Input and runtime details for job 4894743 (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 4894743 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:26 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:36:09 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 05:38:38 CET 2018
	Post-Processing Finished		@ Sat Feb 17 05:38:45 CET 2018
	Job Completed		@ Sat Feb 17 05:39:16 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4894743&toolName=CopraRNA ( 30 days expiry )

Description of the job

SR1

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	Additional homologs
22	0.0005922	0.1011	bsu09965	yhaJ	-9.39	0.394896	264 -- 275	174 -- 185	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16845009; Product type pf : factor'		_____________263___________276\n_____________\|_____________\|\n5'-ACU...AACCC___AU________UUGUU...CCU-3'\n______________CAU__UUCGCAGU\n______________\|\|\|__\|:\|\|\|\|\|:\n______________GUA__AGGCGUCG\n3'-AUU...UAACU___AC________UUCAA...CAA-5'\n_____________\|_____________\|\n_____________186___________173\n	68 -- 74	133 -- 139	-12.4018 kcal/mol	1.72698 kcal/mol	5.12932 kcal/mol	263 276@LB@ \| \|@LB@5'-ACU...AACCC AU UUGUU...CCU-3'@LB@ CAU UUCGCAGU@LB@ \|\|\| \|:\|\|\|\|\|:@LB@ GUA AGGCGUCG@LB@3'-AUU...UAACU AC UUCAA...CAA-5'@LB@ \| \|@LB@ 186 173@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.4018 kcal/mol@LB@Unfolding Energy - mRNA 1.72698 kcal/mol@LB@Unfolding Energy - sRNA 5.12932 kcal/mol@LB@@LB@Position - mRNA 264 -- 275@LB@Position - sRNA 174 -- 185@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 133 -- 139@LB@
113	0.005141	0.1741	bsu36080	ywrF	-10.09	0.302867	265 -- 274	38 -- 47	Evidence 4: Homologs of previously reported genes of unknown function		_____________264________275\n_____________\|__________\|\n5'-UGG...UACCG__________CCCCA...UUU-3'\n______________UUAUUCCCCG\n______________\|\|\|\|\|\|\|\|\|:\n______________AAUAAGGGGU\n3'-AUU...UAGAG__________AAAGA...CAA-5'\n_____________\|__________\|\n_____________48_________37\n	268 -- 274	38 -- 44	-13.6226 kcal/mol	1.45475 kcal/mol	3.86656 kcal/mol	264 275@LB@ \| \|@LB@5'-UGG...UACCG CCCCA...UUU-3'@LB@ UUAUUCCCCG@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AAUAAGGGGU@LB@3'-AUU...UAGAG AAAGA...CAA-5'@LB@ \| \|@LB@ 48 37@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -13.6226 kcal/mol@LB@Unfolding Energy - mRNA 1.45475 kcal/mol@LB@Unfolding Energy - sRNA 3.86656 kcal/mol@LB@@LB@Position - mRNA 265 -- 274@LB@Position - sRNA 38 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 38 -- 44@LB@
26	0.0007049	0.1051	bsu24750	yqhB	-20.67	0.002015	266 -- 294	134 -- 164	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pm: membrane component'		_____________265_____________________________295\n_____________\|_______________________________\|\n5'-UUC...CUCAU______________UUUU_____________AAUUUU-3'\n______________UUUGUUAACAGGAU_____CGUUG_CCGUAG\n______________\|\|::\|:\|\|\|\|\|\|\|:_____\|:\|\|\|_\|\|\|:\|\|\n______________AAGUAGUUGUCCUG_____GUAAC_GGCGUC\n3'-AUU...AUGAG______________UAACU_____A______GUUCA...CAA-5'\n_____________\|_______________________________\|\n_____________165_____________________________133\n	273 -- 279	151 -- 157	-31.5872 kcal/mol	2.9023 kcal/mol	8.693 kcal/mol	265 295@LB@ \| \|@LB@5'-UUC...CUCAU UUUU AAUUUU-3'@LB@ UUUGUUAACAGGAU CGUUG CCGUAG@LB@ \|\|::\|:\|\|\|\|\|\|\|: \|:\|\|\| \|\|\|:\|\|@LB@ AAGUAGUUGUCCUG GUAAC GGCGUC@LB@3'-AUU...AUGAG UAACU A GUUCA...CAA-5'@LB@ \| \|@LB@ 165 133@LB@@LB@@LB@Energy -20.67 kcal/mol@LB@Hybridization Energy -31.5872 kcal/mol@LB@Unfolding Energy - mRNA 2.9023 kcal/mol@LB@Unfolding Energy - sRNA 8.693 kcal/mol@LB@@LB@Position - mRNA 266 -- 294@LB@Position - sRNA 134 -- 164@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 151 -- 157@LB@
