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
144	0.03753	0.6968	lmo2422	N/A	-16.62	0.048504	29 -- 68	172 -- 209	two-component response regulator	_____________28___________________________________69\n_____________\|____________________________________\|\n5'-AUG...AUUCG____________AAAU_______G___U________UUUAU...AUG-3'\n______________CUAUGU__GACG____UGAGGCA_AGA_UAUGAAUU\n______________\|\|\|\|\|:__:\|\|\|____\|\|\|\|\|\|\|_\|\|\|_:\|\|\|\|\|:\|\n______________GAUACG__UUGC____ACUCCGU_UCU_GUACUUGA\n3'-GUU...CCGCG______UA____CCU________A____________UGUGC...GGA-5'\n_____________\|____________________________________\|\n_____________210__________________________________171\n	39 -- 45	194 -- 200	-29.3631 kcal/mol	6.47642 kcal/mol	13.3074 kcal/mol	28 69@LB@ \| \|@LB@5'-AUG...AUUCG AAAU G U UUUAU...AUG-3'@LB@ CUAUGU GACG UGAGGCA AGA UAUGAAUU@LB@ \|\|\|\|\|: :\|\|\| \|\|\|\|\|\|\| \|\|\| :\|\|\|\|\|:\|@LB@ GAUACG UUGC ACUCCGU UCU GUACUUGA@LB@3'-GUU...CCGCG UA CCU A UGUGC...GGA-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -29.3631 kcal/mol@LB@Unfolding Energy - mRNA 6.47642 kcal/mol@LB@Unfolding Energy - sRNA 13.3074 kcal/mol@LB@@LB@Position - mRNA 29 -- 68@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 194 -- 200@LB@
9	0.002066	0.4469	lmo0669	N/A	-20.91	0.006284	33 -- 77	156 -- 211	oxidoreductase	_____________32__________________78\n_____________\|___________________\|\n5'-AAU...UAAAG___________________GGGAA...UUC-3'\n______________UAAUGGGG_GGAUGAAAAU\n______________:\|\|\|\|:\|:_\|:\|\|\|\|\|\|\|:\n______________GUUACUCU_CUUACUUUUG\n3'-GUU...UGCCG________A__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________212_________________155\n	71 -- 77	156 -- 162	-16.6504 kcal/mol	2.4241 kcal/mol	0.944687 kcal/mol	32 78@LB@ \| \|@LB@5'-AAU...UAAAG GGGAA...UUC-3'@LB@ UAAUGGGG GGAUGAAAAU@LB@ :\|\|\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ GUUACUCU CUUACUUUUG@LB@3'-GUU...UGCCG A UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -20.91 kcal/mol@LB@Hybridization Energy -16.6504 kcal/mol@LB@Unfolding Energy - mRNA 2.4241 kcal/mol@LB@Unfolding Energy - sRNA 0.944687 kcal/mol@LB@@LB@Position - mRNA 33 -- 77@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 156 -- 162@LB@
189	0.05497	0.7607	lmo1156	N/A	-15.46	0.080118	37 -- 70	155 -- 186	diol dehydratase-reactivating factor large subunit	_____________36________________71\n_____________\|_________________\|\n5'-UAU...AAAUG______A__________UAUAU...CUA-3'\n______________CGGUGA_AUGAAUGAAG\n______________\|::\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________GUUACU_UACUUACUUU\n3'-GUU...UGCCG______C__________UGUUU...GGA-5'\n_____________\|_________________\|\n_____________187_______________154\n	200 -- 206	158 -- 164	-15.35 kcal/mol	3.5534 kcal/mol	0.871719 kcal/mol	36 71@LB@ \| \|@LB@5'-UAU...AAAUG A UAUAU...CUA-3'@LB@ CGGUGA AUGAAUGAAG@LB@ \|::\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ GUUACU UACUUACUUU@LB@3'-GUU...UGCCG C UGUUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -15.35 kcal/mol@LB@Unfolding Energy - mRNA 3.5534 kcal/mol@LB@Unfolding Energy - sRNA 0.871719 kcal/mol@LB@@LB@Position - mRNA 37 -- 70@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
