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
89	0.02343	0.6733	lmo1651	N/A	-15.38	0.082912	189 -- 217	147 -- 170	ABC transporter ATP-binding protein	_____________188___________________________218\n_____________\|_____________________________\|\n5'-GAA...AGAAG______UAGCA___________UG_____ACAAG...UUC-3'\n______________GGGGUG_____GAUGGAAGCGA__AAUGA\n______________\|:\|:\|\|_____:\|\|\|:\|\|:\|:\|__\|\|\|\|\|\n______________CUCUAC_____UUACUUUUGUU__UUACU\n3'-GUU...GGUUA______________________UA_____AAAAC...GGA-5'\n_____________\|_____________________________\|\n_____________171___________________________146\n	204 -- 210	154 -- 160	-21.1438 kcal/mol	4.28476 kcal/mol	5.93585 kcal/mol	188 218@LB@ \| \|@LB@5'-GAA...AGAAG UAGCA UG ACAAG...UUC-3'@LB@ GGGGUG GAUGGAAGCGA AAUGA@LB@ \|:\|:\|\| :\|\|\|:\|\|:\|:\| \|\|\|\|\|@LB@ CUCUAC UUACUUUUGUU UUACU@LB@3'-GUU...GGUUA UA AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -21.1438 kcal/mol@LB@Unfolding Energy - mRNA 4.28476 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 189 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
180	0.05132	0.7607	lmo1643	N/A	-15.34	0.084306	231 -- 286	157 -- 207	lmo1643	_____________230_______________287\n_____________\|_________________\|\n5'-CGA...UAGUA_______GAU_______AGAAG...CUG-3'\n______________AGUGAGG___AUGAAAA\n______________\|:\|\|\|\|:___\|\|\|\|\|\|\|\n______________UUACUCU___UACUUUU\n3'-GUU...GCCGG_______ACU_______GUUUA...GGA-5'\n_____________\|_________________\|\n_____________208_______________156\n	280 -- 286	157 -- 163	-13.3165 kcal/mol	1.24234 kcal/mol	0.930085 kcal/mol	230 287@LB@ \| \|@LB@5'-CGA...UAGUA GAU AGAAG...CUG-3'@LB@ AGUGAGG AUGAAAA@LB@ \|:\|\|\|\|: \|\|\|\|\|\|\|@LB@ UUACUCU UACUUUU@LB@3'-GUU...GCCGG ACU GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -13.3165 kcal/mol@LB@Unfolding Energy - mRNA 1.24234 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 231 -- 286@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 157 -- 163@LB@
170	0.04745	0.7511	lmo2203	N/A	-15.31	0.085499	133 -- 190	99 -- 165	N-acetylmuramoyl-L-alanine amidase	_____________132___________________________________191\n_____________\|_____________________________________\|\n5'-AUA...AGGUU_________________A________AA_________ACUAA...CAG-3'\n______________AACAGA_____GAC_AG__GCCAUUU__AUUGGGGGA\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UUGUCU_____CUG_UC__CGGUAAG__UAACCUUCU\n3'-GUU...CAGAU______ACAGA___A__AA_______A__________ACCUA...GGA-5'\n_____________\|_____________________________________\|\n_____________166___________________________________98\n	184 -- 190	99 -- 105	-25.8209 kcal/mol	4.57897 kcal/mol	9.42764 kcal/mol	132 191@LB@ \| \|@LB@5'-AUA...AGGUU A AA ACUAA...CAG-3'@LB@ AACAGA GAC AG GCCAUUU AUUGGGGGA@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UUGUCU CUG UC CGGUAAG UAACCUUCU@LB@3'-GUU...CAGAU ACAGA A AA A ACCUA...GGA-5'@LB@ \| \|@LB@ 166 98@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -25.8209 kcal/mol@LB@Unfolding Energy - mRNA 4.57897 kcal/mol@LB@Unfolding Energy - sRNA 9.42764 kcal/mol@LB@@LB@Position - mRNA 133 -- 190@LB@Position - sRNA 99 -- 165@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 99 -- 105@LB@
