Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
65	0.009342	0.4523	b0871	poxB	-9.00	0.151653	248 -- 256	51 -- 59	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________247_______257\n_____________\|_________\|\n5'-CCG...UCGGC_________ACGCA...GUG-3'\n______________AGGGGUGAA\n______________\|\|\|\|\|\|:\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	250 -- 256	51 -- 57	-12.9194 kcal/mol	3.39064 kcal/mol	0.532875 kcal/mol	247 257@LB@ \| \|@LB@5'-CCG...UCGGC ACGCA...GUG-3'@LB@ AGGGGUGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -12.9194 kcal/mol@LB@Unfolding Energy - mRNA 3.39064 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 248 -- 256@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 51 -- 57@LB@
138	0.02287	0.526	b0081	mraZ	-12.90	0.022954	180 -- 193	52 -- 64	RsmH methytransferase inhibitor	_____________179____________194\n_____________\|______________\|\n5'-GAU...AAGUG_____A________GGCUG...AAA-3'\n______________GGAAU_AGGGGUGA\n______________\|:\|\|\|_\|\|\|\|\|\|:\|\n______________CUUUA_UCCCCAUU\n3'-UUU...GCCAA______________UGUCU...UCG-5'\n_____________\|______________\|\n_____________65_____________51\n	187 -- 193	52 -- 58	-14.7021 kcal/mol	1.72638 kcal/mol	0.0778991 kcal/mol	179 194@LB@ \| \|@LB@5'-GAU...AAGUG A GGCUG...AAA-3'@LB@ GGAAU AGGGGUGA@LB@ \|:\|\|\| \|\|\|\|\|\|:\|@LB@ CUUUA UCCCCAUU@LB@3'-UUU...GCCAA UGUCU...UCG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 1.72638 kcal/mol@LB@Unfolding Energy - sRNA 0.0778991 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 52 -- 58@LB@
154	0.02518	0.526	b1602	pntB	-9.01	0.150855	190 -- 197	52 -- 59	pyridine nucleotide transhydrogenase beta subunit	_____________189______198\n_____________\|________\|\n5'-GCU...AAUUA________CAUAU...GUA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	191 -- 197	52 -- 58	-12.5664 kcal/mol	3.49825 kcal/mol	0.0599826 kcal/mol	189 198@LB@ \| \|@LB@5'-GCU...AAUUA CAUAU...GUA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -12.5664 kcal/mol@LB@Unfolding Energy - mRNA 3.49825 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 190 -- 197@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
156	0.02543	0.526	b2805	fucR	-9.08	0.146396	128 -- 135	52 -- 59	l-fucose operon activator	_____________127______136\n_____________\|________\|\n5'-CAC...AAAAA________CACCG...AAA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	129 -- 135	52 -- 58	-12.2757 kcal/mol	3.13783 kcal/mol	0.0599826 kcal/mol	127 136@LB@ \| \|@LB@5'-CAC...AAAAA CACCG...AAA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -12.2757 kcal/mol@LB@Unfolding Energy - mRNA 3.13783 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 128 -- 135@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 52 -- 58@LB@
160	0.02589	0.526	b3297	rpsK	-10.33	0.083340	178 -- 193	52 -- 64	30S ribosomal subunit protein S11	_____________177______________194\n_____________\|________________\|\n5'-CGA...AUCAA______AUC_______UUGAA...CUA-3'\n______________GAAAUA___GGGGUGA\n______________\|\|\|\|\|\|___\|\|\|\|\|:\|\n______________CUUUAU___CCCCAUU\n3'-UUU...GCCAA________________UGUCU...UCG-5'\n_____________\|________________\|\n_____________65_______________51\n	187 -- 193	52 -- 58	-13.1856 kcal/mol	2.77978 kcal/mol	0.0778991 kcal/mol	177 194@LB@ \| \|@LB@5'-CGA...AUCAA AUC UUGAA...CUA-3'@LB@ GAAAUA GGGGUGA@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ CUUUAU CCCCAUU@LB@3'-UUU...GCCAA UGUCU...UCG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -13.1856 kcal/mol@LB@Unfolding Energy - mRNA 2.77978 kcal/mol@LB@Unfolding Energy - sRNA 0.0778991 kcal/mol@LB@@LB@Position - mRNA 178 -- 193@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 52 -- 58@LB@
