Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
18	6.719e-05	0.01313	b2935	tktA	-10.85	0.025018	263 -- 275	52 -- 64	transketolase 1 thiamine triphosphate-binding	_____________262___________276\n_____________\|_____________\|\n5'-AAG...CAGAA_____________CACCC...UGG-3'\n______________AGCCAAAUCCGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGGUUUAGGCUA\n3'-AUU...AUAAG_____________AUGCA...AUG-5'\n_____________\|_____________\|\n_____________65____________51\n	269 -- 275	52 -- 58	-21.1603 kcal/mol	4.16811 kcal/mol	6.16128 kcal/mol	262 276@LB@ \| \|@LB@5'-AAG...CAGAA CACCC...UGG-3'@LB@ AGCCAAAUCCGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGGUUUAGGCUA@LB@3'-AUU...AUAAG AUGCA...AUG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -21.1603 kcal/mol@LB@Unfolding Energy - mRNA 4.16811 kcal/mol@LB@Unfolding Energy - sRNA 6.16128 kcal/mol@LB@@LB@Position - mRNA 263 -- 275@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 52 -- 58@LB@
16	5.617e-05	0.01183	b0116	lpd	-12.59	0.006546	264 -- 293	29 -- 63	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase	_____________263__________________________________294\n_____________\|____________________________________\|\n5'-CCG...CCGCU___U____________C___UUU_____________ACCGUAA-3'\n______________GCC___UCCG_UUGCG_UGA______AGGUCUGGAA\n______________\|\|\|___\|\|\|\|_\|\|:\|\|_\|\|\|______\|\|\|\|\|\|\|:\|\|\n______________CGG___AGGC_AAUGC_ACU______UCCAGACUUU\n3'-AUU...UAAGU___UUU____U_________UCAUUU__________CUAUC...AUG-5'\n_____________\|____________________________________\|\n_____________64___________________________________28\n	286 -- 292	30 -- 36	-30.8342 kcal/mol	7.36676 kcal/mol	10.8887 kcal/mol	263 294@LB@ \| \|@LB@5'-CCG...CCGCU U C UUU ACCGUAA-3'@LB@ GCC UCCG UUGCG UGA AGGUCUGGAA@LB@ \|\|\| \|\|\|\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|:\|\|@LB@ CGG AGGC AAUGC ACU UCCAGACUUU@LB@3'-AUU...UAAGU UUU U UCAUUU CUAUC...AUG-5'@LB@ \| \|@LB@ 64 28@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -30.8342 kcal/mol@LB@Unfolding Energy - mRNA 7.36676 kcal/mol@LB@Unfolding Energy - sRNA 10.8887 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 29 -- 63@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 30 -- 36@LB@
5	1.055e-05	0.007422	b1287	yciW	-9.98	0.045809	266 -- 289	4 -- 27	putative oxidoreductase	_____________265______________________290\n_____________\|________________________\|\n5'-GUC...ACGGA___U______C________GU___GGAAG...CAA-3'\n______________GUA_GACGUU_UGCCUCUG__CCC\n______________:\|\|_:\|\|:\|:_\|:\|\|\|\|\|\|__\|\|\|\n______________UAU_UUGUAG_AUGGAGAC__GGG\n3'-AUU...CUUUC___C______A________AU___AUG-5'\n_____________\|________________________\|\n_____________28_______________________3\n	278 -- 284	9 -- 15	-26.8114 kcal/mol	8.80708 kcal/mol	8.0435 kcal/mol	265 290@LB@ \| \|@LB@5'-GUC...ACGGA U C GU GGAAG...CAA-3'@LB@ GUA GACGUU UGCCUCUG CCC@LB@ :\|\| :\|\|:\|: \|:\|\|\|\|\|\| \|\|\|@LB@ UAU UUGUAG AUGGAGAC GGG@LB@3'-AUU...CUUUC C A AU AUG-5'@LB@ \| \|@LB@ 28 3@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -26.8114 kcal/mol@LB@Unfolding Energy - mRNA 8.80708 kcal/mol@LB@Unfolding Energy - sRNA 8.0435 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 4 -- 27@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 9 -- 15@LB@
