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
60	0.01449	0.6412	lmo0835	N/A	-17.67	0.030280	187 -- 229	146 -- 187	peptidoglycan binding protein	_____________186______________________________________________230\n_____________\|________________________________________________\|\n5'-UUU...UAUGA_____UUGGAGGA____________UAAA____U____A_________UAACU...CAG-3'\n______________GAACU________AUGGUCAGUGAG____AAUG_AAAA_AAAUAGUGA\n______________\|\|\|\|\|________\|:\|\|:\|\|:\|\|\|\|____\|\|\|\|_\|\|\|\|_\|\|\|\|\|:\|\|\|\n______________CUUGA________UGCCGGUUACUC____UUAC_UUUU_UUUAUUACU\n3'-GUU...CUGUA_____UG__________________UAC__________G_________AAAAC...GGA-5'\n_____________\|________________________________________________\|\n_____________188______________________________________________145\n	199 -- 205	168 -- 174	-31.6389 kcal/mol	7.07372 kcal/mol	14.4129 kcal/mol	186 230@LB@ \| \|@LB@5'-UUU...UAUGA UUGGAGGA UAAA U A UAACU...CAG-3'@LB@ GAACU AUGGUCAGUGAG AAUG AAAA AAAUAGUGA@LB@ \|\|\|\|\| \|:\|\|:\|\|:\|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CUUGA UGCCGGUUACUC UUAC UUUU UUUAUUACU@LB@3'-GUU...CUGUA UG UAC G AAAAC...GGA-5'@LB@ \| \|@LB@ 188 145@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -31.6389 kcal/mol@LB@Unfolding Energy - mRNA 7.07372 kcal/mol@LB@Unfolding Energy - sRNA 14.4129 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 146 -- 187@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 168 -- 174@LB@
4	0.0009641	0.4469	lmo0851	N/A	-23.35	0.001728	188 -- 220	172 -- 201	lmo0851	_____________187_______________________________221\n_____________\|_________________________________\|\n5'-GGU...AUAGA__________U_______AAAAGAA________CCAAC...UAA-3'\n______________GUGAGGCAUA_ACAUGAA_______GCGGUUAA\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|_______:\|\|\|::\|\|\n______________UACUCCGUAU_UGUACUU_______UGCCGGUU\n3'-GUU...UGCCC__________C_______GAUG___________ACUCU...GGA-5'\n_____________\|_________________________________\|\n_____________202_______________________________171\n	214 -- 220	172 -- 178	-33.261 kcal/mol	3.18896 kcal/mol	13.3764 kcal/mol	187 221@LB@ \| \|@LB@5'-GGU...AUAGA U AAAAGAA CCAAC...UAA-3'@LB@ GUGAGGCAUA ACAUGAA GCGGUUAA@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| :\|\|\|::\|\|@LB@ UACUCCGUAU UGUACUU UGCCGGUU@LB@3'-GUU...UGCCC C GAUG ACUCU...GGA-5'@LB@ \| \|@LB@ 202 171@LB@@LB@@LB@Energy -23.35 kcal/mol@LB@Hybridization Energy -33.261 kcal/mol@LB@Unfolding Energy - mRNA 3.18896 kcal/mol@LB@Unfolding Energy - sRNA 13.3764 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 172 -- 201@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 172 -- 178@LB@
6	0.001395	0.4469	lmo2078	N/A	-19.77	0.011149	188 -- 240	154 -- 207		_____________187___________________________________________________________________241\n_____________\|_____________________________________________________________________\|\n5'-GAU...UUUAU_____C______U__________U____UA____________AAUG____A_G________________UUCGA...AGG-3'\n______________UUUGG_GCGUCU_UGU_____GG_AUGA__UGUAGA___GAA____AUGG_C_GGUGAGGU_AAUGGAA\n______________\|\|:\|\|_\|\|\|:\|\|_\|\|:_____\|\|_\|\|\|\|__::\|\|\|\|___\|\|\|____\|:\|\|_\|_::\|\|\|\|:\|_\|\|\|\|:\|\|\n______________AAGCC_CGCGGA_ACG_____CC_UACU__GUAUCU___CUU____UGCC_G_UUACUCUA_UUACUUU\n3'-GUU...AGUAC____________U___UAUUG__C____CC______GUA___GAUG______G________C_______UGUUU...GGA-5'\n_____________\|_____________________________________________________________________\|\n_____________208___________________________________________________________________153\n	