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
153	0.04013	0.7027	lmo0979	N/A	-16.44	0.052648	251 -- 296	172 -- 207	daunorubicin resistance ATP-binding protein	_____________250_____________________________297\n_____________\|_______________________________\|\n5'-AAU...UUGAA__________UU____G_AAA_______G__AUUU-3'\n______________GGGUGUAGAU__UGAA_U___ACAUGGC_AA\n______________:\|\|::\|\|\|\|:__\|\|\|\|_\|___\|\|\|:\|\|\|_\|\|\n______________UCCGUAUCUG__ACUU_A___UGUGCCG_UU\n3'-GUU...CCUAC__________U_____G___________G__ACUCU...GGA-5'\n_____________\|_______________________________\|\n_____________208_____________________________171\n	287 -- 293	175 -- 181	-27.1075 kcal/mol	4.53663 kcal/mol	13.3233 kcal/mol	250 297@LB@ \| \|@LB@5'-AAU...UUGAA UU G AAA G AUUU-3'@LB@ GGGUGUAGAU UGAA U ACAUGGC AA@LB@ :\|\|::\|\|\|\|: \|\|\|\| \| \|\|\|:\|\|\| \|\|@LB@ UCCGUAUCUG ACUU A UGUGCCG UU@LB@3'-GUU...CCUAC U G G ACUCU...GGA-5'@LB@ \| \|@LB@ 208 171@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -27.1075 kcal/mol@LB@Unfolding Energy - mRNA 4.53663 kcal/mol@LB@Unfolding Energy - sRNA 13.3233 kcal/mol@LB@@LB@Position - mRNA 251 -- 296@LB@Position - sRNA 172 -- 207@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 175 -- 181@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@
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@
165	0.04532	0.7392	lmo2091	argH	-16.36	0.054421	189 -- 262	141 -- 199	argininosuccinate lyase	_____________188_________________263\n_____________\|___________________\|\n5'-UCA...GGUCA_______G__GAG______AAAUC...AAG-3'\n______________UGCCAUU_UA___GGAAGA\n______________\|\|\|\|\|\|\|_\|\|___\|\|\|\|\|\|\n______________ACGGUAA_AU___CCUUCU\n3'-GUU...GAUCA_______G__AA_______ACCUA...GGA-5'\n_____________\|___________________\|\n_____________200_________________140\n	20 -- 26	110 -- 116	-20.7676 kcal/mol	3.64063 kcal/mol	5.20705 kcal/mol	188 263@LB@ \| \|@LB@5'-UCA...GGUCA G GAG AAAUC...AAG-3'@LB@ UGCCAUU UA GGAAGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ ACGGUAA AU CCUUCU@LB@3'-GUU...GAUCA G AA ACCUA...GGA-5'@LB@ \| \|@LB@ 200 140@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -20.7676 kcal/mol@LB@Unfolding Energy - mRNA 3.64063 kcal/mol@LB@Unfolding Energy - sRNA 5.20705 kcal/mol@LB@@LB@Position - mRNA 189 -- 262@LB@Position - sRNA 141 -- 199@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 110 -- 116@LB@
104	0.02699	0.6733	lmo1327	rbfA	-16.36	0.054483	188 -- 240	157 -- 199	ribosome-binding factor A	_____________187________________241\n_____________\|__________________\|\n5'-ACA...CGUGU_______CA_________AAGAA...CUG-3'\n______________CAGUGAG___AAUGAAAA\n______________\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\n______________GUUACUC___UUACUUUU\n3'-GUU...UGCCG_______UAC________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________200________________156\n	234 -- 240	157 -- 163	-12.7883 kcal/mol	2.00785 kcal/mol	0.933292 kcal/mol	187 241@LB@ \| \|@LB@5'-ACA...CGUGU CA AAGAA...CUG-3'@LB@ CAGUGAG AAUGAAAA@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUACUC UUACUUUU@LB@3'-GUU...UGCCG UAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -12.7883 kcal/mol@LB@Unfolding Energy - mRNA 2.00785 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 157 -- 163@LB@
166	0.04633	0.7403	lmo1152	N/A	-16.33	0.055198	97 -- 188	95 -- 169	PduB protein	_____________96_______________189\n_____________\|________________\|\n5'-GGC...AAGUC________________AAUAA...AAG-3'\n______________AGAUGAGUGA__GCAA\n______________\|\|\|\|\|\|:\|\|\|__:\|\|\|\n______________UCUACUUACU__UGUU\n3'-GUU...GUUAC__________UU____UAUUA...GGA-5'\n_____________\|________________\|\n_____________170______________94\n	100 -- 106	160 -- 166	-13.7881 kcal/mol	2.27776 kcal/mol	0.924402 kcal/mol	96 189@LB@ \| \|@LB@5'-GGC...AAGUC AAUAA...AAG-3'@LB@ AGAUGAGUGA GCAA@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\|@LB@ UCUACUUACU UGUU@LB@3'-GUU...GUUAC UU UAUUA...GGA-5'@LB@ \| \|@LB@ 170 94@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -13.7881 kcal/mol@LB@Unfolding Energy - mRNA 2.27776 kcal/mol@LB@Unfolding Energy - sRNA 0.924402 kcal/mol@LB@@LB@Position - mRNA 97 -- 188@LB@Position - sRNA 95 -- 169@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 160 -- 166@LB@