199	0.00902	0.1751	bsu30990	thiT	-13.50	0.067771	270 -- 291	126 -- 147	thiamine transporter ThiT		_____________269_____________________292\n_____________\|_______________________\|\n5'-AUG...UUUUA______________G__U_____UUAGC...UGC-3'\n______________GACAUUGUCU_CAG_AA_GUUUC\n______________\|\|\|\|\|\|\|\|\|:_\|\|\|_\|\|_\|\|\|:\|\n______________CUGUAACAGG_GUC_UU_CAAGG\n3'-AUU...UGUAA__________C___G________UAUAU...CAA-5'\n_____________\|_______________________\|\n_____________148_____________________125\n	273 -- 279	138 -- 144	-23.3567 kcal/mol	5.16312 kcal/mol	6.80985 kcal/mol	269 292@LB@ \| \|@LB@5'-AUG...UUUUA G U UUAGC...UGC-3'@LB@ GACAUUGUCU CAG AA GUUUC@LB@ \|\|\|\|\|\|\|\|\|: \|\|\| \|\| \|\|\|:\|@LB@ CUGUAACAGG GUC UU CAAGG@LB@3'-AUU...UGUAA C G UAUAU...CAA-5'@LB@ \| \|@LB@ 148 125@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -23.3567 kcal/mol@LB@Unfolding Energy - mRNA 5.16312 kcal/mol@LB@Unfolding Energy - sRNA 6.80985 kcal/mol@LB@@LB@Position - mRNA 270 -- 291@LB@Position - sRNA 126 -- 147@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 138 -- 144@LB@
37	0.00122	0.1206	bsu31150	yubB	-14.80	0.036692	271 -- 292	145 -- 165	undecaprenyl-diphosphatase		_____________270____________________293\n_____________\|______________________\|\n5'-UAU...GCCGG____U____________A____CAUAGUAG-3'\n______________UUUC_UCGACAGGACAU_UGAU\n______________:\|\|\|_\|\|:\|\|\|\|\|\|\|\|\|_\|\|\|:\n______________GAAG_AGUUGUCCUGUA_ACUG\n3'-AUU...AAUGA____U_________________UAACA...CAA-5'\n_____________\|______________________\|\n_____________166____________________144\n	281 -- 287	149 -- 155	-24.6442 kcal/mol	4.4819 kcal/mol	7.11846 kcal/mol	270 293@LB@ \| \|@LB@5'-UAU...GCCGG U A CAUAGUAG-3'@LB@ UUUC UCGACAGGACAU UGAU@LB@ :\|\|\| \|\|:\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ GAAG AGUUGUCCUGUA ACUG@LB@3'-AUU...AAUGA U UAACA...CAA-5'@LB@ \| \|@LB@ 166 144@LB@@LB@@LB@Energy -14.80 kcal/mol@LB@Hybridization Energy -24.6442 kcal/mol@LB@Unfolding Energy - mRNA 4.4819 kcal/mol@LB@Unfolding Energy - sRNA 7.11846 kcal/mol@LB@@LB@Position - mRNA 271 -- 292@LB@Position - sRNA 145 -- 165@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 149 -- 155@LB@
164	0.007653	0.1751	bsu02110	ybyB	-7.82	0.651200	271 -- 286	38 -- 56	Evidence 4: Homologs of previously reported genes of unknown function		_____________270_____287\n_____________\|_______\|\n5'-UUG...AAAAG_______AAAUC...AAU-3'\n______________ACCCGUC\n______________\|\|\|\|:\|\|\n______________UGGGUAG\n3'-AUU...UAGCA_______AGAAU...CAA-5'\n_____________\|_______\|\n_____________57______37\n	271 -- 277	50 -- 56	-11.5721 kcal/mol	0.816393 kcal/mol	3.06627 kcal/mol	270 287@LB@ \| \|@LB@5'-UUG...AAAAG AAAUC...AAU-3'@LB@ ACCCGUC@LB@ \|\|\|\|:\|\|@LB@ UGGGUAG@LB@3'-AUU...UAGCA AGAAU...CAA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -11.5721 kcal/mol@LB@Unfolding Energy - mRNA 0.816393 kcal/mol@LB@Unfolding Energy - sRNA 3.06627 kcal/mol@LB@@LB@Position - mRNA 271 -- 286@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 50 -- 56@LB@
