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
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@
12	0.002293	0.5385	b1823	cspC	-13.69	0.023618	13 -- 32	14 -- 35	stress protein member of the CspA-family	_____________12_____________________33\n_____________\|______________________\|\n5'-UAU...UAACA________________C_____ACAGU...UCU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	20 -- 26	20 -- 26	-23.8593 kcal/mol	6.83349 kcal/mol	3.33183 kcal/mol	12 33@LB@ \| \|@LB@5'-UAU...UAACA C ACAGU...UCU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -23.8593 kcal/mol@LB@Unfolding Energy - mRNA 6.83349 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 20 -- 26@LB@
13	0.002299	0.5385	b3663	yicN	-11.49	0.058154	241 -- 256	60 -- 78	DUF1198 family protein	_____________240_________________257\n_____________\|___________________\|\n5'-CUU...GUUUG___________________GCUGA...AUC-3'\n______________UGGU__UGGUU_UUCGGGU\n______________\|\|\|:__\|:\|\|\|_\|\|\|\|:\|\|\n______________ACCG__AUCAA_AAGCUCA\n3'-CGC...GUGCA____AA_____U_______ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	250 -- 256	60 -- 66	-15.2298 kcal/mol	2.94333 kcal/mol	0.797083 kcal/mol	240 257@LB@ \| \|@LB@5'-CUU...GUUUG GCUGA...AUC-3'@LB@ UGGU UGGUU UUCGGGU@LB@ \|\|\|: \|:\|\|\| \|\|\|\|:\|\|@LB@ ACCG AUCAA AAGCUCA@LB@3'-CGC...GUGCA AA U ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.94333 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 241 -- 256@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 60 -- 66@LB@
14	0.002739	0.5385	b0903	pflB	-11.82	0.050867	80 -- 105	57 -- 81	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________79_________________________106\n_____________\|__________________________\|\n5'-CAC...AUUAU__G____GGUUU____G_________CAUAC...ACU-3'\n______________CG_UGGU_____GUUG_UUGGGUUGA\n______________\|\|_\|\|\|:_____\|\|\|:_\|:\|:\|\|\|\|\|\n______________GC_ACCG_____CAAU_AGCUCAACU\n3'-CGC...CAAGU__A____AAAU_____A_________CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________82_________________________56\n	99 -- 105	57 -- 63	-19.5015 kcal/mol	6.38537 kcal/mol	1.29708 kcal/mol	79 106@LB@ \| \|@LB@5'-CAC...AUUAU G GGUUU G CAUAC...ACU-3'@LB@ CG UGGU GUUG UUGGGUUGA@LB@ \|\| \|\|\|: \|\|\|: \|:\|:\|\|\|\|\|@LB@ GC ACCG CAAU AGCUCAACU@LB@3'-CGC...CAAGU A AAAU A CUUUG...AAG-5'@LB@ \| \|@LB@ 82 56@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -19.5015 kcal/mol@LB@Unfolding Energy - mRNA 6.38537 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 80 -- 105@LB@Position - sRNA 57 -- 81@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 57 -- 63@LB@
15	0.002894	0.5385	b2780	pyrG	-11.46	0.058961	111 -- 140	60 -- 90	CTP synthetase	_____________110_______________________________141\n_____________\|_________________________________\|\n5'-UGU...AUAAU________________ACA___CA_________AUACU...GCC-3'\n______________GAAAGUUUG___UGGC___GGU__UGUUCGGGU\n______________:\|\|\|\|\|\|::___\|\|\|\|___:\|\|__\|:\|\|\|\|:\|\|\n______________UUUUCAAGU___ACCG___UCA__AUAAGCUCA\n3'-CGC...AGGCG_________GCA____AAA______________ACUCU...AAG-5'\n_____________\|_________________________________\|\n_____________91________________________________59\n	134 -- 140	60 -- 66	-21.5125 kcal/mol	8.34782 kcal/mol	1.70935 kcal/mol	110 141@LB@ \| \|@LB@5'-UGU...AUAAU ACA CA AUACU...GCC-3'@LB@ GAAAGUUUG UGGC GGU UGUUCGGGU@LB@ :\|\|\|\|\|\|:: \|\|\|\| :\|\| \|:\|\|\|\|:\|\|@LB@ UUUUCAAGU ACCG UCA AUAAGCUCA@LB@3'-CGC...AGGCG GCA AAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -21.5125 kcal/mol@LB@Unfolding Energy - mRNA 8.34782 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 111 -- 140@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 60 -- 66@LB@
16	0.002981	0.5385	b3428	glgP	-10.45	0.088230	278 -- 289	76 -- 86	glycogen phosphorylase	_____________277__________290\n_____________\|____________\|\n5'-CCA...CUGAU_______A____AAAGG...CGG-3'\n______________GUUUACG_UUGG\n______________\|\|\|:\|\|\|_\|\|\|\|\n______________CAAGUGC_AACC\n3'-CGC...GUUUU____________GAAAU...AAG-5'\n_____________\|____________\|\n_____________87___________75\n	278 -- 284	80 -- 86	-12.981 kcal/mol	2.0211 kcal/mol	0.505081 kcal/mol	277 290@LB@ \| \|@LB@5'-CCA...CUGAU A AAAGG...CGG-3'@LB@ GUUUACG UUGG@LB@ \|\|\|:\|\|\| \|\|\|\|@LB@ CAAGUGC AACC@LB@3'-CGC...GUUUU GAAAU...AAG-5'@LB@ \| \|@LB@ 87 75@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -12.981 kcal/mol@LB@Unfolding Energy - mRNA 2.0211 kcal/mol@LB@Unfolding Energy - sRNA 0.505081 kcal/mol@LB@@LB@Position - mRNA 278 -- 289@LB@Position - sRNA 76 -- 86@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 80 -- 86@LB@
