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@
160	0.04276	0.7192	lmo0415	N/A	-19.07	0.015641	183 -- 241	108 -- 171	endo-1 4-beta-xylanase	_____________182_________________________________________________________________242\n_____________\|___________________________________________________________________\|\n5'-UUU...UUUUC_________GU______UAAU____AAA__A____GA______________C_______________CAUUA...AGU-3'\n______________UGAGGUGAG_____GCA____GUGA___UU_GGUG__UUAGAC_____UUU_ACUAGUUGCCAUUCU\n______________\|\|\|\|:\|\|\|:_____:\|\|____:\|\|\|___\|\|_\|\|\|\|__:\|\|:\|\|_____\|:\|_\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACUCUACUU_____UGU____UACU___AA_CCAC__GAUUUG_____AGA_UGAUCAACGGUAAGA\n3'-GUU...CGGUU_________ACUUU___UUAU____A____A____A_______UCUAC___C_______________UAACC...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________172_________________________________________________________________107\n	235 -- 241	108 -- 114	-46.29 kcal/mol	15.9956 kcal/mol	19.2069 kcal/mol	182 242@LB@ \| \|@LB@5'-UUU...UUUUC GU UAAU AAA A GA C CAUUA...AGU-3'@LB@ UGAGGUGAG GCA GUGA UU GGUG UUAGAC UUU ACUAGUUGCCAUUCU@LB@ \|\|\|\|:\|\|\|: :\|\| :\|\|\| \|\| \|\|\|\| :\|\|:\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACUCUACUU UGU UACU AA CCAC GAUUUG AGA UGAUCAACGGUAAGA@LB@3'-GUU...CGGUU ACUUU UUAU A A A UCUAC C UAACC...GGA-5'@LB@ \| \|@LB@ 172 107@LB@@LB@@LB@Energy -19.07 kcal/mol@LB@Hybridization Energy -46.29 kcal/mol@LB@Unfolding Energy - mRNA 15.9956 kcal/mol@LB@Unfolding Energy - sRNA 19.2069 kcal/mol@LB@@LB@Position - mRNA 183 -- 241@LB@Position - sRNA 108 -- 171@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 108 -- 114@LB@
113	0.02939	0.6968	lmo0232	clpC	-17.21	0.037249	171 -- 212	159 -- 202	endopeptidase Clp ATP-binding chain C	_____________170___________________________________________213\n_____________\|_____________________________________________\|\n5'-AUU...UAAAU________U__C____A___GGAA__AA___________UU____CGAUU...AUA-3'\n______________GAUGAGGC_UA_GAUA_GGA____AC___CAAUGA__UG__UGGA\n______________\|\|\|\|\|\|\|\|_\|\|_\|\|:\|_\|:\|____\|\|___\|\|\|\|\|\|__\|\|__\|\|:\|\n______________CUACUCCG_AU_CUGU_CUU____UG___GUUACU__AC__ACUU\n3'-GUU...UUGCC________U_______A___GAUG__CCG______CU__UU____UUGUU...GGA-5'\n_____________\|_____________________________________________\|\n_____________203___________________________________________158\n	172 -- 178	195 -- 201	-28.9894 kcal/mol	4.99237 kcal/mol	13.9304 kcal/mol	170 213@LB@ \| \|@LB@5'-AUU...UAAAU U C A GGAA AA UU CGAUU...AUA-3'@LB@ GAUGAGGC UA GAUA GGA AC CAAUGA UG UGGA@LB@ \|\|\|\|\|\|\|\| \|\| \|\|:\| \|:\| \|\| \|\|\|\|\|\| \|\| \|\|:\|@LB@ CUACUCCG AU CUGU CUU UG GUUACU AC ACUU@LB@3'-GUU...UUGCC U A GAUG CCG CU UU UUGUU...GGA-5'@LB@ \| \|@LB@ 203 158@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.9894 kcal/mol@LB@Unfolding Energy - mRNA 4.99237 kcal/mol@LB@Unfolding Energy - sRNA 13.9304 kcal/mol@LB@@LB@Position - mRNA 171 -- 212@LB@Position - sRNA 159 -- 202@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 195 -- 201@LB@
