Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
40	0.008109	0.5385	b0784	moaD	-13.26	0.028244	179 -- 200	15 -- 38	molybdopterin synthase small subunit	_____________178______________________201\n_____________\|________________________\|\n5'-GCA...AGUCG_____________________C__AUGAU...AGC-3'\n______________GGUGACUUUAAGG__UGGAAG_GG\n______________:\|\|\|\|\|\|\|:\|\|\|\|__\|::\|\|\|_\|\|\n______________UCACUGAAGUUCC__AUUUUC_CC\n3'-CGC...GCCCG_____________CA______U__ACGGC...AAG-5'\n_____________\|________________________\|\n_____________39_______________________14\n	185 -- 191	26 -- 32	-24.646 kcal/mol	4.81525 kcal/mol	6.57247 kcal/mol	178 201@LB@ \| \|@LB@5'-GCA...AGUCG C AUGAU...AGC-3'@LB@ GGUGACUUUAAGG UGGAAG GG@LB@ :\|\|\|\|\|\|\|:\|\|\|\| \|::\|\|\| \|\|@LB@ UCACUGAAGUUCC AUUUUC CC@LB@3'-CGC...GCCCG CA U ACGGC...AAG-5'@LB@ \| \|@LB@ 39 14@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -24.646 kcal/mol@LB@Unfolding Energy - mRNA 4.81525 kcal/mol@LB@Unfolding Energy - sRNA 6.57247 kcal/mol@LB@@LB@Position - mRNA 179 -- 200@LB@Position - sRNA 15 -- 38@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 26 -- 32@LB@
22	0.004141	0.5385	b0462	acrB	-13.08	0.030428	256 -- 265	75 -- 84	multidrug efflux system protein	_____________255________266\n_____________\|__________\|\n5'-AAG...UAUCA__________AGGGG...CGC-3'\n______________UCAUGUUGGC\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	259 -- 265	75 -- 81	-16.8887 kcal/mol	3.30616 kcal/mol	0.505918 kcal/mol	255 266@LB@ \| \|@LB@5'-AAG...UAUCA AGGGG...CGC-3'@LB@ UCAUGUUGGC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -16.8887 kcal/mol@LB@Unfolding Energy - mRNA 3.30616 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 256 -- 265@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 75 -- 81@LB@
44	0.009138	0.5385	b4148	sugE	-12.73	0.035076	273 -- 288	62 -- 77	multidrug efflux system protein	_____________272______________289\n_____________\|________________\|\n5'-CGC...CCCAC_________C______CGCCG...UUA-3'\n______________GGCUUUAGU_GUUUGA\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|\|\n______________CCGAAAUCA_UAAGCU\n3'-CGC...UGCAA_________A______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	275 -- 281	69 -- 75	-18.0703 kcal/mol	4.60455 kcal/mol	0.736118 kcal/mol	272 289@LB@ \| \|@LB@5'-CGC...CCCAC C CGCCG...UUA-3'@LB@ GGCUUUAGU GUUUGA@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\|\|@LB@ CCGAAAUCA UAAGCU@LB@3'-CGC...UGCAA A CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -18.0703 kcal/mol@LB@Unfolding Energy - mRNA 4.60455 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 273 -- 288@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 69 -- 75@LB@
7	0.001275	0.5385	b2175	mepS	-13.85	0.022182	178 -- 188	25 -- 35	murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase	_____________177_________189\n_____________\|___________\|\n5'-CAA...UUAAG___________AAAAC...CAA-3'\n______________GACUUCAAGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________CUGAAGUUCCC\n3'-CGC...CGUCA___________AAUUU...AAG-5'\n_____________\|___________\|\n_____________36__________24\n	182 -- 188	25 -- 31	-19.9152 kcal/mol	2.73903 kcal/mol	3.32958 kcal/mol	177 189@LB@ \| \|@LB@5'-CAA...UUAAG AAAAC...CAA-3'@LB@ GACUUCAAGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ CUGAAGUUCCC@LB@3'-CGC...CGUCA AAUUU...AAG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 2.73903 kcal/mol@LB@Unfolding Energy - sRNA 3.32958 kcal/mol@LB@@LB@Position - mRNA 178 -- 188@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 25 -- 31@LB@
24	0.00428	0.5385	b0090	murG	-10.85	0.075280	191 -- 203	77 -- 89	N-acetylglucosaminyl transferase	_____________190___________204\n_____________\|_____________\|\n5'-AUU...UGUAC__________A__AGUGG...GUU-3'\n______________GAGGUUCACG_UG\n______________:\|:\|\|\|\|\|\|\|_\|\|\n______________UUUCAAGUGC_AC\n3'-CGC...GGCGU__________A__CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	194 -- 200	80 -- 86	-14.5499 kcal/mol	3.18923 kcal/mol	0.510111 kcal/mol	190 204@LB@ \| \|@LB@5'-AUU...UGUAC A AGUGG...GUU-3'@LB@ GAGGUUCACG UG@LB@ :\|:\|\|\|\|\|\|\| \|\|@LB@ UUUCAAGUGC AC@LB@3'-CGC...GGCGU A CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -14.5499 kcal/mol@LB@Unfolding Energy - mRNA 3.18923 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 80 -- 86@LB@
