Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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	Additional homologs
151	0.0157	0.3349	b0586	entF	-8.26	0.051334	189 -- 199	37 -- 47	enterobactin synthase multienzyme complex component ATP-dependent		_____________188_________200\n_____________\|___________\|\n5'-CCC...CAGUU___________AAUGA...UUG-3'\n______________GCAGGAGGCAC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	193 -- 199	37 -- 43	-17.6877 kcal/mol	4.1913 kcal/mol	5.23944 kcal/mol	188 200@LB@ \| \|@LB@5'-CCC...CAGUU AAUGA...UUG-3'@LB@ GCAGGAGGCAC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -17.6877 kcal/mol@LB@Unfolding Energy - mRNA 4.1913 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
16	0.0003675	0.07398	b0566	envY	-6.67	0.133095	149 -- 159	37 -- 47	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________148_________160\n_____________\|___________\|\n5'-GGC...CUCAU___________AGAUC...ACU-3'\n______________GCAGGAAGCAU\n______________\|\|\|:\|\|\|\|\|\|:\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	153 -- 159	37 -- 43	-16.6622 kcal/mol	4.74809 kcal/mol	5.23944 kcal/mol	148 160@LB@ \| \|@LB@5'-GGC...CUCAU AGAUC...ACU-3'@LB@ GCAGGAAGCAU@LB@ \|\|\|:\|\|\|\|\|\|:@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -16.6622 kcal/mol@LB@Unfolding Energy - mRNA 4.74809 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 149 -- 159@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 37 -- 43@LB@
40	0.001639	0.1292	b0156	erpA	-9.82	0.018424	105 -- 133	14 -- 48	iron-sulfur cluster insertion protein		_____________104_________________________________134\n_____________\|___________________________________\|\n5'-UAG...CAGCC________________________AA_________UAUUA...UAC-3'\n______________AGCGAGAA_UACUUGAA_____CG__AUACCAGGG\n______________\|\|\|:\|\|\|\|_:\|\|\|\|:\|\|_____\|\|__\|:\|\|\|\|\|\|:\n______________UCGUUCUU_GUGAAUUU_____GC__UGUGGUCCU\n3'-UUU...CGAAU________C________UUUAA__AA_________UUAGA...CAA-5'\n_____________\|___________________________________\|\n_____________49__________________________________13\n	127 -- 133	14 -- 20	-29.1703 kcal/mol	5.55319 kcal/mol	13.801 kcal/mol	104 134@LB@ \| \|@LB@5'-UAG...CAGCC AA UAUUA...UAC-3'@LB@ AGCGAGAA UACUUGAA CG AUACCAGGG@LB@ \|\|\|:\|\|\|\| :\|\|\|\|:\|\| \|\| \|:\|\|\|\|\|\|:@LB@ UCGUUCUU GUGAAUUU GC UGUGGUCCU@LB@3'-UUU...CGAAU C UUUAA AA UUAGA...CAA-5'@LB@ \| \|@LB@ 49 13@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -29.1703 kcal/mol@LB@Unfolding Energy - mRNA 5.55319 kcal/mol@LB@Unfolding Energy - sRNA 13.801 kcal/mol@LB@@LB@Position - mRNA 105 -- 133@LB@Position - sRNA 14 -- 48@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 14 -- 20@LB@
133	0.0127	0.3077	b2452	eutH	-4.80	0.352106	186 -- 194	38 -- 46	ethanolamine transporter		_____________185_______195\n_____________\|_________\|\n5'-UUG...ACUAA_________AAGGC...UCC-3'\n______________CAGGGAGUA\n______________\|\|:\|:\|\|:\|\n______________GUUCUUCGU\n3'-UUU...AAUUC_________GAAUU...CAA-5'\n_____________\|_________\|\n_____________47________37\n	188 -- 194	38 -- 44	-8.62764 kcal/mol	1.2009 kcal/mol	2.62609 kcal/mol	185 195@LB@ \| \|@LB@5'-UUG...ACUAA AAGGC...UCC-3'@LB@ CAGGGAGUA@LB@ \|\|:\|:\|\|:\|@LB@ GUUCUUCGU@LB@3'-UUU...AAUUC GAAUU...CAA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.80 kcal/mol@LB@Hybridization Energy -8.62764 kcal/mol@LB@Unfolding Energy - mRNA 1.2009 kcal/mol@LB@Unfolding Energy - sRNA 2.62609 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 38 -- 44@LB@
