Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
135	0.01297	0.3104	b3409	feoB	-9.25	0.161231	74 -- 82	5 -- 13	ferrous iron transporter protein B and GTP-binding protein; membrane protein	_____________73________83\n_____________\|_________\|\n5'-CCG...AUGUG_________GCUCC...GGG-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	76 -- 82	5 -- 11	-15.2985 kcal/mol	4.89519 kcal/mol	1.15134 kcal/mol	73 83@LB@ \| \|@LB@5'-CCG...AUGUG GCUCC...GGG-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.2985 kcal/mol@LB@Unfolding Energy - mRNA 4.89519 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 74 -- 82@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 5 -- 11@LB@
47	0.003448	0.2484	b0614	citX	-10.13	0.115098	76 -- 91	4 -- 17	apo-citrate lyase phosphoribosyl-dephospho-CoA transferase	_____________75_______________92\n_____________\|________________\|\n5'-UUA...GCUGC____AC__________GCUGA...UCA-3'\n______________GCGA__GUGCGCGUCU\n______________:\|:\|__:\|\|\|\|\|\|\|\|\|\n______________UGUU__UACGCGCAGA\n3'-UUU...ACUAU________________AAG-5'\n_____________\|________________\|\n_____________18_______________3\n	85 -- 91	4 -- 10	-19.1919 kcal/mol	7.83057 kcal/mol	1.22888 kcal/mol	75 92@LB@ \| \|@LB@5'-UUA...GCUGC AC GCUGA...UCA-3'@LB@ GCGA GUGCGCGUCU@LB@ :\|:\| :\|\|\|\|\|\|\|\|\|@LB@ UGUU UACGCGCAGA@LB@3'-UUU...ACUAU AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -19.1919 kcal/mol@LB@Unfolding Energy - mRNA 7.83057 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 76 -- 91@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 4 -- 10@LB@
200	0.0195	0.3104	b3183	obgE	-7.01	0.355777	76 -- 83	4 -- 11	GTPase involved in cell partioning and DNA repair	_____________75_______84\n_____________\|________\|\n5'-UUU...UCUCG________GUCGU...GCC-3'\n______________GUGCGUUU\n______________\|:\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	77 -- 83	4 -- 10	-11.428 kcal/mol	3.26207 kcal/mol	1.15639 kcal/mol	75 84@LB@ \| \|@LB@5'-UUU...UCUCG GUCGU...GCC-3'@LB@ GUGCGUUU@LB@ \|:\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.428 kcal/mol@LB@Unfolding Energy - mRNA 3.26207 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 4 -- 10@LB@
77	0.007102	0.3087	b0832	gsiD	-8.78	0.192254	77 -- 85	7 -- 15	glutathione ABC transporter permease	_____________76________86\n_____________\|_________\|\n5'-UUG...CGUAG_________AUUAC...GAU-3'\n______________AAAUGCGUG\n______________\|\|\|\|\|\|\|:\|\n______________UUUACGCGC\n3'-UUU...UAUUG_________AGAAAG-5'\n_____________\|_________\|\n_____________16________6\n	79 -- 85	7 -- 13	-12.0627 kcal/mol	2.10506 kcal/mol	1.17837 kcal/mol	76 86@LB@ \| \|@LB@5'-UUG...CGUAG AUUAC...GAU-3'@LB@ AAAUGCGUG@LB@ \|\|\|\|\|\|\|:\|@LB@ UUUACGCGC@LB@3'-UUU...UAUUG AGAAAG-5'@LB@ \| \|@LB@ 16 6@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -12.0627 kcal/mol@LB@Unfolding Energy - mRNA 2.10506 kcal/mol@LB@Unfolding Energy - sRNA 1.17837 kcal/mol@LB@@LB@Position - mRNA 77 -- 85@LB@Position - sRNA 7 -- 15@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 7 -- 13@LB@
118	0.01199	0.3104	b2573	rpoE	-10.72	0.091300	77 -- 87	8 -- 18	RNA polymerase sigma E factor	_____________76__________88\n_____________\|___________\|\n5'-ACA...ACAAA___________UACGG...UGG-3'\n______________AACAGAUGCGU\n______________\|\|\|\|:\|\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	81 -- 87	8 -- 14	-15.0531 kcal/mol	3.12642 kcal/mol	1.20363 kcal/mol	76 88@LB@ \| \|@LB@5'-ACA...ACAAA UACGG...UGG-3'@LB@ AACAGAUGCGU@LB@ \|\|\|\|:\|\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.0531 kcal/mol@LB@Unfolding Energy - mRNA 3.12642 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 77 -- 87@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 8 -- 14@LB@
147	0.01411	0.3104	b0441	ppiD	-10.51	0.099467	81 -- 98	3 -- 21	periplasmic folding chaperone has an inactive PPIase domain	_____________80__________________99\n_____________\|___________________\|\n5'-GUA...UAUUC______UUUC_________GUGGG...ACC-3'\n______________GGUGAC_____UGCGUCUU\n______________\|:\|:\|\|_____:\|\|\|\|\|\|\|\n______________CUAUUG_____GCGCAGAA\n3'-UUU...UACUA______UUUAC________AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	92 -- 98	3 -- 9	-17.0331 kcal/mol	5.27038 kcal/mol	1.257 kcal/mol	80 99@LB@ \| \|@LB@5'-GUA...UAUUC UUUC GUGGG...ACC-3'@LB@ GGUGAC UGCGUCUU@LB@ \|:\|:\|\| :\|\|\|\|\|\|\|@LB@ CUAUUG GCGCAGAA@LB@3'-UUU...UACUA UUUAC AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -17.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.27038 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 81 -- 98@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 3 -- 9@LB@
