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
158	0.04144	0.7058	lmo1958	fhuB	-14.94	0.099691	191 -- 222	150 -- 181	ferrichrome ABC transporter permease	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GUU...AAGGA_____U__A________A___C___________AAAUG...UCG-3'\n______________ACAUG_GC_GAUG_GAU_AGU_AAAACAGAUAA\n______________\|\|\|:\|_\|\|_:\|\|\|_\|\|\|_\|:\|_\|\|\|\|\|\|:\|\|\|\|\n______________UGUGC_CG_UUAC_CUA_UUA_UUUUGUUUAUU\n3'-GUU...CUUGA________G____U___C___C___________ACUAA...GGA-5'\n_____________\|_________________________________\|\n_____________182_______________________________149\n	214 -- 220	152 -- 158	-22.8664 kcal/mol	3.81003 kcal/mol	11.9534 kcal/mol	190 223@LB@ \| \|@LB@5'-GUU...AAGGA U A A C AAAUG...UCG-3'@LB@ ACAUG GC GAUG GAU AGU AAAACAGAUAA@LB@ \|\|\|:\| \|\| :\|\|\| \|\|\| \|:\| \|\|\|\|\|\|:\|\|\|\|@LB@ UGUGC CG UUAC CUA UUA UUUUGUUUAUU@LB@3'-GUU...CUUGA G U C C ACUAA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -22.8664 kcal/mol@LB@Unfolding Energy - mRNA 3.81003 kcal/mol@LB@Unfolding Energy - sRNA 11.9534 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 152 -- 158@LB@
26	0.004866	0.5029	lmo0682	flgG	-18.63	0.019297	177 -- 239	156 -- 207	flagellar basal body rod protein FlgG	_____________176__________________________________________240\n_____________\|____________________________________________\|\n5'-GAA...ACCAA_______GU_______CGGA__G___________AC____A___GGCAG...UCA-3'\n______________AGA_GUC__UGGCUAG____GC_G_UUUGUUGGA__GGAU_GGA\n______________\|\|\|_\|\|\|__\|\|:\|\|\|\|____\|\|_:_\|:\|:\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UCU_CAG__ACUGAUC____CG_U_AGAUAACCU__UCUA_CCU\n3'-GUU...AUUUG___A____________AA____G_A___________________AUGUG...GGA-5'\n_____________\|____________________________________________\|\n_____________208__________________________________________155\n	171 -- 177	102 -- 108	-30.3451 kcal/mol	11.2986 kcal/mol	9.4836 kcal/mol	176 240@LB@ \| \|@LB@5'-GAA...ACCAA GU CGGA G AC A GGCAG...UCA-3'@LB@ AGA GUC UGGCUAG GC G UUUGUUGGA GGAU GGA@LB@ \|\|\| \|\|\| \|\|:\|\|\|\| \|\| : \|:\|:\|\|\|\|\| :\|\|\| \|\|\|@LB@ UCU CAG ACUGAUC CG U AGAUAACCU UCUA CCU@LB@3'-GUU...AUUUG A AA G A AUGUG...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -30.3451 kcal/mol@LB@Unfolding Energy - mRNA 11.2986 kcal/mol@LB@Unfolding Energy - sRNA 9.4836 kcal/mol@LB@@LB@Position - mRNA 177 -- 239@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 102 -- 108@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@
121	0.03234	0.6968	lmo0198	glmU	-15.85	0.067914	228 -- 259	153 -- 184	bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase	_____________227______________________________260\n_____________\|________________________________\|\n5'-UAC...UGCUU_____________GGCACAC________U___AACUU...UGG-3'\n______________GCUGC_UGGCCAA_______GGAUGAAA_CAA\n______________:\|\|:\|_:\|\|\|\|\|\|_______\|:\|\|\|\|\|\|_\|\|\|\n______________UGAUG_GCCGGUU_______CUUACUUU_GUU\n3'-GUU...GUACU_____U_______ACUCUA_________U___UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________185______________________________152\n	248 -- 254	158 -- 164	-25.2592 kcal/mol	7.21839 kcal/mol	9.59579 kcal/mol	227 260@LB@ \| \|@LB@5'-UAC...UGCUU GGCACAC U AACUU...UGG-3'@LB@ GCUGC UGGCCAA GGAUGAAA CAA@LB@ :\|\|:\| :\|\|\|\|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGAUG GCCGGUU CUUACUUU GUU@LB@3'-GUU...GUACU U ACUCUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 185 152@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -25.2592 kcal/mol@LB@Unfolding Energy - mRNA 7.21839 kcal/mol@LB@Unfolding Energy - sRNA 9.59579 kcal/mol@LB@@LB@Position - mRNA 228 -- 259@LB@Position - sRNA 153 -- 184@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 158 -- 164@LB@