83	0.005546	0.2146	b0221	fadE	-11.24	0.006780	20 -- 32	37 -- 49	acyl coenzyme A dehydrogenase		_____________19____________33\n_____________\|_____________\|\n5'-GUG...GCCAA_____________GGGCA...GGA-3'\n______________AAGCGAGAAGUAC\n______________\|\|\|\|:\|\|\|\|\|:\|\|\n______________UUCGUUCUUCGUG\n3'-UUU...ACGAA_____________AAUUU...CAA-5'\n_____________\|_____________\|\n_____________50____________36\n	26 -- 32	37 -- 43	-19.9972 kcal/mol	2.7283 kcal/mol	6.03369 kcal/mol	19 33@LB@ \| \|@LB@5'-GUG...GCCAA GGGCA...GGA-3'@LB@ AAGCGAGAAGUAC@LB@ \|\|\|\|:\|\|\|\|\|:\|\|@LB@ UUCGUUCUUCGUG@LB@3'-UUU...ACGAA AAUUU...CAA-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.24 kcal/mol@LB@Hybridization Energy -19.9972 kcal/mol@LB@Unfolding Energy - mRNA 2.7283 kcal/mol@LB@Unfolding Energy - sRNA 6.03369 kcal/mol@LB@@LB@Position - mRNA 20 -- 32@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 37 -- 43@LB@
49	0.002267	0.1465	b0592	fepB	-6.35	0.159662	143 -- 160	24 -- 40	ferrienterobactin ABC transporter periplasmic binding protein		_____________142________________161\n_____________\|__________________\|\n5'-AUA...AUUGU______UGUC________CAUUA...UUA-3'\n______________GCGCUU____GAAUUUGU\n______________\|\|:\|\|\|____:\|\|\|\|:\|\|\n______________CGUGAA____UUUAAGCA\n3'-UUU...UUCUU______UUU_________AUGUG...CAA-5'\n_____________\|__________________\|\n_____________41_________________23\n	154 -- 160	24 -- 30	-12.773 kcal/mol	4.77335 kcal/mol	1.64869 kcal/mol	142 161@LB@ \| \|@LB@5'-AUA...AUUGU UGUC CAUUA...UUA-3'@LB@ GCGCUU GAAUUUGU@LB@ \|\|:\|\|\| :\|\|\|\|:\|\|@LB@ CGUGAA UUUAAGCA@LB@3'-UUU...UUCUU UUU AUGUG...CAA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.35 kcal/mol@LB@Hybridization Energy -12.773 kcal/mol@LB@Unfolding Energy - mRNA 4.77335 kcal/mol@LB@Unfolding Energy - sRNA 1.64869 kcal/mol@LB@@LB@Position - mRNA 143 -- 160@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 24 -- 30@LB@
9	7.531e-05	0.02695	b0491	fetB	-11.86	0.004271	187 -- 209	25 -- 47	iron export ABC transporter permease; peroxide resistance protein		_____________186_____________________210\n_____________\|_______________________\|\n5'-GCC...GAAAU___________GCUAU___C___CAUAA...AGA-3'\n______________GCAGGAAGCAC_____GAA_UCG\n______________\|\|\|:\|\|\|\|\|\|\|_____:\|\|_\|\|\|\n______________CGUUCUUCGUG_____UUU_AGC\n3'-UUU...GAAUU___________AAUUU___A___AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	191 -- 197	37 -- 43	-22.8314 kcal/mol	4.71887 kcal/mol	6.25056 kcal/mol	186 210@LB@ \| \|@LB@5'-GCC...GAAAU GCUAU C CAUAA...AGA-3'@LB@ GCAGGAAGCAC GAA UCG@LB@ \|\|\|:\|\|\|\|\|\|\| :\|\| \|\|\|@LB@ CGUUCUUCGUG UUU AGC@LB@3'-UUU...GAAUU AAUUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -22.8314 kcal/mol@LB@Unfolding Energy - mRNA 4.71887 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