101	0.004166	0.1594	bsu11270	yjzD	-8.07	0.607351	275 -- 290	119 -- 136	Evidence 4: Homologs of previously reported genes of unknown function		_____________274________________291\n_____________\|__________________\|\n5'-UAG...AUGAA________UA________UUCAA...CAU-3'\n______________CAGC__GU__CGUAUAAU\n______________\|\|\|\|__\|\|__\|:\|\|\|\|\|\|\n______________GUCG__CA__GUAUAUUA\n3'-AUU...CAGGC____UU__AG________CAACA...CAA-5'\n_____________\|__________________\|\n_____________137________________118\n	284 -- 290	119 -- 125	-12.692 kcal/mol	1.37877 kcal/mol	3.96273 kcal/mol	274 291@LB@ \| \|@LB@5'-UAG...AUGAA UA UUCAA...CAU-3'@LB@ CAGC GU CGUAUAAU@LB@ \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ GUCG CA GUAUAUUA@LB@3'-AUU...CAGGC UU AG CAACA...CAA-5'@LB@ \| \|@LB@ 137 118@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -12.692 kcal/mol@LB@Unfolding Energy - mRNA 1.37877 kcal/mol@LB@Unfolding Energy - sRNA 3.96273 kcal/mol@LB@@LB@Position - mRNA 275 -- 290@LB@Position - sRNA 119 -- 136@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 119 -- 125@LB@
188	0.008618	0.1751	bsu31720	degQ	-9.47	0.382925	276 -- 300	147 -- 170	degradation enzyme regulation protein DegQ		_____________275______________301\n_____________\|________________\|\n5'-GAA...AUUCA____GAAA________AAAGC...UUG-3'\n______________UUAC____CAUUAACA\n______________\|\|\|\|____\|\|\|:\|\|\|\|\n______________AAUG____GUAGUUGU\n3'-AUU...AAAAA____AGAA________CCUGU...CAA-5'\n_____________\|________________\|\n_____________171______________146\n	285 -- 291	155 -- 161	-9.46814 kcal/mol	0.995164 kcal/mol	1.41808 kcal/mol	275 301@LB@ \| \|@LB@5'-GAA...AUUCA GAAA AAAGC...UUG-3'@LB@ UUAC CAUUAACA@LB@ \|\|\|\| \|\|\|:\|\|\|\|@LB@ AAUG GUAGUUGU@LB@3'-AUU...AAAAA AGAA CCUGU...CAA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -9.46814 kcal/mol@LB@Unfolding Energy - mRNA 0.995164 kcal/mol@LB@Unfolding Energy - sRNA 1.41808 kcal/mol@LB@@LB@Position - mRNA 276 -- 300@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 155 -- 161@LB@
109	0.004595	0.1633	bsu02700	estA	-7.85	0.646397	289 -- 295	181 -- 187	lipase EstA	bsu08350	_____________288_______296\n_____________\|_________\|\n5'-AUC...CUUAA_________AAAAA...AAC-3'\n______________AAUUUCUUU\n______________\|\|\|\|\|\|\|\|\|\n______________UUAAAGAAA\n3'-AUU...GCGAA_________ACAA-5'\n_____________\|_________\|\n_____________188_______180\n	109 -- 115	5 -- 11	-6.84044 kcal/mol	1.42932 kcal/mol	0.176622 kcal/mol	288 296@LB@ \| \|@LB@5'-AUC...CUUAA AAAAA...AAC-3'@LB@ AAUUUCUUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUAAAGAAA@LB@3'-AUU...GCGAA ACAA-5'@LB@ \| \|@LB@ 188 180@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -6.84044 kcal/mol@LB@Unfolding Energy - mRNA 1.42932 kcal/mol@LB@Unfolding Energy - sRNA 0.176622 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 181 -- 187@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 5 -- 11@LB@
36	0.001118	0.1204	bsu17650	yncE	-8.56	0.524973	291 -- 300	61 -- 70	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type h: extrachromosomal origin'		_____________290_______300\n_____________\|_________\|\n5'-GUA...AUAGG__________-3'\n______________UGGCAAACGA\n______________\|\|\|\|\|\|\|\|:\|\n______________ACCGUUUGUU\n3'-AUU...UUAGA__________AGCAU...CAA-5'\n_____________\|__________\|\n_____________71_________60\n	294 -- 300	61 -- 67	-13.5985 kcal/mol	0.387687 kcal/mol	4.67716 kcal/mol	290 300@LB@ \| \|@LB@5'-GUA...AUAGG -3'@LB@ UGGCAAACGA@LB@ \|\|\|\|\|\|\|\|:\|@LB@ ACCGUUUGUU@LB@3'-AUU...UUAGA AGCAU...CAA-5'@LB@ \| \|@LB@ 71 60@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -13.5985 kcal/mol@LB@Unfolding Energy - mRNA 0.387687 kcal/mol@LB@Unfolding Energy - sRNA 4.67716 kcal/mol@LB@@LB@Position - mRNA 291 -- 300@LB@Position - sRNA 61 -- 70@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 61 -- 67@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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