Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
138	0.01215	0.2883	bsu17940	yneI	-15.06	0.029368	176 -- 197	30 -- 52	plasmid maintenance protein CcdB	_____________175_____________________198\n_____________\|_______________________\|\n5'-GAA...AUCUG____AA_C____GU_________AAUAU...CGG-3'\n______________UGGA__U_GAUU___UGGAGGGG\n______________:\|\|\|__\|_\|\|\|:___\|:\|\|\|\|\|\|\n______________GCCU__A_CUAG___AUCUCCCC\n3'-UUU...AAAAA____AG_A____ACU________AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	191 -- 197	30 -- 36	-21.3361 kcal/mol	5.29839 kcal/mol	0.979974 kcal/mol	175 198@LB@ \| \|@LB@5'-GAA...AUCUG AA C GU AAUAU...CGG-3'@LB@ UGGA U GAUU UGGAGGGG@LB@ :\|\|\| \| \|\|\|: \|:\|\|\|\|\|\|@LB@ GCCU A CUAG AUCUCCCC@LB@3'-UUU...AAAAA AG A ACU AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -21.3361 kcal/mol@LB@Unfolding Energy - mRNA 5.29839 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 30 -- 36@LB@
139	0.01217	0.2883	bsu30960	glgD	-11.28	0.137516	171 -- 191	30 -- 50	glycogen biosynthesis protein GlgD	_____________170____________________192\n_____________\|______________________\|\n5'-ACU...GAAUU_____AAUUA____________GCAGA...UUG-3'\n______________GAUUU_____CUGA_AGAGGGG\n______________\|\|\|:\|_____\|\|\|\|_\|\|\|\|\|\|\|\n______________CUAGA_____GACU_UCUCCCC\n3'-UUU...AAAGC_____ACUA_____A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	185 -- 191	30 -- 36	-19.1028 kcal/mol	6.84884 kcal/mol	0.974272 kcal/mol	170 192@LB@ \| \|@LB@5'-ACU...GAAUU AAUUA GCAGA...UUG-3'@LB@ GAUUU CUGA AGAGGGG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CUAGA GACU UCUCCCC@LB@3'-UUU...AAAGC ACUA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -19.1028 kcal/mol@LB@Unfolding Energy - mRNA 6.84884 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 30 -- 36@LB@
145	0.01267	0.2913	bsu36760	murAA	-10.92	0.156018	188 -- 194	30 -- 36	UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	_____________187_____195\n_____________\|_______\|\n5'-UAG...GACGC_______AAUAC...UAU-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.3986 kcal/mol	2.34028 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UAG...GACGC AAUAC...UAU-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -13.3986 kcal/mol@LB@Unfolding Energy - mRNA 2.34028 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
150	0.01344	0.2966	bsu27040	levG	-16.98	0.011562	166 -- 191	30 -- 50	PTS system-fructose-specific transporter subunit IID	_____________165_________________________192\n_____________\|___________________________\|\n5'-UUC...AUGAU_________GCCUAAAC__________GAAGA...CAA-3'\n______________GAUCUUGAU________GAU_GAGGGG\n______________\|\|\|\|\|\|\|\|\|________\|\|\|_\|\|\|\|\|\|\n______________CUAGAACUA________CUA_CUCCCC\n3'-UUU...AAAGC_________GA_________U______AACCC...AUA-5'\n_____________\|___________________________\|\n_____________51__________________________29\n	168 -- 174	42 -- 48	-23.2775 kcal/mol	5.32128 kcal/mol	0.974272 kcal/mol	165 192@LB@ \| \|@LB@5'-UUC...AUGAU GCCUAAAC GAAGA...CAA-3'@LB@ GAUCUUGAU GAU GAGGGG@LB@ \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ CUAGAACUA CUA CUCCCC@LB@3'-UUU...AAAGC GA U AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -23.2775 kcal/mol@LB@Unfolding Energy - mRNA 5.32128 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 166 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 42 -- 48@LB@
152	0.01351	0.2966	bsu25600	comER	-9.59	0.243237	173 -- 194	30 -- 51	ComE operon protein 4	_____________172____________________195\n_____________\|______________________\|\n5'-AGC...UUAGA____AAUAGCUCAAA_______AAACC...CAA-3'\n______________GGAU___________GGAGGGG\n______________\|\|\|\|___________:\|\|\|\|\|\|\n______________CCUA___________UCUCCCC\n3'-UUU...AAAAG____GAACUAGACUA_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	188 -- 194	30 -- 36	-16.7526 kcal/mol	6.18889 kcal/mol	0.974282 kcal/mol	172 195@LB@ \| \|@LB@5'-AGC...UUAGA AAUAGCUCAAA AAACC...CAA-3'@LB@ GGAU GGAGGGG@LB@ \|\|\|\| :\|\|\|\|\|\|@LB@ CCUA UCUCCCC@LB@3'-UUU...AAAAG GAACUAGACUA AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -16.7526 kcal/mol@LB@Unfolding Energy - mRNA 6.18889 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 173 -- 194@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
