Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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	Additional homologs
105	0.003867	0.1238	b0716	ybgO	-11.28	0.093728	281 -- 296	25 -- 40	putative fimbrial protein	b3048	_____________280______________297\n_____________\|________________\|\n5'-GCC...UGCUA__________U_____GGCG-3'\n______________UUUUGGUACA_CUGGU\n______________\|::\|\|\|\|\|\|\|_\|\|:\|:\n______________AGGACCAUGU_GAUCG\n3'-UUU...CACCA__________C_____UAAAA...UCG-5'\n_____________\|________________\|\n_____________41_______________24\n	284 -- 290	31 -- 37	-18.2853 kcal/mol	2.44789 kcal/mol	4.55365 kcal/mol	280 297@LB@ \| \|@LB@5'-GCC...UGCUA U GGCG-3'@LB@ UUUUGGUACA CUGGU@LB@ \|::\|\|\|\|\|\|\| \|\|:\|:@LB@ AGGACCAUGU GAUCG@LB@3'-UUU...CACCA C UAAAA...UCG-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -18.2853 kcal/mol@LB@Unfolding Energy - mRNA 2.44789 kcal/mol@LB@Unfolding Energy - sRNA 4.55365 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 31 -- 37@LB@
139	0.00635	0.1535	b0800	ybiB	-9.74	0.186276	120 -- 129	27 -- 36	putative family 3 glycosyltransferase		_____________119________130\n_____________\|__________\|\n5'-GCC...CUGAA__________AAAAG...UCA-3'\n______________GGUAUAGUUA\n______________\|\|\|\|:\|\|:\|\|\n______________CCAUGUCGAU\n3'-UUU...AAGGA__________CGUAA...UCG-5'\n_____________\|__________\|\n_____________37_________26\n	123 -- 129	27 -- 33	-12.0711 kcal/mol	1.15693 kcal/mol	1.17709 kcal/mol	119 130@LB@ \| \|@LB@5'-GCC...CUGAA AAAAG...UCA-3'@LB@ GGUAUAGUUA@LB@ \|\|\|\|:\|\|:\|\|@LB@ CCAUGUCGAU@LB@3'-UUU...AAGGA CGUAA...UCG-5'@LB@ \| \|@LB@ 37 26@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.0711 kcal/mol@LB@Unfolding Energy - mRNA 1.15693 kcal/mol@LB@Unfolding Energy - sRNA 1.17709 kcal/mol@LB@@LB@Position - mRNA 120 -- 129@LB@Position - sRNA 27 -- 36@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 27 -- 33@LB@
59	0.00143	0.08147	b0848	ybjM	-6.77	0.507403	86 -- 118	1 -- 33	inner membrane protein		_____________85_________________________________119\n_____________\|__________________________________\|\n5'-GAA...UAUCA___________GAAU__C____GCCUAUA_____AUGGA...GGG-3'\n______________ACGGCUA_UAU____UG_GUUG_______UUAGC\n______________\|\|:\|\|\|\|_:\|\|____\|\|_\|\|\|:_______\|:\|\|\|\n______________UGUCGAU_GUA____AC_CAAU_______AGUCG\n3'-UUU...GACCA_______C___AAAU__C____ACAAAA______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	86 -- 92	27 -- 33	-17.6492 kcal/mol	9.38597 kcal/mol	1.49313 kcal/mol	85 119@LB@ \| \|@LB@5'-GAA...UAUCA GAAU C GCCUAUA AUGGA...GGG-3'@LB@ ACGGCUA UAU UG GUUG UUAGC@LB@ \|\|:\|\|\|\| :\|\| \|\| \|\|\|: \|:\|\|\|@LB@ UGUCGAU GUA AC CAAU AGUCG@LB@3'-UUU...GACCA C AAAU C ACAAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -17.6492 kcal/mol@LB@Unfolding Energy - mRNA 9.38597 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 86 -- 118@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 27 -- 33@LB@
138	0.006247	0.1521	b1063	yceB	-7.15	0.457702	84 -- 117	1 -- 32	lipoprotein DUF1439 family		_____________83__________________________________118\n_____________\|___________________________________\|\n5'-UGC...CGCGG____CU_____CGC_______CCGCCG________UUUUU...ACC-3'\n______________CAGC__GUAUU____GGGUUG______UUUUCAGU\n______________\|\|\|\|__\|:\|\|\|____\|\|\|\|\|:______\|\|\|\|\|\|\|:\n______________GUCG__CGUAA____CCCAAU______AAAAGUCG\n3'-UUU...ACCAU____AU_____AAUA______ACA___________-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	111 -- 117	1 -- 7	-22.6034 kcal/mol	13.9644 kcal/mol	1.49075 kcal/mol	83 118@LB@ \| \|@LB@5'-UGC...CGCGG CU CGC CCGCCG UUUUU...ACC-3'@LB@ CAGC GUAUU GGGUUG UUUUCAGU@LB@ \|\|\|\| \|:\|\|\| \|\|\|\|\|: \|\|\|\|\|\|\|:@LB@ GUCG CGUAA CCCAAU AAAAGUCG@LB@3'-UUU...ACCAU AU AAUA ACA -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -22.6034 kcal/mol@LB@Unfolding Energy - mRNA 13.9644 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 84 -- 117@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 1 -- 7@LB@