155	0.04112	0.7058	lmo1165	N/A	-16.89	0.043077	88 -- 150	155 -- 206	ethanolamine utilization protein EutE	_____________87_______________________________151\n_____________\|________________________________\|\n5'-AAG...AAUGG____________G___C_______G_______UCCAC...CAA-3'\n______________GGAUUA_GCGGC_GAU_AG_UGGA_GAAGAUA\n______________\|:\|:\|\|_:\|\|\|\|_:\|\|_\|\|_\|\|:\|_\|\|\|:\|:\|\n______________CUUGAU_UGCCG_UUA_UC_ACUU_CUUUUGU\n3'-GUU...CUGUA______G_____G___C__U____A_______UUAUU...GGA-5'\n_____________\|________________________________\|\n_____________207______________________________154\n	144 -- 150	155 -- 161	-24.1777 kcal/mol	5.41964 kcal/mol	9.66922 kcal/mol	87 151@LB@ \| \|@LB@5'-AAG...AAUGG G C G UCCAC...CAA-3'@LB@ GGAUUA GCGGC GAU AG UGGA GAAGAUA@LB@ \|:\|:\|\| :\|\|\|\| :\|\| \|\| \|\|:\| \|\|\|:\|:\|@LB@ CUUGAU UGCCG UUA UC ACUU CUUUUGU@LB@3'-GUU...CUGUA G G C U A UUAUU...GGA-5'@LB@ \| \|@LB@ 207 154@LB@@LB@@LB@Energy -16.89 kcal/mol@LB@Hybridization Energy -24.1777 kcal/mol@LB@Unfolding Energy - mRNA 5.41964 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 88 -- 150@LB@Position - sRNA 155 -- 206@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 155 -- 161@LB@
17	0.003248	0.4469	lmo1161	N/A	-22.54	0.002685	189 -- 238	155 -- 204	ethanolamine utilization protein EutJ	_____________188___________________________________________________239\n_____________\|_____________________________________________________\|\n5'-GGU...GUAAG_____GGAAAA________U_______AACA________AC____________GCUUG...AAG-3'\n______________GAGGU______AUGGAUAU___UUACA____GCCAAUGA___GAAUGGAA_CA\n______________\|\|\|\|:______\|\|:\|\|:\|\|___:\|\|\|\|____\|\|\|\|\|\|\|\|___\|\|\|\|\|:\|\|_\|\|\n______________CUCCG______UAUCUGUA___GAUGU____CGGUUACU___CUUACUUU_GU\n3'-GUU...CCCUA___________________CUU_____GC__________CUA________U__UUAUU...GGA-5'\n_____________\|_____________________________________________________\|\n_____________205___________________________________________________154\n	230 -- 236	158 -- 164	-34.4634 kcal/mol	5.85583 kcal/mol	13.9822 kcal/mol	188 239@LB@ \| \|@LB@5'-GGU...GUAAG GGAAAA U AACA AC GCUUG...AAG-3'@LB@ GAGGU AUGGAUAU UUACA GCCAAUGA GAAUGGAA CA@LB@ \|\|\|\|: \|\|:\|\|:\|\| :\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\| \|\|@LB@ CUCCG UAUCUGUA GAUGU CGGUUACU CUUACUUU GU@LB@3'-GUU...CCCUA CUU GC CUA U UUAUU...GGA-5'@LB@ \| \|@LB@ 205 154@LB@@LB@@LB@Energy -22.54 kcal/mol@LB@Hybridization Energy -34.4634 kcal/mol@LB@Unfolding Energy - mRNA 5.85583 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 189 -- 238@LB@Position - sRNA 155 -- 204@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 158 -- 164@LB@
