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
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@
35	0.00718	0.552	lmo0397	N/A	-24.49	0.000911	178 -- 232	160 -- 211		_____________177_________________________________________________________________________233\n_____________\|___________________________________________________________________________\|\n5'-AAU...ACAAA_______AAAAUGAAAGCAAAU_____________G__UU_G______GAG___AU__AA___C___________UAUGA...CGA-3'\n______________CUGUGCG_______________UGGCGGGA___GG_AU__A_AUGAAC___GCA__CG__CGA_GAGAUGA_UGA\n______________\|\|:\|\|\|:_______________\|::\|\|\|\|\|___\|\|_\|\|__\|_\|\|\|\|\|\|___:\|\|__\|\|__\|:\|_\|\|\|\|\|\|\|_\|\|\|\n______________GAUACGU_______________AUUGCCCU___CC_UA__U_UACUUG___UGU__GC__GUU_CUCUACU_ACU\n3'-GUU...CCGCG______________________________ACU__G__UC_G______A_________CG___A_______U___UUUGU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________212_________________________________________________________________________159\n	223 -- 229	164 -- 170	-45.3132 kcal/mol	12.0365 kcal/mol	19.7814 kcal/mol	177 233@LB@ \| \|@LB@5'-AAU...ACAAA AAAAUGAAAGCAAAU G UU G GAG AU AA C UAUGA...CGA-3'@LB@ CUGUGCG UGGCGGGA GG AU A AUGAAC GCA CG CGA GAGAUGA UGA@LB@ \|\|:\|\|\|: \|::\|\|\|\|\| \|\| \|\| \| \|\|\|\|\|\| :\|\| \|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ GAUACGU AUUGCCCU CC UA U UACUUG UGU GC GUU CUCUACU ACU@LB@3'-GUU...CCGCG ACU G UC G A CG A U UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -24.49 kcal/mol@LB@Hybridization Energy -45.3132 kcal/mol@LB@Unfolding Energy - mRNA 12.0365 kcal/mol@LB@Unfolding Energy - sRNA 19.7814 kcal/mol@LB@@LB@Position - mRNA 178 -- 232@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 164 -- 170@LB@
71	0.01891	0.6733	lmo2349	N/A	-17.22	0.037183	66 -- 119	160 -- 206	amino acid ABC transporter substrate-binding protein	_____________65______________________________________________________________________________________________________________________120\n_____________\|_______________________________________________________________________________________________________________________\|\n5'-ACC...GCACU___A_______CUUCUGCCAGA___________UG_______GA_____A__U__________________UU_______C__UUUU_A_______GA_G___________U_______UUAUG...AAG-3'\n______________GAC_CUUGGAA___________AAACA__UCCA__GUUGCUG__UAUGU_UC__GCGCC________GCGG__AUGAGGU_UA____G_ACAUGAG__A_ACGGC____GA_GUGGGUG\n______________\|\|\|_\|\|:\|:\|\|___________\|\|\|\|\|__\|\|\|\|__\|\|\|\|\|::__:\|\|\|\|_\|\|__\|\|\|\|\|________:\|\|\|__\|\|\|\|\|\|:_\|\|____\|_\|\|\|\|\|\|:__\|_\|\|\|\|\|____\|\|_:\|\|::\|\|\n______________CUG_GAGCUUU___________UUUGU__AGGU__CAACGGU__GUACA_AG__CGCGG________UGCC__UACUCCG_AU____C_UGUACUU__U_UGCCG____CU_UACUUAC\n___3'-GUUUUUUU___C_______A_______________AA____CG_______A_________CC_____AUACGUAU____C________U_______________GA_G_____GUUA__C_______UUUUG...GGA-5'\n_____________\|_______________________________________________________________________________________________________________________\|\n_____________207_____________________________________________________________________________________________________________________159\n	107 -- 113	161 -- 167	-71.8793 kcal/mol	29.0166 kcal/mol	34.5254 kcal/mol	65 120@LB@ \| \|@LB@5'-ACC...GCACU A CUUCUGCCAGA UG GA A U UU C UUUU A GA G U UUAUG...AAG-3'@LB@ GAC CUUGGAA AAACA UCCA GUUGCUG UAUGU UC GCGCC GCGG