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
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@
3	0.0004111	0.3688	lmo0196	N/A	-23.83	0.001321	198 -- 256	156 -- 209	regulatory protein SpoVG	_____________197________________257\n_____________\|__________________\|\n5'-ACU...AGACA__________________UAUUU...ACA-3'\n______________GAUGGGA_GAAUGAAAGC\n______________:\|\|\|:\|\|_\|\|\|\|\|\|\|\|:\|\n______________UUACUCU_CUUACUUUUG\n3'-GUU...GCCGG_______A__________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________210________________155\n	250 -- 256	156 -- 162	-19.3926 kcal/mol	2.92904 kcal/mol	0.941471 kcal/mol	197 257@LB@ \| \|@LB@5'-ACU...AGACA UAUUU...ACA-3'@LB@ GAUGGGA GAAUGAAAGC@LB@ :\|\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU CUUACUUUUG@LB@3'-GUU...GCCGG A UUUAU...GGA-5'@LB@ \| \|@LB@ 210 155@LB@@LB@@LB@Energy -23.83 kcal/mol@LB@Hybridization Energy -19.3926 kcal/mol@LB@Unfolding Energy - mRNA 2.92904 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 198 -- 256@LB@Position - sRNA 156 -- 209@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 156 -- 162@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@
13	0.002947	0.4469	lmo0233	N/A	-20.88	0.006381	238 -- 276	156 -- 198	DNA repair protein RadA	_____________237_____________________________________________277\n_____________\|_______________________________________________\|\n5'-AAA...GUGUC______GU__________________AA___________________UCCGA...CNN-3'\n______________AGGCAU__GGAUAUGAAU____CGGC__AAUG_GAUGG__GAAAAUG\n______________\|\|\|\|\|\|__:\|\|:\|\|\|\|\|:____\|\|\|\|__\|\|\|\|_\|\|\|\|:__\|\|\|\|\|::\n______________UCCGUA__UCUGUACUUG____GCCG__UUAC_CUACU__CUUUUGU\n3'-GUU...CCUAC__________________AUGU____G_____U_____UA_______UUAUU...GGA-5'\n_____________\|_______________________________________________\|\n_____________199_____________________________________________155\n	271 -- 277	155 -- 161	-35.3246 kcal/mol	8.28493 kcal/mol	13.976 kcal/mol	237 277@LB@ \| \|@LB@5'-AAA...GUGUC GU AA UCCGA...CNN-3'@LB@ AGGCAU GGAUAUGAAU CGGC AAUG GAUGG GAAAAUG@LB@ \|\|\|\|\|\| :\|\|:\|\|\|\|\|: \|\|\|\| \|\|\|\| \|\|\|\|: \|\|\|\|\|::@LB@ UCCGUA UCUGUACUUG GCCG UUAC CUACU CUUUUGU@LB@3'-GUU...CCUAC AUGU G U UA UUAUU...GGA-5'@LB@ \| \|@LB@ 199 155@LB@@LB@@LB@Energy -20.88 kcal/mol@LB@Hybridization Energy -35.3246 kcal/mol@LB@Unfolding Energy - mRNA 8.28493 kcal/mol@LB@Unfolding Energy - sRNA 13.976 kcal/mol@LB@@LB@Position - mRNA 238 -- 276@LB@Position - sRNA 156 -- 198@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 155 -- 161@LB@
20	0.003655	0.4469	lmo1591	argC	-21.66	0.004270	183 -- 240	156 -- 208	N-acetyl-gamma-glutamyl-phosphate reductase	_____________182___________________________________________________________241\n_____________\|_____________________________________________________________\|\n5'-AAA...AUAAU________A________________AGUUUCAAU__U____G___C_______UG______UUGAG...GUU-3'\n______________UAACGGGG_GGGGU_UAGG_AUGAA_________CA_UGGC_CGA_GGGGU_A__GAGGAC\n______________\|\|\|\|\|\|\|:_\|:\|\|:_\|\|\|:_\|\|\|\|\|_________\|\|_:\|\|\|_\|:\|_\|:\|:\|_\|__\|\|::\|\|\n______________AUUGCCCU_CUCCG_AUCU_UACUU_________GU_GCCG_GUU_CUCUA_U__CUUUUG\n3'-GUU...UACGU________A_____U____G_____GAU_________________A_____C_UA______UUUAU...GGA-5'\n_____________\|_____________________________________________________________\|\n_____________209___________________________________________________________155\n	184 -- 190	201 -- 207	-40.8209 kcal/mol	11.7 kcal/mol	18.6528 kcal/mol	182 241@LB@ \| \|@LB@5'-AAA...AUAAU