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	Additional homologs
1	1.731e-05	0.04657	lmo1883	N/A	-26.54	0.000269	199 -- 265	114 -- 169	chitinase		_____________198_________________________________________________________________266\n_____________\|___________________________________________________________________\|\n5'-GCG...AAAGU________G_________________GG___UU_____UU__UUUUAGUU____CGG______GG__AUUUG...ACG-3'\n______________AGAUGAAU_GAAAACAAGUAAUGGUU__UGG__UGUCU__AC________GGUG___GACUGG__GC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|\|:\|\|\|\|\|:\|\|__\|\|\|__\|\|\|\|\|__\|\|________\|:\|\|___\|\|\|\|:\|__\|\|\n______________UCUACUUA_CUUUUGUUUAUUACUAA__ACC__ACAGA__UG________CUAC___CUGAUC__CG\n3'-GUU...GUUAC__________________________A___________UU__U___________AGA______AA__GUAAG...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________170_________________________________________________________________113\n	210 -- 216	153 -- 159	-51.3221 kcal/mol	15.9506 kcal/mol	18.5045 kcal/mol	198 266@LB@ \| \|@LB@5'-GCG...AAAGU G GG UU UU UUUUAGUU CGG GG AUUUG...ACG-3'@LB@ AGAUGAAU GAAAACAAGUAAUGGUU UGG UGUCU AC GGUG GACUGG GC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|:\|\|\|\|\|:\|\| \|\|\| \|\|\|\|\| \|\| \|:\|\| \|\|\|\|:\| \|\|@LB@ UCUACUUA CUUUUGUUUAUUACUAA ACC ACAGA UG CUAC CUGAUC CG@LB@3'-GUU...GUUAC A UU U AGA AA GUAAG...GGA-5'@LB@ \| \|@LB@ 170 113@LB@@LB@@LB@Energy -26.54 kcal/mol@LB@Hybridization Energy -51.3221 kcal/mol@LB@Unfolding Energy - mRNA 15.9506 kcal/mol@LB@Unfolding Energy - sRNA 18.5045 kcal/mol@LB@@LB@Position - mRNA 199 -- 265@LB@Position - sRNA 114 -- 169@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 153 -- 159@LB@
2	0.0002774	0.3688	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
3	0.0004111	0.3688	lmo0196	N/A	-23.83	0.001321	198 -- 256	156 -- 209	regulatory protein SpoVG		_____________197________________257\n_____________\|__________________\|\n5'-ACU...AGACA__________________UAUUU...ACA-3'\n______________GAUGGGA_GAAUGAAAGC\n______________:\|\|\|:\|\|_\|\|\|\|\|\|\|\|:\|\n______________UUACUCU_CUUACUUUUG\n3'-GUU...GCCGG_______A__________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________210________________155\n	250 -- 256	156 -- 162	-19.3926 kcal/mol	2.92904 kcal/mol	0.941471 kcal/mol	197 257@LB@ \| \|@LB@5'-ACU...AGACA UAUUU...ACA-3'@LB@ GAUGGGA GAAUGAAAGC@LB@ :\|\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU CUUACUUUUG@LB@3'-GUU...GCCGG A UUUAU...GGA-5'@LB@ \| \|@LB@ 210 155@LB@@LB@@LB@Energy -23.83 kcal/mol@LB@Hybridization Energy -19.3926 kcal/mol@LB@Unfolding Energy - mRNA 2.92904 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 198 -- 256@LB@Position - sRNA 156 -- 209@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 156 -- 162@LB@
4	0.0009641	0.4469	lmo0851	N/A	-23.35	0.001728	188 -- 220	172 -- 201	lmo0851		_____________187_______________________________221\n_____________\|_________________________________\|\n5'-GGU...AUAGA__________U_______AAAAGAA________CCAAC...UAA-3'\n______________GUGAGGCAUA_ACAUGAA_______GCGGUUAA\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|_______:\|\|\|::\|\|\n______________UACUCCGUAU_UGUACUU_______UGCCGGUU\n3'-GUU...UGCCC__________C_______GAUG___________ACUCU...GGA-5'\n_____________\|_________________________________\|\n_____________202_______________________________171\n	214 -- 220	172 -- 178	-33.261 kcal/mol	3.18896 kcal/mol	13.3764 kcal/mol	187 221@LB@ \| \|@LB@5'-GGU...AUAGA U AAAAGAA CCAAC...UAA-3'@LB@ GUGAGGCAUA ACAUGAA GCGGUUAA@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| :\|\|\|::\|\|@LB@ UACUCCGUAU UGUACUU UGCCGGUU@LB@3'-GUU...UGCCC C GAUG ACUCU...GGA-5'@LB@ \| \|@LB@ 202 171@LB@@LB@@LB@Energy -23.35 kcal/mol@LB@Hybridization Energy -33.261 kcal/mol@LB@Unfolding Energy - mRNA 3.18896 kcal/mol@LB@Unfolding Energy - sRNA 13.3764 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 172 -- 201@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 172 -- 178@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@
