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
119	0.03213	0.6968	lmo2454	N/A	-17.21	0.037384	166 -- 217	153 -- 209	lmo2454	_____________165_____________218\n_____________\|_______________\|\n5'-GUG...GACGC__U____C_______AAGCC...AAA-3'\n______________UG_GGUG_AUGAAAA\n______________\|\|_\|:\|\|_\|\|\|\|\|\|\|\n______________AC_CUAC_UACUUUU\n3'-GUU...CGGUU__U____U_______GUUUA...GGA-5'\n_____________\|_______________\|\n_____________210_____________152\n	274 -- 280	157 -- 163	-10.6243 kcal/mol	2.77636 kcal/mol	0.905109 kcal/mol	165 218@LB@ \| \|@LB@5'-GUG...GACGC U C AAGCC...AAA-3'@LB@ UG GGUG AUGAAAA@LB@ \|\| \|:\|\| \|\|\|\|\|\|\|@LB@ AC CUAC UACUUUU@LB@3'-GUU...CGGUU U U GUUUA...GGA-5'@LB@ \| \|@LB@ 210 152@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -10.6243 kcal/mol@LB@Unfolding Energy - mRNA 2.77636 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 166 -- 217@LB@Position - sRNA 153 -- 209@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 157 -- 163@LB@
139	0.03644	0.6968	lmo2566	N/A	-16.54	0.050390	198 -- 240	121 -- 170	lmo2566	_____________197_________________241\n_____________\|___________________\|\n5'-GAA...ACAUA_________AUA_______CCUUA...CAG-3'\n______________GAGAUGAAU___GAAAACA\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUCUACUUA___CUUUUGU\n3'-GUU...GGUUA___________________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________171_________________120\n	210 -- 216	155 -- 161	-17.6586 kcal/mol	1.26524 kcal/mol	0.929544 kcal/mol	197 241@LB@ \| \|@LB@5'-GAA...ACAUA AUA CCUUA...CAG-3'@LB@ GAGAUGAAU GAAAACA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUCUACUUA CUUUUGU@LB@3'-GUU...GGUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 171 120@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 1.26524 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 198 -- 240@LB@Position - sRNA 121 -- 170@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 155 -- 161@LB@
28	0.005366	0.5157	lmo2793	N/A	-19.39	0.013418	199 -- 253	121 -- 174	lmo2793	_____________198__________________254\n_____________\|____________________\|\n5'-AAA...UGUAG_________UUU________AUUGG...GUU-3'\n______________CAGUGAGGU___UGAAGAUA\n______________\|\|:\|\|\|\|:\|___\|\|\|\|:\|:\|\n______________GUUACUCUA___ACUUUUGU\n3'-GUU...UGCCG_________CUU________UUAUU...GGA-5'\n_____________\|____________________\|\n_____________175__________________120\n	212 -- 218	155 -- 161	-16.7389 kcal/mol	5.68665 kcal/mol	0.95817 kcal/mol	198 254@LB@ \| \|@LB@5'-AAA...UGUAG UUU AUUGG...GUU-3'@LB@ CAGUGAGGU UGAAGAUA@LB@ \|\|:\|\|\|\|:\| \|\|\|\|:\|:\|@LB@ GUUACUCUA ACUUUUGU@LB@3'-GUU...UGCCG CUU UUAUU...GGA-5'@LB@ \| \|@LB@ 175 120@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -16.7389 kcal/mol@LB@Unfolding Energy - mRNA 5.68665 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 199 -- 253@LB@Position - sRNA 121 -- 174@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@LB@
150	0.03884	0.6968	lmo1709	N/A	-16.64	0.048121	221 -- 241	163 -- 181	methionine aminopeptidase	_____________220__________242\n_____________\|____________\|\n5'-UCA...GAAAU____________AGCAG...CUG-3'\n______________CGAUGAGAUGAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________GUUACUCUACUU\n3'-GUU...UGCCG____________ACUUU...GGA-5'\n_____________\|____________\|\n_____________182__________162\n	235 -- 241	163 -- 169	-15.3561 kcal/mol	3.44721 kcal/mol	0.694462 kcal/mol	220 242@LB@ \| \|@LB@5'-UCA...GAAAU AGCAG...CUG-3'@LB@ CGAUGAGAUGAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ GUUACUCUACUU@LB@3'-GUU...UGCCG ACUUU...GGA-5'@LB@ \| \|@LB@ 182 162@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -15.3561 kcal/mol@LB@Unfolding Energy - mRNA 3.44721 kcal/mol@LB@Unfolding Energy - sRNA 0.694462 kcal/mol@LB@@LB@Position - mRNA 221 -- 241@LB@Position - sRNA 163 -- 181@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 163 -- 169@LB@
