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
45	0.009513	0.5385	b2513	yfgM	-9.58	0.124672	177 -- 189	15 -- 27	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________176___________190\n_____________\|_____________\|\n5'-GGC...UUACU_________A___AGAAG...UUG-3'\n______________GGGUUAAGG_AGG\n______________\|\|\|\|\|\|\|::_\|\|\|\n______________CCCAAUUUU_UCC\n3'-CGC...AAGUU_________C___ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	179 -- 185	19 -- 25	-14.0675 kcal/mol	1.24912 kcal/mol	3.23583 kcal/mol	176 190@LB@ \| \|@LB@5'-GGC...UUACU A AGAAG...UUG-3'@LB@ GGGUUAAGG AGG@LB@ \|\|\|\|\|\|\|:: \|\|\|@LB@ CCCAAUUUU UCC@LB@3'-CGC...AAGUU C ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.0675 kcal/mol@LB@Unfolding Energy - mRNA 1.24912 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 19 -- 25@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@
120	0.02045	0.5385	b0979	cbdB	-12.05	0.046235	177 -- 194	16 -- 34	cytochrome bd-II oxidase subunit II	_____________176_________________195\n_____________\|___________________\|\n5'-AUA...ACGCA__AA_______________AAAAU...GCU-3'\n______________GC__CAGGGG_UAAAGGAG\n______________:\|__\|\|:\|\|\|_\|\|\|\|:\|\|\|\n______________UG__GUUCCC_AUUUUCUC\n3'-CGC...GUCAC__AA______A________CACGG...AAG-5'\n_____________\|___________________\|\n_____________35__________________15\n	188 -- 194	16 -- 22	-18.7902 kcal/mol	3.40633 kcal/mol	3.33043 kcal/mol	176 195@LB@ \| \|@LB@5'-AUA...ACGCA AA AAAAU...GCU-3'@LB@ GC CAGGGG UAAAGGAG@LB@ :\| \|\|:\|\|\| \|\|\|\|:\|\|\|@LB@ UG GUUCCC AUUUUCUC@LB@3'-CGC...GUCAC AA A CACGG...AAG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -18.7902 kcal/mol@LB@Unfolding Energy - mRNA 3.40633 kcal/mol@LB@Unfolding Energy - sRNA 3.33043 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 16 -- 22@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@
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@
11	0.002269	0.5385	b1205	ychH	-11.36	0.061344	181 -- 195	75 -- 90	DUF2583 family putative inner membrane protein	_____________180______________196\n_____________\|________________\|\n5'-CAA...ACCCA___________GA___GACAU...UAC-3'\n______________GAAAGUUC_CG__GGU\n______________:\|\|\|\|\|\|\|_\|\|__\|\|:\n______________UUUUCAAG_GC__CCG\n3'-CGC...AGGCG________U__AA___AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	182 -- 188	83 -- 89	-14.0006 kcal/mol	2.12575 kcal/mol	0.517251 kcal/mol	180 196@LB@ \| \|@LB@5'-CAA...ACCCA GA GACAU...UAC-3'@LB@ GAAAGUUC CG GGU@LB@ :\|\|\|\|\|\|\| \|\| \|\|:@LB@ UUUUCAAG GC CCG@LB@3'-CGC...AGGCG U AA AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.0006 kcal/mol@LB@Unfolding Energy - mRNA 2.12575 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 83 -- 89@LB@
99	0.01653	0.5385	b0004	thrC	-7.16	0.308279	183 -- 210	49 -- 64	L-threonine synthase	_____________182__________________________211\n_____________\|____________________________\|\n5'-CGC...GCGCA_____AC___AAAACUAAAU________ACAAU...ACG-3'\n______________CGAGU__UGG__________GAAACUCU\n______________\|\|\|\|\|__\|\|:__________\|\|\|\|\|\|\|\|\n______________GCUCA__ACU__________CUUUGAGA\n3'-CGC...AAUAA____________________________GCUUU...AAG-5'\n_____________\|____________________________\|\n_____________65___________________________48\n	204 -- 210	49 -- 55	-14.0058 kcal/mol	2.63666 kcal/mol	4.20534 kcal/mol	182 211@LB@ \| \|@LB@5'-CGC...GCGCA AC AAAACUAAAU ACAAU...ACG-3'@LB@ CGAGU UGG GAAACUCU@LB@ \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|@LB@ GCUCA ACU CUUUGAGA@LB@3'-CGC...AAUAA GCUUU...AAG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -14.0058 kcal/mol@LB@Unfolding Energy - mRNA 2.63666 kcal/mol@LB@Unfolding Energy - sRNA 4.20534 kcal/mol@LB@@LB@Position - mRNA 183 -- 210@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 49 -- 55@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@
73	0.0135	0.5385	b3362	yhfG	-12.23	0.043008	184 -- 212	50 -- 86	putative antitoxin for Fic	_____________183___________________________________213\n_____________\|_____________________________________\|\n5'-GAU...GACAC_____G_GA___A__________A___GA________ACCGA...CUU-3'\n______________GUUCA_G__GGC_________UC_AGU__AGAAACUC\n______________\|\|\|\|\|_\|__\|\|\|_________\|\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________CAAGU_C__CCG_________AG_UCA__UCUUUGAG\n3'-CGC...GUUUU_____G_AA___AAAUCAAUA__C___AC________AGCUU...AAG-5'\n_____________\|_____________________________________\|\n_____________87____________________________________49\n	206 -- 212	50 -- 56	-25.6976 kcal/mol	9.05881 kcal/mol	4.40785 kcal/mol	183 213@LB@ \| \|@LB@5'-GAU...GACAC G GA A A GA ACCGA...CUU-3'@LB@ GUUCA G GGC UC AGU AGAAACUC@LB@ \|\|\|\|\| \| \|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CAAGU C CCG AG UCA UCUUUGAG@LB@3'-CGC...GUUUU G AA AAAUCAAUA C AC AGCUU...AAG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -25.6976 kcal/mol@LB@Unfolding Energy - mRNA 9.05881 kcal/mol@LB@Unfolding Energy - sRNA 4.40785 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 50 -- 56@LB@
98	0.0165	0.5385	b0151	fhuC	-12.15	0.044517	184 -- 202	66 -- 85	iron(3+)-hydroxamate import ABC transporter ATPase	_____________183____________________203\n_____________\|______________________\|\n5'-CUG...CCCAU_____AA_______________GCAGG...CCU-3'\n______________UUCAC__GUUGGCU___GUUAU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAGUG__CAACCGA___CAAUA\n3'-CGC...UUUUC______________AAU_____AGCUC...AAG-5'\n_____________\|______________________\|\n_____________86_____________________65\n	191 -- 197	74 -- 80	-16.912 kcal/mol	4.1925 kcal/mol	0.573112 kcal/mol	183 203@LB@ \| \|@LB@5'-CUG...CCCAU AA GCAGG...CCU-3'@LB@ UUCAC GUUGGCU GUUAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAGUG CAACCGA CAAUA@LB@3'-CGC...UUUUC AAU AGCUC...AAG-5'@LB@ \| \|@LB@ 86 65@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -16.912 kcal/mol@LB@Unfolding Energy - mRNA 4.1925 kcal/mol@LB@Unfolding Energy - sRNA 0.573112 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 85@LB@Position Seed - mRNA 191 -- 197@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)

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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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