200	0.05675	0.7607	lmo0115	lmaD	-15.21	0.089253	167 -- 203	151 -- 184		_____________166_________________204\n_____________\|___________________\|\n5'-AUG...GUGGG____________A______UUUUA...UGG-3'\n______________AAUG_GAUGGAU_GAAAAC\n______________\|\|\|\|_\|\|\|\|:\|\|_\|\|\|\|\|\|\n______________UUAC_CUACUUA_CUUUUG\n3'-GUU...GCCGG____U______________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________185_________________150\n	200 -- 206	162 -- 168	-16.3044 kcal/mol	1.75857 kcal/mol	0.941471 kcal/mol	166 204@LB@ \| \|@LB@5'-AUG...GUGGG A UUUUA...UGG-3'@LB@ AAUG GAUGGAU GAAAAC@LB@ \|\|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|@LB@ UUAC CUACUUA CUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 185 150@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -16.3044 kcal/mol@LB@Unfolding Energy - mRNA 1.75857 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 167 -- 203@LB@Position - sRNA 151 -- 184@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 162 -- 168@LB@
193	0.05586	0.7607	lmo1772	purC	-15.19	0.089756	256 -- 291	97 -- 135	phosphoribosylaminoimidazole-succinocarboxamide synthase	_____________255_____________________________________292\n_____________\|_______________________________________\|\n5'-UUA...AGAAG____________U__GU______UAUAA______C____CGACA...CGC-3'\n______________AAGCAGGUGUCU_GC__GUUGCU________GGA_GAUG\n______________\|\|:\|\|\|:\|\|\|\|\|_:\|__\|\|\|\|\|:________\|\|\|_\|\|\|\|\n______________UUUGUCUACAGA_UG__CAACGG________CCU_CUAC\n3'-GUU...ACAGA____________C__AU______UAAGAUAA___U____CUAUG...GGA-5'\n_____________\|_______________________________________\|\n_____________136_____________________________________96\n	261 -- 267	124 -- 130	-33.6761 kcal/mol	9.14329 kcal/mol	9.45249 kcal/mol	255 292@LB@ \| \|@LB@5'-UUA...AGAAG U GU UAUAA C CGACA...CGC-3'@LB@ AAGCAGGUGUCU GC GUUGCU GGA GAUG@LB@ \|\|:\|\|\|:\|\|\|\|\| :\| \|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UUUGUCUACAGA UG CAACGG CCU CUAC@LB@3'-GUU...ACAGA C AU UAAGAUAA U CUAUG...GGA-5'@LB@ \| \|@LB@ 136 96@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -33.6761 kcal/mol@LB@Unfolding Energy - mRNA 9.14329 kcal/mol@LB@Unfolding Energy - sRNA 9.45249 kcal/mol@LB@@LB@Position - mRNA 256 -- 291@LB@Position - sRNA 97 -- 135@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 124 -- 130@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@
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@
194	0.05602	0.7607	lmo1602	N/A	-15.08	0.094256	153 -- 204	160 -- 207		_____________152_______________________________________205\n_____________\|_________________________________________\|\n5'-UUU...ACUCA_________AAAA___________A_____U____A_____UAGUA...CAA-3'\n______________GGGUAUAGA____GGA__AUAUGG__GGUG_GGAU_GAUGA\n______________:\|\|:\|\|\|\|\|____\|:\|__\|:\|:\|\|__::\|\|_:\|\|\|_:\|\|\|\|\n______________UCCGUAUCU____CUU__UGUGCC__UUAC_UCUA_UUACU\n3'-GUU...CCUAC_________GUA____GA______GG_________C_____UUUGU...GGA-5'\n_____________\|_________________________________________\|\n_____________208_______________________________________159\n	