14	9.306e-05	0.02121	b1205	ychH	-11.92	0.068307	242 -- 277	15 -- 49	DUF2583 family putative inner membrane protein		_____________241____________________________________278\n_____________\|______________________________________\|\n5'-CAA...CUCAU____U___G________GUAAU_G____CGGC______GUAUU...UAC-3'\n______________GGGG_UGG__UCUGGUG_____G_UGGU_____GUGGG\n______________\|\|:\|_\|\|\|__:\|\|\|\|\|:_____\|_\|:\|:_____:\|\|\|\|\n______________CCUC_ACC__GGACCAU_____C_AUCG_____UACCC\n3'-UUU...CGAUU____C___AA_______GU____G____UAAAA_____AAUAC...UCG-5'\n_____________\|______________________________________\|\n_____________50_____________________________________14\n	251 -- 257	33 -- 39	-28.7764 kcal/mol	12.2787 kcal/mol	4.57366 kcal/mol	241 278@LB@ \| \|@LB@5'-CAA...CUCAU U G GUAAU G CGGC GUAUU...UAC-3'@LB@ GGGG UGG UCUGGUG G UGGU GUGGG@LB@ \|\|:\| \|\|\| :\|\|\|\|\|: \| \|:\|: :\|\|\|\|@LB@ CCUC ACC GGACCAU C AUCG UACCC@LB@3'-UUU...CGAUU C AA GU G UAAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -28.7764 kcal/mol@LB@Unfolding Energy - mRNA 12.2787 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 242 -- 277@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 33 -- 39@LB@
6	7.051e-06	0.00395	b1213	ychQ	-11.22	0.096653	74 -- 98	15 -- 40	SIRB family inner membrane protein		_____________73___________________________99\n_____________\|____________________________\|\n5'-GAC...UCUGC______AAC__________GCA______CGAAG...AUC-3'\n______________UUCUGG___AUGGCUGGCA______GGG\n______________\|:\|\|\|\|___\|::\|\|\|:\|\|\|______\|\|\|\n______________AGGACC___UGUCGAUCGU______CCC\n3'-UUU...CACCA______A____________AAAAUA___AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________41___________________________14\n	86 -- 92	24 -- 30	-24.2509 kcal/mol	8.46179 kcal/mol	4.56973 kcal/mol	73 99@LB@ \| \|@LB@5'-GAC...UCUGC AAC GCA CGAAG...AUC-3'@LB@ UUCUGG AUGGCUGGCA GGG@LB@ \|:\|\|\|\| \|::\|\|\|:\|\|\| \|\|\|@LB@ AGGACC UGUCGAUCGU CCC@LB@3'-UUU...CACCA A AAAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 41 14@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -24.2509 kcal/mol@LB@Unfolding Energy - mRNA 8.46179 kcal/mol@LB@Unfolding Energy - sRNA 4.56973 kcal/mol@LB@@LB@Position - mRNA 74 -- 98@LB@Position - sRNA 15 -- 40@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 24 -- 30@LB@
81	0.002689	0.1082	b1498	ydeN	-15.88	0.005981	253 -- 275	21 -- 44	putative Ser-type periplasmic non-aryl sulfatase	b3678 b3801	_____________252______________________276\n_____________\|________________________\|\n5'-AUU...GAUAC___CA___________________GCUGC...UAA-3'\n______________UGG__UCUGGUAUGGCU_GCAUUU\n______________\|\|\|__:\|\|\|\|\|\|::\|\|\|_\|\|\|\|\|\|\n______________ACC__GGACCAUGUCGA_CGUAAA\n3'-UUU...CCUCC___AA____________U______AUACC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________20\n	263 -- 269	28 -- 34	-26.8614 kcal/mol	6.42389 kcal/mol	4.55918 kcal/mol	252 276@LB@ \| \|@LB@5'-AUU...GAUAC CA GCUGC...UAA-3'@LB@ UGG UCUGGUAUGGCU GCAUUU@LB@ \|\|\| :\|\|\|\|\|\|::\|\|\| \|\|\|\|\|\|@LB@ ACC GGACCAUGUCGA CGUAAA@LB@3'-UUU...CCUCC AA U AUACC...UCG-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -15.88 kcal/mol@LB@Hybridization Energy -26.8614 kcal/mol@LB@Unfolding Energy - mRNA 6.42389 kcal/mol@LB@Unfolding Energy - sRNA 4.55918 kcal/mol@LB@@LB@Position - mRNA 253 -- 275@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
