Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
173	0.03478	0.6177	b1234	rssA	-4.70	0.418234	181 -- 188	43 -- 50	putative patatin-like family phospholipase	_____________180______189\n_____________\|________\|\n5'-GAU...AUUCC________CUUGC...AAA-3'\n______________AGGGGAAU\n______________\|\|:\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	182 -- 188	43 -- 49	-9.05148 kcal/mol	3.5051 kcal/mol	0.845564 kcal/mol	180 189@LB@ \| \|@LB@5'-GAU...AUUCC CUUGC...AAA-3'@LB@ AGGGGAAU@LB@ \|\|:\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -9.05148 kcal/mol@LB@Unfolding Energy - mRNA 3.5051 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 181 -- 188@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
3	9.453e-06	0.01014	b0681	chiP	-16.40	0.001982	182 -- 193	45 -- 56	chitoporin uptake of chitosugars	_____________181__________194\n_____________\|____________\|\n5'-CUU...UUAUA____________UUAAC...AAG-3'\n______________CGUCAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCCU\n3'-UUU...ACCGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	187 -- 193	45 -- 51	-19.4659 kcal/mol	2.1233 kcal/mol	0.938337 kcal/mol	181 194@LB@ \| \|@LB@5'-CUU...UUAUA UUAAC...AAG-3'@LB@ CGUCAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCCU@LB@3'-UUU...ACCGG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -19.4659 kcal/mol@LB@Unfolding Energy - mRNA 2.1233 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
35	0.00713	0.6129	b2025	hisF	-8.66	0.076851	182 -- 193	46 -- 57	imidazole glycerol phosphate synthase catalytic subunit with HisH	_____________181__________194\n_____________\|____________\|\n5'-UCG...AUUCA____G_______CCAUC...UGC-3'\n______________CCGU_AAGGAGG\n______________\|\|\|\|_\|\|:\|\|\|\|\n______________GGCA_UUUCUCC\n3'-UUU...AACCG____G_______UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	187 -- 193	46 -- 52	-16.1254 kcal/mol	4.72855 kcal/mol	2.7365 kcal/mol	181 194@LB@ \| \|@LB@5'-UCG...AUUCA G CCAUC...UGC-3'@LB@ CCGU AAGGAGG@LB@ \|\|\|\| \|\|:\|\|\|\|@LB@ GGCA UUUCUCC@LB@3'-UUU...AACCG G UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -16.1254 kcal/mol@LB@Unfolding Energy - mRNA 4.72855 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 46 -- 52@LB@
63	0.01324	0.6177	b3140	agaD	-9.33	0.056359	182 -- 192	45 -- 55	N-acetylgalactosamine-specific enzyme IID component of PTS	_____________181_________193\n_____________\|___________\|\n5'-GCG...AAAAU_AA________CUACA...GUU-3'\n______________G__GAAGAGGA\n______________\|__:\|\|\|\|\|\|\|\n______________C__UUUCUCCU\n3'-UUU...CCGGG_AG________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	186 -- 192	45 -- 51	-11.186 kcal/mol	0.927202 kcal/mol	0.930875 kcal/mol	181 193@LB@ \| \|@LB@5'-GCG...AAAAU AA CUACA...GUU-3'@LB@ G GAAGAGGA@LB@ \| :\|\|\|\|\|\|\|@LB@ C UUUCUCCU@LB@3'-UUU...CCGGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -11.186 kcal/mol@LB@Unfolding Energy - mRNA 0.927202 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 182 -- 192@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
109	0.02227	0.6177	b4040	ubiA	-8.97	0.066674	182 -- 194	44 -- 55	p-hydroxybenzoate octaprenyltransferase	_____________181___________195\n_____________\|_____________\|\n5'-AGC...CCGUU__A_U________AAAAA...UAU-3'\n______________GU_C_AAGAGGAA\n______________\|\|_\|_\|\|\|\|\|\|\|\|\n______________CA_G_UUCUCCUU\n3'-UUU...CCGGG____U________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	188 -- 194	44 -- 50	-10.7786 kcal/mol	0.870226 kcal/mol	0.941432 kcal/mol	181 195@LB@ \| \|@LB@5'-AGC...CCGUU A U AAAAA...UAU-3'@LB@ GU C AAGAGGAA@LB@ \|\| \| \|\|\|\|\|\|\|\|@LB@ CA G UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -10.7786 kcal/mol@LB@Unfolding Energy - mRNA 0.870226 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