81	0.005437	0.2146	b1073	flgB	-5.23	0.286610	229 -- 247	36 -- 53	flagellar component of cell-proximal portion of basal-body rod		_____________228_________________248\n_____________\|___________________\|\n5'-UGA...CUUAC____UCAA___________CAAUC...CCG-3'\n______________GUUU____CAAGAGGCGCU\n______________\|:\|\|____\|\|\|\|\|:\|\|:\|\|\n______________CGAA____GUUCUUCGUGA\n3'-UUU...UUGAA____UUC____________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________35\n	241 -- 247	36 -- 42	-18.0666 kcal/mol	6.73003 kcal/mol	6.10238 kcal/mol	228 248@LB@ \| \|@LB@5'-UGA...CUUAC UCAA CAAUC...CCG-3'@LB@ GUUU CAAGAGGCGCU@LB@ \|:\|\| \|\|\|\|\|:\|\|:\|\|@LB@ CGAA GUUCUUCGUGA@LB@3'-UUU...UUGAA UUC AUUUU...CAA-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -18.0666 kcal/mol@LB@Unfolding Energy - mRNA 6.73003 kcal/mol@LB@Unfolding Energy - sRNA 6.10238 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 36 -- 42@LB@
196	0.02353	0.3864	b1948	fliP	-9.61	0.021211	171 -- 185	45 -- 59	flagellar biosynthesis protein		_____________170_____________186\n_____________\|_______________\|\n5'-AUU...AUGAA_______________UAGCG...GCG-3'\n______________AAAUUUGCUUAAGCG\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|:\n______________UUUGAACGAAUUCGU\n3'-UUU...CCUAC_______________UCUUC...CAA-5'\n_____________\|_______________\|\n_____________60______________44\n	178 -- 184	46 -- 52	-18.3894 kcal/mol	2.75936 kcal/mol	6.02152 kcal/mol	170 186@LB@ \| \|@LB@5'-AUU...AUGAA UAGCG...GCG-3'@LB@ AAAUUUGCUUAAGCG@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|:@LB@ UUUGAACGAAUUCGU@LB@3'-UUU...CCUAC UCUUC...CAA-5'@LB@ \| \|@LB@ 60 44@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -18.3894 kcal/mol@LB@Unfolding Energy - mRNA 2.75936 kcal/mol@LB@Unfolding Energy - sRNA 6.02152 kcal/mol@LB@@LB@Position - mRNA 171 -- 185@LB@Position - sRNA 45 -- 59@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 46 -- 52@LB@
125	0.01132	0.2916	b4152	frdC	-8.74	0.037729	137 -- 154	25 -- 41	fumarate reductase (anaerobic) membrane anchor subunit		_____________136________________155\n_____________\|__________________\|\n5'-AGA...AGCAG____AAG___________AAAGA...CGG-3'\n______________GGCA___UAGAAAGUUCG\n______________:\|\|\|___\|\|:\|\|\|:\|\|\|\|\n______________UCGU___AUUUUUUAAGC\n3'-UUU...GUUCU____GA____________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	148 -- 154	25 -- 31	-13.3883 kcal/mol	3.00162 kcal/mol	1.64839 kcal/mol	136 155@LB@ \| \|@LB@5'-AGA...AGCAG AAG AAAGA...CGG-3'@LB@ GGCA UAGAAAGUUCG@LB@ :\|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ UCGU AUUUUUUAAGC@LB@3'-UUU...GUUCU GA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -13.3883 kcal/mol@LB@Unfolding Energy - mRNA 3.00162 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 137 -- 154@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 25 -- 31@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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usability assessment

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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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