AUGAGGU UA G ACAUGAG A ACGGC GA GUGGGUG@LB@ \|\|\| \|\|:\|:\|\| \|\|\|\|\| \|\|\|\| \|\|\|\|\|:: :\|\|\|\| \|\| \|\|\|\|\| :\|\|\| \|\|\|\|\|\|: \|\| \| \|\|\|\|\|\|: \| \|\|\|\|\| \|\| :\|\|::\|\|@LB@ CUG GAGCUUU UUUGU AGGU CAACGGU GUACA AG CGCGG UGCC UACUCCG AU C UGUACUU U UGCCG CU UACUUAC@LB@ 3'-GUUUUUUU C A AA CG A CC AUACGUAU C U GA G GUUA C UUUUG...GGA-5'@LB@ \| \|@LB@ 207 159@LB@@LB@@LB@Energy -17.22 kcal/mol@LB@Hybridization Energy -71.8793 kcal/mol@LB@Unfolding Energy - mRNA 29.0166 kcal/mol@LB@Unfolding Energy - sRNA 34.5254 kcal/mol@LB@@LB@Position - mRNA 66 -- 119@LB@Position - sRNA 160 -- 206@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 161 -- 167@LB@
90	0.02372	0.6733	lmo2712	N/A	-17.76	0.029098	218 -- 285	160 -- 210	gluconate kinase	_____________217________286\n_____________\|__________\|\n5'-AGA...AAAAU__________CUGUU...CGA-3'\n______________GCGGGGUGAG\n______________:\|\|\|\|:\|\|\|\|\n______________UGCCCUACUC\n3'-GUU...CGUAU__________CGUAU...GGA-5'\n_____________\|__________\|\n_____________211________159\n	190 -- 196	197 -- 203	-16.6296 kcal/mol	4.31289 kcal/mol	0.38676 kcal/mol	217 286@LB@ \| \|@LB@5'-AGA...AAAAU CUGUU...CGA-3'@LB@ GCGGGGUGAG@LB@ :\|\|\|\|:\|\|\|\|@LB@ UGCCCUACUC@LB@3'-GUU...CGUAU CGUAU...GGA-5'@LB@ \| \|@LB@ 211 159@LB@@LB@@LB@Energy -17.76 kcal/mol@LB@Hybridization Energy -16.6296 kcal/mol@LB@Unfolding Energy - mRNA 4.31289 kcal/mol@LB@Unfolding Energy - sRNA 0.38676 kcal/mol@LB@@LB@Position - mRNA 218 -- 285@LB@Position - sRNA 160 -- 210@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 197 -- 203@LB@
105	0.02711	0.6733	lmo0347	N/A	-16.41	0.053410	62 -- 87	160 -- 186	dihydroxyacetone kinase	_____________61____________________________88\n_____________\|_____________________________\|\n5'-AUC...GUUGG__________ACU________________UUGGU...AUU-3'\n______________GAACUACGCG___UCGAUG_GAU__AUGA\n______________\|\|\|\|\|\|\|:\|\|___:\|:\|\|\|_\|\|\|__\|\|\|\|\n______________CUUGAUGUGC___GGUUAC_CUA__UACU\n3'-GUU...CUGUA__________C________U___CU____UUUGU...GGA-5'\n_____________\|_____________________________\|\n_____________187___________________________159\n	65 -- 71	177 -- 183	-23.7931 kcal/mol	4.23572 kcal/mol	9.57505 kcal/mol	61 88@LB@ \| \|@LB@5'-AUC...GUUGG ACU UUGGU...AUU-3'@LB@ GAACUACGCG UCGAUG GAU AUGA@LB@ \|\|\|\|\|\|\|:\|\| :\|:\|\|\| \|\|\| \|\|\|\|@LB@ CUUGAUGUGC GGUUAC CUA UACU@LB@3'-GUU...CUGUA C U CU UUUGU...GGA-5'@LB@ \| \|@LB@ 187 159@LB@@LB@@LB@Energy -16.41 kcal/mol@LB@Hybridization Energy -23.7931 kcal/mol@LB@Unfolding Energy - mRNA 4.23572 kcal/mol@LB@Unfolding Energy - sRNA 9.57505 kcal/mol@LB@@LB@Position - mRNA 62 -- 87@LB@Position - sRNA 160 -- 186@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 177 -- 183@LB@
163	0.04467	0.7375	lmo1286	parE	-16.49	0.051436	172 -- 223	160 -- 211	DNA topoisomerase IV subunit B	_____________171____________________________224\n_____________\|______________________________\|\n5'-CUU...AAUCA______UAA__________AU_________UUUUA...UAC-3'\n______________GCUAGU___UGCUAUUCUG____AAGGUGG\n______________:\|\|\|\|\|___\|\|\|:\|\|\|\|\|:____\|\|\|:\|\|\|\n______________UGAUCA___ACGGUAAGAU____UUCUACC\n3'-GUU...CAGAC___________________AACC_______UAUGU...GGA-5'\n_____________\|______________________________\|\n_____________212____________________________159\n	135 -- 141	96 -- 102	-24.989 kcal/mol	7.49229 kcal/mol	9.10061 kcal/mol	171 224@LB@ \| \|@LB@5'-CUU...AAUCA UAA AU UUUUA...UAC-3'@LB@ GCUAGU UGCUAUUCUG AAGGUGG@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|: \|\|\|:\|\|\|@LB@ UGAUCA ACGGUAAGAU UUCUACC@LB@3'-GUU...CAGAC AACC UAUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -24.989 kcal/mol@LB@Unfolding Energy - mRNA 7.49229 kcal/mol@LB@Unfolding Energy - sRNA 9.10061 kcal/mol@LB@@LB@Position - mRNA 172 -- 223@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 96 -- 102@LB@
