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
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@
183	0.0534	0.7607	lmo2583	N/A	-16.44	0.052604	178 -- 212	151 -- 181	DNA-binding response regulator	_____________177___________________________213\n_____________\|_____________________________\|\n5'-UAA...AAAUA_G_____AA______C_____________AACAA...AUG-3'\n______________A_ACGGU__GGUGAG___GGUGAAAAUGA\n______________\|_\|\|\|\|:__::\|\|\|\|___::\|\|\|\|\|\|::\|\n______________U_UGCCG__UUACUC___UUACUUUUGUU\n3'-GUU...CUUGA_G_____G_______UAC___________UAUUA...GGA-5'\n_____________\|_____________________________\|\n_____________182___________________________150\n	197 -- 203	155 -- 161	-21.6156 kcal/mol	3.93053 kcal/mol	8.33518 kcal/mol	177 213@LB@ \| \|@LB@5'-UAA...AAAUA G AA C AACAA...AUG-3'@LB@ A ACGGU GGUGAG GGUGAAAAUGA@LB@ \| \|\|\|\|: ::\|\|\|\| ::\|\|\|\|\|\|::\|@LB@ U UGCCG UUACUC UUACUUUUGUU@LB@3'-GUU...CUUGA G G UAC UAUUA...GGA-5'@LB@ \| \|@LB@ 182 150@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -21.6156 kcal/mol@LB@Unfolding Energy - mRNA 3.93053 kcal/mol@LB@Unfolding Energy - sRNA 8.33518 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 151 -- 181@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
45	0.0103	0.599	lmo0066	N/A	-17.00	0.040990	179 -- 207	157 -- 199	toxin	_____________178___________208\n_____________\|_____________\|\n5'-AAA...AGGCC_____________AAGUC...AUU-3'\n______________AGAUGAAUGAAAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCUACUUACUUUU\n3'-GUU...GUUAC_____________GUUUA...GGA-5'\n_____________\|_____________\|\n_____________200___________156\n	201 -- 207	157 -- 163	-14.7839 kcal/mol	1.76886 kcal/mol	0.884237 kcal/mol	178 208@LB@ \| \|@LB@5'-AAA...AGGCC AAGUC...AUU-3'@LB@ AGAUGAAUGAAAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCUACUUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -14.7839 kcal/mol@LB@Unfolding Energy - mRNA 1.76886 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 179 -- 207@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
59	0.0137	0.6248	lmo0642	N/A	-14.84	0.103863	179 -- 256	168 -- 213	lmo0642	_____________178________257\n_____________\|__________\|\n5'-UUC...GAUUG__________CAUGA...CAA-3'\n______________GAGAUGAGUG\n______________\|\|\|\|\|\|\|:\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________214________167\n	193 -- 199	161 -- 167	-14.0942 kcal/mol	3.54513 kcal/mol	0.812237 kcal/mol	178 257@LB@ \| \|@LB@5'-UUC...GAUUG CAUGA...CAA-3'@LB@ GAGAUGAGUG@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 214 167@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -14.0942 kcal/mol@LB@Unfolding Energy - mRNA 3.54513 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 179 -- 256@LB@Position - sRNA 168 -- 213@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
128	0.03459	0.6968	lmo1993	pdp	-15.44	0.080912	179 -- 212	139 -- 174	pyrimidine-nucleoside phosphorylase	_____________178_________________213\n_____________\|___________________\|\n5'-AUU...GAAAG____A___GA_________GGUGG...UUC-3'\n______________GGUG_AGA__AAUGAGAAU\n______________::\|\|_\|\|\|__\|\|\|\|\|:\|\|:\n______________UUAC_UCU__UUACUUUUG\n3'-GUU...GCCGG________AC_________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________175_________________138\n	202 -- 208	156 -- 162	-13.005 kcal/mol	2.24337 kcal/mol	0.941471 kcal/mol	178 213@LB@ \| \|@LB@5'-AUU...GAAAG A GA GGUGG...UUC-3'@LB@ GGUG AGA AAUGAGAAU@LB@ ::\|\| \|\|\| \|\|\|\|\|:\|\|:@LB@ UUAC UCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -13.005 kcal/mol@LB@Unfolding Energy - mRNA 2.24337 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@LB@