168 -- 174	191 -- 197	-27.2651 kcal/mol	6.9826 kcal/mol	13.8637 kcal/mol	152 205@LB@ \| \|@LB@5'-UUU...ACUCA AAAA A U A UAGUA...CAA-3'@LB@ GGGUAUAGA GGA AUAUGG GGUG GGAU GAUGA@LB@ :\|\|:\|\|\|\|\| \|:\| \|:\|:\|\| ::\|\| :\|\|\| :\|\|\|\|@LB@ UCCGUAUCU CUU UGUGCC UUAC UCUA UUACU@LB@3'-GUU...CCUAC GUA GA GG C UUUGU...GGA-5'@LB@ \| \|@LB@ 208 159@LB@@LB@@LB@Energy -15.08 kcal/mol@LB@Hybridization Energy -27.2651 kcal/mol@LB@Unfolding Energy - mRNA 6.9826 kcal/mol@LB@Unfolding Energy - sRNA 13.8637 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 160 -- 207@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 191 -- 197@LB@
148	0.03863	0.6968	lmo1766	purN	-15.06	0.094934	1 -- 35	156 -- 188	phosphoribosylglycinamide formyltransferase	______________1__________________________________36\n______________\|__________________________________\|\n___________5'-_____GAA___________UAAAC_A_________GUAUG...AUA-3'\n______________GUGAA___AUACGGCCAAU_____G_AAUGGAAAU\n______________:\|\|\|\|___\|:\|\|\|\|\|\|\|\|\|_____\|_\|\|\|\|:\|\|\|:\n______________UACUU___UGUGCCGGUUA_____C_UUACUUUUG\n3'-GUU...AUCUG_____GA____________CUCUA___________UUUAU...GGA-5'\n_____________\|___________________________________\|\n_____________189_________________________________155\n	29 -- 35	156 -- 162	-25.7257 kcal/mol	7.32217 kcal/mol	9.72027 kcal/mol	1 36@LB@ \| \|@LB@ 5'- GAA UAAAC A GUAUG...AUA-3'@LB@ GUGAA AUACGGCCAAU G AAUGGAAAU@LB@ :\|\|\|\| \|:\|\|\|\|\|\|\|\|\| \| \|\|\|\|:\|\|\|:@LB@ UACUU UGUGCCGGUUA C UUACUUUUG@LB@3'-GUU...AUCUG GA CUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 189 155@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -25.7257 kcal/mol@LB@Unfolding Energy - mRNA 7.32217 kcal/mol@LB@Unfolding Energy - sRNA 9.72027 kcal/mol@LB@@LB@Position - mRNA 1 -- 35@LB@Position - sRNA 156 -- 188@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 156 -- 162@LB@
137	0.03627	0.6968	lmo2666	N/A	-15.01	0.096662	42 -- 111	153 -- 211	PTS galacticol transporter subunit IIB	_____________41__________________112\n_____________\|___________________\|\n5'-CUC...ACUCA___CGAAA___________AGUAA...UGG-3'\n______________GAG_____GAUGAAGACGA\n______________\|\|\|_____:\|\|\|\|\|:\|\|:\|\n______________CUC_____UUACUUUUGUU\n3'-GUU...GGUUA___UAC_____________UAUUA...GGA-5'\n_____________\|___________________\|\n_____________212_________________152\n	104 -- 110	154 -- 160	-11.8615 kcal/mol	1.60013 kcal/mol	0.933796 kcal/mol	41 112@LB@ \| \|@LB@5'-CUC...ACUCA CGAAA AGUAA...UGG-3'@LB@ GAG GAUGAAGACGA@LB@ \|\|\| :\|\|\|\|\|:\|\|:\|@LB@ CUC UUACUUUUGUU@LB@3'-GUU...GGUUA UAC UAUUA...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -11.8615 kcal/mol@LB@Unfolding Energy - mRNA 1.60013 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 42 -- 111@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 154 -- 160@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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service.

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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