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
187	0.05427	0.7607	lmo2654	fus	-15.17	0.090605	196 -- 212	168 -- 184	elongation factor G	_____________195____________213\n_____________\|______________\|\n5'-GAG...AUACA__________A___UUCUC...AUA-3'\n______________ACAUGGCUAG_GAG\n______________\|\|\|:\|\|\|:\|:_\|\|\|\n______________UGUGCCGGUU_CUC\n3'-GUU...CUUGA__________A___UACUU...GGA-5'\n_____________\|______________\|\n_____________185____________167\n	202 -- 208	172 -- 178	-17.9516 kcal/mol	0.731619 kcal/mol	6.23346 kcal/mol	195 213@LB@ \| \|@LB@5'-GAG...AUACA A UUCUC...AUA-3'@LB@ ACAUGGCUAG GAG@LB@ \|\|\|:\|\|\|:\|: \|\|\|@LB@ UGUGCCGGUU CUC@LB@3'-GUU...CUUGA A UACUU...GGA-5'@LB@ \| \|@LB@ 185 167@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -17.9516 kcal/mol@LB@Unfolding Energy - mRNA 0.731619 kcal/mol@LB@Unfolding Energy - sRNA 6.23346 kcal/mol@LB@@LB@Position - mRNA 196 -- 212@LB@Position - sRNA 168 -- 184@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 172 -- 178@LB@
190	0.0551	0.7607	lmo0641	N/A	-14.65	0.112053	196 -- 245	175 -- 211	heavy metal-transporting ATPase	_____________195_____________________246\n_____________\|_______________________\|\n5'-AUU...GAGCA______AA__U____________GAAUU...ACU-3'\n______________UAAUGA__GA_UGGAUGAAG_CA\n______________:\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\|:_\|\|\n______________GUUACU__CU_ACUUACUUU_GU\n3'-GUU...UGCCG____________________U__UUAUU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________174\n	212 -- 218	158 -- 164	-12.4633 kcal/mol	2.08827 kcal/mol	0.95817 kcal/mol	195 246@LB@ \| \|@LB@5'-AUU...GAGCA AA U GAAUU...ACU-3'@LB@ UAAUGA GA UGGAUGAAG CA@LB@ :\|\|\|\|\| \|\| \|\|:\|\|\|\|\|: \|\|@LB@ GUUACU CU ACUUACUUU GU@LB@3'-GUU...UGCCG U UUAUU...GGA-5'@LB@ \| \|@LB@ 212 174@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -12.4633 kcal/mol@LB@Unfolding Energy - mRNA 2.08827 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 196 -- 245@LB@Position - sRNA 175 -- 211@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 158 -- 164@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@
122	0.03252	0.6968	lmo0926	N/A	-16.71	0.046694	198 -- 274	155 -- 207	TetR family transcriptional regulator	_____________197______________275\n_____________\|________________\|\n5'-GCU...AACCA_____________G__GCGCC...UCG-3'\n______________AGAUGAGUGAAAA_CA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|_\|\|\n______________UCUACUUACUUUU_GU\n3'-GUU...GUUAC________________UUAUU...GGA-5'\n_____________\|________________\|\n_____________208______________154\n	265 -- 271	157 -- 163	-16.1904 kcal/mol	1.95479 kcal/mol	0.920152 kcal/mol	197 275@LB@ \| \|@LB@5'-GCU...AACCA G GCGCC...UCG-3'@LB@ AGAUGAGUGAAAA CA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\| \|\|@LB@ UCUACUUACUUUU GU@LB@3'-GUU...GUUAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 154@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -16.1904 kcal/mol@LB@Unfolding Energy - mRNA 1.95479 kcal/mol@LB@Unfolding Energy - sRNA 0.920152 kcal/mol@LB@@LB@Position - mRNA 198 -- 274@LB@Position - sRNA 155 -- 207@LB@Position Seed - mRNA 265 -- 271@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@
