Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
5	0.0001254	0.08442	b4481	wecF	-11.27	0.155862	165 -- 206	62 -- 99	TDP-Fuc4NAc:lipidIIFuc4NAc transferase	_____________164_____________________________________207\n_____________\|_______________________________________\|\n5'-UUU...GCGUC___G_____U_____UC__GC___________CAG____CUUUA...ACG-3'\n______________ACU_CGGUU_UAUAU__UG__GG_AAGUCAGC___UUCA\n______________\|\|\|_\|:\|\|:_:\|:\|\|__\|\|__\|\|_\|\|\|\|\|\|:\|___\|\|\|\|\n______________UGA_GUCAG_GUGUA__AC__CC_UUCAGUUG___AAGU\n3'-UUU...GGUUA_________U_____CU__GU__G________A______CUUAA...UAG-5'\n_____________\|_______________________________________\|\n_____________100_____________________________________61\n	54 -- 60	149 -- 155	-25.8626 kcal/mol	10.7241 kcal/mol	8.38318 kcal/mol	164 207@LB@ \| \|@LB@5'-UUU...GCGUC G U UC GC CAG CUUUA...ACG-3'@LB@ ACU CGGUU UAUAU UG GG AAGUCAGC UUCA@LB@ \|\|\| \|:\|\|: :\|:\|\| \|\| \|\| \|\|\|\|\|\|:\| \|\|\|\|@LB@ UGA GUCAG GUGUA AC CC UUCAGUUG AAGU@LB@3'-UUU...GGUUA U CU GU G A CUUAA...UAG-5'@LB@ \| \|@LB@ 100 61@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -25.8626 kcal/mol@LB@Unfolding Energy - mRNA 10.7241 kcal/mol@LB@Unfolding Energy - sRNA 8.38318 kcal/mol@LB@@LB@Position - mRNA 165 -- 206@LB@Position - sRNA 62 -- 99@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 149 -- 155@LB@
166	0.01886	0.3812	b3300	secY	-11.48	0.141920	168 -- 177	196 -- 205	preprotein translocase membrane subunit	_____________167_______________178\n_____________\|_________________\|\n5'-CCU...UCGAA____C_G__________CGAGG...UCC-3'\n______________GCUG_U_GCGGUAAAAU\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAC_A_CGCCAUUUUA\n3'-UUU...UGAAG______G__________UCACG...UAG-5'\n_____________\|_________________\|\n_____________206_______________195\n	177 -- 183	44 -- 50	-20.9884 kcal/mol	6.84834 kcal/mol	6.15722 kcal/mol	167 178@LB@ \| \|@LB@5'-CCU...UCGAA C G CGAGG...UCC-3'@LB@ GCUG U GCGGUAAAAU@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAC A CGCCAUUUUA@LB@3'-UUU...UGAAG G UCACG...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.9884 kcal/mol@LB@Unfolding Energy - mRNA 6.84834 kcal/mol@LB@Unfolding Energy - sRNA 6.15722 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 44 -- 50@LB@
14	0.00083	0.1886	b2721	hycE	-15.91	0.017607	169 -- 185	190 -- 205	hydrogenase 3 large subunit	_____________168_______________186\n_____________\|_________________\|\n5'-UUC...UCUCC__________C______AAAGA...UGA-3'\n______________UUGCUGGCGG_GUGAUU\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GACGACCGCC_CACUAA\n3'-UUU...UAUUA_________________AAUGU...UAG-5'\n_____________\|_________________\|\n_____________206_______________189\n	172 -- 178	196 -- 202	-26.9802 kcal/mol	6.4269 kcal/mol	9.06848 kcal/mol	168 186@LB@ \| \|@LB@5'-UUC...UCUCC C AAAGA...UGA-3'@LB@ UUGCUGGCGG GUGAUU@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GACGACCGCC CACUAA@LB@3'-UUU...UAUUA AAUGU...UAG-5'@LB@ \| \|@LB@ 206 189@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -26.9802 kcal/mol@LB@Unfolding Energy - mRNA 6.4269 kcal/mol@LB@Unfolding Energy - sRNA 9.06848 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 190 -- 205@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 196 -- 202@LB@
