LB@Unfolding Energy - sRNA 4.55979 kcal/mol@LB@@LB@Position - mRNA 80 -- 105@LB@Position - sRNA 22 -- 49@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 43 -- 49@LB@
119	0.005024	0.1407	b2342	fadI	-9.59	0.197573	199 -- 214	6 -- 21	beta-ketoacyl-CoA thiolase anaerobic subunit		_____________198______________215\n_____________\|________________\|\n5'-UCC...GAGUG________CAG_____ACCGC...AUG-3'\n______________UUAUGGGU___GUUUU\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAUACCCA___CAAAA\n3'-UUU...CGUAA________AUA_____AGUCG-5'\n_____________\|________________\|\n_____________22_______________5\n	200 -- 206	14 -- 20	-13.0434 kcal/mol	3.24348 kcal/mol	0.208077 kcal/mol	198 215@LB@ \| \|@LB@5'-UCC...GAGUG CAG ACCGC...AUG-3'@LB@ UUAUGGGU GUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAUACCCA CAAAA@LB@3'-UUU...CGUAA AUA AGUCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0434 kcal/mol@LB@Unfolding Energy - mRNA 3.24348 kcal/mol@LB@Unfolding Energy - sRNA 0.208077 kcal/mol@LB@@LB@Position - mRNA 199 -- 214@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 14 -- 20@LB@
120	0.005024	0.1407	b2564	pdxJ	-10.23	0.151404	275 -- 296	21 -- 43	pyridoxine 5'-phosphate synthase		_____________274_____________________297\n_____________\|_______________________\|\n5'-AAA...UACCC__A___________GCC______AUUG-3'\n______________GG_UCC_GGUGCAG___GCGUUU\n______________\|\|_\|\|\|_\|\|\|:\|\|\|___\|\|:\|\|\|\n______________CC_AGG_CCAUGUC___CGUAAA\n3'-UUU...CUCCA__A___A_______GAU______AUACC...UCG-5'\n_____________\|_______________________\|\n_____________44______________________20\n	281 -- 287	30 -- 36	-24.4803 kcal/mol	9.69131 kcal/mol	4.55861 kcal/mol	274 297@LB@ \| \|@LB@5'-AAA...UACCC A GCC AUUG-3'@LB@ GG UCC GGUGCAG GCGUUU@LB@ \|\| \|\|\| \|\|\|:\|\|\| \|\|:\|\|\|@LB@ CC AGG CCAUGUC CGUAAA@LB@3'-UUU...CUCCA A A GAU AUACC...UCG-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -24.4803 kcal/mol@LB@Unfolding Energy - mRNA 9.69131 kcal/mol@LB@Unfolding Energy - sRNA 4.55861 kcal/mol@LB@@LB@Position - mRNA 275 -- 296@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 30 -- 36@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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