70	0.01838	0.6733	lmo0265	N/A	-16.33	0.055331	156 -- 199	158 -- 207	succinyl-diaminopimelate desuccinylase	_____________155_____200\n_____________\|_______\|\n5'-UUU...UAGAG_______AAACA...UGU-3'\n______________AACGGGA\n______________\|\|\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________208_____157\n	156 -- 162	201 -- 207	-11.1784 kcal/mol	0.573427 kcal/mol	0.326294 kcal/mol	155 200@LB@ \| \|@LB@5'-UUU...UAGAG AAACA...UGU-3'@LB@ AACGGGA@LB@ \|\|\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 208 157@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -11.1784 kcal/mol@LB@Unfolding Energy - mRNA 0.573427 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 156 -- 199@LB@Position - sRNA 158 -- 207@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 201 -- 207@LB@
175	0.04975	0.7607	lmo0194	N/A	-16.29	0.056201	181 -- 242	155 -- 212	ABC transporter ATP-binding protein	_____________180________________________243\n_____________\|__________________________\|\n_______5'-AAGA________AAACGAAAAA________AAUUU...AGC-3'\n______________CAAUGGGA__________AGUGAAGA\n______________\|\|\|\|\|:\|\|__________\|:\|\|\|\|:\|\n______________GUUACUCU__________UUACUUUU\n3'-GUU...UGCCG________AC________________GUUUA...GGA-5'\n_____________\|__________________________\|\n_____________213________________________154\n	24 -- 30	157 -- 163	-10.5893 kcal/mol	0.67181 kcal/mol	0.933292 kcal/mol	180 243@LB@ \| \|@LB@ 5'-AAGA AAACGAAAAA AAUUU...AGC-3'@LB@ CAAUGGGA AGUGAAGA@LB@ \|\|\|\|\|:\|\| \|:\|\|\|\|:\|@LB@ GUUACUCU UUACUUUU@LB@3'-GUU...UGCCG AC GUUUA...GGA-5'@LB@ \| \|@LB@ 213 154@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -10.5893 kcal/mol@LB@Unfolding Energy - mRNA 0.67181 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 181 -- 242@LB@Position - sRNA 155 -- 212@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 157 -- 163@LB@
159	0.04218	0.7139	lmo1454	rpoD	-16.27	0.056776	172 -- 217	153 -- 211	RNA polymerase sigma factor RpoD	_____________171_______________218\n_____________\|_________________\|\n5'-AGA...GUUAA___G________U____UAAUA...UAA-3'\n______________ACA_CGGCCAAU_GGAU\n______________\|\|\|_\|\|\|\|\|\|\|\|_:\|\|\|\n______________UGU_GCCGGUUA_UCUA\n3'-GUU...CUUGA____________C____CUUAC...GGA-5'\n_____________\|_________________\|\n_____________212_______________152\n	92 -- 98	171 -- 177	-19.258 kcal/mol	2.66151 kcal/mol	6.2749 kcal/mol	171 218@LB@ \| \|@LB@5'-AGA...GUUAA G U UAAUA...UAA-3'@LB@ ACA CGGCCAAU GGAU@LB@ \|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGU GCCGGUUA UCUA@LB@3'-GUU...CUUGA C CUUAC...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -16.27 kcal/mol@LB@Hybridization Energy -19.258 kcal/mol@LB@Unfolding Energy - mRNA 2.66151 kcal/mol@LB@Unfolding Energy - sRNA 6.2749 kcal/mol@LB@@LB@Position - mRNA 172 -- 217@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 171 -- 177@LB@
131	0.03528	0.6968	lmo0788	N/A	-16.25	0.057193	177 -- 197	197 -- 213	lmo0788	_____________176______198\n_____________\|________\|\n5'-AAA...CGAAA________AAAAU...AUU-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________214______196\n	191 -- 197	197 -- 203	-13.9782 kcal/mol	1.18818 kcal/mol	0.386531 kcal/mol	176 198@LB@ \| \|@LB@5'-AAA...CGAAA AAAAU...AUU-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 214 196@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -13.9782 kcal/mol@LB@Unfolding Energy - mRNA 1.18818 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 197 -- 213@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 197 -- 203@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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