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
57	0.01133	0.5385	b0026	ileS	-8.45	0.192830	289 -- 299	74 -- 83	isoleucyl-tRNA synthetase	_____________288_________300\n_____________\|___________\|\n5'-AUG...GCUGG________A__G-3'\n______________CGCGUUGG_CU\n______________\|:\|\|\|\|\|\|_\|\|\n______________GUGCAACC_GA\n3'-CGC...UUCAA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________84__________73\n	290 -- 296	76 -- 82	-13.1796 kcal/mol	4.23376 kcal/mol	0.494551 kcal/mol	288 300@LB@ \| \|@LB@5'-AUG...GCUGG A G-3'@LB@ CGCGUUGG CU@LB@ \|:\|\|\|\|\|\| \|\|@LB@ GUGCAACC GA@LB@3'-CGC...UUCAA AAUCA...AAG-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -13.1796 kcal/mol@LB@Unfolding Energy - mRNA 4.23376 kcal/mol@LB@Unfolding Energy - sRNA 0.494551 kcal/mol@LB@@LB@Position - mRNA 289 -- 299@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 76 -- 82@LB@
64	0.01278	0.5385	b1718	infC	-10.82	0.076139	1 -- 9	71 -- 79	translation initiation factor IF-3	______________1________10\n______________\|________\|\n___________5'-_________AAAUC...AGC-3'\n______________UUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	3 -- 9	71 -- 77	-11.2516 kcal/mol	0.206511 kcal/mol	0.222833 kcal/mol	1 10@LB@ \| \|@LB@ 5'- AAAUC...AGC-3'@LB@ UUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -11.2516 kcal/mol@LB@Unfolding Energy - mRNA 0.206511 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 1 -- 9@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 71 -- 77@LB@
178	0.03115	0.5559	b2528	iscA	-9.66	0.120899	187 -- 207	62 -- 80	FeS cluster assembly protein	_____________186___________________208\n_____________\|_____________________\|\n5'-UUC...UAAGA____A_G_________G____UUACA...CCG-3'\n______________GUUG_G_UUUGGUUAU_UCGA\n______________\|\|\|\|_\|_\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CAAC_C_AAAUCAAUA_AGCU\n3'-CGC...AAGUG______G______________CAACU...AAG-5'\n_____________\|_____________________\|\n_____________81____________________61\n	196 -- 202	66 -- 72	-17.7068 kcal/mol	7.30815 kcal/mol	0.737855 kcal/mol	186 208@LB@ \| \|@LB@5'-UUC...UAAGA A G G UUACA...CCG-3'@LB@ GUUG G UUUGGUUAU UCGA@LB@ \|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CAAC C AAAUCAAUA AGCU@LB@3'-CGC...AAGUG G CAACU...AAG-5'@LB@ \| \|@LB@ 81 61@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -17.7068 kcal/mol@LB@Unfolding Energy - mRNA 7.30815 kcal/mol@LB@Unfolding Energy - sRNA 0.737855 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 62 -- 80@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 66 -- 72@LB@
43	0.009109	0.5385	b2531	iscR	-9.39	0.134324	275 -- 298	62 -- 87	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________274________________________299\n_____________\|__________________________\|\n5'-AUG...GGCCC___A__________GAUAUUUC____AC-3'\n______________GGU_C_CGUUGGCU_________CGA\n______________:\|\|_\|_\|\|\|\|\|\|\|\|_________\|\|\|\n______________UCA_G_GCAACCGA_________GCU\n3'-CGC...CGUUU___A_U________AAUCAAUAA___CAACU...AAG-5'\n_____________\|__________________________\|\n_____________88_________________________61\n	281 -- 287	74 -- 80	-16.3089 kcal/mol	5.20915 kcal/mol	1.70771 kcal/mol	274 299@LB@ \| \|@LB@5'-AUG...GGCCC A GAUAUUUC AC-3'@LB@ GGU C CGUUGGCU CGA@LB@ :\|\| \| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCA G GCAACCGA GCU@LB@3'-CGC...CGUUU A U AAUCAAUAA CAACU...AAG-5'@LB@ \| \|@LB@ 88 61@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -16.3089 kcal/mol@LB@Unfolding Energy - mRNA 5.20915 kcal/mol@LB@Unfolding Energy - sRNA 1.70771 kcal/mol@LB@@LB@Position - mRNA 275 -- 298@LB@Position - sRNA 62 -- 87@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 74 -- 80@LB@
69	0.01301	0.5385	b0174	ispU	-11.35	0.061456	97 -- 106	71 -- 80	undecaprenyl pyrophosphate synthase	_____________96_________107\n_____________\|__________\|\n5'-CGU...AAGUA__________UAAGG...AAA-3'\n______________GUUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CAACCGAAAU\n3'-CGC...AAGUG__________CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	100 -- 106	71 -- 77	-14.3232 kcal/mol	2.73321 kcal/mol	0.236872 kcal/mol	96 107@LB@ \| \|@LB@5'-CGU...AAGUA UAAGG...AAA-3'@LB@ GUUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CAACCGAAAU@LB@3'-CGC...AAGUG CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -14.3232 kcal/mol@LB@Unfolding Energy - mRNA 2.73321 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 97 -- 106@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 71 -- 77@LB@