200 -- 206	158 -- 164	-46.039 kcal/mol	12.924 kcal/mol	22.2029 kcal/mol	187 241@LB@ \| \|@LB@5'-GAU...UUUAU C U U UA AAUG A G UUCGA...AGG-3'@LB@ UUUGG GCGUCU UGU GG AUGA UGUAGA GAA AUGG C GGUGAGGU AAUGGAA@LB@ \|\|:\|\| \|\|\|:\|\| \|\|: \|\| \|\|\|\| ::\|\|\|\| \|\|\| \|:\|\| \| ::\|\|\|\|:\| \|\|\|\|:\|\|@LB@ AAGCC CGCGGA ACG CC UACU GUAUCU CUU UGCC G UUACUCUA UUACUUU@LB@3'-GUU...AGUAC U UAUUG C CC GUA GAUG G C UGUUU...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -19.77 kcal/mol@LB@Hybridization Energy -46.039 kcal/mol@LB@Unfolding Energy - mRNA 12.924 kcal/mol@LB@Unfolding Energy - sRNA 22.2029 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
87	0.02294	0.6733	lmo2765	N/A	-17.07	0.039744	188 -- 213	176 -- 199	PTS cellbiose transporter subunit IIA	_____________187_________________214\n_____________\|___________________\|\n5'-UUA...UAGAC________A__________GUUAU...AUU-3'\n______________AUGA_AUG_AAUGGAAACA\n______________\|\|\|\|_\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________UACU_UAC_UUACUUUUGU\n3'-GUU...CCGGU____C______________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________200_________________175\n	212 -- 218	155 -- 161	-13.3886 kcal/mol	2.47541 kcal/mol	0.935542 kcal/mol	187 214@LB@ \| \|@LB@5'-UUA...UAGAC A GUUAU...AUU-3'@LB@ AUGA AUG AAUGGAAACA@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UACU UAC UUACUUUUGU@LB@3'-GUU...CCGGU C UUAUU...GGA-5'@LB@ \| \|@LB@ 200 175@LB@@LB@@LB@Energy -17.07 kcal/mol@LB@Hybridization Energy -13.3886 kcal/mol@LB@Unfolding Energy - mRNA 2.47541 kcal/mol@LB@Unfolding Energy - sRNA 0.935542 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 176 -- 199@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@LB@
94	0.02439	0.6733	lmo0952	N/A	-17.21	0.037353	188 -- 223	166 -- 199	lmo0952	_____________187__________________________________224\n_____________\|____________________________________\|\n5'-AAC...AAACG________UU__GAU_____A___AA__________AGUAC...UAA-3'\n______________GAGGCAUA__CA___GAUUA_ACG__CUGGUGAGAU\n______________\|\|\|\|\|\|\|\|__\|\|___:\|:\|\|_\|\|\|__\|:::\|\|\|\|\|\|\n______________CUCCGUAU__GU___UUGAU_UGC__GGUUACUCUA\n3'-GUU...CCCUA________CU__AC______G___C___________CUUAC...GGA-5'\n_____________\|____________________________________\|\n_____________200__________________________________165\n	217 -- 223	166 -- 172	-30.0979 kcal/mol	6.14462 kcal/mol	13.4403 kcal/mol	187 224@LB@ \| \|@LB@5'-AAC...AAACG UU GAU A AA AGUAC...UAA-3'@LB@ GAGGCAUA CA GAUUA ACG CUGGUGAGAU@LB@ \|\|\|\|\|\|\|\| \|\| :\|:\|\| \|\|\| \|:::\|\|\|\|\|\|@LB@ CUCCGUAU GU UUGAU UGC GGUUACUCUA@LB@3'-GUU...CCCUA CU AC G C CUUAC...GGA-5'@LB@ \| \|@LB@ 200 165@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -30.0979 kcal/mol@LB@Unfolding Energy - mRNA 6.14462 kcal/mol@LB@Unfolding Energy - sRNA 13.4403 kcal/mol@LB@@LB@Position - mRNA 188 -- 223@LB@Position - sRNA 166 -- 199@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 166 -- 172@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@