186	0.01069	0.1919	b1614	ydgA	-8.85	0.262719	182 -- 191	16 -- 25	DUF945 family protein		_____________181________192\n_____________\|__________\|\n5'-ACA...GAUUU__________AUAAU...UCG-3'\n______________CAUUUUAUGG\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUAAAAUACC\n3'-UUU...CGAUC__________CAAUA...UCG-5'\n_____________\|__________\|\n_____________26_________15\n	185 -- 191	16 -- 22	-11.3536 kcal/mol	2.1555 kcal/mol	0.346409 kcal/mol	181 192@LB@ \| \|@LB@5'-ACA...GAUUU AUAAU...UCG-3'@LB@ CAUUUUAUGG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUAAAAUACC@LB@3'-UUU...CGAUC CAAUA...UCG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -11.3536 kcal/mol@LB@Unfolding Energy - mRNA 2.1555 kcal/mol@LB@Unfolding Energy - sRNA 0.346409 kcal/mol@LB@@LB@Position - mRNA 182 -- 191@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 16 -- 22@LB@
67	0.00183	0.09081	b1607	ydgC	-12.69	0.045650	228 -- 262	1 -- 36	GlpM family inner membrane protein		_____________227__________________________________263\n_____________\|____________________________________\|\n5'-AUG...CGCUC_____________GUGCUGUUGAUUG__G_______AAAAA...CAC-3'\n______________GGUGC_GCUGGUA_____________GU_UUUUAGC\n______________\|\|\|:\|_\|\|\|:\|:\|_____________\|\|_\|\|\|:\|\|\|\n______________CCAUG_CGAUCGU_____________CA_AAAGUCG\n3'-UUU...AAGGA_____U_______AAAAUACCCAAUA__A_______-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	256 -- 262	1 -- 7	-24.769 kcal/mol	10.5859 kcal/mol	1.49509 kcal/mol	227 263@LB@ \| \|@LB@5'-AUG...CGCUC GUGCUGUUGAUUG G AAAAA...CAC-3'@LB@ GGUGC GCUGGUA GU UUUUAGC@LB@ \|\|\|:\| \|\|\|:\|:\| \|\| \|\|\|:\|\|\|@LB@ CCAUG CGAUCGU CA AAAGUCG@LB@3'-UUU...AAGGA U AAAAUACCCAAUA A -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.769 kcal/mol@LB@Unfolding Energy - mRNA 10.5859 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 228 -- 262@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 1 -- 7@LB@
28	0.000409	0.0491	b1688	ydiK	-9.69	0.189548	195 -- 219	1 -- 33	UPF0118 family inner membrane protein		_____________194_______________________________220\n_____________\|_________________________________\|\n5'-AUG...GAAAA__________________UAA_____CG_____CCAGG...CCU-3'\n______________GUAGUUA________UGG___AUGUU__UCAGC\n______________::\|\|:\|\|________\|\|\|___\|\|\|\|\|__\|\|\|\|\|\n______________UGUCGAU________ACC___UACAA__AGUCG\n3'-UUU...GACCA_______CGUAAAAU___CAA_____AA_____-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	195 -- 201	27 -- 33	-14.5165 kcal/mol	3.32905 kcal/mol	1.49313 kcal/mol	194 220@LB@ \| \|@LB@5'-AUG...GAAAA UAA CG CCAGG...CCU-3'@LB@ GUAGUUA UGG AUGUU UCAGC@LB@ ::\|\|:\|\| \|\|\| \|\|\|\|\| \|\|\|\|\|@LB@ UGUCGAU ACC UACAA AGUCG@LB@3'-UUU...GACCA CGUAAAAU CAA AA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -14.5165 kcal/mol@LB@Unfolding Energy - mRNA 3.32905 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 195 -- 219@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 27 -- 33@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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