Input and runtime details for job 8257533 (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 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

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_003210 Listeria monocytogenes EGD-e

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
63	0.01551	0.6624	lmo2613	rplO	-17.63	0.030853	185 -- 213	177 -- 203	50S ribosomal protein L15	_____________184______214\n_____________\|________\|\n5'-AAU...AUUCG________UCACU...GCG-3'\n______________UGGGAUGA\n______________:\|\|\|\|\|\|\|\n______________GCCCUACU\n3'-GUU...GUAUU________CCGUA...GGA-5'\n_____________\|________\|\n_____________204______176\n	98 -- 104	198 -- 204	-11.9514 kcal/mol	5.35707 kcal/mol	0.374397 kcal/mol	184 214@LB@ \| \|@LB@5'-AAU...AUUCG UCACU...GCG-3'@LB@ UGGGAUGA@LB@ :\|\|\|\|\|\|\|@LB@ GCCCUACU@LB@3'-GUU...GUAUU CCGUA...GGA-5'@LB@ \| \|@LB@ 204 176@LB@@LB@@LB@Energy -17.63 kcal/mol@LB@Hybridization Energy -11.9514 kcal/mol@LB@Unfolding Energy - mRNA 5.35707 kcal/mol@LB@Unfolding Energy - sRNA 0.374397 kcal/mol@LB@@LB@Position - mRNA 185 -- 213@LB@Position - sRNA 177 -- 203@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 198 -- 204@LB@
101	0.026	0.6733	lmo2768	N/A	-17.52	0.032492	230 -- 251	161 -- 179	hypothetical membrane protein	_____________229__________252\n_____________\|____________\|\n5'-UUA...GUAAU____________CUUUU...UAA-3'\n______________AUGAGAUGGAUG\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________UACUCUACUUAC\n3'-GUU...CCGGU____________UUUUG...GGA-5'\n_____________\|____________\|\n_____________180__________160\n	245 -- 251	161 -- 167	-15.292 kcal/mol	2.52317 kcal/mol	0.818518 kcal/mol	229 252@LB@ \| \|@LB@5'-UUA...GUAAU CUUUU...UAA-3'@LB@ AUGAGAUGGAUG@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ UACUCUACUUAC@LB@3'-GUU...CCGGU UUUUG...GGA-5'@LB@ \| \|@LB@ 180 160@LB@@LB@@LB@Energy -17.52 kcal/mol@LB@Hybridization Energy -15.292 kcal/mol@LB@Unfolding Energy - mRNA 2.52317 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 230 -- 251@LB@Position - sRNA 161 -- 179@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 161 -- 167@LB@
74	0.01955	0.6733	lmo0190	ipk	-17.49	0.032930	174 -- 210	154 -- 192	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	_____________173_______________________________________211\n_____________\|_________________________________________\|\n5'-AUA...AAAAG____UU_________GA___________AA___________GCAUU...CAA-3'\n______________AGAU__UGAAC_GCG__GGCCA___AGA__AAUGAAAAUAA\n______________\|\|\|:__\|\|\|\|\|_:\|:__\|\|\|\|\|___\|\|\|__\|\|\|\|\|\|\|\|:\|\|\n______________UCUG__ACUUG_UGU__CCGGU___UCU__UUACUUUUGUU\n3'-GUU...CCGUA____U______A___G______UAC___AC___________UAUUA...GGA-5'\n_____________\|_________________________________________\|\n_____________193_______________________________________153\n	204 -- 210	154 -- 160	-28.6344 kcal/mol	5.15958 kcal/mol	12.1365 kcal/mol	173 211@LB@ \| \|@LB@5'-AUA...AAAAG UU GA AA GCAUU...CAA-3'@LB@ AGAU UGAAC GCG GGCCA AGA AAUGAAAAUAA@LB@ \|\|\|: \|\|\|\|\| :\|: \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ UCUG ACUUG UGU CCGGU UCU UUACUUUUGUU@LB@3'-GUU...CCGUA U A G UAC AC UAUUA...GGA-5'@LB@ \| \|@LB@ 193 153@LB@@LB@@LB@Energy -17.49 kcal/mol@LB@Hybridization Energy -28.6344 kcal/mol@LB@Unfolding Energy - mRNA 5.15958 kcal/mol@LB@Unfolding Energy - sRNA 12.1365 kcal/mol@LB@@LB@Position - mRNA 174 -- 210@LB@Position - sRNA 154 -- 192@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