149	0.0387	0.6968	lmo1809	plsX	-16.53	0.050633	188 -- 233	156 -- 203	glycerol-3-phosphate acyltransferase PlsX	_____________187________________234\n_____________\|__________________\|\n5'-ACA...CUGUA____C_____________CACGC...UUC-3'\n______________GAUG_GAUGGGUGGAGAU\n______________:\|\|\|_\|\|\|\|::\|\|:\|:\|:\n______________UUAC_CUACUUACUUUUG\n3'-GUU...GCCGG____U_____________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________204________________155\n	227 -- 233	156 -- 162	-17.4325 kcal/mol	7.3364 kcal/mol	0.941471 kcal/mol	187 234@LB@ \| \|@LB@5'-ACA...CUGUA C CACGC...UUC-3'@LB@ GAUG GAUGGGUGGAGAU@LB@ :\|\|\| \|\|\|\|::\|\|:\|:\|:@LB@ UUAC CUACUUACUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 204 155@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -17.4325 kcal/mol@LB@Unfolding Energy - mRNA 7.3364 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 188 -- 233@LB@Position - sRNA 156 -- 203@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 156 -- 162@LB@
157	0.0414	0.7058	lmo0010	N/A	-15.41	0.081879	188 -- 219	167 -- 203	mevalonate kinase	_____________187_____220\n_____________\|_______\|\n5'-AUC...AUGCG_______UGCAG...UAG-3'\n______________GAGAACA\n______________\|\|:\|\|\|\|\n______________CUUUUGU\n3'-GUU...ACUUA_______UUAUU...GGA-5'\n_____________\|_______\|\n_____________204_____166\n	241 -- 247	155 -- 161	-5.76961 kcal/mol	0.621388 kcal/mol	0.528569 kcal/mol	187 220@LB@ \| \|@LB@5'-AUC...AUGCG UGCAG...UAG-3'@LB@ GAGAACA@LB@ \|\|:\|\|\|\|@LB@ CUUUUGU@LB@3'-GUU...ACUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 204 166@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -5.76961 kcal/mol@LB@Unfolding Energy - mRNA 0.621388 kcal/mol@LB@Unfolding Energy - sRNA 0.528569 kcal/mol@LB@@LB@Position - mRNA 188 -- 219@LB@Position - sRNA 167 -- 203@LB@Position Seed - mRNA 241 -- 247@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@
89	0.02343	0.6733	lmo1651	N/A	-15.38	0.082912	189 -- 217	147 -- 170	ABC transporter ATP-binding protein	_____________188___________________________218\n_____________\|_____________________________\|\n5'-GAA...AGAAG______UAGCA___________UG_____ACAAG...UUC-3'\n______________GGGGUG_____GAUGGAAGCGA__AAUGA\n______________\|:\|:\|\|_____:\|\|\|:\|\|:\|:\|__\|\|\|\|\|\n______________CUCUAC_____UUACUUUUGUU__UUACU\n3'-GUU...GGUUA______________________UA_____AAAAC...GGA-5'\n_____________\|_____________________________\|\n_____________171___________________________146\n	204 -- 210	154 -- 160	-21.1438 kcal/mol	4.28476 kcal/mol	5.93585 kcal/mol	188 218@LB@ \| \|@LB@5'-GAA...AGAAG UAGCA UG ACAAG...UUC-3'@LB@ GGGGUG GAUGGAAGCGA AAUGA@LB@ \|:\|:\|\| :\|\|\|:\|\|:\|:\| \|\|\|\|\|@LB@ CUCUAC UUACUUUUGUU UUACU@LB@3'-GUU...GGUUA UA AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -21.1438 kcal/mol@LB@Unfolding Energy - mRNA 4.28476 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 189 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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