177	0.05015	0.7607	lmo1905	cca	-16.43	0.052746	154 -- 208	160 -- 211	tRNA CCA-pyrophosphorylase	_____________153_______________209\n_____________\|_________________\|\n5'-UUA...AGGAG______CA_________CGUUU...UGC-3'\n______________CGAUGA__GAUGAAUGA\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________GUUACU__CUACUUACU\n3'-GUU...UGCCG_________________UUUGU...GGA-5'\n_____________\|_________________\|\n_____________212_______________159\n	202 -- 208	160 -- 166	-15.3935 kcal/mol	2.32419 kcal/mol	0.846187 kcal/mol	153 209@LB@ \| \|@LB@5'-UUA...AGGAG CA CGUUU...UGC-3'@LB@ CGAUGA GAUGAAUGA@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUUACU CUACUUACU@LB@3'-GUU...UGCCG UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -15.3935 kcal/mol@LB@Unfolding Energy - mRNA 2.32419 kcal/mol@LB@Unfolding Energy - sRNA 0.846187 kcal/mol@LB@@LB@Position - mRNA 154 -- 208@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 160 -- 166@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@
69	0.01791	0.6733	lmo0011	N/A	-18.87	0.017267	48 -- 93	161 -- 209	mevalonate diphosphate decarboxylase	_____________47_________94\n_____________\|__________\|\n5'-AGU...CGGUA__________CAUUA...CCU-3'\n______________GAGGUGGAUG\n______________\|\|\|:\|\|:\|\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________210________160\n	87 -- 93	161 -- 167	-12.2828 kcal/mol	3.75931 kcal/mol	0.812237 kcal/mol	47 94@LB@ \| \|@LB@5'-AGU...CGGUA CAUUA...CCU-3'@LB@ GAGGUGGAUG@LB@ \|\|\|:\|\|:\|\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 210 160@LB@@LB@@LB@Energy -18.87 kcal/mol@LB@Hybridization Energy -12.2828 kcal/mol@LB@Unfolding Energy - mRNA 3.75931 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 48 -- 93@LB@Position - sRNA 161 -- 209@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 161 -- 167@LB@
101	0.026	0.6733	lmo2768	N/A	-17.52	0.032492	230 -- 251	161 -- 179	hypothetical membrane protein	_____________229__________252\n_____________\|____________\|\n5'-UUA...GUAAU____________CUUUU...UAA-3'\n______________AUGAGAUGGAUG\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________UACUCUACUUAC\n3'-GUU...CCGGU____________UUUUG...GGA-5'\n_____________\|____________\|\n_____________180__________160\n	245 -- 251	161 -- 167	-15.292 kcal/mol	2.52317 kcal/mol	0.818518 kcal/mol	229 252@LB@ \| \|@LB@5'-UUA...GUAAU CUUUU...UAA-3'@LB@ AUGAGAUGGAUG@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ UACUCUACUUAC@LB@3'-GUU...CCGGU UUUUG...GGA-5'@LB@ \| \|@LB@ 180 160@LB@@LB@@LB@Energy -17.52 kcal/mol@LB@Hybridization Energy -15.292 kcal/mol@LB@Unfolding Energy - mRNA 2.52317 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 230 -- 251@LB@Position - sRNA 161 -- 179@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 161 -- 167@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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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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