A AGUUUCAAU U G C UG UUGAG...GUU-3'@LB@ UAACGGGG GGGGU UAGG AUGAA CA UGGC CGA GGGGU A GAGGAC@LB@ \|\|\|\|\|\|\|: \|:\|\|: \|\|\|: \|\|\|\|\| \|\| :\|\|\| \|:\| \|:\|:\| \| \|\|::\|\|@LB@ AUUGCCCU CUCCG AUCU UACUU GU GCCG GUU CUCUA U CUUUUG@LB@3'-GUU...UACGU A U G GAU A C UA UUUAU...GGA-5'@LB@ \| \|@LB@ 209 155@LB@@LB@@LB@Energy -21.66 kcal/mol@LB@Hybridization Energy -40.8209 kcal/mol@LB@Unfolding Energy - mRNA 11.7 kcal/mol@LB@Unfolding Energy - sRNA 18.6528 kcal/mol@LB@@LB@Position - mRNA 183 -- 240@LB@Position - sRNA 156 -- 208@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 201 -- 207@LB@
26	0.004866	0.5029	lmo0682	flgG	-18.63	0.019297	177 -- 239	156 -- 207	flagellar basal body rod protein FlgG	_____________176__________________________________________240\n_____________\|____________________________________________\|\n5'-GAA...ACCAA_______GU_______CGGA__G___________AC____A___GGCAG...UCA-3'\n______________AGA_GUC__UGGCUAG____GC_G_UUUGUUGGA__GGAU_GGA\n______________\|\|\|_\|\|\|__\|\|:\|\|\|\|____\|\|_:_\|:\|:\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UCU_CAG__ACUGAUC____CG_U_AGAUAACCU__UCUA_CCU\n3'-GUU...AUUUG___A____________AA____G_A___________________AUGUG...GGA-5'\n_____________\|____________________________________________\|\n_____________208__________________________________________155\n	171 -- 177	102 -- 108	-30.3451 kcal/mol	11.2986 kcal/mol	9.4836 kcal/mol	176 240@LB@ \| \|@LB@5'-GAA...ACCAA GU CGGA G AC A GGCAG...UCA-3'@LB@ AGA GUC UGGCUAG GC G UUUGUUGGA GGAU GGA@LB@ \|\|\| \|\|\| \|\|:\|\|\|\| \|\| : \|:\|:\|\|\|\|\| :\|\|\| \|\|\|@LB@ UCU CAG ACUGAUC CG U AGAUAACCU UCUA CCU@LB@3'-GUU...AUUUG A AA G A AUGUG...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -30.3451 kcal/mol@LB@Unfolding Energy - mRNA 11.2986 kcal/mol@LB@Unfolding Energy - sRNA 9.4836 kcal/mol@LB@@LB@Position - mRNA 177 -- 239@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 102 -- 108@LB@
40	0.00848	0.5705	lmo2399	N/A	-21.52	0.004592	127 -- 195	156 -- 207		_____________126_________________________________________________________________196\n_____________\|___________________________________________________________________\|\n5'-AUU...UCGAC_________GU_______CUUGUGGUUUAAAC____AGA____G__UAGA______A___G______GCUAA...CUG-3'\n______________GGUGAGGCA__GGCG_GA______________GCUA___ACGG_UA____AUGGGG_GAA_GAGGAU\n______________\|:\|\|\|\|\|\|\|__\|:\|:_\|\|______________:\|\|\|___\|\|\|\|_:\|____\|\|\|:\|:_\|\|\|_\|\|::\|:\n______________CUACUCCGU__CUGU_CU______________UGAU___UGCC_GU____UACUCU_CUU_CUUUUG\n3'-GUU...UUGCC_________AU____A____________________G______G____________A___A______UUUAU...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________208_________________________________________________________________155\n	132 -- 138	194 -- 200	-37.8581 kcal/mol	11.6457 kcal/mol	14.014 kcal/mol	126 196@LB@ \| \|@LB@5'-AUU...UCGAC GU CUUGUGGUUUAAAC AGA G UAGA A G GCUAA...CUG-3'@LB@ GGUGAGGCA GGCG GA GCUA ACGG UA AUGGGG GAA GAGGAU@LB@ \|:\|\|\|\|\|\|\| \|:\|: \|\| :\|\|\| \|\|\|\| :\| \|\|\|:\|: \|\|\| \|\|::\|:@LB@ CUACUCCGU CUGU CU UGAU UGCC GU UACUCU CUU CUUUUG@LB@3'-GUU...UUGCC AU A G G A A UUUAU...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -21.52 kcal/mol@LB@Hybridization Energy -37.8581 kcal/mol@LB@Unfolding Energy - mRNA 11.6457 kcal/mol@LB@Unfolding Energy - sRNA 14.014 kcal/mol@LB@@LB@Position - mRNA 127 -- 195@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@LB@
