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
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@
69	0.00357	0.1645	b0571	cusR	-5.90	0.203942	86 -- 99	6 -- 21	response regulator in two-component regulatory system with CusS	b1969	_____________85_______________100\n_____________\|________________\|\n5'-AGC...UUACU_______C________UUUCC...GGC-3'\n______________CGCCAGG___UCUGAU\n______________\|:\|\|\|\|\|___\|\|\|\|\|\|\n______________GUGGUCC___AGACUA\n3'-UUU...GCAAU_______UUU______CACAA-5'\n_____________\|________________\|\n_____________22_______________5\n	86 -- 92	15 -- 21	-18.4182 kcal/mol	4.95815 kcal/mol	7.56001 kcal/mol	85 100@LB@ \| \|@LB@5'-AGC...UUACU C UUUCC...GGC-3'@LB@ CGCCAGG UCUGAU@LB@ \|:\|\|\|\|\| \|\|\|\|\|\|@LB@ GUGGUCC AGACUA@LB@3'-UUU...GCAAU UUU CACAA-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -18.4182 kcal/mol@LB@Unfolding Energy - mRNA 4.95815 kcal/mol@LB@Unfolding Energy - sRNA 7.56001 kcal/mol@LB@@LB@Position - mRNA 86 -- 99@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 15 -- 21@LB@
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@
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@
43	0.001794	0.1344	b0631	ybeD	-7.18	0.099343	171 -- 193	16 -- 40	UPF0250 family protein		_____________170________________________194\n_____________\|__________________________\|\n5'-GCU...GAGUU__U______UUA______________AGCUG...AAG-3'\n______________GC_AUUUAA______CGUUACGCCGG\n______________\|\|_\|:\|\|\|\|______\|\|\|\|\|\|:\|\|:\|\n______________CG_UGAAUU______GCAAUGUGGUC\n3'-UUU...UUCUU_________UUUUAA___________CUUUA...CAA-5'\n_____________\|__________________________\|\n_____________41_________________________15\n	187 -- 193	16 -- 22	-19.4847 kcal/mol	3.10673 kcal/mol	9.1996 kcal/mol	170 194@LB@ \| \|@LB@5'-GCU...GAGUU U UUA AGCUG...AAG-3'@LB@ GC AUUUAA CGUUACGCCGG@LB@ \|\| \|:\|\|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ CG UGAAUU GCAAUGUGGUC@LB@3'-UUU...UUCUU UUUUAA CUUUA...CAA-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -19.4847 kcal/mol@LB@Unfolding Energy - mRNA 3.10673 kcal/mol@LB@Unfolding Energy - sRNA 9.1996 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 16 -- 22@LB@
110	0.009505	0.2693	b0632	dacA	-12.82	0.002052	146 -- 175	26 -- 57	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)		_____________145______________________________176\n_____________\|________________________________\|\n5'-CCU...AGUGC_______AU______________UUUU_____CAUCA...AUA-3'\n______________AUUUGCU__AGUAGG__GCACUU____AAUUC\n______________\|:\|\|\|\|\|__\|\|:\|:\|__\|\|\|\|\|\|____\|\|\|\|\|\n______________UGAACGA__UCGUUC__CGUGAA____UUAAG\n3'-UUU...UACUU_______AU______UU______UUUU_____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	146 -- 152	51 -- 57	-23.8315 kcal/mol	4.73353 kcal/mol	6.27605 kcal/mol	145 176@LB@ \| \|@LB@5'-CCU...AGUGC AU UUUU CAUCA...AUA-3'@LB@ AUUUGCU AGUAGG GCACUU AAUUC@LB@ \|:\|\|\|\|\| \|\|:\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ UGAACGA UCGUUC CGUGAA UUAAG@LB@3'-UUU...UACUU AU UU UUUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.8315 kcal/mol@LB@Unfolding Energy - mRNA 4.73353 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 146 -- 175@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 51 -- 57@LB@