172	0.02805	0.531	b1912	pgsA	-10.33	0.083391	160 -- 169	52 -- 61	phosphatidylglycerophosphate synthetase	_____________159________170\n_____________\|__________\|\n5'-GUC...GCAAC__________UCUUA...UUG-3'\n______________AUAGGGGUAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAUCCCCAUU\n3'-UUU...AACUU__________UGUCU...UCG-5'\n_____________\|__________\|\n_____________62_________51\n	163 -- 169	52 -- 58	-13.9577 kcal/mol	3.55629 kcal/mol	0.0747282 kcal/mol	159 170@LB@ \| \|@LB@5'-GUC...GCAAC UCUUA...UUG-3'@LB@ AUAGGGGUAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAUCCCCAUU@LB@3'-UUU...AACUU UGUCU...UCG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -13.9577 kcal/mol@LB@Unfolding Energy - mRNA 3.55629 kcal/mol@LB@Unfolding Energy - sRNA 0.0747282 kcal/mol@LB@@LB@Position - mRNA 160 -- 169@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
31	0.00291	0.3081	b1205	ychH	-11.03	0.059536	152 -- 163	53 -- 64	DUF2583 family putative inner membrane protein	_____________151__________164\n_____________\|____________\|\n5'-CAA...CAUAA____G_______UUCCC...UAC-3'\n______________GGAA_AGGGGUA\n______________\|:\|\|_\|\|\|\|\|\|\|\n______________CUUU_UCCCCAU\n3'-UUU...GCCAA____A_______UUGUC...UCG-5'\n_____________\|____________\|\n_____________65___________52\n	157 -- 163	53 -- 59	-13.5677 kcal/mol	2.46117 kcal/mol	0.0747267 kcal/mol	151 164@LB@ \| \|@LB@5'-CAA...CAUAA G UUCCC...UAC-3'@LB@ GGAA AGGGGUA@LB@ \|:\|\| \|\|\|\|\|\|\|@LB@ CUUU UCCCCAU@LB@3'-UUU...GCCAA A UUGUC...UCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.5677 kcal/mol@LB@Unfolding Energy - mRNA 2.46117 kcal/mol@LB@Unfolding Energy - sRNA 0.0747267 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 53 -- 59@LB@
82	0.0113	0.4523	b3747	kup	-9.05	0.148352	64 -- 70	53 -- 59	potassium transporter	_____________63______71\n_____________\|_______\|\n5'-AAA...AAAGG_______UUUUU...GUG-3'\n______________GGGGGUA\n______________:\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	64 -- 70	53 -- 59	-11.6233 kcal/mol	2.51972 kcal/mol	0.0564539 kcal/mol	63 71@LB@ \| \|@LB@5'-AAA...AAAGG UUUUU...GUG-3'@LB@ GGGGGUA@LB@ :\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -11.6233 kcal/mol@LB@Unfolding Energy - mRNA 2.51972 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 64 -- 70@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 53 -- 59@LB@
162	0.02632	0.526	b1886	tar	-10.00	0.096892	244 -- 251	53 -- 60	methyl-accepting chemotaxis protein II	_____________243______252\n_____________\|________\|\n5'-UGC...GGUGC________UUCGC...UUC-3'\n______________UGGGGGUA\n______________\|:\|\|\|\|\|\|\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	245 -- 251	53 -- 59	-12.2006 kcal/mol	2.12623 kcal/mol	0.0710089 kcal/mol	243 252@LB@ \| \|@LB@5'-UGC...GGUGC UUCGC...UUC-3'@LB@ UGGGGGUA@LB@ \|:\|\|\|\|\|\|@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -12.2006 kcal/mol@LB@Unfolding Energy - mRNA 2.12623 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 244 -- 251@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 53 -- 59@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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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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