46	0.01036	0.599	lmo2695	N/A	-19.87	0.010617	150 -- 211	156 -- 209	dihydroxyacetone kinase subunit DhaK	_____________149_________________________________________________________________212\n_____________\|___________________________________________________________________\|\n5'-UUA...UUCUA____A____AAU_____________________UAUAAAGGA____UUU__UC______________UCUUA...CUC-3'\n______________GUAA_GGGA___UGAGGUA_AGA___GGACUAU_________GGUU___UG__AGAUGAA_GAAGAU\n______________:\|\|\|_\|\|\|\|___\|\|\|\|\|:\|_\|\|\|___\|:\|\|\|\|:_________\|\|::___\|\|__\|\|\|\|\|\|\|_\|\|\|:\|:\n______________UAUU_CCCU___ACUCCGU_UCU___CUUGAUG_________CCGG___AC__UCUACUU_CUUUUG\n3'-GUU...AUACG____G______________A___GUA_______UG___________UU____________A______UUUAU...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________210_________________________________________________________________155\n	199 -- 205	163 -- 169	-36.4151 kcal/mol	9.16424 kcal/mol	18.7057 kcal/mol	149 212@LB@ \| \|@LB@5'-UUA...UUCUA A AAU UAUAAAGGA UUU UC UCUUA...CUC-3'@LB@ GUAA GGGA UGAGGUA AGA GGACUAU GGUU UG AGAUGAA GAAGAU@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|\| \|:\|\|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|:\|:@LB@ UAUU CCCU ACUCCGU UCU CUUGAUG CCGG AC UCUACUU CUUUUG@LB@3'-GUU...AUACG G A GUA UG UU A UUUAU...GGA-5'@LB@ \| \|@LB@ 210 155@LB@@LB@@LB@Energy -19.87 kcal/mol@LB@Hybridization Energy -36.4151 kcal/mol@LB@Unfolding Energy - mRNA 9.16424 kcal/mol@LB@Unfolding Energy - sRNA 18.7057 kcal/mol@LB@@LB@Position - mRNA 150 -- 211@LB@Position - sRNA 156 -- 209@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@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@
88	0.02298	0.6733	lmo0666	N/A	-13.39	0.184164	127 -- 173	156 -- 211		_____________126__________________________________________________________________________________174\n_____________\|____________________________________________________________________________________\|\n5'-AAG...AUUCA____A__GAACC______AA__C___AGU____AC___A__AAA_____GUUA______G_____GC_________________UCGUU...AUG-3'\n______________GCCA_CA______GGCGC__AU_GCA___AUGG__GGU_AG___AUAGA____GA___A_ACGGC_________GAAUGGAGAC\n______________\|\|\|\|_\|\|______\|\|\|\|\|__\|\|_\|\|\|___\|:\|\|__\|:\|_\|\|___\|\|\|\|\|____\|\|___\|_\|\|\|\|\|_________\|\|\|\|\|:\|:\|\|\n______________CGGU_GU______CCGCG__UA_CGU___UGCC__CUA_UC___UAUCU____CU___U_UGCCG_________CUUACUUUUG\n3'-GUU...CGCAA____A__ACAAGC_____GA______AU__________C__CG______GUA___UGA_G_____GUUACUCUA__________UUUAU...GGA-5'\n_____________\|____________________________________________________________________________________\|\n_____________212__________________________________________________________________________________155\n	167 -- 173	156 -- 162	-45.3275 kcal/mol	14.8697 kcal/mol	22.6898 kcal/mol	126 174@LB@ \| \|@LB@5'-AAG...AUUCA A GAACC AA C AGU AC A AAA GUUA G GC UCGUU...AUG-3'@LB@ GCCA CA GGCGC AU GCA AUGG GGU AG AUAGA GA A ACGGC GAAUGGAGAC@LB@ \|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\| \|:\|\| \|:\| \|\| \|\|\|\|\| \|\| \| \|\|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CGGU GU CCGCG UA CGU UGCC CUA UC UAUCU CU U UGCCG CUUACUUUUG@LB@3'-GUU...CGCAA A ACAAGC GA AU C CG GUA UGA G GUUACUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -13.39 kcal/mol@LB@Hybridization Energy -45.3275 kcal/mol@LB@Unfolding Energy - mRNA 14.8697 kcal/mol@LB@Unfolding Energy - sRNA 22.6898 kcal/mol@LB@@LB@Position - mRNA 127 -- 173@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 156 -- 162@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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