108	0.003398	0.1101	b0973	hyaB	-11.40	0.016694	267 -- 275	48 -- 56	hydrogenase 1 large subunit	_____________266_______276\n_____________\|_________\|\n5'-GGU...UCGAC_________CGCAU...GCG-3'\n______________CCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	269 -- 275	48 -- 54	-14.3171 kcal/mol	1.33562 kcal/mol	1.55919 kcal/mol	266 276@LB@ \| \|@LB@5'-GGU...UCGAC CGCAU...GCG-3'@LB@ CCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -14.3171 kcal/mol@LB@Unfolding Energy - mRNA 1.33562 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 267 -- 275@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
129	0.004413	0.1199	b0062	araA	-8.60	0.109835	267 -- 273	1 -- 7	L-arabinose isomerase	_____________266_____274\n_____________\|_______\|\n5'-CGC...CGGAA_______GUCAG...ACG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	267 -- 273	1 -- 7	-12.3746 kcal/mol	1.75625 kcal/mol	2.03949 kcal/mol	266 274@LB@ \| \|@LB@5'-CGC...CGGAA GUCAG...ACG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.3746 kcal/mol@LB@Unfolding Energy - mRNA 1.75625 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 267 -- 273@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
106	0.003365	0.1101	b0955	ycbZ	-10.52	0.031644	269 -- 288	48 -- 66	putative peptidase	_____________268__________________289\n_____________\|____________________\|\n5'-UUG...UUUGC_______C_________A__AAAAC...CUU-3'\n______________UCAGCCA_AUUUGAUUG_CG\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|:_\|\|\n______________AGUCGGU_UAGGCUAAU_GC\n3'-AUU...UUAUA_______U____________ACUUC...AUG-5'\n_____________\|____________________\|\n_____________67___________________47\n	279 -- 285	50 -- 56	-21.5915 kcal/mol	3.60671 kcal/mol	7.48271 kcal/mol	268 289@LB@ \| \|@LB@5'-UUG...UUUGC C A AAAAC...CUU-3'@LB@ UCAGCCA AUUUGAUUG CG@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|: \|\|@LB@ AGUCGGU UAGGCUAAU GC@LB@3'-AUU...UUAUA U ACUUC...AUG-5'@LB@ \| \|@LB@ 67 47@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -21.5915 kcal/mol@LB@Unfolding Energy - mRNA 3.60671 kcal/mol@LB@Unfolding Energy - sRNA 7.48271 kcal/mol@LB@@LB@Position - mRNA 269 -- 288@LB@Position - sRNA 48 -- 66@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 50 -- 56@LB@
43	0.0004631	0.03766	b4346	mcrB	-12.47	0.007188	270 -- 300	1 -- 31	5-methylcytosine-specific restriction enzyme McrBC subunit McrB	_____________269_______________________________300\n_____________\|_________________________________\|\n5'-UUU...CCACU______UAUCC_________________A_____-3'\n______________AAAGAU_____AACGUCUUACC___GUA_CCUGC\n______________\|\|\|\|\|\|_____\|\|\|:\|\|\|\|\|\|\|___\|\|\|_\|\|\|:\|\n______________UUUCUA_____UUGUAGAAUGG___CAU_GGAUG\n3'-AUU...CAGAC______UC______________AGA___G_____-5'\n_____________\|_________________________________\|\n_____________32________________________________1\n	285 -- 291	13 -- 19	-24.3421 kcal/mol	3.83264 kcal/mol	8.05889 kcal/mol	269 300@LB@ \| \|@LB@5'-UUU...CCACU UAUCC A -3'@LB@ AAAGAU AACGUCUUACC GUA CCUGC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|\| \|\|\| \|\|\|:\|@LB@ UUUCUA UUGUAGAAUGG CAU GGAUG@LB@3'-AUU...CAGAC UC AGA G -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -24.3421 kcal/mol@LB@Unfolding Energy - mRNA 3.83264 kcal/mol@LB@Unfolding Energy - sRNA 8.05889 kcal/mol@LB@@LB@Position - mRNA 270 -- 300@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 13 -- 19@LB@