95	0.01635	0.5385	b2287	nuoB	-8.27	0.206762	33 -- 42	71 -- 80	NADH:ubiquinone oxidoreductase chain B	_____________32_________43\n_____________\|__________\|\n5'-CAU...GCUGG__A_______UGGAA...UUA-3'\n______________GU_GGCUUUG\n______________\|\|_\|\|\|\|\|\|:\n______________CA_CCGAAAU\n3'-CGC...AAGUG__A_______CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	36 -- 42	71 -- 77	-10.0496 kcal/mol	1.54713 kcal/mol	0.236872 kcal/mol	32 43@LB@ \| \|@LB@5'-CAU...GCUGG A UGGAA...UUA-3'@LB@ GU GGCUUUG@LB@ \|\| \|\|\|\|\|\|:@LB@ CA CCGAAAU@LB@3'-CGC...AAGUG A CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -10.0496 kcal/mol@LB@Unfolding Energy - mRNA 1.54713 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 33 -- 42@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 71 -- 77@LB@
51	0.01052	0.5385	b0751	pnuC	-11.84	0.050492	77 -- 89	77 -- 89	nicotinamide riboside transporter	_____________76____________90\n_____________\|_____________\|\n5'-CGC...AUCAC_____________AUGAA...GGU-3'\n______________GAGGUUCAUGUUG\n______________:\|:\|\|\|\|\|:\|\|\|\|\n______________UUUCAAGUGCAAC\n3'-CGC...GGCGU_____________CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	83 -- 89	77 -- 83	-16.9239 kcal/mol	4.57656 kcal/mol	0.510111 kcal/mol	76 90@LB@ \| \|@LB@5'-CGC...AUCAC AUGAA...GGU-3'@LB@ GAGGUUCAUGUUG@LB@ :\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUCAAGUGCAAC@LB@3'-CGC...GGCGU CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -11.84 kcal/mol@LB@Hybridization Energy -16.9239 kcal/mol@LB@Unfolding Energy - mRNA 4.57656 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 77 -- 83@LB@
155	0.02668	0.5559	b1625	cnu	-8.12	0.218326	240 -- 246	81 -- 87	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________239_____247\n_____________\|_______\|\n5'-UUU...AAAUC_______UCGAA...AUC-3'\n______________AGUUCAC\n______________\|\|\|\|\|\|\|\n______________UCAAGUG\n3'-CGC...CGUUU_______CAACC...AAG-5'\n_____________\|_______\|\n_____________88______80\n	240 -- 246	81 -- 87	-9.1905 kcal/mol	0.576286 kcal/mol	0.494577 kcal/mol	239 247@LB@ \| \|@LB@5'-UUU...AAAUC UCGAA...AUC-3'@LB@ AGUUCAC@LB@ \|\|\|\|\|\|\|@LB@ UCAAGUG@LB@3'-CGC...CGUUU CAACC...AAG-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.1905 kcal/mol@LB@Unfolding Energy - mRNA 0.576286 kcal/mol@LB@Unfolding Energy - sRNA 0.494577 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 81 -- 87@LB@
92	0.01569	0.5385	b1246	oppD	-11.32	0.062179	266 -- 290	69 -- 90	oligopeptide ABC transporter ATPase	_____________265_______________________291\n_____________\|_________________________\|\n5'-AGC...AACGU_____A_______GUCAC_______ACCCC...ACG-3'\n______________GAAAG_UUUGCGU_____CUUUAGU\n______________:\|\|\|\|_\|\|::\|\|\|_____\|\|\|\|\|\|\|\n______________UUUUC_AAGUGCA_____GAAAUCA\n3'-CGC...AGGCG_____________ACC_________AUAAG...AAG-5'\n_____________\|_________________________\|\n_____________91________________________68\n	284 -- 290	69 -- 75	-14.6652 kcal/mol	2.76867 kcal/mol	0.572281 kcal/mol	265 291@LB@ \| \|@LB@5'-AGC...AACGU A GUCAC ACCCC...ACG-3'@LB@ GAAAG UUUGCGU CUUUAGU@LB@ :\|\|\|\| \|\|::\|\|\| \|\|\|\|\|\|\|@LB@ UUUUC AAGUGCA GAAAUCA@LB@3'-CGC...AGGCG ACC AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -14.6652 kcal/mol@LB@Unfolding Energy - mRNA 2.76867 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
126	0.02177	0.5385	b4162	orn	-9.93	0.108535	62 -- 89	61 -- 86	oligoribonuclease	_____________61___________________________90\n_____________\|____________________________\|\n5'-ACA...UUGGC_______CG_C___GC___CCU__G___AGUUU...CCG-3'\n______________GUUCACG__G_GCU__UGG___UU_GAG\n______________\|\|\|\|\|\|\|__\|_\|\|\|__\|:\|___\|\|_\|\|\|\n______________CAAGUGC__C_CGA__AUC___AA_CUC\n3'-CGC...GUUUU_______AA_____A____AAU__G___AACUC...AAG-5'\n_____________\|____________________________\|\n_____________87___________________________60\n	62 -- 68	80 -- 86	-20.598 kcal/mol	8.95458 kcal/mol	1.70915 kcal/mol	61 90@LB@ \| \|@LB@5'-ACA...UUGGC CG C GC CCU G AGUUU...CCG-3'@LB@ GUUCACG G GCU UGG UU GAG@LB@ \|\|\|\|\|\|\| \| \|\|\| \|:\| \|\| \|\|\|@LB@ CAAGUGC C CGA AUC AA CUC@LB@3'-CGC...GUUUU AA A AAU G AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -20.598 kcal/mol@LB@Unfolding Energy - mRNA 8.95458 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 62 -- 89@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 80 -- 86@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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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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