78	0.01399	0.5385	b3526	kdgK	-7.99	0.228654	189 -- 197	80 -- 88	2-dehydro-3-deoxygluconokinase	_____________188_______198\n_____________\|_________\|\n5'-CCC...AGAUC_________ACUAU...CUU-3'\n______________AGGUUCACG\n______________\|:\|\|\|\|\|\|\|\n______________UUCAAGUGC\n3'-CGC...GCGUU_________AACCG...AAG-5'\n_____________\|_________\|\n_____________89________79\n	191 -- 197	80 -- 86	-11.7911 kcal/mol	3.29177 kcal/mol	0.504555 kcal/mol	188 198@LB@ \| \|@LB@5'-CCC...AGAUC ACUAU...CUU-3'@LB@ AGGUUCACG@LB@ \|:\|\|\|\|\|\|\|@LB@ UUCAAGUGC@LB@3'-CGC...GCGUU AACCG...AAG-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.7911 kcal/mol@LB@Unfolding Energy - mRNA 3.29177 kcal/mol@LB@Unfolding Energy - sRNA 0.504555 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 80 -- 86@LB@
145	0.02443	0.5467	b2569	lepA	-12.53	0.038132	5 -- 17	71 -- 85	back-translocating elongation factor EF4 GTPase	_____________4_______________18\n_____________\|_______________\|\n_______5'-UGAU_______________UUGCA...ACC-3'\n______________UUCAC__UGGCUUUG\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\n______________AAGUG__ACCGAAAU\n3'-CGC...UUUUC_____CA________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	11 -- 17	71 -- 77	-14.3569 kcal/mol	1.27074 kcal/mol	0.560731 kcal/mol	4 18@LB@ \| \|@LB@ 5'-UGAU UUGCA...ACC-3'@LB@ UUCAC UGGCUUUG@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AAGUG ACCGAAAU@LB@3'-CGC...UUUUC CA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.3569 kcal/mol@LB@Unfolding Energy - mRNA 1.27074 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 5 -- 17@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 71 -- 77@LB@
72	0.0135	0.5385	b1117	lolD	-8.66	0.177865	184 -- 202	66 -- 83	outer membrane-specific lipoprotein transporter subunit	_____________183_________________203\n_____________\|___________________\|\n5'-GCU...CAACC___UGA_______C_____GAAUA...GCG-3'\n______________CGC___GGCUUUA_GUUAU\n______________\|:\|___\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GUG___CCGAAAU_CAAUA\n3'-CGC...UUCAA___CAA_____________AGCUC...AAG-5'\n_____________\|___________________\|\n_____________84__________________65\n	190 -- 196	71 -- 77	-15.2298 kcal/mol	6.00943 kcal/mol	0.556032 kcal/mol	183 203@LB@ \| \|@LB@5'-GCU...CAACC UGA C GAAUA...GCG-3'@LB@ CGC GGCUUUA GUUAU@LB@ \|:\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ GUG CCGAAAU CAAUA@LB@3'-CGC...UUCAA CAA AGCUC...AAG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 6.00943 kcal/mol@LB@Unfolding Energy - sRNA 0.556032 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 71 -- 77@LB@
89	0.01549	0.5385	b3147	lpoA	-11.44	0.059349	235 -- 255	64 -- 83	OM lipoprotein stimulator of MrcA transpeptidase	_____________234___________________256\n_____________\|_____________________\|\n5'-UAU...AGCCG_______U__GCCU_______UGGCA...AUC-3'\n______________CGCGUUG_CU____GUUGUUC\n______________\|:\|\|\|\|\|_\|\|____\|\|\|:\|\|\|\n______________GUGCAAC_GA____CAAUAAG\n3'-CGC...UUCAA_______C__AAU________CUCAA...AAG-5'\n_____________\|_____________________\|\n_____________84____________________63\n	249 -- 255	64 -- 70	-16.9353 kcal/mol	4.93537 kcal/mol	0.560651 kcal/mol	234 256@LB@ \| \|@LB@5'-UAU...AGCCG U GCCU UGGCA...AUC-3'@LB@ CGCGUUG CU GUUGUUC@LB@ \|:\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ GUGCAAC GA CAAUAAG@LB@3'-CGC...UUCAA C AAU CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -16.9353 kcal/mol@LB@Unfolding Energy - mRNA 4.93537 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 235 -- 255@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
48	0.009918	0.5385	b0641	lptE	-9.88	0.110832	177 -- 184	74 -- 81	LPS assembly OM complex LptDE lipoprotein component	_____________176______185\n_____________\|________\|\n5'-ACG...CUGGU________AAGCG...UGA-3'\n______________CGUUGGCU\n______________\|\|\|\|\|\|\|\|\n______________GCAACCGA\n3'-CGC...CAAGU________AAUCA...AAG-5'\n_____________\|________\|\n_____________82_______73\n	178 -- 184	74 -- 80	-13.2047 kcal/mol	2.99134 kcal/mol	0.332056 kcal/mol	176 185@LB@ \| \|@LB@5'-ACG...CUGGU AAGCG...UGA-3'@LB@ CGUUGGCU@LB@ \|\|\|\|\|\|\|\|@LB@ GCAACCGA@LB@3'-CGC...CAAGU AAUCA...AAG-5'@LB@ \| \|@LB@ 82 73@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.2047 kcal/mol@LB@Unfolding Energy - mRNA 2.99134 kcal/mol@LB@Unfolding Energy - sRNA 0.332056 kcal/mol@LB@@LB@Position - mRNA 177 -- 184@LB@Position - sRNA 74 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 74 -- 80@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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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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