32	0.0009536	0.09599	b0637	rsfS	-12.32	0.003012	197 -- 230	23 -- 59	ribosomal silencing factor		_____________196___________________________________231\n_____________\|_____________________________________\|\n5'-AUU...GGGGA________A_______________CC____U______AUCGA...UCA-3'\n______________AAACUUGC__GGGUA__AAGCACU__AGGA_UUUGUU\n______________\|\|\|\|\|\|\|\|__::\|:\|__\|\|\|\|\|\|\|__\|::\|_\|\|:\|\|\|\n______________UUUGAACG__UUCGU__UUCGUGA__UUUU_AAGCAA\n3'-UUU...CCUAC________AA_____UC_______AU____U______UGUGG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________22\n	211 -- 217	36 -- 42	-25.7611 kcal/mol	7.16036 kcal/mol	6.27609 kcal/mol	196 231@LB@ \| \|@LB@5'-AUU...GGGGA A CC U AUCGA...UCA-3'@LB@ AAACUUGC GGGUA AAGCACU AGGA UUUGUU@LB@ \|\|\|\|\|\|\|\| ::\|:\| \|\|\|\|\|\|\| \|::\| \|\|:\|\|\|@LB@ UUUGAACG UUCGU UUCGUGA UUUU AAGCAA@LB@3'-UUU...CCUAC AA UC AU U UGUGG...CAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -12.32 kcal/mol@LB@Hybridization Energy -25.7611 kcal/mol@LB@Unfolding Energy - mRNA 7.16036 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 197 -- 230@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 36 -- 42@LB@
108	0.009338	0.2693	b0639	nadD	-9.48	0.023112	42 -- 61	34 -- 53	nicotinic acid mononucleotide adenylyltransferase NAD(P)-dependent		_____________41___________________62\n_____________\|____________________\|\n5'-AUG...AAAUC________C___C___G___CGUCA...CGC-3'\n______________GCUUAAGU_AGA_GCA_UUA\n______________\|\|\|\|\|\|\|:_\|\|\|_\|\|\|_\|\|\|\n______________CGAAUUCG_UCU_CGU_AAU\n3'-UUU...UUGAA________U___U___G___UUUUU...CAA-5'\n_____________\|____________________\|\n_____________54___________________33\n	42 -- 48	47 -- 53	-20.1483 kcal/mol	4.55179 kcal/mol	6.11529 kcal/mol	41 62@LB@ \| \|@LB@5'-AUG...AAAUC C C G CGUCA...CGC-3'@LB@ GCUUAAGU AGA GCA UUA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\| \|\|\|@LB@ CGAAUUCG UCU CGU AAU@LB@3'-UUU...UUGAA U U G UUUUU...CAA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -20.1483 kcal/mol@LB@Unfolding Energy - mRNA 4.55179 kcal/mol@LB@Unfolding Energy - sRNA 6.11529 kcal/mol@LB@@LB@Position - mRNA 42 -- 61@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 47 -- 53@LB@
143	0.01412	0.3181	b0642	leuS	-6.82	0.122159	244 -- 266	37 -- 58	leucyl-tRNA synthetase		_____________243_____________________267\n_____________\|_______________________\|\n5'-AAU...AGUAC_____CA_____A__________ACAUU...AGA-3'\n______________AGCUU__UUGGG_UGAGAAGCGC\n______________\|:\|\|\|__\|\|::\|_::\|\|\|\|\|\|:\|\n______________UUGAA__AAUUC_GUUCUUCGUG\n3'-UUU...CUACU_____CG________________AAUUU...CAA-5'\n_____________\|_______________________\|\n_____________59______________________36\n	260 -- 266	37 -- 43	-20.1861 kcal/mol	7.11823 kcal/mol	6.24354 kcal/mol	243 267@LB@ \| \|@LB@5'-AAU...AGUAC CA A ACAUU...AGA-3'@LB@ AGCUU UUGGG UGAGAAGCGC@LB@ \|:\|\|\| \|\|::\| ::\|\|\|\|\|\|:\|@LB@ UUGAA AAUUC GUUCUUCGUG@LB@3'-UUU...CUACU CG AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.82 kcal/mol@LB@Hybridization Energy -20.1861 kcal/mol@LB@Unfolding Energy - mRNA 7.11823 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 244 -- 266@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 37 -- 43@LB@
162	0.01764	0.3508	b0654	gltJ	-6.81	0.123116	18 -- 45	15 -- 42	glutamate/aspartate ABC transporter permease		_____________17___________________________46\n_____________\|____________________________\|\n5'-CAA...UGACA_______GAACU____ACAAGA______GGCGG...UCG-3'\n______________AGGCACU_____AAUU______ACCAGG\n______________\|:\|\|\|\|\|_____\|\|\|\|______\|\|\|\|\|\|\n______________UUCGUGA_____UUAA______UGGUCC\n3'-UUU...CGUUC_______AUUUU____GCAAUG______UUUAG...CAA-5'\n_____________\|____________________________\|\n_____________43___________________________14\n	18 -- 24	36 -- 42	-19.3193 kcal/mol	3.30421 kcal/mol	9.20431 kcal/mol	17 46@LB@ \| \|@LB@5'-CAA...UGACA GAACU ACAAGA GGCGG...UCG-3'@LB@ AGGCACU AAUU ACCAGG@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UUCGUGA UUAA UGGUCC@LB@3'-UUU...CGUUC AUUUU GCAAUG UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -19.3193 kcal/mol@LB@Unfolding Energy - mRNA 3.30421 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@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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