140	0.0365	0.6968	lmo1717	N/A	-17.46	0.033387	195 -- 217	147 -- 170		_____________194______________________218\n_____________\|________________________\|\n5'-UAG...AGUAG____C___________________AACAC...AAA-3'\n______________GAGA__GAUGAAAAUGGAUAGUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|:::\|\|\|:\|\|\|\n______________CUCU__UUACUUUUGUUUAUUACU\n3'-GUU...GGUUA____AC__________________AAAAC...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	203 -- 209	155 -- 161	-21.6361 kcal/mol	2.67158 kcal/mol	5.93585 kcal/mol	194 218@LB@ \| \|@LB@5'-UAG...AGUAG C AACAC...AAA-3'@LB@ GAGA GAUGAAAAUGGAUAGUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|:::\|\|\|:\|\|\|@LB@ CUCU UUACUUUUGUUUAUUACU@LB@3'-GUU...GGUUA AC AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -21.6361 kcal/mol@LB@Unfolding Energy - mRNA 2.67158 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 195 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
115	0.03087	0.6968	lmo0059	N/A	-17.38	0.034592	142 -- 189	155 -- 211		_____________141_______________________________________________190\n_____________\|_________________________________________________\|\n5'-AAG...UUAGC____G_____UU___U________________UUUU_____A_______GGGAG...CAU-3'\n______________AGGC__GGAU__AUG_GGCUGCGCG__CAAUG____UGAAU_GAAAGCG\n______________\|\|\|\|__:\|\|:__\|\|\|_::\|\|:\|:\|\|__\|\|\|\|\|____\|\|\|\|\|_\|\|\|\|:\|:\n______________UCCG__UCUG__UAC_UUGAUGUGC__GUUAC____ACUUA_CUUUUGU\n3'-GUU...CCUAC____UA___________________CG_____UCU______________UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________212_______________________________________________154\n	183 -- 189	155 -- 161	-35.3318 kcal/mol	12.9952 kcal/mol	13.976 kcal/mol	141 190@LB@ \| \|@LB@5'-AAG...UUAGC G UU U UUUU A GGGAG...CAU-3'@LB@ AGGC GGAU AUG GGCUGCGCG CAAUG UGAAU GAAAGCG@LB@ \|\|\|\| :\|\|: \|\|\| ::\|\|:\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|:@LB@ UCCG UCUG UAC UUGAUGUGC GUUAC ACUUA CUUUUGU@LB@3'-GUU...CCUAC UA CG UCU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 154@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -35.3318 kcal/mol@LB@Unfolding Energy - mRNA 12.9952 kcal/mol@LB@Unfolding Energy - sRNA 13.976 kcal/mol@LB@@LB@Position - mRNA 142 -- 189@LB@Position - sRNA 155 -- 211@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 155 -- 161@LB@
172	0.04804	0.7516	lmo0111	N/A	-17.34	0.035270	180 -- 204	147 -- 170	lmo0111	_____________179______________________205\n_____________\|________________________\|\n5'-AAU...AUAGA____A_A________G________GGACU...CAG-3'\n______________GAGG_G_AAUGAGAA_GGAUGAUG\n______________\|\|\|:_\|_\|\|\|\|\|:\|\|_::\|\|:\|\|\|\n______________CUCU_C_UUACUUUU_UUUAUUAC\n3'-GUU...GGUUA____A__________G________UAAAA...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	188 -- 194	157 -- 163	-20.9699 kcal/mol	2.01501 kcal/mol	5.93381 kcal/mol	179 205@LB@ \| \|@LB@5'-AAU...AUAGA A A G GGACU...CAG-3'@LB@ GAGG G AAUGAGAA GGAUGAUG@LB@ \|\|\|: \| \|\|\|\|\|:\|\| ::\|\|:\|\|\|@LB@ CUCU C UUACUUUU UUUAUUAC@LB@3'-GUU...GGUUA A G UAAAA...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.34 kcal/mol@LB@Hybridization Energy -20.9699 kcal/mol@LB@Unfolding Energy - mRNA 2.01501 kcal/mol@LB@Unfolding Energy - sRNA 5.93381 kcal/mol@LB@@LB@Position - mRNA 180 -- 204@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 157 -- 163@LB@
