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
99	0.02562	0.6733	lmo2201	N/A	-18.35	0.022079	190 -- 255	101 -- 170	3-oxoacyl-ACP synthase	_____________189_____________________________________________________________________256\n_____________\|_______________________________________________________________________\|\n5'-AAC...AUAAG________________________GAAGA__A___GUU__U______G__GCU___A___C__________ACGAU...AUG-3'\n______________GAGAUGAGU__AAAUGGAUAA_GA_____GU_GUU___AC_GGUGUU_GA___GUU__CA__CUAUUGGAA\n______________\|\|\|\|\|\|\|:\|__\|\|\|:::\|\|\|\|_\|\|_____\|\|_\|\|:___\|\|_\|:\|\|\|:_\|\|___\|\|\|__\|\|__\|\|\|\|\|\|\|\|\|\n______________CUCUACUUA__UUUGUUUAUU_CU_____CA_CAG___UG_CUACAG_CU___CAA__GU__GAUAACCUU\n3'-GUU...GGUUA_________CU__________A__AAAAC______AUU__U______A__GAU___CG__AA_________CUACC...GGA-5'\n_____________\|_______________________________________________________________________\|\n_____________171_____________________________________________________________________100\n	249 -- 255	101 -- 107	-41.8612 kcal/mol	11.5076 kcal/mol	19.339 kcal/mol	189 256@LB@ \| \|@LB@5'-AAC...AUAAG GAAGA A GUU U G GCU A C ACGAU...AUG-3'@LB@ GAGAUGAGU AAAUGGAUAA GA GU GUU AC GGUGUU GA GUU CA CUAUUGGAA@LB@ \|\|\|\|\|\|\|:\| \|\|\|:::\|\|\|\| \|\| \|\| \|\|: \|\| \|:\|\|\|: \|\| \|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ CUCUACUUA UUUGUUUAUU CU CA CAG UG CUACAG CU CAA GU GAUAACCUU@LB@3'-GUU...GGUUA CU A AAAAC AUU U A GAU CG AA CUACC...GGA-5'@LB@ \| \|@LB@ 171 100@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -41.8612 kcal/mol@LB@Unfolding Energy - mRNA 11.5076 kcal/mol@LB@Unfolding Energy - sRNA 19.339 kcal/mol@LB@@LB@Position - mRNA 190 -- 255@LB@Position - sRNA 101 -- 170@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 101 -- 107@LB@
74	0.01955	0.6733	lmo0190	ipk	-17.49	0.032930	174 -- 210	154 -- 192	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	_____________173_______________________________________211\n_____________\|_________________________________________\|\n5'-AUA...AAAAG____UU_________GA___________AA___________GCAUU...CAA-3'\n______________AGAU__UGAAC_GCG__GGCCA___AGA__AAUGAAAAUAA\n______________\|\|\|:__\|\|\|\|\|_:\|:__\|\|\|\|\|___\|\|\|__\|\|\|\|\|\|\|\|:\|\|\n______________UCUG__ACUUG_UGU__CCGGU___UCU__UUACUUUUGUU\n3'-GUU...CCGUA____U______A___G______UAC___AC___________UAUUA...GGA-5'\n_____________\|_________________________________________\|\n_____________193_______________________________________153\n	204 -- 210	154 -- 160	-28.6344 kcal/mol	5.15958 kcal/mol	12.1365 kcal/mol	173 211@LB@ \| \|@LB@5'-AUA...AAAAG UU GA AA GCAUU...CAA-3'@LB@ AGAU UGAAC GCG GGCCA AGA AAUGAAAAUAA@LB@ \|\|\|: \|\|\|\|\| :\|: \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ UCUG ACUUG UGU CCGGU UCU UUACUUUUGUU@LB@3'-GUU...CCGUA U A G UAC AC UAUUA...GGA-5'@LB@ \| \|@LB@ 193 153@LB@@LB@@LB@Energy -17.49 kcal/mol@LB@Hybridization Energy -28.6344 kcal/mol@LB@Unfolding Energy - mRNA 5.15958 kcal/mol@LB@Unfolding Energy - sRNA 12.1365 kcal/mol@LB@@LB@Position - mRNA 174 -- 210@LB@Position - sRNA 154 -- 192@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
171	0.04778	0.7516	lmo0498	N/A	-14.78	0.106331	152 -- 199	154 -- 211	5-phosphate isomerase	_____________151__________________200\n_____________\|____________________\|\n5'-AUC...AUCAA_______AA___________ACAUG...GUU-3'\n______________GGUGAGA__GGA_GAGGAUA\n______________::\|\|\|\|\|__\|:\|_\|\|::\|:\|\n______________UUACUCU__CUU_CUUUUGU\n3'-GUU...GCCGG_______A____A_______UUAUU...GGA-5'\n_____________\|____________________\|\n_____________212__________________153\n	192 -- 198	155 -- 161	-12.5427 kcal/mol	2.39386 kcal/mol	0.954976 kcal/mol	151 200@LB@ \| \|@LB@5'-AUC...AUCAA AA ACAUG...GUU-3'@LB@ GGUGAGA GGA GAGGAUA@LB@ ::\|\|\|\|\| \|:\| \|\|::\|:\|@LB@ UUACUCU CUU CUUUUGU@LB@3'-GUU...GCCGG A A UUAUU...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -12.5427 kcal/mol@LB@Unfolding Energy - mRNA 2.39386 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 152 -- 199@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 155 -- 161@LB@