75	0.01961	0.6733	lmo0383	N/A	-20.23	0.008871	224 -- 265	150 -- 186	methylmalonate-semialdehyde dehydrogenase	_____________223________________________________________266\n_____________\|__________________________________________\|\n5'-UUC...UUAAA_______AUUG_____G______UC___A_U___________AUAUG...AAG-3'\n______________GAAUUAU____ACGGC_AAUGGG__GAG_G_AAGACAGAUAA\n______________\|\|\|:\|\|:____\|\|\|\|\|_\|\|\|\|:\|__\|\|:_\|_\|\|:\|\|\|:\|\|\|\|\n______________CUUGAUG____UGCCG_UUACUC__CUU_C_UUUUGUUUAUU\n3'-GUU...CUGUA________________G______UA___A_____________ACUAA...GGA-5'\n_____________\|__________________________________________\|\n_____________187________________________________________149\n	257 -- 263	152 -- 158	-34.2826 kcal/mol	8.25616 kcal/mol	13.66 kcal/mol	223 266@LB@ \| \|@LB@5'-UUC...UUAAA AUUG G UC A U AUAUG...AAG-3'@LB@ GAAUUAU ACGGC AAUGGG GAG G AAGACAGAUAA@LB@ \|\|\|:\|\|: \|\|\|\|\| \|\|\|\|:\| \|\|: \| \|\|:\|\|\|:\|\|\|\|@LB@ CUUGAUG UGCCG UUACUC CUU C UUUUGUUUAUU@LB@3'-GUU...CUGUA G UA A ACUAA...GGA-5'@LB@ \| \|@LB@ 187 149@LB@@LB@@LB@Energy -20.23 kcal/mol@LB@Hybridization Energy -34.2826 kcal/mol@LB@Unfolding Energy - mRNA 8.25616 kcal/mol@LB@Unfolding Energy - sRNA 13.66 kcal/mol@LB@@LB@Position - mRNA 224 -- 265@LB@Position - sRNA 150 -- 186@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 152 -- 158@LB@
69	0.01791	0.6733	lmo0011	N/A	-18.87	0.017267	48 -- 93	161 -- 209	mevalonate diphosphate decarboxylase	_____________47_________94\n_____________\|__________\|\n5'-AGU...CGGUA__________CAUUA...CCU-3'\n______________GAGGUGGAUG\n______________\|\|\|:\|\|:\|\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________210________160\n	87 -- 93	161 -- 167	-12.2828 kcal/mol	3.75931 kcal/mol	0.812237 kcal/mol	47 94@LB@ \| \|@LB@5'-AGU...CGGUA CAUUA...CCU-3'@LB@ GAGGUGGAUG@LB@ \|\|\|:\|\|:\|\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 210 160@LB@@LB@@LB@Energy -18.87 kcal/mol@LB@Hybridization Energy -12.2828 kcal/mol@LB@Unfolding Energy - mRNA 3.75931 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 48 -- 93@LB@Position - sRNA 161 -- 209@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 161 -- 167@LB@
157	0.0414	0.7058	lmo0010	N/A	-15.41	0.081879	188 -- 219	167 -- 203	mevalonate kinase	_____________187_____220\n_____________\|_______\|\n5'-AUC...AUGCG_______UGCAG...UAG-3'\n______________GAGAACA\n______________\|\|:\|\|\|\|\n______________CUUUUGU\n3'-GUU...ACUUA_______UUAUU...GGA-5'\n_____________\|_______\|\n_____________204_____166\n	241 -- 247	155 -- 161	-5.76961 kcal/mol	0.621388 kcal/mol	0.528569 kcal/mol	187 220@LB@ \| \|@LB@5'-AUC...AUGCG UGCAG...UAG-3'@LB@ GAGAACA@LB@ \|\|:\|\|\|\|@LB@ CUUUUGU@LB@3'-GUU...ACUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 204 166@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -5.76961 kcal/mol@LB@Unfolding Energy - mRNA 0.621388 kcal/mol@LB@Unfolding Energy - sRNA 0.528569 kcal/mol@LB@@LB@Position - mRNA 188 -- 219@LB@Position - sRNA 167 -- 203@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 155 -- 161@LB@
