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
23	0.00382	0.4469	lmo1572	accA	-20.61	0.007329	192 -- 226	157 -- 188	acetyl-CoA carboxylase carboxyltransferase subunit alpha	_____________191______________________________________________________________________________227\n_____________\|________________________________________________________________________________\|\n5'-AGG...UUUAA__AU______GAAA__A____GA_____________A__UG__________________G___________AUU______ACCGA...CCA-3'\n______________GC__UCAUGU____GC_CCUG___GUAG_GGGGUGA_GU_______________AUGGC_AAUGAGAUGGA___UGAGAA\n______________\|\|__\|\|\|\|\|\|____\|\|_\|\|\|:___:\|\|:_\|\|\|:\|\|\|_\|:_______________\|:\|\|\|_\|\|\|\|\|\|\|\|\|:\|___\|\|\|:\|\|\n______________CG__AGUACA____CG_GGAU___UAUU_CCCUACU_CG_______________UGCCG_UUACUCUACUU___ACUUUU\n3'-GUU...CGCAA__GU______AGCC__C____ACG____G_______C__UAUCUGUACUUGAUG_____G____________________GUUUA...GGA-5'\n_____________\|________________________________________________________________________________\|\n_____________189______________________________________________________________________________156\n	211 -- 217	163 -- 169	-59.1532 kcal/mol	18.9584 kcal/mol	22.6787 kcal/mol	191 227@LB@ \| \|@LB@5'-AGG...UUUAA AU GAAA A GA A UG G AUU ACCGA...CCA-3'@LB@ GC UCAUGU GC CCUG GUAG GGGGUGA GU AUGGC AAUGAGAUGGA UGAGAA@LB@ \|\| \|\|\|\|\|\| \|\| \|\|\|: :\|\|: \|\|\|:\|\|\| \|: \|:\|\|\| \|\|\|\|\|\|\|\|\|:\| \|\|\|:\|\|@LB@ CG AGUACA CG GGAU UAUU CCCUACU CG UGCCG UUACUCUACUU ACUUUU@LB@3'-GUU...CGCAA GU AGCC C ACG G C UAUCUGUACUUGAUG G GUUUA...GGA-5'@LB@ \| \|@LB@ 189 156@LB@@LB@@LB@Energy -20.61 kcal/mol@LB@Hybridization Energy -59.1532 kcal/mol@LB@Unfolding Energy - mRNA 18.9584 kcal/mol@LB@Unfolding Energy - sRNA 22.6787 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 157 -- 188@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@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@
165	0.04532	0.7392	lmo2091	argH	-16.36	0.054421	189 -- 262	141 -- 199	argininosuccinate lyase	_____________188_________________263\n_____________\|___________________\|\n5'-UCA...GGUCA_______G__GAG______AAAUC...AAG-3'\n______________UGCCAUU_UA___GGAAGA\n______________\|\|\|\|\|\|\|_\|\|___\|\|\|\|\|\|\n______________ACGGUAA_AU___CCUUCU\n3'-GUU...GAUCA_______G__AA_______ACCUA...GGA-5'\n_____________\|___________________\|\n_____________200_________________140\n	20 -- 26	110 -- 116	-20.7676 kcal/mol	3.64063 kcal/mol	5.20705 kcal/mol	188 263@LB@ \| \|@LB@5'-UCA...GGUCA G GAG AAAUC...AAG-3'@LB@ UGCCAUU UA GGAAGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ ACGGUAA AU CCUUCU@LB@3'-GUU...GAUCA G AA ACCUA...GGA-5'@LB@ \| \|@LB@ 200 140@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -20.7676 kcal/mol@LB@Unfolding Energy - mRNA 3.64063 kcal/mol@LB@Unfolding Energy - sRNA 5.20705 kcal/mol@LB@@LB@Position - mRNA 189 -- 262@LB@Position - sRNA 141 -- 199@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 110 -- 116@LB@