178	0.02044	0.3833	b3433	asd	-8.72	0.462346	170 -- 185	58 -- 71	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________169__________________186\n_____________\|____________________\|\n5'-UCA...UUAUA___________CUU______AAAAA...UCU-3'\n______________CAG_CACACAU___UGCAGG\n______________\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GUC_GUGUGUA___ACGUCC\n3'-UUU...UAUGA___A_______CU_______GUUCA...UAG-5'\n_____________\|____________________\|\n_____________72___________________57\n	173 -- 179	166 -- 172	-22.5694 kcal/mol	4.04779 kcal/mol	7.34152 kcal/mol	169 186@LB@ \| \|@LB@5'-UCA...UUAUA CUU AAAAA...UCU-3'@LB@ CAG CACACAU UGCAGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUC GUGUGUA ACGUCC@LB@3'-UUU...UAUGA A CU GUUCA...UAG-5'@LB@ \| \|@LB@ 72 57@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -22.5694 kcal/mol@LB@Unfolding Energy - mRNA 4.04779 kcal/mol@LB@Unfolding Energy - sRNA 7.34152 kcal/mol@LB@@LB@Position - mRNA 170 -- 185@LB@Position - sRNA 58 -- 71@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 166 -- 172@LB@
72	0.007293	0.3408	b3240	aaeB	-15.57	0.020683	172 -- 248	45 -- 133	p-hydroxybenzoic acid efflux system component	_____________171________________249\n_____________\|__________________\|\n5'-ACU...ACAUA__________________CUGGC...UGG-3'\n______________UUCGCU_UUGCGGUAAAA\n______________\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\|\|\n______________AAGCGA_AGCGCCAUUUU\n3'-UUU...UGUUG______C___________AUCAC...UAG-5'\n_____________\|__________________\|\n_____________134________________44\n	240 -- 246	47 -- 53	-22.573 kcal/mol	5.7072 kcal/mol	6.14031 kcal/mol	171 249@LB@ \| \|@LB@5'-ACU...ACAUA CUGGC...UGG-3'@LB@ UUCGCU UUGCGGUAAAA@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|\|\|\|@LB@ AAGCGA AGCGCCAUUUU@LB@3'-UUU...UGUUG C AUCAC...UAG-5'@LB@ \| \|@LB@ 134 44@LB@@LB@@LB@Energy -15.57 kcal/mol@LB@Hybridization Energy -22.573 kcal/mol@LB@Unfolding Energy - mRNA 5.7072 kcal/mol@LB@Unfolding Energy - sRNA 6.14031 kcal/mol@LB@@LB@Position - mRNA 172 -- 248@LB@Position - sRNA 45 -- 133@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 47 -- 53@LB@
163	0.01822	0.376	b1073	flgB	-9.73	0.308533	172 -- 220	24 -- 70	flagellar component of cell-proximal portion of basal-body rod	_____________171_______221\n_____________\|_________\|\n5'-UGA...AACAU_________CG-3'\n______________CGCCAAUGC\n______________\|:\|\|\|\|\|:\|\n______________GUGGUUAUG\n3'-UUU...AAAAU_________AGUCA...UAG-5'\n_____________\|_________\|\n_____________71________23\n	292 -- 298	178 -- 184	-11.5881 kcal/mol	1.63005 kcal/mol	3.31726 kcal/mol	171 221@LB@ \| \|@LB@5'-UGA...AACAU CG-3'@LB@ CGCCAAUGC@LB@ \|:\|\|\|\|\|:\|@LB@ GUGGUUAUG@LB@3'-UUU...AAAAU AGUCA...UAG-5'@LB@ \| \|@LB@ 71 23@LB@@LB@@LB@Energy -9.73 kcal/mol@LB@Hybridization Energy -11.5881 kcal/mol@LB@Unfolding Energy - mRNA 1.63005 kcal/mol@LB@Unfolding Energy - sRNA 3.31726 kcal/mol@LB@@LB@Position - mRNA 172 -- 220@LB@Position - sRNA 24 -- 70@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 178 -- 184@LB@
12	0.0007005	0.1842	b1101	ptsG	-16.86	0.011310	173 -- 192	168 -- 187	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________172__________________193\n_____________\|____________________\|\n5'-CAU...AAAAA_____C________GA____UCUCA...GUU-3'\n______________GCACC_AUACUCAG__GCAC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|__:\|\|\|\n______________UGUGG_UAUGAGUC__UGUG\n3'-UUU...UAAAA_____U________AG____UACUA...UAG-5'\n_____________\|____________________\|\n_____________188__________________167\n	180 -- 186	174 -- 180	-27.3381 kcal/mol	3.90127 kcal/mol	4.88067 kcal/mol	172 193@LB@ \| \|@LB@5'-CAU...AAAAA C GA UCUCA...GUU-3'@LB@ GCACC AUACUCAG GCAC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGUGG UAUGAGUC UGUG@LB@3'-UUU...UAAAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -16.86 kcal/mol@LB@Hybridization Energy -27.3381 kcal/mol@LB@Unfolding Energy - mRNA 3.90127 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 174 -- 180@LB@