192	0.05535	0.7607	lmo2025	nadA	-15.59	0.075878	179 -- 223	172 -- 209	quinolinate synthetase	_____________178________________________________224\n_____________\|__________________________________\|\n5'-GAU...AAUAA_________U____UAGAA________ACA____ACAAU...CCC-3'\n______________AGGCAUGAA_UUAC_____ACGGUCGA___AGAU\n______________\|\|:\|\|\|\|\|\|_:\|\|\|_____\|\|\|\|:\|:\|___\|\|\|\|\n______________UCUGUACUU_GAUG_____UGCCGGUU___UCUA\n3'-GUU...CCGUA___________________________AC_____CUUAC...GGA-5'\n_____________\|__________________________________\|\n_____________210________________________________171\n	217 -- 223	172 -- 178	-24.6997 kcal/mol	5.14719 kcal/mol	11.5853 kcal/mol	178 224@LB@ \| \|@LB@5'-GAU...AAUAA U UAGAA ACA ACAAU...CCC-3'@LB@ AGGCAUGAA UUAC ACGGUCGA AGAU@LB@ \|\|:\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|:\| \|\|\|\|@LB@ UCUGUACUU GAUG UGCCGGUU UCUA@LB@3'-GUU...CCGUA AC CUUAC...GGA-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -24.6997 kcal/mol@LB@Unfolding Energy - mRNA 5.14719 kcal/mol@LB@Unfolding Energy - sRNA 11.5853 kcal/mol@LB@@LB@Position - mRNA 179 -- 223@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 172 -- 178@LB@
61	0.01458	0.6412	lmo2589	N/A	-18.59	0.019740	180 -- 258	153 -- 210	TetR family transcriptional regulator	_____________179__________259\n_____________\|____________\|\n5'-ACU...AACAG____________UGUUU...CUG-3'\n______________AAC_GGGUGGGG\n______________\|\|\|_\|\|:\|\|:\|\|\n______________UUG_CCUACUCC\n3'-GUU...ACGUA___C________GUAUC...GGA-5'\n_____________\|____________\|\n_____________211__________152\n	186 -- 192	197 -- 203	-13.3669 kcal/mol	1.19489 kcal/mol	3.58567 kcal/mol	179 259@LB@ \| \|@LB@5'-ACU...AACAG UGUUU...CUG-3'@LB@ AAC GGGUGGGG@LB@ \|\|\| \|\|:\|\|:\|\|@LB@ UUG CCUACUCC@LB@3'-GUU...ACGUA C GUAUC...GGA-5'@LB@ \| \|@LB@ 211 152@LB@@LB@@LB@Energy -18.59 kcal/mol@LB@Hybridization Energy -13.3669 kcal/mol@LB@Unfolding Energy - mRNA 1.19489 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 180 -- 258@LB@Position - sRNA 153 -- 210@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 197 -- 203@LB@
138	0.03642	0.6968	lmo0509	prs	-15.18	0.090372	180 -- 241	157 -- 211	phosphoribosyl pyrophosphate synthetase	_____________179____________________________________242\n_____________\|______________________________________\|\n5'-AAC...GAAGA_____G______G__AG_____A_C_____C_______AUGAA...UCC-3'\n______________AAUUA_UAUGGC_GA__GAGAU_G_AAUGG_AGGCAAA\n______________\|\|:\|\|_:\|:\|\|\|_:\|__\|\|\|\|\|_\|_\|\|\|\|:_\|::\|\|\|\|\n______________UUGAU_GUGCCG_UU__CUCUA_C_UUACU_UUUGUUU\n3'-GUU...UGUAC____________G__A______________________AUUAC...GGA-5'\n_____________\|______________________________________\|\n_____________212____________________________________156\n	206 -- 212	153 -- 159	-24.2745 kcal/mol	6.00947 kcal/mol	10.6652 kcal/mol	179 242@LB@ \| \|@LB@5'-AAC...GAAGA G G AG A C C AUGAA...UCC-3'@LB@ AAUUA UAUGGC GA GAGAU G AAUGG AGGCAAA@LB@ \|\|:\|\| :\|:\|\|\| :\| \|\|\|\|\| \| \|\|\|\|: \|::\|\|\|\|@LB@ UUGAU GUGCCG UU CUCUA C UUACU UUUGUUU@LB@3'-GUU...UGUAC G A AUUAC...GGA-5'@LB@ \| \|@LB@ 212 156@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -24.2745 kcal/mol@LB@Unfolding Energy - mRNA 6.00947 kcal/mol@LB@Unfolding Energy - sRNA 10.6652 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 157 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 153 -- 159@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@
92	0.02404	0.6733	lmo1947	resE	-16.63	0.048416	181 -- 212	141 -- 170	two-component sensor histidine kinas	_____________180_________________213\n_____________\|___________________\|\n5'-AAG...ACCGA_______AUA_________UUGGA...UUU-3'\n______________GGUGAGA___GAUGAAGAU\n______________::\|\|\|\|\|___:\|\|\|\|\|:\|:\n______________UUACUCU___UUACUUUUG\n3'-GUU...GCCGG_______AC__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________171_________________140\n	202 -- 208	156 -- 162	-13.4823 kcal/mol	2.25638 kcal/mol	0.941471 kcal/mol	180 213@LB@ \| \|@LB@5'-AAG...ACCGA AUA UUGGA...UUU-3'@LB@ GGUGAGA GAUGAAGAU@LB@ ::\|\|\|\|\| :\|\|\|\|\|:\|:@LB@ UUACUCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 171 140@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -13.4823 kcal/mol@LB@Unfolding Energy - mRNA 2.25638 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 181 -- 212@LB@Position - sRNA 141 -- 170@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@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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