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
23	0.001281	0.182	b3541	dppD	-11.06	0.072175	116 -- 139	1 -- 23	dipeptide/heme ABC transporter ATPas	_____________115______________________140\n_____________\|________________________\|\n5'-UUU...CGAUC___C________CU_____U____CUGAU...GCG-3'\n______________CUG_UGACGGUG__GGCAU_UAAC\n______________\|\|\|_\|\|\|\|::\|:__\|\|\|\|\|_\|\|\|\|\n______________GAC_ACUGUUAU__CCGUA_AUUG\n3'-UUU...UUUUA____________UU_____U____-5'\n_____________\|_______________________\|\n_____________24______________________1\n	121 -- 127	13 -- 19	-21.9665 kcal/mol	6.28511 kcal/mol	4.61692 kcal/mol	115 140@LB@ \| \|@LB@5'-UUU...CGAUC C CU U CUGAU...GCG-3'@LB@ CUG UGACGGUG GGCAU UAAC@LB@ \|\|\| \|\|\|\|::\|: \|\|\|\|\| \|\|\|\|@LB@ GAC ACUGUUAU CCGUA AUUG@LB@3'-UUU...UUUUA UU U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -21.9665 kcal/mol@LB@Unfolding Energy - mRNA 6.28511 kcal/mol@LB@Unfolding Energy - sRNA 4.61692 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 13 -- 19@LB@
73	0.006265	0.2822	b2452	eutH	-10.44	0.098342	69 -- 89	40 -- 58	ethanolamine transporter	_____________68____________________90\n_____________\|_____________________\|\n5'-UUG...UCCGC________CG_______U___GGAUG...UCC-3'\n______________CAGUGGCG__GUGCAAU_GCC\n______________\|\|\|\|\|\|\|:__:\|\|\|\|\|\|_\|\|\|\n______________GUCACCGU__UACGUUA_CGG\n3'-UUU...UUUUA_________________C___GUUGU...UUG-5'\n_____________\|_____________________\|\n_____________59____________________39\n	79 -- 85	44 -- 50	-25.8936 kcal/mol	9.38235 kcal/mol	6.06808 kcal/mol	68 90@LB@ \| \|@LB@5'-UUG...UCCGC CG U GGAUG...UCC-3'@LB@ CAGUGGCG GUGCAAU GCC@LB@ \|\|\|\|\|\|\|: :\|\|\|\|\|\| \|\|\|@LB@ GUCACCGU UACGUUA CGG@LB@3'-UUU...UUUUA C GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -25.8936 kcal/mol@LB@Unfolding Energy - mRNA 9.38235 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 69 -- 89@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 44 -- 50@LB@
125	0.01291	0.3474	b3006	exbB	-11.08	0.071576	189 -- 220	46 -- 66	membrane spanning protein in TonB-ExbB-ExbD complex	_____________188______________________________221\n_____________\|________________________________\|\n5'-CGC...CGUCC______UACA______GUAAUAAUU_______GACGG...CCU-3'\n______________UGGAGA____CAGUGG_________UAAUGCA\n______________\|\|\|\|:\|____\|\|\|\|\|\|_________:\|\|\|\|\|\|\n______________ACCUUU____GUCACC_________GUUACGU\n3'-UUU...AUACA______UA________________________UACCG...UUG-5'\n_____________\|________________________________\|\n_____________67_______________________________45\n	214 -- 220	46 -- 52	-19.4381 kcal/mol	4.26886 kcal/mol	4.08842 kcal/mol	188 221@LB@ \| \|@LB@5'-CGC...CGUCC UACA GUAAUAAUU GACGG...CCU-3'@LB@ UGGAGA CAGUGG UAAUGCA@LB@ \|\|\|\|:\| \|\|\|\|\|\| :\|\|\|\|\|\|@LB@ ACCUUU GUCACC GUUACGU@LB@3'-UUU...AUACA UA UACCG...UUG-5'@LB@ \| \|@LB@ 67 45@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -19.4381 kcal/mol@LB@Unfolding Energy - mRNA 4.26886 kcal/mol@LB@Unfolding Energy - sRNA 4.08842 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 46 -- 66@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 46 -- 52@LB@
196	0.02524	0.4256	b1805	fadD	-8.19	0.269381	280 -- 298	55 -- 72	acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase)	_____________279_________________299\n_____________\|___________________\|\n5'-UUG...GGUAG_______U___C_______CG-3'\n______________AUAUGUU_GAG_AGUCGGU\n______________\|\|\|\|\|\|\|_\|\|:_\|:\|\|:\|\|\n______________UAUACAA_CUU_UUAGUCA\n3'-UUU...AAAAA_______C___________CCGUU...UUG-5'\n_____________\|___________________\|\n_____________73__________________54\n	292 -- 298	55 -- 61	-14.048 kcal/mol	3.20699 kcal/mol	2.64594 kcal/mol	279 299@LB@ \| \|@LB@5'-UUG...GGUAG U C CG-3'@LB@ AUAUGUU GAG AGUCGGU@LB@ \|\|\|\|\|\|\| \|\|: \|:\|\|:\|\|@LB@ UAUACAA CUU UUAGUCA@LB@3'-UUU...AAAAA C CCGUU...UUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -14.048 kcal/mol@LB@Unfolding Energy - mRNA 3.20699 kcal/mol@LB@Unfolding Energy - sRNA 2.64594 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 55 -- 61@LB@