64	0.005939	0.3087	b3237	argR	-9.39	0.153279	85 -- 104	1 -- 19	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________84____________________105\n_____________\|_____________________\|\n5'-ACA...AAAUU_______AUCC__________AUAAC...UGC-3'\n______________UGAUAAA____CGC_UCUUUC\n______________\|:\|:\|\|\|____\|\|\|_\|\|\|\|\|\|\n______________AUUGUUU____GCG_AGAAAG\n3'-UUU...CUACU_______AC_____C______-5'\n_____________\|____________________\|\n_____________20___________________1\n	85 -- 91	13 -- 19	-12.1021 kcal/mol	1.46458 kcal/mol	1.25156 kcal/mol	84 105@LB@ \| \|@LB@5'-ACA...AAAUU AUCC AUAAC...UGC-3'@LB@ UGAUAAA CGC UCUUUC@LB@ \|:\|:\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AUUGUUU GCG AGAAAG@LB@3'-UUU...CUACU AC C -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.46458 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 85 -- 104@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 13 -- 19@LB@
31	0.001974	0.2094	b1080	flgI	-10.59	0.096403	87 -- 101	7 -- 21	putative flagellar basal body protein	_____________86______________102\n_____________\|_______________\|\n5'-AUU...ACUCA_______________CAUUG...AAA-3'\n______________GGUGGCGGAUGCGCG\n______________\|:\|::\|::\|\|\|\|\|\|\|\n______________CUAUUGUUUACGCGC\n3'-UUU...UACUA_______________AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	95 -- 101	7 -- 13	-22.6939 kcal/mol	10.8668 kcal/mol	1.24179 kcal/mol	86 102@LB@ \| \|@LB@5'-AUU...ACUCA CAUUG...AAA-3'@LB@ GGUGGCGGAUGCGCG@LB@ \|:\|::\|::\|\|\|\|\|\|\|@LB@ CUAUUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -22.6939 kcal/mol@LB@Unfolding Energy - mRNA 10.8668 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 87 -- 101@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 7 -- 13@LB@
109	0.01118	0.3104	b3195	mlaF	-11.81	0.058997	89 -- 105	1 -- 18	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________88_________________106\n_____________\|__________________\|\n5'-UUU...AGUAA___________AG_____GCUAA...GAG-3'\n______________AACAAAUGC_C__CUUUC\n______________\|\|\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUGUUUACG_G__GAAAG\n3'-UUU...UACUA_________C_CA_____-5'\n_____________\|_________________\|\n_____________19________________1\n	91 -- 97	10 -- 16	-16.9522 kcal/mol	3.89814 kcal/mol	1.24077 kcal/mol	88 106@LB@ \| \|@LB@5'-UUU...AGUAA AG GCUAA...GAG-3'@LB@ AACAAAUGC C CUUUC@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUGUUUACG G GAAAG@LB@3'-UUU...UACUA C CA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -16.9522 kcal/mol@LB@Unfolding Energy - mRNA 3.89814 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 89 -- 105@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 10 -- 16@LB@
113	0.01159	0.3104	b1279	yciS	-9.20	0.164515	90 -- 101	6 -- 18	DUF1049 family inner membrane protein function unknown	_____________89____________102\n_____________\|_____________\|\n5'-ACC...UCAUC_____________GGAUG...UGU-3'\n______________AAC_AAUGCGUGU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________UUG_UUACGCGCA\n3'-UUU...UACUA___U_________GAAAG-5'\n_____________\|_____________\|\n_____________19____________5\n	95 -- 101	6 -- 12	-13.4585 kcal/mol	3.04139 kcal/mol	1.21878 kcal/mol	89 102@LB@ \| \|@LB@5'-ACC...UCAUC GGAUG...UGU-3'@LB@ AAC AAUGCGUGU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ UUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 19 5@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -13.4585 kcal/mol@LB@Unfolding Energy - mRNA 3.04139 kcal/mol@LB@Unfolding Energy - sRNA 1.21878 kcal/mol@LB@@LB@Position - mRNA 90 -- 101@LB@Position - sRNA 6 -- 18@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 6 -- 12@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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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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