6	0.001395	0.4469	lmo2078	N/A	-19.77	0.011149	188 -- 240	154 -- 207			_____________187___________________________________________________________________241\n_____________\|_____________________________________________________________________\|\n5'-GAU...UUUAU_____C______U__________U____UA____________AAUG____A_G________________UUCGA...AGG-3'\n______________UUUGG_GCGUCU_UGU_____GG_AUGA__UGUAGA___GAA____AUGG_C_GGUGAGGU_AAUGGAA\n______________\|\|:\|\|_\|\|\|:\|\|_\|\|:_____\|\|_\|\|\|\|__::\|\|\|\|___\|\|\|____\|:\|\|_\|_::\|\|\|\|:\|_\|\|\|\|:\|\|\n______________AAGCC_CGCGGA_ACG_____CC_UACU__GUAUCU___CUU____UGCC_G_UUACUCUA_UUACUUU\n3'-GUU...AGUAC____________U___UAUUG__C____CC______GUA___GAUG______G________C_______UGUUU...GGA-5'\n_____________\|_____________________________________________________________________\|\n_____________208___________________________________________________________________153\n	200 -- 206	158 -- 164	-46.039 kcal/mol	12.924 kcal/mol	22.2029 kcal/mol	187 241@LB@ \| \|@LB@5'-GAU...UUUAU C U U UA AAUG A G UUCGA...AGG-3'@LB@ UUUGG GCGUCU UGU GG AUGA UGUAGA GAA AUGG C GGUGAGGU AAUGGAA@LB@ \|\|:\|\| \|\|\|:\|\| \|\|: \|\| \|\|\|\| ::\|\|\|\| \|\|\| \|:\|\| \| ::\|\|\|\|:\| \|\|\|\|:\|\|@LB@ AAGCC CGCGGA ACG CC UACU GUAUCU CUU UGCC G UUACUCUA UUACUUU@LB@3'-GUU...AGUAC U UAUUG C CC GUA GAUG G C UGUUU...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -19.77 kcal/mol@LB@Hybridization Energy -46.039 kcal/mol@LB@Unfolding Energy - mRNA 12.924 kcal/mol@LB@Unfolding Energy - sRNA 22.2029 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
7	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
8	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
9	0.002066	0.4469	lmo0669	N/A	-20.91	0.006284	33 -- 77	156 -- 211	oxidoreductase		_____________32__________________78\n_____________\|___________________\|\n5'-AAU...UAAAG___________________GGGAA...UUC-3'\n______________UAAUGGGG_GGAUGAAAAU\n______________:\|\|\|\|:\|:_\|:\|\|\|\|\|\|\|:\n______________GUUACUCU_CUUACUUUUG\n3'-GUU...UGCCG________A__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________212_________________155\n	71 -- 77	156 -- 162	-16.6504 kcal/mol	2.4241 kcal/mol	0.944687 kcal/mol	32 78@LB@ \| \|@LB@5'-AAU...UAAAG GGGAA...UUC-3'@LB@ UAAUGGGG GGAUGAAAAU@LB@ :\|\|\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ GUUACUCU CUUACUUUUG@LB@3'-GUU...UGCCG A UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -20.91 kcal/mol@LB@Hybridization Energy -16.6504 kcal/mol@LB@Unfolding Energy - mRNA 2.4241 kcal/mol@LB@Unfolding Energy - sRNA 0.944687 kcal/mol@LB@@LB@Position - mRNA 33 -- 77@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 156 -- 162@LB@
10	0.002311	0.4469	lmo2106	N/A	-20.89	0.006356	172 -- 222	159 -- 207			_____________171__________________________________________________223\n_____________\|____________________________________________________\|\n5'-AGU...UAAUA_______AC__CAA______G_____AAA____U__UUAA_______G____UUAUA...AUG-3'\n______________AAUGGGA__AG___CAUAGA_GUGAA____AUG_CU____AGAUGAA_UGGA\n______________\|\|:\|\|\|\|__\|\|___\|\|\|\|\|\|_:\|\|\|\|____\|:\|_\|:____\|\|\|\|\|\|\|_\|\|:\|\n______________UUGCCCU__UC___GUAUCU_UACUU____UGC_GG____UCUACUU_ACUU\n3'-GUU...ACGUA_______AC__C________G_____GAUG___C__UUAC____________UUGUU...GGA-5'\n_____________\|____________________________________________________\|\n_____________208__________________________________________________158\n	211 -- 217	163 -- 169	-34.9864 kcal/mol	6.68059 kcal/mol	18.5724 kcal/mol	171 223@LB@ \| \|@LB@5'-AGU...UAAUA AC CAA G AAA U UUAA G UUAUA...AUG-3'@LB@ AAUGGGA AG CAUAGA GUGAA AUG CU AGAUGAA UGGA@LB@ \|\|:\|\|\|\| \|\| \|\|\|\|\|\| :\|\|\|\| \|:\| \|: \|\|\|\|\|\|\| \|\|:\|@LB@ UUGCCCU UC GUAUCU UACUU UGC GG UCUACUU ACUU@LB@3'-GUU...ACGUA AC C G GAUG C UUAC UUGUU...GGA-5'@LB@ \| \|@LB@ 208 158@LB@@LB@@LB@Energy -20.89 kcal/mol@LB@Hybridization Energy -34.9864 kcal/mol@LB@Unfolding Energy - mRNA 6.68059 kcal/mol@LB@Unfolding Energy - sRNA 18.5724 kcal/mol@LB@@LB@Position - mRNA 172 -- 222@LB@Position - sRNA 159 -- 207@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@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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