63	0.01551	0.6624	lmo2613	rplO	-17.63	0.030853	185 -- 213	177 -- 203	50S ribosomal protein L15	_____________184______214\n_____________\|________\|\n5'-AAU...AUUCG________UCACU...GCG-3'\n______________UGGGAUGA\n______________:\|\|\|\|\|\|\|\n______________GCCCUACU\n3'-GUU...GUAUU________CCGUA...GGA-5'\n_____________\|________\|\n_____________204______176\n	98 -- 104	198 -- 204	-11.9514 kcal/mol	5.35707 kcal/mol	0.374397 kcal/mol	184 214@LB@ \| \|@LB@5'-AAU...AUUCG UCACU...GCG-3'@LB@ UGGGAUGA@LB@ :\|\|\|\|\|\|\|@LB@ GCCCUACU@LB@3'-GUU...GUAUU CCGUA...GGA-5'@LB@ \| \|@LB@ 204 176@LB@@LB@@LB@Energy -17.63 kcal/mol@LB@Hybridization Energy -11.9514 kcal/mol@LB@Unfolding Energy - mRNA 5.35707 kcal/mol@LB@Unfolding Energy - sRNA 0.374397 kcal/mol@LB@@LB@Position - mRNA 185 -- 213@LB@Position - sRNA 177 -- 203@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 198 -- 204@LB@
22	0.003708	0.4469	lmo1689	N/A	-20.94	0.006216	185 -- 218	155 -- 186	A/G-specific adenine glycosylase	_____________184________________________________219\n_____________\|__________________________________\|\n5'-UGA...UAUUA________A__GGAA_______AA________G_CUAAC...CGU-3'\n______________GAAUUACG_GG____AAUGAGA__AAUGAAGA_A\n______________\|\|\|:\|\|\|:_\|\|____\|\|\|\|\|\|\|__\|\|\|\|\|\|:\|_\|\n______________CUUGAUGU_CC____UUACUCU__UUACUUUU_U\n3'-GUU...CUGUA________G__GG_________AC________G_UUAUU...GGA-5'\n_____________\|__________________________________\|\n_____________187________________________________154\n	210 -- 216	157 -- 163	-27.9128 kcal/mol	3.65812 kcal/mol	9.66922 kcal/mol	184 219@LB@ \| \|@LB@5'-UGA...UAUUA A GGAA AA G CUAAC...CGU-3'@LB@ GAAUUACG GG AAUGAGA AAUGAAGA A@LB@ \|\|\|:\|\|\|: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|@LB@ CUUGAUGU CC UUACUCU UUACUUUU U@LB@3'-GUU...CUGUA G GG AC G UUAUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -20.94 kcal/mol@LB@Hybridization Energy -27.9128 kcal/mol@LB@Unfolding Energy - mRNA 3.65812 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 157 -- 163@LB@
29	0.005638	0.5232	lmo0014	qoxB	-19.61	0.012062	164 -- 215	168 -- 211	AA3-600 quinol oxidase subunit I	_____________163____________216\n_____________\|______________\|\n5'-CGG...CGCGA_____A________AAAUG...CUU-3'\n______________AGAUG_AAUGAAGA\n______________\|\|\|\|\|_\|\|\|\|\|\|:\|\n______________UCUAC_UUACUUUU\n3'-GUU...GUUAC______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________212____________167\n	111 -- 117	157 -- 163	-11.9482 kcal/mol	0.56531 kcal/mol	0.884237 kcal/mol	163 216@LB@ \| \|@LB@5'-CGG...CGCGA A AAAUG...CUU-3'@LB@ AGAUG AAUGAAGA@LB@ \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ UCUAC UUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 212 167@LB@@LB@@LB@Energy -19.61 kcal/mol@LB@Hybridization Energy -11.9482 kcal/mol@LB@Unfolding Energy - mRNA 0.56531 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 164 -- 215@LB@Position - sRNA 168 -- 211@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 157 -- 163@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@
58	0.0137	0.6248	lmo1724	N/A	-17.96	0.026530	144 -- 212	156 -- 211	ABC transporter ATP-binding protein	_____________143__________213\n_____________\|____________\|\n5'-UUA...CAACC____________CUGAU...UCA-3'\n______________AUGAAUGAAAAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________212__________155\n	206 -- 212	156 -- 162	-13.4321 kcal/mol	1.37849 kcal/mol	0.849227 kcal/mol	143 213@LB@ \| \|@LB@5'-UUA...CAACC CUGAU...UCA-3'@LB@ AUGAAUGAAAAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -17.96 kcal/mol@LB@Hybridization Energy -13.4321 kcal/mol@LB@Unfolding Energy - mRNA 1.37849 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 144 -- 212@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 156 -- 162@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@
129	0.03464	0.6968	lmo0756	N/A	-20.18	0.009099	160 -- 214	175 -- 223	ABC transporter ATP-binding protein	_____________159__________215\n_____________\|____________\|\n5'-AGU...AUAGA_______G____AGAAG...UUU-3'\n______________GACGGGA_GGGG\n______________:\|\|\|\|\|\|_\|:\|\|\n______________UUGCCCU_CUCC\n3'-GUU...ACGUA_______A____GUAUC...GGA-5'\n_____________\|____________\|\n_____________224__________174\n	181 -- 187	201 -- 207	-16.8336 kcal/mol	1.76926 kcal/mol	3.58567 kcal/mol	159 215@LB@ \| \|@LB@5'-AGU...AUAGA G AGAAG...UUU-3'@LB@ GACGGGA GGGG@LB@ :\|\|\|\|\|\| \|:\|\|@LB@ UUGCCCU CUCC@LB@3'-GUU...ACGUA A GUAUC...GGA-5'@LB@ \| \|@LB@ 224 174@LB@@LB@@LB@Energy -20.18 kcal/mol@LB@Hybridization Energy -16.8336 kcal/mol@LB@Unfolding Energy - mRNA 1.76926 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 160 -- 214@LB@Position - sRNA 175 -- 223@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 201 -- 207@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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