84	0.00705	0.2822	b2341	fadJ	-9.52	0.152421	171 -- 187	39 -- 55	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase	_____________170_______________188\n_____________\|_________________\|\n5'-CAU...GGGCU_____CG__________UGGAG...CGG-3'\n______________UGGCG__GCAAUGGUUC\n______________\|\|\|\|:__\|\|\|\|\|\|\|::\|\n______________ACCGU__CGUUACCGGG\n3'-UUU...UAGUC_____UA__________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________56________________38\n	181 -- 187	39 -- 45	-22.4983 kcal/mol	8.21876 kcal/mol	4.76312 kcal/mol	170 188@LB@ \| \|@LB@5'-CAU...GGGCU CG UGGAG...CGG-3'@LB@ UGGCG GCAAUGGUUC@LB@ \|\|\|\|: \|\|\|\|\|\|\|::\|@LB@ ACCGU CGUUACCGGG@LB@3'-UUU...UAGUC UA UUGUC...UUG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -22.4983 kcal/mol@LB@Unfolding Energy - mRNA 8.21876 kcal/mol@LB@Unfolding Energy - sRNA 4.76312 kcal/mol@LB@@LB@Position - mRNA 171 -- 187@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 39 -- 45@LB@
66	0.005339	0.2645	b1476	fdnI	-10.79	0.082799	156 -- 194	9 -- 48	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________155________________________________________195\n_____________\|__________________________________________\|\n5'-CGU...CAUCG___U________AUA_____________GA______G_____AUCAU...UUU-3'\n______________GUA_UGGCCCGA___AGGAAGUGGA__C__UGACGA__GAGG\n______________\|:\|_\|\|\|\|\|\|:\|___\|\|:\|\|:\|::\|__\|__\|\|\|\|:\|__:\|\|\|\n______________CGU_ACCGGGUU___UCUUUUAUUU__G__ACUGUU__UUCC\n3'-UUU...CGUUA___U________G____________UA_AC______AU____GUAUAUUG-5'\n_____________\|__________________________________________\|\n_____________49_________________________________________8\n	161 -- 167	37 -- 43	-34.1322 kcal/mol	12.2398 kcal/mol	11.1008 kcal/mol	155 195@LB@ \| \|@LB@5'-CGU...CAUCG U AUA GA G AUCAU...UUU-3'@LB@ GUA UGGCCCGA AGGAAGUGGA C UGACGA GAGG@LB@ \|:\| \|\|\|\|\|\|:\| \|\|:\|\|:\|::\| \| \|\|\|\|:\| :\|\|\|@LB@ CGU ACCGGGUU UCUUUUAUUU G ACUGUU UUCC@LB@3'-UUU...CGUUA U G UA AC AU GUAUAUUG-5'@LB@ \| \|@LB@ 49 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -34.1322 kcal/mol@LB@Unfolding Energy - mRNA 12.2398 kcal/mol@LB@Unfolding Energy - sRNA 11.1008 kcal/mol@LB@@LB@Position - mRNA 156 -- 194@LB@Position - sRNA 9 -- 48@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 37 -- 43@LB@
164	0.01912	0.392	b0585	fes	-11.27	0.064985	233 -- 253	39 -- 56	enterobactin/ferrienterobactin esterase	_____________232____________________254\n_____________\|______________________\|\n5'-CAU...AGCUG____________AACA______GGAAU...GGU-3'\n______________GUGGCAGU_CGA____UGGCCC\n______________\|\|\|\|\|\|:\|_\|:\|____\|\|\|\|\|\|\n______________CACCGUUA_GUU____ACCGGG\n3'-UUU...UUAGU________C_____________UUGUC...UUG-5'\n_____________\|______________________\|\n_____________57_____________________38\n	234 -- 240	49 -- 55	-24.6014 kcal/mol	8.56812 kcal/mol	4.76336 kcal/mol	232 254@LB@ \| \|@LB@5'-CAU...AGCUG AACA GGAAU...GGU-3'@LB@ GUGGCAGU CGA UGGCCC@LB@ \|\|\|\|\|\|:\| \|:\| \|\|\|\|\|\|@LB@ CACCGUUA GUU ACCGGG@LB@3'-UUU...UUAGU C UUGUC...UUG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -24.6014 kcal/mol@LB@Unfolding Energy - mRNA 8.56812 kcal/mol@LB@Unfolding Energy - sRNA 4.76336 kcal/mol@LB@@LB@Position - mRNA 233 -- 253@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 49 -- 55@LB@