156	0.04133	0.7058	lmo1481	holA	-16.45	0.052293	189 -- 224	151 -- 199	DNA polymerase III subunit delta	_____________188_________225\n_____________\|___________\|\n5'-CAA...UGCCA___________GAUAC...UUU-3'\n______________GAAUGGAAACA\n______________\|\|\|\|\|:\|\|\|\|\|\n______________CUUACUUUUGU\n3'-GUU...CUCUA___________UUAUU...GGA-5'\n_____________\|___________\|\n_____________200_________150\n	213 -- 219	156 -- 162	-12.8572 kcal/mol	1.78423 kcal/mol	0.853601 kcal/mol	188 225@LB@ \| \|@LB@5'-CAA...UGCCA GAUAC...UUU-3'@LB@ GAAUGGAAACA@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ CUUACUUUUGU@LB@3'-GUU...CUCUA UUAUU...GGA-5'@LB@ \| \|@LB@ 200 150@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -12.8572 kcal/mol@LB@Unfolding Energy - mRNA 1.78423 kcal/mol@LB@Unfolding Energy - sRNA 0.853601 kcal/mol@LB@@LB@Position - mRNA 189 -- 224@LB@Position - sRNA 151 -- 199@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 156 -- 162@LB@
41	0.008795	0.5772	lmo1984	ilvB	-19.06	0.015768	187 -- 229	157 -- 201	acetolactate synthase	_____________186____________________________________________230\n_____________\|______________________________________________\|\n5'-AUU...AAAAA_______G___A______UUG_____A_________CA________AGCGA...ACA-3'\n______________AUGAGGU_AUA_GCGUGA___AUACG__CGA__AGA__AAUGAAAA\n______________\|\|\|\|\|\|:_\|\|\|_:\|:\|\|\|___\|:\|\|\|__\|:\|__\|\|\|__\|\|\|\|\|\|\|\|\n______________UACUCCG_UAU_UGUACU___UGUGC__GUU__UCU__UUACUUUU\n3'-GUU...UGCCC___________C______UGA_____CG___AC___AC________GUUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________202____________________________________________156\n	223 -- 229	157 -- 163	-31.6948 kcal/mol	5.6221 kcal/mol	13.9999 kcal/mol	186 230@LB@ \| \|@LB@5'-AUU...AAAAA G A UUG A CA AGCGA...ACA-3'@LB@ AUGAGGU AUA GCGUGA AUACG CGA AGA AAUGAAAA@LB@ \|\|\|\|\|\|: \|\|\| :\|:\|\|\| \|:\|\|\| \|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UACUCCG UAU UGUACU UGUGC GUU UCU UUACUUUU@LB@3'-GUU...UGCCC C UGA CG AC AC GUUUA...GGA-5'@LB@ \| \|@LB@ 202 156@LB@@LB@@LB@Energy -19.06 kcal/mol@LB@Hybridization Energy -31.6948 kcal/mol@LB@Unfolding Energy - mRNA 5.6221 kcal/mol@LB@Unfolding Energy - sRNA 13.9999 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 157 -- 201@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 157 -- 163@LB@
74	0.01955	0.6733	lmo0190	ipk	-17.49	0.032930	174 -- 210	154 -- 192	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	_____________173_______________________________________211\n_____________\|_________________________________________\|\n5'-AUA...AAAAG____UU_________GA___________AA___________GCAUU...CAA-3'\n______________AGAU__UGAAC_GCG__GGCCA___AGA__AAUGAAAAUAA\n______________\|\|\|:__\|\|\|\|\|_:\|:__\|\|\|\|\|___\|\|\|__\|\|\|\|\|\|\|\|:\|\|\n______________UCUG__ACUUG_UGU__CCGGU___UCU__UUACUUUUGUU\n3'-GUU...CCGUA____U______A___G______UAC___AC___________UAUUA...GGA-5'\n_____________\|_________________________________________\|\n_____________193_______________________________________153\n	