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@
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@
79	0.02126	0.6733	lmo1172	N/A	-17.83	0.028138	200 -- 242	163 -- 210	two-component response regulator	_____________199_________243\n_____________\|___________\|\n5'-CAC...CAGGA___________AAUUG...UAG-3'\n______________AUGAAUGGAAG\n______________\|\|\|\|\|\|\|:\|\|:\n______________UACUUACUUUU\n3'-GUU...UACUC___________GUUUA...GGA-5'\n_____________\|___________\|\n_____________211_________162\n	214 -- 220	157 -- 163	-10.013 kcal/mol	1.15656 kcal/mol	0.82573 kcal/mol	199 243@LB@ \| \|@LB@5'-CAC...CAGGA AAUUG...UAG-3'@LB@ AUGAAUGGAAG@LB@ \|\|\|\|\|\|\|:\|\|:@LB@ UACUUACUUUU@LB@3'-GUU...UACUC GUUUA...GGA-5'@LB@ \| \|@LB@ 211 162@LB@@LB@@LB@Energy -17.83 kcal/mol@LB@Hybridization Energy -10.013 kcal/mol@LB@Unfolding Energy - mRNA 1.15656 kcal/mol@LB@Unfolding Energy - sRNA 0.82573 kcal/mol@LB@@LB@Position - mRNA 200 -- 242@LB@Position - sRNA 163 -- 210@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 157 -- 163@LB@
118	0.03209	0.6968	lmo0654	N/A	-17.15	0.038336	200 -- 225	156 -- 180	lmo0654	_____________199________________________226\n_____________\|__________________________\|\n5'-GAA...GCGCG_______C______AUUUAA______UAGAA...CAC-3'\n______________UAUGGCC_AUGAGA______GAGAAC\n______________:\|:\|\|\|\|_\|\|\|\|\|\|______\|\|:\|\|\|\n______________GUGCCGG_UACUCU______CUUUUG\n3'-GUU...UUGAU_______U______ACUUA_______UUUAU...GGA-5'\n_____________\|__________________________\|\n_____________181________________________155\n	200 -- 206	174 -- 180	-23.3306 kcal/mol	3.96502 kcal/mol	8.29586 kcal/mol	199 226@LB@ \| \|@LB@5'-GAA...GCGCG C AUUUAA UAGAA...CAC-3'@LB@ UAUGGCC AUGAGA GAGAAC@LB@ :\|:\|\|\|\| \|\|\|\|\|\| \|\|:\|\|\|@LB@ GUGCCGG UACUCU CUUUUG@LB@3'-GUU...UUGAU U ACUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 181 155@LB@@LB@@LB@Energy -17.15 kcal/mol@LB@Hybridization Energy -23.3306 kcal/mol@LB@Unfolding Energy - mRNA 3.96502 kcal/mol@LB@Unfolding Energy - sRNA 8.29586 kcal/mol@LB@@LB@Position - mRNA 200 -- 225@LB@Position - sRNA 156 -- 180@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 174 -- 180@LB@
199	0.05673	0.7607	lmo0888	N/A	-13.34	0.187096	200 -- 237	174 -- 211		_____________199___________________238\n_____________\|_____________________\|\n5'-AAG...GGCGG_____A__UAU__________ACGCA...AUA-3'\n______________AGUGA_GU___AAUGGAAGCA\n______________\|:\|\|\|_:\|___\|\|\|\|:\|\|:\|\|\n______________UUACU_UA___UUACUUUUGU\n3'-GUU...GCCGG_____C__C____________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________212___________________173\n	32 -- 38	155 -- 161	-11.9538 kcal/mol	2.24583 kcal/mol	0.954976 kcal/mol	199 238@LB@ \| \|@LB@5'-AAG...GGCGG A UAU ACGCA...AUA-3'@LB@ AGUGA GU AAUGGAAGCA@LB@ \|:\|\|\| :\| \|\|\|\|:\|\|:\|\|@LB@ UUACU UA UUACUUUUGU@LB@3'-GUU...GCCGG C C UUAUU...GGA-5'@LB@ \| \|@LB@ 212 173@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -11.9538 kcal/mol@LB@Unfolding Energy - mRNA 2.24583 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 200 -- 237@LB@Position - sRNA 174 -- 211@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 155 -- 161@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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