136	0.03623	0.6968	lmo1567	citZ	-17.33	0.035419	8 -- 31	169 -- 198	citrate synthase	_____________7______________________________32\n_____________\|______________________________\|\n____5'-CGAAAAA__________________________U___UCCAC...ACG-3'\n______________AGGUGUAG______GCUAUAUGGCCG_UGA\n______________\|\|\|::\|\|\|______:\|\|\|:\|:\|\|\|\|:_\|\|\|\n______________UCCGUAUC______UGAUGUGCCGGU_ACU\n3'-GUU...CCUAC________UGUACU____________U___CUACU...GGA-5'\n_____________\|______________________________\|\n_____________199____________________________168\n	21 -- 27	173 -- 179	-29.4881 kcal/mol	5.57901 kcal/mol	13.3393 kcal/mol	7 32@LB@ \| \|@LB@ 5'-CGAAAAA U UCCAC...ACG-3'@LB@ AGGUGUAG GCUAUAUGGCCG UGA@LB@ \|\|\|::\|\|\| :\|\|\|:\|:\|\|\|\|: \|\|\|@LB@ UCCGUAUC UGAUGUGCCGGU ACU@LB@3'-GUU...CCUAC UGUACU U CUACU...GGA-5'@LB@ \| \|@LB@ 199 168@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -29.4881 kcal/mol@LB@Unfolding Energy - mRNA 5.57901 kcal/mol@LB@Unfolding Energy - sRNA 13.3393 kcal/mol@LB@@LB@Position - mRNA 8 -- 31@LB@Position - sRNA 169 -- 198@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 173 -- 179@LB@
96	0.02498	0.6733	lmo1278	clpQ	-17.33	0.035430	185 -- 216	173 -- 203	ATP-dependent protease peptidase subunit	_____________184_____217\n_____________\|_______\|\n5'-AAA...UCAAC_______AAAAG...UGA-3'\n______________AUGACGG\n______________\|\|:\|\|\|\|\n______________UAUUGCC\n3'-GUU...AUACG_______CUACU...GGA-5'\n_____________\|_______\|\n_____________204_____172\n	238 -- 244	203 -- 209	-8.20287 kcal/mol	1.40847 kcal/mol	0.374301 kcal/mol	184 217@LB@ \| \|@LB@5'-AAA...UCAAC AAAAG...UGA-3'@LB@ AUGACGG@LB@ \|\|:\|\|\|\|@LB@ UAUUGCC@LB@3'-GUU...AUACG CUACU...GGA-5'@LB@ \| \|@LB@ 204 172@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -8.20287 kcal/mol@LB@Unfolding Energy - mRNA 1.40847 kcal/mol@LB@Unfolding Energy - sRNA 0.374301 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 173 -- 203@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 203 -- 209@LB@
124	0.03258	0.6968	lmo1611	N/A	-17.32	0.035574	130 -- 182	121 -- 173	aminopeptidase	_____________129_______________________183\n_____________\|_________________________\|\n5'-CAU...AGAGA_______C___C_____________AUUUG...UUG-3'\n______________AGUGAGG_GAG_GGAAACGGAUAAU\n______________\|:\|\|\|\|:_\|\|:_\|:\|\|\|\|::\|\|\|\|\|\n______________UUACUCU_CUU_CUUUUGUUUAUUA\n3'-GUU...GCCGG_______A___A_____________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________174_______________________120\n	143 -- 149	154 -- 160	-22.8649 kcal/mol	4.94187 kcal/mol	5.58154 kcal/mol	129 183@LB@ \| \|@LB@5'-CAU...AGAGA C C AUUUG...UUG-3'@LB@ AGUGAGG GAG GGAAACGGAUAAU@LB@ \|:\|\|\|\|: \|\|: \|:\|\|\|\|::\|\|\|\|\|@LB@ UUACUCU CUU CUUUUGUUUAUUA@LB@3'-GUU...GCCGG A A CUAAA...GGA-5'@LB@ \| \|@LB@ 174 120@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -22.8649 kcal/mol@LB@Unfolding Energy - mRNA 4.94187 kcal/mol@LB@Unfolding Energy - sRNA 5.58154 kcal/mol@LB@@LB@Position - mRNA 130 -- 182@LB@Position - sRNA 121 -- 173@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 154 -- 160@LB@
110	0.02752	0.6733	lmo0057	N/A	-17.32	0.035592	178 -- 213	150 -- 185		_____________177_________________214\n_____________\|___________________\|\n5'-AAA...GCGGG_______CA__________AAGUA...AAG-3'\n______________AGUGGGA__UGAAUGAAGA\n______________\|:\|\|:\|\|__\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__ACUUACUUUU\n3'-GUU...GCCGG___________________GUUUA...GGA-5'\n_____________\|___________________\|\n_____________186_________________149\n	201 -- 207	157 -- 163	-16.939 kcal/mol	2.5385 kcal/mol	0.930085 kcal/mol	177 214@LB@ \| \|@LB@5'-AAA...GCGGG CA AAGUA...AAG-3'@LB@ AGUGGGA UGAAUGAAGA@LB@ \|:\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU ACUUACUUUU@LB@3'-GUU...GCCGG GUUUA...GGA-5'@LB@ \| \|@LB@ 186 149@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -16.939 kcal/mol@LB@Unfolding Energy - mRNA 2.5385 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 178 -- 213@LB@Position - sRNA 150 -- 185@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@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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