155	0.01391	0.2994	bsu24780	yqgY	-10.29	0.193646	188 -- 194	30 -- 36	Evidence 4: Homologs of previously reported genes of unknown function	_____________187_____195\n_____________\|_______\|\n5'-UGU...UCUCG_______AUAAA...GAC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.7207 kcal/mol	3.29345 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGU...UCUCG AUAAA...GAC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -13.7207 kcal/mol@LB@Unfolding Energy - mRNA 3.29345 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
157	0.01433	0.3008	bsu38150	qoxC	-14.65	0.035334	274 -- 297	30 -- 53	quinol oxidase subunit 3	_____________273_______________________298\n_____________\|_________________________\|\n5'-ACC...UAUUC__________G____UUUU______CAG-3'\n______________UCGGGUUUUG_AUCU_____AGGGG\n______________\|\|\|\|:\|:\|\|\|_\|\|\|\|_____\|\|\|\|\|\n______________AGCCUAGAAC_UAGA_____UCCCC\n3'-UUU...AAAAA_______________CUAUC_____AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	277 -- 283	44 -- 50	-24.1532 kcal/mol	8.5194 kcal/mol	0.985344 kcal/mol	273 298@LB@ \| \|@LB@5'-ACC...UAUUC G UUUU CAG-3'@LB@ UCGGGUUUUG AUCU AGGGG@LB@ \|\|\|\|:\|:\|\|\| \|\|\|\| \|\|\|\|\|@LB@ AGCCUAGAAC UAGA UCCCC@LB@3'-UUU...AAAAA CUAUC AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -24.1532 kcal/mol@LB@Unfolding Energy - mRNA 8.5194 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 274 -- 297@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 44 -- 50@LB@
164	0.01535	0.3122	bsu39720	iolE	-13.03	0.070250	182 -- 189	30 -- 37	inosose dehydratase	_____________181______190\n_____________\|________\|\n5'-GUU...AGUAU________AGGCA...UAA-3'\n______________UAGAGGGG\n______________\|\|\|\|\|\|\|\|\n______________AUCUCCCC\n3'-UUU...AGACU________AACCC...AUA-5'\n_____________\|________\|\n_____________38_______29\n	183 -- 189	30 -- 36	-14.5397 kcal/mol	1.33978 kcal/mol	0.165704 kcal/mol	181 190@LB@ \| \|@LB@5'-GUU...AGUAU AGGCA...UAA-3'@LB@ UAGAGGGG@LB@ \|\|\|\|\|\|\|\|@LB@ AUCUCCCC@LB@3'-UUU...AGACU AACCC...AUA-5'@LB@ \| \|@LB@ 38 29@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -14.5397 kcal/mol@LB@Unfolding Energy - mRNA 1.33978 kcal/mol@LB@Unfolding Energy - sRNA 0.165704 kcal/mol@LB@@LB@Position - mRNA 182 -- 189@LB@Position - sRNA 30 -- 37@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
165	0.01546	0.3127	bsu02230	purT	-12.11	0.100898	185 -- 195	30 -- 39	phosphoribosylglycinamide formyltransferase	_____________184_________196\n_____________\|___________\|\n5'-GAU...GAACA___A_______CAAAG...UUG-3'\n______________GAU_GGAGGGG\n______________\|\|\|_:\|\|\|\|\|\|\n______________CUA_UCUCCCC\n3'-UUU...CUAGA___________AACCC...AUA-5'\n_____________\|___________\|\n_____________40__________29\n	189 -- 195	30 -- 36	-15.5568 kcal/mol	2.66346 kcal/mol	0.779184 kcal/mol	184 196@LB@ \| \|@LB@5'-GAU...GAACA A CAAAG...UUG-3'@LB@ GAU GGAGGGG@LB@ \|\|\| :\|\|\|\|\|\|@LB@ CUA UCUCCCC@LB@3'-UUU...CUAGA AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.5568 kcal/mol@LB@Unfolding Energy - mRNA 2.66346 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
189	0.01911	0.3269	bsu24290	xseB	-12.91	0.073825	187 -- 193	30 -- 36	exodeoxyribonuclease 7 small subunit	_____________186_____194\n_____________\|_______\|\n5'-CAU...AAAAG_______AAGAA...UAG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	187 -- 193	30 -- 36	-14.0184 kcal/mol	0.973532 kcal/mol	0.133643 kcal/mol	186 194@LB@ \| \|@LB@5'-CAU...AAAAG AAGAA...UAG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.91 kcal/mol@LB@Hybridization Energy -14.0184 kcal/mol@LB@Unfolding Energy - mRNA 0.973532 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@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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