154	0.01792	0.3828	b2610	ffh	-8.53	0.234957	246 -- 258	48 -- 60	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________245___________259\n_____________\|_____________\|\n5'-AGG...GCAAU_________C___GACGC...AAG-3'\n______________AUCAGUGGC_GUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|\n______________UAGUCACCG_UAC\n3'-UUU...CCUUU_________U___GUUAC...UUG-5'\n_____________\|_____________\|\n_____________61____________47\n	248 -- 254	52 -- 58	-18.214 kcal/mol	6.29175 kcal/mol	3.39422 kcal/mol	245 259@LB@ \| \|@LB@5'-AGG...GCAAU C GACGC...AAG-3'@LB@ AUCAGUGGC GUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|@LB@ UAGUCACCG UAC@LB@3'-UUU...CCUUU U GUUAC...UUG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.214 kcal/mol@LB@Unfolding Energy - mRNA 6.29175 kcal/mol@LB@Unfolding Energy - sRNA 3.39422 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 52 -- 58@LB@
184	0.02285	0.4143	b4312	fimB	-10.59	0.091292	169 -- 221	1 -- 58	tyrosine recombinase/inversion of on/off regulator of fimA	_____________168________________________________________________________________222\n_____________\|__________________________________________________________________\|\n5'-AUG...ACAGC_____C___UC______UA_____G________________________AGAAUA____UG_____AAAAA...GUA-3'\n______________UAGUG_GCG__UGUAAU____UAA_GGAAAA___________ACGAUGA______AGGC__AUAAC\n______________:\|\|\|\|_\|\|:__\|\|:\|\|\|____:\|\|_:\|\|\|\|\|___________\|\|:\|\|:\|______\|\|\|\|__\|\|\|\|\|\n______________GUCAC_CGU__ACGUUA____GUU_UCUUUU___________UGUUAUU______UCCG__UAUUG\n3'-UUU...UUUUA_________U_______CCGG___G______AUUUUAGACAC_________________UA_____-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	198 -- 204	12 -- 18	-31.4649 kcal/mol	8.72248 kcal/mol	12.1476 kcal/mol	168 222@LB@ \| \|@LB@5'-AUG...ACAGC C UC UA G AGAAUA UG AAAAA...GUA-3'@LB@ UAGUG GCG UGUAAU UAA GGAAAA ACGAUGA AGGC AUAAC@LB@ :\|\|\|\| \|\|: \|\|:\|\|\| :\|\| :\|\|\|\|\| \|\|:\|\|:\| \|\|\|\| \|\|\|\|\|@LB@ GUCAC CGU ACGUUA GUU UCUUUU UGUUAUU UCCG UAUUG@LB@3'-UUU...UUUUA U CCGG G AUUUUAGACAC UA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -31.4649 kcal/mol@LB@Unfolding Energy - mRNA 8.72248 kcal/mol@LB@Unfolding Energy - sRNA 12.1476 kcal/mol@LB@@LB@Position - mRNA 169 -- 221@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
77	0.006658	0.2822	b3347	fkpA	-8.74	0.214444	80 -- 111	4 -- 28	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)	_____________79________________________________112\n_____________\|_________________________________\|\n5'-UGG...CAAAA________AAAAUAGA_________________CUGUA...CAG-3'\n______________AGAGUCUG________UGAUAAU_AGGGCGUGU\n______________\|:\|:\|\|\|\|________\|\|\|:\|\|\|_\|:\|\|\|:\|:\|\n______________UUUUAGAC________ACUGUUA_UUCCGUAUA\n3'-UUU...UUUUA_______________________U_________UUG-5'\n_____________\|_________________________________\|\n_____________29________________________________3\n	104 -- 110	5 -- 11	-22.6947 kcal/mol	9.05802 kcal/mol	4.89231 kcal/mol	79 112@LB@ \| \|@LB@5'-UGG...CAAAA AAAAUAGA CUGUA...CAG-3'@LB@ AGAGUCUG UGAUAAU AGGGCGUGU@LB@ \|:\|:\|\|\|\| \|\|\|:\|\|\| \|:\|\|\|:\|:\|@LB@ UUUUAGAC ACUGUUA UUCCGUAUA@LB@3'-UUU...UUUUA U UUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -22.6947 kcal/mol@LB@Unfolding Energy - mRNA 9.05802 kcal/mol@LB@Unfolding Energy - sRNA 4.89231 kcal/mol@LB@@LB@Position - mRNA 80 -- 111@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 5 -- 11@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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