57	0.01283	0.6057	lmo2379	N/A	-18.13	0.024463	194 -- 217	150 -- 173	monovalent cation/H+ antiporter subunit B	_____________193__________________218\n_____________\|____________________\|\n5'-GUA...AACGA_______AU___________AUGAC...AUA-3'\n______________GGUGAGA__GAUGAAAACGA\n______________::\|\|\|\|\|__:\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__UUACUUUUGUU\n3'-GUU...GCCGG_______AC___________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________149\n	207 -- 213	154 -- 160	-18.1864 kcal/mol	2.62553 kcal/mol	0.959215 kcal/mol	193 218@LB@ \| \|@LB@5'-GUA...AACGA AU AUGAC...AUA-3'@LB@ GGUGAGA GAUGAAAACGA@LB@ ::\|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UUACUCU UUACUUUUGUU@LB@3'-GUU...GCCGG AC UAUUA...GGA-5'@LB@ \| \|@LB@ 174 149@LB@@LB@@LB@Energy -18.13 kcal/mol@LB@Hybridization Energy -18.1864 kcal/mol@LB@Unfolding Energy - mRNA 2.62553 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 194 -- 217@LB@Position - sRNA 150 -- 173@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 154 -- 160@LB@
20	0.003655	0.4469	lmo1591	argC	-21.66	0.004270	183 -- 240	156 -- 208	N-acetyl-gamma-glutamyl-phosphate reductase	_____________182___________________________________________________________241\n_____________\|_____________________________________________________________\|\n5'-AAA...AUAAU________A________________AGUUUCAAU__U____G___C_______UG______UUGAG...GUU-3'\n______________UAACGGGG_GGGGU_UAGG_AUGAA_________CA_UGGC_CGA_GGGGU_A__GAGGAC\n______________\|\|\|\|\|\|\|:_\|:\|\|:_\|\|\|:_\|\|\|\|\|_________\|\|_:\|\|\|_\|:\|_\|:\|:\|_\|__\|\|::\|\|\n______________AUUGCCCU_CUCCG_AUCU_UACUU_________GU_GCCG_GUU_CUCUA_U__CUUUUG\n3'-GUU...UACGU________A_____U____G_____GAU_________________A_____C_UA______UUUAU...GGA-5'\n_____________\|_____________________________________________________________\|\n_____________209___________________________________________________________155\n	184 -- 190	201 -- 207	-40.8209 kcal/mol	11.7 kcal/mol	18.6528 kcal/mol	182 241@LB@ \| \|@LB@5'-AAA...AUAAU A AGUUUCAAU U G C UG UUGAG...GUU-3'@LB@ UAACGGGG GGGGU UAGG AUGAA CA UGGC CGA GGGGU A GAGGAC@LB@ \|\|\|\|\|\|\|: \|:\|\|: \|\|\|: \|\|\|\|\| \|\| :\|\|\| \|:\| \|:\|:\| \| \|\|::\|\|@LB@ AUUGCCCU CUCCG AUCU UACUU GU GCCG GUU CUCUA U CUUUUG@LB@3'-GUU...UACGU A U G GAU A C UA UUUAU...GGA-5'@LB@ \| \|@LB@ 209 155@LB@@LB@@LB@Energy -21.66 kcal/mol@LB@Hybridization Energy -40.8209 kcal/mol@LB@Unfolding Energy - mRNA 11.7 kcal/mol@LB@Unfolding Energy - sRNA 18.6528 kcal/mol@LB@@LB@Position - mRNA 183 -- 240@LB@Position - sRNA 156 -- 208@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 201 -- 207@LB@
18	0.003504	0.4469	lmo0129	N/A	-18.06	0.025228	187 -- 226	176 -- 203	N-acetylmuramoyl-L-alanine amidase	_____________186____________227\n_____________\|______________\|\n5'-UUU...GUCAG______________AAAAC...AAC-3'\n______________GAGA_GGAUGAGGA\n______________\|\|\|\|_\|:\|\|\|\|::\|\n______________CUCU_CUUACUUUU\n3'-GUU...GGUUA____A_________GUUUA...GGA-5'\n_____________\|______________\|\n_____________204____________175\n	189 -- 195	157 -- 163	-12.9517 kcal/mol	0.542108 kcal/mol	0.904482 kcal/mol	186 227@LB@ \| \|@LB@5'-UUU...GUCAG AAAAC...AAC-3'@LB@ GAGA GGAUGAGGA@LB@ \|\|\|\| \|:\|\|\|\|::\|@LB@ CUCU CUUACUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 204 175@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -12.9517 kcal/mol@LB@Unfolding Energy - mRNA 0.542108 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 187 -- 226@LB@Position - sRNA 176 -- 203@LB@Position Seed - mRNA 189 -- 195@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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