172	0.007198	0.1466	b2395	yfeA	-7.88	0.166321	272 -- 292	49 -- 69	putative diguanylate cyclase	_____________271____________________293\n_____________\|______________________\|\n5'-ACC...GUACU__________UC____UU____UUCGCCAC-3'\n______________UAUUCAGCUA___CCG__UUAU\n______________\|\|\|\|\|\|\|\|:\|___\|\|\|__\|\|\|:\n______________AUAAGUCGGU___GGC__AAUG\n3'-AUU...AUUUU__________UUA___U_____CACUU...AUG-5'\n_____________\|______________________\|\n_____________70_____________________48\n	275 -- 281	60 -- 66	-16.2546 kcal/mol	2.18624 kcal/mol	6.21499 kcal/mol	271 293@LB@ \| \|@LB@5'-ACC...GUACU UC UU UUCGCCAC-3'@LB@ UAUUCAGCUA CCG UUAU@LB@ \|\|\|\|\|\|\|\|:\| \|\|\| \|\|\|:@LB@ AUAAGUCGGU GGC AAUG@LB@3'-AUU...AUUUU UUA U CACUU...AUG-5'@LB@ \| \|@LB@ 70 48@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -16.2546 kcal/mol@LB@Unfolding Energy - mRNA 2.18624 kcal/mol@LB@Unfolding Energy - sRNA 6.21499 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 49 -- 69@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 60 -- 66@LB@
3	0	0	b2564	pdxJ	-5.03	0.588876	273 -- 283	52 -- 62	pyridoxine 5'-phosphate synthase	_____________272_________284\n_____________\|___________\|\n5'-AAA...CUUAC___________GCAGG...UUG-3'\n______________CCGGAUCCGGU\n______________\|\|::\|\|\|\|\|:\|\n______________GGUUUAGGCUA\n3'-AUU...AAGUC___________AUGCA...AUG-5'\n_____________\|___________\|\n_____________63__________51\n	277 -- 283	52 -- 58	-14.6263 kcal/mol	4.30712 kcal/mol	5.31395 kcal/mol	272 284@LB@ \| \|@LB@5'-AAA...CUUAC GCAGG...UUG-3'@LB@ CCGGAUCCGGU@LB@ \|\|::\|\|\|\|\|:\|@LB@ GGUUUAGGCUA@LB@3'-AUU...AAGUC AUGCA...AUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -14.6263 kcal/mol@LB@Unfolding Energy - mRNA 4.30712 kcal/mol@LB@Unfolding Energy - sRNA 5.31395 kcal/mol@LB@@LB@Position - mRNA 273 -- 283@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 52 -- 58@LB@
136	0.004892	0.1265	b2349	intS	-8.19	0.139381	273 -- 281	3 -- 11	CPS-53 (KpLE1) prophage; putative prophage CPS-53 integrase	_____________272_______282\n_____________\|_________\|\n5'-AAG...AUGGC_________UAUGU...GGA-3'\n______________CUGUACCUU\n______________\|\|\|\|\|\|\|:\|\n______________GACAUGGGA\n3'-AUU...AUGGA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	275 -- 281	3 -- 9	-13.0022 kcal/mol	1.37836 kcal/mol	3.45478 kcal/mol	272 282@LB@ \| \|@LB@5'-AAG...AUGGC UAUGU...GGA-3'@LB@ CUGUACCUU@LB@ \|\|\|\|\|\|\|:\|@LB@ GACAUGGGA@LB@3'-AUU...AUGGA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -13.0022 kcal/mol@LB@Unfolding Energy - mRNA 1.37836 kcal/mol@LB@Unfolding Energy - sRNA 3.45478 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@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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