102	0.02619	0.6733	lmo1799	N/A	-17.02	0.040600	38 -- 69	171 -- 207	peptidoglycan binding protein	_____________37______________70\n_____________\|_______________\|\n5'-CUA...AAAAC__G____________UUGGC...UGG-3'\n______________GA_GGGA_GGGGCAU\n______________:\|_\|\|\|\|_\|:\|\|\|\|\|\n______________UU_CCCU_CUCCGUA\n3'-GUU...ACGUA__G____A_______UCUGU...GGA-5'\n_____________\|_______________\|\n_____________208_____________170\n	45 -- 51	193 -- 199	-19.1902 kcal/mol	1.80232 kcal/mol	8.95053 kcal/mol	37 70@LB@ \| \|@LB@5'-CUA...AAAAC G UUGGC...UGG-3'@LB@ GA GGGA GGGGCAU@LB@ :\| \|\|\|\| \|:\|\|\|\|\|@LB@ UU CCCU CUCCGUA@LB@3'-GUU...ACGUA G A UCUGU...GGA-5'@LB@ \| \|@LB@ 208 170@LB@@LB@@LB@Energy -17.02 kcal/mol@LB@Hybridization Energy -19.1902 kcal/mol@LB@Unfolding Energy - mRNA 1.80232 kcal/mol@LB@Unfolding Energy - sRNA 8.95053 kcal/mol@LB@@LB@Position - mRNA 38 -- 69@LB@Position - sRNA 171 -- 207@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 193 -- 199@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@
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@
65	0.01641	0.6733	lmo0040	N/A	-17.01	0.040772	52 -- 100	171 -- 220	agmatine deiminase	_____________51______________101\n_____________\|_______________\|\n5'-GUC...AAUAG____A__________GGGAC...CUG-3'\n______________GAGG_GAAUGAGGAU\n______________\|\|\|:_\|\|\|\|\|\|::\|:\n______________CUCU_CUUACUUUUG\n3'-GUU...GGUUA____A__________UUUAU...GGA-5'\n_____________\|_______________\|\n_____________221_____________170\n	196 -- 202	156 -- 162	-15.5399 kcal/mol	0.994344 kcal/mol	0.916023 kcal/mol	51 101@LB@ \| \|@LB@5'-GUC...AAUAG A GGGAC...CUG-3'@LB@ GAGG GAAUGAGGAU@LB@ \|\|\|: \|\|\|\|\|\|::\|:@LB@ CUCU CUUACUUUUG@LB@3'-GUU...GGUUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 221 170@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -15.5399 kcal/mol@LB@Unfolding Energy - mRNA 0.994344 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 52 -- 100@LB@Position - sRNA 171 -- 220@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 156 -- 162@LB@
178	0.05066	0.7607	lmo0216	N/A	-18.27	0.022949	55 -- 114	166 -- 213		_____________54__________________________________________________________________________________115\n_____________\|___________________________________________________________________________________\|\n5'-GCG...UCCAA__AAU______A______A__A___G__________UUUCCUUGUUUUU___CUA______A______U___U____A_____UUUGU...CGG-3'\n______________GC_____UGUU___GUGC_CU_GUG_GUGGCGGGAU_____________GCA___AGAUAU_AAUUAC_CGG_CCAA__AGAU\n______________\|\|_____\|\|\|\|___\|:\|\|_\|\|_:\|\|_:\|::\|\|\|\|\|\|_____________\|\|\|___\|\|\|:\|\|_\|\|:\|\|\|_\|\|\|_\|\|\|\|__\|\|\|\|\n______________CG_____ACAA___CGCG_GA_UAC_UAUUGCCCUA_____________CGU___UCUGUA_UUGAUG_GCC_GGUU__UCUA\n3'-GUU...CGCAA__GUAGU____GCC___________G__________CUC_____________A________C______U________AC____CUUAC...GGA-5'\n_____________\|___________________________________________________________________________________\|\n_____________214_________________________________________________________________________________165\n	62 -- 68	200 -- 206	-50.1796 kcal/mol	16.7648 kcal/mol	22.1647 kcal/mol	54 115@LB@ \| \|@LB@5'-GCG...UCCAA AAU A A A G UUUCCUUGUUUUU CUA A U U A UUUGU...CGG-3'@LB@ GC UGUU GUGC CU GUG GUGGCGGGAU GCA AGAUAU AAUUAC CGG CCAA AGAU@LB@ \|\| \|\|\|\| \|:\|\| \|\| :\|\| :\|::\|\|\|\|\|\| \|\|\| \|\|\|:\|\| \|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|@LB@ CG ACAA CGCG GA UAC UAUUGCCCUA CGU UCUGUA UUGAUG GCC GGUU UCUA@LB@3'-GUU...CGCAA GUAGU GCC G CUC A C U AC CUUAC...GGA-5'@LB@ \| \|@LB@ 214 165@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -50.1796 kcal/mol@LB@Unfolding Energy - mRNA 16.7648 kcal/mol@LB@Unfolding Energy - sRNA 22.1647 kcal/mol@LB@@LB@Position - mRNA 55 -- 114@LB@Position - sRNA 166 -- 213@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 200 -- 206@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@
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@

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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