5	0.001245	0.4469	lmo1835	carB	-22.95	0.002153	176 -- 228	154 -- 207	carbamoyl-phosphate synthetase	_____________175____________________________________________________________229\n_____________\|______________________________________________________________\|\n5'-AAA...UGGAA___AUG_______AA_______________________C____AC_C__C__UAUA______AUUCU...CUU-3'\n______________AUG___AAUGGGA__GAGG___AGG_GUGAACUACAUG_CUAA__G_GA_GA____AAAACA\n______________\|\|\|___\|\|:\|\|\|\|__\|\|\|\|___\|\|:_:\|\|\|\|\|\|\|\|\|:\|_\|:\|\|__\|_\|\|_\|\|____\|\|\|\|\|\|\n______________UAC___UUGCCCU__CUCC___UCU_UACUUGAUGUGC_GGUU__C_CU_CU____UUUUGU\n3'-GUU...GCGGA___GUA_______A_____GUA___G____________C____A__U__A__UAC_______UUAUU...GGA-5'\n_____________\|______________________________________________________________\|\n_____________208____________________________________________________________153\n	194 -- 200	180 -- 186	-39.6119 kcal/mol	8.25276 kcal/mol	19.5968 kcal/mol	175 229@LB@ \| \|@LB@5'-AAA...UGGAA AUG AA C AC C C UAUA AUUCU...CUU-3'@LB@ AUG AAUGGGA GAGG AGG GUGAACUACAUG CUAA G GA GA AAAACA@LB@ \|\|\| \|\|:\|\|\|\| \|\|\|\| \|\|: :\|\|\|\|\|\|\|\|\|:\| \|:\|\| \| \|\| \|\| \|\|\|\|\|\|@LB@ UAC UUGCCCU CUCC UCU UACUUGAUGUGC GGUU C CU CU UUUUGU@LB@3'-GUU...GCGGA GUA A GUA G C A U A UAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -39.6119 kcal/mol@LB@Unfolding Energy - mRNA 8.25276 kcal/mol@LB@Unfolding Energy - sRNA 19.5968 kcal/mol@LB@@LB@Position - mRNA 176 -- 228@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 180 -- 186@LB@
152	0.04001	0.7027	lmo1203	cbiL	-16.49	0.051377	174 -- 199	155 -- 181	cobalt-precorrin-2 C(20)-methyltransferase	_____________173___________________200\n_____________\|_____________________\|\n5'-ACA...CACUG____A________________CGUGG...CAC-3'\n______________CAAU_GAGA_GGGUGAAAACA\n______________\|\|\|\|_\|\|\|\|_\|::\|\|\|\|\|\|\|\|\n______________GUUA_CUCU_CUUACUUUUGU\n3'-GUU...UGCCG_________A___________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________182___________________154\n	193 -- 199	155 -- 161	-18.5314 kcal/mol	4.87195 kcal/mol	0.95817 kcal/mol	173 200@LB@ \| \|@LB@5'-ACA...CACUG A CGUGG...CAC-3'@LB@ CAAU GAGA GGGUGAAAACA@LB@ \|\|\|\| \|\|\|\| \|::\|\|\|\|\|\|\|\|@LB@ GUUA CUCU CUUACUUUUGU@LB@3'-GUU...UGCCG A UUAUU...GGA-5'@LB@ \| \|@LB@ 182 154@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -18.5314 kcal/mol@LB@Unfolding Energy - mRNA 4.87195 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 174 -- 199@LB@Position - sRNA 155 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@LB@
177	0.05015	0.7607	lmo1905	cca	-16.43	0.052746	154 -- 208	160 -- 211	tRNA CCA-pyrophosphorylase	_____________153_______________209\n_____________\|_________________\|\n5'-UUA...AGGAG______CA_________CGUUU...UGC-3'\n______________CGAUGA__GAUGAAUGA\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________GUUACU__CUACUUACU\n3'-GUU...UGCCG_________________UUUGU...GGA-5'\n_____________\|_________________\|\n_____________212_______________159\n	202 -- 208	160 -- 166	-15.3935 kcal/mol	2.32419 kcal/mol	0.846187 kcal/mol	153 209@LB@ \| \|@LB@5'-UUA...AGGAG CA CGUUU...UGC-3'@LB@ CGAUGA GAUGAAUGA@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUUACU CUACUUACU@LB@3'-GUU...UGCCG UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -15.3935 kcal/mol@LB@Unfolding Energy - mRNA 2.32419 kcal/mol@LB@Unfolding Energy - sRNA 0.846187 kcal/mol@LB@@LB@Position - mRNA 154 -- 208@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 160 -- 166@LB@