190	0.02217	0.3833	b2754	ygbF	-10.33	0.238061	176 -- 225	124 -- 165	CRISPR adaptation ssRNA endonuclease	_____________175____________226\n_____________\|______________\|\n5'-UGG...AAAAU________GC____ACGAG...GUG-3'\n______________GUACCUCC__GCUU\n______________\|:\|\|\|:\|\|__\|\|\|\|\n______________CGUGGGGG__CGAA\n3'-UUU...UACCC________AA____GUAG-5'\n_____________\|______________\|\n_____________166____________123\n	232 -- 238	11 -- 17	-17.8256 kcal/mol	3.33543 kcal/mol	6.90657 kcal/mol	175 226@LB@ \| \|@LB@5'-UGG...AAAAU GC ACGAG...GUG-3'@LB@ GUACCUCC GCUU@LB@ \|:\|\|\|:\|\| \|\|\|\|@LB@ CGUGGGGG CGAA@LB@3'-UUU...UACCC AA GUAG-5'@LB@ \| \|@LB@ 166 123@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -17.8256 kcal/mol@LB@Unfolding Energy - mRNA 3.33543 kcal/mol@LB@Unfolding Energy - sRNA 6.90657 kcal/mol@LB@@LB@Position - mRNA 176 -- 225@LB@Position - sRNA 124 -- 165@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
34	0.002769	0.2736	b2416	ptsI	-14.05	0.042463	178 -- 225	128 -- 177	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________177_________________________________________226\n_____________\|___________________________________________\|\n5'-GUG...AAAAA_________AGUAAGGUAGGGU______UU______UU_____AUCCC...CCG-3'\n______________UCAGUCACA_____________UAUGAU__CAGGCA__UUAGC\n______________\|\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|__\|\|\|\|\|\|__\|:\|:\|\n______________AGUCAGUGU_____________GUACUA__GUCCGU__AGUUG\n3'-UUU...UUAUG____________________________C_______UC_____AAAGU...UAG-5'\n_____________\|___________________________________________\|\n_____________178_________________________________________127\n	180 -- 186	169 -- 175	-30.6202 kcal/mol	5.78851 kcal/mol	8.17404 kcal/mol	177 226@LB@ \| \|@LB@5'-GUG...AAAAA AGUAAGGUAGGGU UU UU AUCCC...CCG-3'@LB@ UCAGUCACA UAUGAU CAGGCA UUAGC@LB@ \|\|\|\|\|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\| \|:\|:\|@LB@ AGUCAGUGU GUACUA GUCCGU AGUUG@LB@3'-UUU...UUAUG C UC AAAGU...UAG-5'@LB@ \| \|@LB@ 178 127@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -30.6202 kcal/mol@LB@Unfolding Energy - mRNA 5.78851 kcal/mol@LB@Unfolding Energy - sRNA 8.17404 kcal/mol@LB@@LB@Position - mRNA 178 -- 225@LB@Position - sRNA 128 -- 177@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 169 -- 175@LB@
108	0.01175	0.3575	b0723	sdhA	-10.39	0.232370	178 -- 209	28 -- 62	succinate dehydrogenase flavoprotein subunit	_____________177_______________________210\n_____________\|_________________________\|\n5'-GGU...GAAAU__________G_G_AUU________UUGUG...GUG-3'\n______________UGC_CAGUCA_A_A___UGAUGCAG\n______________\|:\|_\|\|\|\|\|\|_\|_\|___\|\|\|\|\|\|\|\|\n______________AUG_GUCAGU_U_U___ACUACGUC\n3'-UUU...UGGUU___A______G_G____________CGUUC...UAG-5'\n_____________\|_________________________\|\n_____________63________________________27\n	225 -- 231	159 -- 165	-22.5908 kcal/mol	8.24888 kcal/mol	4.81331 kcal/mol	177 210@LB@ \| \|@LB@5'-GGU...GAAAU G G AUU UUGUG...GUG-3'@LB@ UGC CAGUCA A A UGAUGCAG@LB@ \|:\| \|\|\|\|\|\| \| \| \|\|\|\|\|\|\|\|@LB@ AUG GUCAGU U U ACUACGUC@LB@3'-UUU...UGGUU A G G CGUUC...UAG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -22.5908 kcal/mol@LB@Unfolding Energy - mRNA 8.24888 kcal/mol@LB@Unfolding Energy - sRNA 4.81331 kcal/mol@LB@@LB@Position - mRNA 178 -- 209@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@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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