14	0.00304	0.4469	lmo1187	N/A	-19.26	0.014311	139 -- 172	153 -- 183	ethanolamine utilization protein EutQ	_____________138_______________________________173\n_____________\|_________________________________\|\n5'-UAA...GGUAU____________CC__AU______GA_______AGCAA...UUU-3'\n______________CUAUAUGGCUAA__GA__GAUGAA__AAAAUAA\n______________\|\|\|:\|:\|\|\|:\|\|__\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________GAUGUGCCGGUU__CU__CUACUU__UUUUGUU\n3'-GUU...UACUU____________A___________AC_______UAUUA...GGA-5'\n_____________\|_________________________________\|\n_____________184_______________________________152\n	165 -- 171	154 -- 160	-25.2263 kcal/mol	3.98561 kcal/mol	9.539 kcal/mol	138 173@LB@ \| \|@LB@5'-UAA...GGUAU CC AU GA AGCAA...UUU-3'@LB@ CUAUAUGGCUAA GA GAUGAA AAAAUAA@LB@ \|\|\|:\|:\|\|\|:\|\| \|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ GAUGUGCCGGUU CU CUACUU UUUUGUU@LB@3'-GUU...UACUU A AC UAUUA...GGA-5'@LB@ \| \|@LB@ 184 152@LB@@LB@@LB@Energy -19.26 kcal/mol@LB@Hybridization Energy -25.2263 kcal/mol@LB@Unfolding Energy - mRNA 3.98561 kcal/mol@LB@Unfolding Energy - sRNA 9.539 kcal/mol@LB@@LB@Position - mRNA 139 -- 172@LB@Position - sRNA 153 -- 183@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 154 -- 160@LB@
103	0.02634	0.6733	lmo2183	N/A	-17.72	0.029644	120 -- 189	95 -- 172	ferrichrome ABC transporter permease	_____________119_______________190\n_____________\|_________________\|\n5'-AGA...UGUGU____UU___________UUAUU...UCC-3'\n______________AUGA__UGGAUGAAAAU\n______________\|\|\|\|__\|\|:\|\|\|\|\|\|\|:\n______________UACU__ACUUACUUUUG\n3'-GUU...CCGGU____CU___________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________173_______________94\n	130 -- 136	156 -- 162	-14.4355 kcal/mol	3.54286 kcal/mol	0.922045 kcal/mol	119 190@LB@ \| \|@LB@5'-AGA...UGUGU UU UUAUU...UCC-3'@LB@ AUGA UGGAUGAAAAU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ UACU ACUUACUUUUG@LB@3'-GUU...CCGGU CU UUUAU...GGA-5'@LB@ \| \|@LB@ 173 94@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -14.4355 kcal/mol@LB@Unfolding Energy - mRNA 3.54286 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 120 -- 189@LB@Position - sRNA 95 -- 172@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 156 -- 162@LB@
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@
142	0.03693	0.6968	lmo2586	N/A	-16.96	0.041696	196 -- 266	151 -- 227	formate dehydrogenase subunit alpha	_____________195______267\n_____________\|________\|\n5'-UUU...GUGGC________UGGUG...AUC-3'\n______________GCGGGAUG\n______________:\|\|\|\|\|\|\|\n______________UGCCCUAC\n3'-GUU...CGUAU________UCCGU...GGA-5'\n_____________\|________\|\n_____________228______150\n	240 -- 246	199 -- 205	-13.0644 kcal/mol	3.68871 kcal/mol	0.331032 kcal/mol	195 267@LB@ \| \|@LB@5'-UUU...GUGGC UGGUG...AUC-3'@LB@ GCGGGAUG@LB@ :\|\|\|\|\|\|\|@LB@ UGCCCUAC@LB@3'-GUU...CGUAU UCCGU...GGA-5'@LB@ \| \|@LB@ 228 150@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -13.0644 kcal/mol@LB@Unfolding Energy - mRNA 3.68871 kcal/mol@LB@Unfolding Energy - sRNA 0.331032 kcal/mol@LB@@LB@Position - mRNA 196 -- 266@LB@Position - sRNA 151 -- 227@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 199 -- 205@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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