204 -- 210	154 -- 160	-28.6344 kcal/mol	5.15958 kcal/mol	12.1365 kcal/mol	173 211@LB@ \| \|@LB@5'-AUA...AAAAG UU GA AA GCAUU...CAA-3'@LB@ AGAU UGAAC GCG GGCCA AGA AAUGAAAAUAA@LB@ \|\|\|: \|\|\|\|\| :\|: \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ UCUG ACUUG UGU CCGGU UCU UUACUUUUGUU@LB@3'-GUU...CCGUA U A G UAC AC UAUUA...GGA-5'@LB@ \| \|@LB@ 193 153@LB@@LB@@LB@Energy -17.49 kcal/mol@LB@Hybridization Energy -28.6344 kcal/mol@LB@Unfolding Energy - mRNA 5.15958 kcal/mol@LB@Unfolding Energy - sRNA 12.1365 kcal/mol@LB@@LB@Position - mRNA 174 -- 210@LB@Position - sRNA 154 -- 192@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
134	0.0358	0.6968	lmo2682	kdpA	-15.50	0.078936	69 -- 121	151 -- 202	potassium-transporting ATPase subunit A	_____________68_____________________________________________122\n_____________\|______________________________________________\|\n5'-ACA...UUGGU___AU___UG_____AAGAG______G___________CG______GGGUG...AAA-3'\n______________AGG__UAG__GUGGA_____UACGGU_AA_GGGGUGAA__GAAAAU\n______________\|\|\|__\|\|\|__:\|\|:\|_____:\|\|\|\|:_\|\|_\|:\|:\|\|\|\|__\|\|\|\|\|:\n______________UCC__AUC__UACUU_____GUGCCG_UU_CUCUACUU__CUUUUG\n3'-GUU...CCUAC___GU___UG_____GAU________G__A________A_______UUUAU...GGA-5'\n_____________\|______________________________________________\|\n_____________203____________________________________________150\n	102 -- 108	163 -- 169	-34.0107 kcal/mol	9.08348 kcal/mol	13.9626 kcal/mol	68 122@LB@ \| \|@LB@5'-ACA...UUGGU AU UG AAGAG G CG GGGUG...AAA-3'@LB@ AGG UAG GUGGA UACGGU AA GGGGUGAA GAAAAU@LB@ \|\|\| \|\|\| :\|\|:\| :\|\|\|\|: \|\| \|:\|:\|\|\|\| \|\|\|\|\|:@LB@ UCC AUC UACUU GUGCCG UU CUCUACUU CUUUUG@LB@3'-GUU...CCUAC GU UG GAU G A A UUUAU...GGA-5'@LB@ \| \|@LB@ 203 150@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -34.0107 kcal/mol@LB@Unfolding Energy - mRNA 9.08348 kcal/mol@LB@Unfolding Energy - sRNA 13.9626 kcal/mol@LB@@LB@Position - mRNA 69 -- 121@LB@Position - sRNA 151 -- 202@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 163 -- 169@LB@
21	0.003699	0.4469	lmo2681	kdpB	-18.50	0.020601	185 -- 204	154 -- 173	potassium-transporting ATPase subunit B	_____________184__________________205\n_____________\|____________________\|\n5'-GCA...UUUCA____________________UGGAA...AUG-3'\n______________AAUGAGGUGAAUGGAAAUGA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|\n______________UUACUCUACUUACUUUUGUU\n3'-GUU...GCCGG____________________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________153\n	197 -- 203	155 -- 161	-22.9313 kcal/mol	3.41 kcal/mol	0.959215 kcal/mol	184 205@LB@ \| \|@LB@5'-GCA...UUUCA UGGAA...AUG-3'@LB@ AAUGAGGUGAAUGGAAAUGA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|@LB@ UUACUCUACUUACUUUUGUU@LB@3'-GUU...GCCGG UAUUA...GGA-5'@LB@ \| \|@LB@ 174 153@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -22.9313 kcal/mol@LB@Unfolding Energy - mRNA 3.41 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 154 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@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@

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)

Job resubmission

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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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