126	0.03359	0.6968	lmo1599	ccpA	-16.59	0.049230	178 -- 221	146 -- 188	catabolite control protein A	_____________177______________222\n_____________\|________________\|\n5'-UUU...GAAUA__________U_____AUUUA...CAA-3'\n______________GAGAUGAAUG__AACA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________CUCUACUUAC__UUGU\n3'-GUU...GGUUA__________UU____UUAUU...GGA-5'\n_____________\|________________\|\n_____________189______________145\n	201 -- 207	161 -- 167	-17.207 kcal/mol	2.33031 kcal/mol	0.929544 kcal/mol	177 222@LB@ \| \|@LB@5'-UUU...GAAUA U AUUUA...CAA-3'@LB@ GAGAUGAAUG AACA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUCUACUUAC UUGU@LB@3'-GUU...GGUUA UU UUAUU...GGA-5'@LB@ \| \|@LB@ 189 145@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -17.207 kcal/mol@LB@Unfolding Energy - mRNA 2.33031 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 178 -- 221@LB@Position - sRNA 146 -- 188@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@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@
113	0.02939	0.6968	lmo0232	clpC	-17.21	0.037249	171 -- 212	159 -- 202	endopeptidase Clp ATP-binding chain C	_____________170___________________________________________213\n_____________\|_____________________________________________\|\n5'-AUU...UAAAU________U__C____A___GGAA__AA___________UU____CGAUU...AUA-3'\n______________GAUGAGGC_UA_GAUA_GGA____AC___CAAUGA__UG__UGGA\n______________\|\|\|\|\|\|\|\|_\|\|_\|\|:\|_\|:\|____\|\|___\|\|\|\|\|\|__\|\|__\|\|:\|\n______________CUACUCCG_AU_CUGU_CUU____UG___GUUACU__AC__ACUU\n3'-GUU...UUGCC________U_______A___GAUG__CCG______CU__UU____UUGUU...GGA-5'\n_____________\|_____________________________________________\|\n_____________203___________________________________________158\n	172 -- 178	195 -- 201	-28.9894 kcal/mol	4.99237 kcal/mol	13.9304 kcal/mol	170 213@LB@ \| \|@LB@5'-AUU...UAAAU U C A GGAA AA UU CGAUU...AUA-3'@LB@ GAUGAGGC UA GAUA GGA AC CAAUGA UG UGGA@LB@ \|\|\|\|\|\|\|\| \|\| \|\|:\| \|:\| \|\| \|\|\|\|\|\| \|\| \|\|:\|@LB@ CUACUCCG AU CUGU CUU UG GUUACU AC ACUU@LB@3'-GUU...UUGCC U A GAUG CCG CU UU UUGUU...GGA-5'@LB@ \| \|@LB@ 203 158@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.9894 kcal/mol@LB@Unfolding Energy - mRNA 4.99237 kcal/mol@LB@Unfolding Energy - sRNA 13.9304 kcal/mol@LB@@LB@Position - mRNA 171 -- 212@LB@Position - sRNA 159 -- 202@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 195 -- 201@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@

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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