17	0.003067	0.5385	b1628	rsxB	-11.62	0.055094	175 -- 198	58 -- 77	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein	_____________174______________________199\n_____________\|________________________\|\n5'-CAC...UUAUG_________G_____GUGA_____UAAUG...ACG-3'\n______________GGCUUUAGU_GUUUG____AGUUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|____\|\|\|\|\|\n______________CCGAAAUCA_UAAGC____UCAAC\n3'-CGC...UGCAA_________A______________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________78_______________________57\n	177 -- 183	69 -- 75	-20.3316 kcal/mol	7.50919 kcal/mol	1.19974 kcal/mol	174 199@LB@ \| \|@LB@5'-CAC...UUAUG G GUGA UAAUG...ACG-3'@LB@ GGCUUUAGU GUUUG AGUUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\| \|\|\|\|\|@LB@ CCGAAAUCA UAAGC UCAAC@LB@3'-CGC...UGCAA A UCUUU...AAG-5'@LB@ \| \|@LB@ 78 57@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -20.3316 kcal/mol@LB@Unfolding Energy - mRNA 7.50919 kcal/mol@LB@Unfolding Energy - sRNA 1.19974 kcal/mol@LB@@LB@Position - mRNA 175 -- 198@LB@Position - sRNA 58 -- 77@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 69 -- 75@LB@
18	0.003137	0.5385	b1824	yobF	-13.30	0.027752	169 -- 188	14 -- 35	DUF2527 family heat-induced protein	_____________168____________________189\n_____________\|______________________\|\n5'-GCC...UAACA________________C_____ACAGU...UGU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	176 -- 182	20 -- 26	-23.4961 kcal/mol	6.86312 kcal/mol	3.33183 kcal/mol	168 189@LB@ \| \|@LB@5'-GCC...UAACA C ACAGU...UGU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -23.4961 kcal/mol@LB@Unfolding Energy - mRNA 6.86312 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 169 -- 188@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
19	0.003195	0.5385	b3739	atpI	-12.12	0.045044	59 -- 85	62 -- 85	ATP synthase membrane-bound accessory factor	_____________58___________________________86\n_____________\|____________________________\|\n5'-GAA...AUUUA_____CUU______AC____________AAUCA...ACC-3'\n______________UUCAC___UUGGCU__UUA_UUGUUUGA\n______________\|\|\|\|\|___\|\|\|\|\|\|__\|\|\|_\|\|:\|\|:\|\|\n______________AAGUG___AACCGA__AAU_AAUAAGCU\n3'-CGC...UUUUC_____C_____________C________CAACU...AAG-5'\n_____________\|____________________________\|\n_____________86___________________________61\n	79 -- 85	62 -- 68	-17.7596 kcal/mol	3.93623 kcal/mol	1.70582 kcal/mol	58 86@LB@ \| \|@LB@5'-GAA...AUUUA CUU AC AAUCA...ACC-3'@LB@ UUCAC UUGGCU UUA UUGUUUGA@LB@ \|\|\|\|\| \|\|\|\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ AAGUG AACCGA AAU AAUAAGCU@LB@3'-CGC...UUUUC C C CAACU...AAG-5'@LB@ \| \|@LB@ 86 61@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -17.7596 kcal/mol@LB@Unfolding Energy - mRNA 3.93623 kcal/mol@LB@Unfolding Energy - sRNA 1.70582 kcal/mol@LB@@LB@Position - mRNA 59 -- 85@LB@Position - sRNA 62 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 62 -- 68@LB@
20	0.003438	0.5385	b3093	exuT	-11.51	0.057623	213 -- 228	75 -- 90	hexuronate transporter	_____________212______________229\n_____________\|________________\|\n5'-GGA...AAAUU_____G__________AUAUG...CGC-3'\n______________AAAGG_UUACGUUGGU\n______________\|\|\|:\|_\|:\|\|\|\|\|\|\|:\n______________UUUUC_AGUGCAACCG\n3'-CGC...AGGCG_____A__________AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	222 -- 228	75 -- 81	-17.0017 kcal/mol	4.97243 kcal/mol	0.517251 kcal/mol	212 229@LB@ \| \|@LB@5'-GGA...AAAUU G AUAUG...CGC-3'@LB@ AAAGG UUACGUUGGU@LB@ \|\|\|:\| \|:\|\|\|\|\|\|\|:@LB@ UUUUC AGUGCAACCG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -17.0017 kcal/mol@LB@Unfolding Energy - mRNA 4.97243 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 213 -- 228@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 75 -- 81@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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