145	0.02855	0.6177	b2252	ais	-5.71	0.282709	182 -- 202	38 -- 55	putative LPS core heptose(II)-phosphate phosphatase	_____________181___________________203\n_____________\|_____________________\|\n5'-ACC...CGCUU___UAU___U_______A___GUUAG...GGA-3'\n______________GUC___AGG_GGAGUUU_CGU\n______________\|\|\|___\|:\|_\|\|\|:\|\|\|_\|:\|\n______________CAG___UUC_CCUUAAA_GUA\n3'-UUU...CCGGG___U_____U___________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	192 -- 198	41 -- 47	-12.7294 kcal/mol	5.84979 kcal/mol	1.17036 kcal/mol	181 203@LB@ \| \|@LB@5'-ACC...CGCUU UAU U A GUUAG...GGA-3'@LB@ GUC AGG GGAGUUU CGU@LB@ \|\|\| \|:\| \|\|\|:\|\|\| \|:\|@LB@ CAG UUC CCUUAAA GUA@LB@3'-UUU...CCGGG U U AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -5.71 kcal/mol@LB@Hybridization Energy -12.7294 kcal/mol@LB@Unfolding Energy - mRNA 5.84979 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 182 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 41 -- 47@LB@
14	0.003078	0.593	b0886	cydC	-10.90	0.026971	183 -- 199	39 -- 56	glutathione/cysteine ABC transporter export permease/ATPase	_____________182________________200\n_____________\|__________________\|\n5'-GCG...CCCAU_____________A____AAUGC...UCG-3'\n______________CGUC_AGGAGGAG_UUUA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|:\|\n______________GCAG_UUCUCCUU_AAGU\n3'-UUU...ACCGG____U________A____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	188 -- 194	44 -- 50	-16.2318 kcal/mol	4.17801 kcal/mol	1.15786 kcal/mol	182 200@LB@ \| \|@LB@5'-GCG...CCCAU A AAUGC...UCG-3'@LB@ CGUC AGGAGGAG UUUA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|:\|@LB@ GCAG UUCUCCUU AAGU@LB@3'-UUU...ACCGG U A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -16.2318 kcal/mol@LB@Unfolding Energy - mRNA 4.17801 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 183 -- 199@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
19	0.003501	0.593	b2019	hisG	-12.73	0.011332	183 -- 194	43 -- 54	ATP phosphoribosyltransferase	_____________182__________195\n_____________\|____________\|\n5'-UUU...CAGGU____________AACAA...AUC-3'\n______________UUAAAGAGGAAU\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUUUCUCCUUA\n3'-UUU...CGGGC____________AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	188 -- 194	43 -- 49	-14.9017 kcal/mol	1.23041 kcal/mol	0.944705 kcal/mol	182 195@LB@ \| \|@LB@5'-UUU...CAGGU AACAA...AUC-3'@LB@ UUAAAGAGGAAU@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUUUCUCCUUA@LB@3'-UUU...CGGGC AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -14.9017 kcal/mol@LB@Unfolding Energy - mRNA 1.23041 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
108	0.0217	0.6177	b0243	proA	-8.76	0.073409	183 -- 193	47 -- 57	gamma-glutamylphosphate reductase	_____________182_________194\n_____________\|___________\|\n5'-AAU...AUUAC___________CAGGC...AUG-3'\n______________CCGUUAAGGAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	187 -- 193	47 -- 53	-14.7866 kcal/mol	3.29159 kcal/mol	2.73556 kcal/mol	182 194@LB@ \| \|@LB@5'-AAU...AUUAC CAGGC...AUG-3'@LB@ CCGUUAAGGAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -14.7866 kcal/mol@LB@Unfolding Energy - mRNA 3.29159 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
157	0.03134	0.6177	b4086	alsC	-8.98	0.066369	183 -- 191	45 -- 53	D-allose ABC transporter permease	_____________182_______192\n_____________\|_________\|\n5'-CGC...AUGAG_________GAUUA...CGA-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	185 -- 191	45 -- 51	-13.528 kcal/mol	3.63363 kcal/mol	0.917553 kcal/mol	182 192@LB@ \| \|@LB@5'-CGC...AUGAG GAUUA...CGA-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.528 kcal/mol@LB@Unfolding Energy - mRNA 3.63363 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 45 -- 51@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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