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
44	0.01013	0.599	lmo0022	N/A	-16.20	0.058356	176 -- 261	150 -- 213	PTS fructose transporter subunit IIB	_____________175________________262\n_____________\|__________________\|\n5'-CCG...GUGAU_______A___A______UGAUG...UCA-3'\n______________GAUGGGG_GGA_GAGGAC\n______________:\|\|\|:\|:_\|:\|_\|\|::\|\|\n______________UUACUCU_CUU_CUUUUG\n3'-GUU...GCCGG_______A___A______UUUAU...GGA-5'\n_____________\|__________________\|\n_____________214________________149\n	181 -- 187	167 -- 173	-14.383 kcal/mol	2.57794 kcal/mol	0.941471 kcal/mol	175 262@LB@ \| \|@LB@5'-CCG...GUGAU A A UGAUG...UCA-3'@LB@ GAUGGGG GGA GAGGAC@LB@ :\|\|\|:\|: \|:\| \|\|::\|\|@LB@ UUACUCU CUU CUUUUG@LB@3'-GUU...GCCGG A A UUUAU...GGA-5'@LB@ \| \|@LB@ 214 149@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -14.383 kcal/mol@LB@Unfolding Energy - mRNA 2.57794 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 176 -- 261@LB@Position - sRNA 150 -- 213@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 167 -- 173@LB@
57	0.01283	0.6057	lmo2379	N/A	-18.13	0.024463	194 -- 217	150 -- 173	monovalent cation/H+ antiporter subunit B	_____________193__________________218\n_____________\|____________________\|\n5'-GUA...AACGA_______AU___________AUGAC...AUA-3'\n______________GGUGAGA__GAUGAAAACGA\n______________::\|\|\|\|\|__:\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__UUACUUUUGUU\n3'-GUU...GCCGG_______AC___________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________149\n	207 -- 213	154 -- 160	-18.1864 kcal/mol	2.62553 kcal/mol	0.959215 kcal/mol	193 218@LB@ \| \|@LB@5'-GUA...AACGA AU AUGAC...AUA-3'@LB@ GGUGAGA GAUGAAAACGA@LB@ ::\|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UUACUCU UUACUUUUGUU@LB@3'-GUU...GCCGG AC UAUUA...GGA-5'@LB@ \| \|@LB@ 174 149@LB@@LB@@LB@Energy -18.13 kcal/mol@LB@Hybridization Energy -18.1864 kcal/mol@LB@Unfolding Energy - mRNA 2.62553 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 194 -- 217@LB@Position - sRNA 150 -- 173@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 154 -- 160@LB@
75	0.01961	0.6733	lmo0383	N/A	-20.23	0.008871	224 -- 265	150 -- 186	methylmalonate-semialdehyde dehydrogenase	_____________223________________________________________266\n_____________\|__________________________________________\|\n5'-UUC...UUAAA_______AUUG_____G______UC___A_U___________AUAUG...AAG-3'\n______________GAAUUAU____ACGGC_AAUGGG__GAG_G_AAGACAGAUAA\n______________\|\|\|:\|\|:____\|\|\|\|\|_\|\|\|\|:\|__\|\|:_\|_\|\|:\|\|\|:\|\|\|\|\n______________CUUGAUG____UGCCG_UUACUC__CUU_C_UUUUGUUUAUU\n3'-GUU...CUGUA________________G______UA___A_____________ACUAA...GGA-5'\n_____________\|__________________________________________\|\n_____________187________________________________________149\n	257 -- 263	152 -- 158	-34.2826 kcal/mol	8.25616 kcal/mol	13.66 kcal/mol	223 266@LB@ \| \|@LB@5'-UUC...UUAAA AUUG G UC A U AUAUG...AAG-3'@LB@ GAAUUAU ACGGC AAUGGG GAG G AAGACAGAUAA@LB@ \|\|\|:\|\|: \|\|\|\|\| \|\|\|\|:\| \|\|: \| \|\|:\|\|\|:\|\|\|\|@LB@ CUUGAUG UGCCG UUACUC CUU C UUUUGUUUAUU@LB@3'-GUU...CUGUA G UA A ACUAA...GGA-5'@LB@ \| \|@LB@ 187 149@LB@@LB@@LB@Energy -20.23 kcal/mol@LB@Hybridization Energy -34.2826 kcal/mol@LB@Unfolding Energy - mRNA 8.25616 kcal/mol@LB@Unfolding Energy - sRNA 13.66 kcal/mol@LB@@LB@Position - mRNA 224 -- 265@LB@Position - sRNA 150 -- 186@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 152 -- 158@LB@
110	0.02752	0.6733	lmo0057	N/A	-17.32	0.035592	178 -- 213	150 -- 185		_____________177_________________214\n_____________\|___________________\|\n5'-AAA...GCGGG_______CA__________AAGUA...AAG-3'\n______________AGUGGGA__UGAAUGAAGA\n______________\|:\|\|:\|\|__\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__ACUUACUUUU\n3'-GUU...GCCGG___________________GUUUA...GGA-5'\n_____________\|___________________\|\n_____________186_________________149\n	201 -- 207	157 -- 163	-16.939 kcal/mol	2.5385 kcal/mol	0.930085 kcal/mol	177 214@LB@ \| \|@LB@5'-AAA...GCGGG CA AAGUA...AAG-3'@LB@ AGUGGGA UGAAUGAAGA@LB@ \|:\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU ACUUACUUUU@LB@3'-GUU...GCCGG GUUUA...GGA-5'@LB@ \| \|@LB@ 186 149@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -16.939 kcal/mol@LB@Unfolding Energy - mRNA 2.5385 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 178 -- 213@LB@Position - sRNA 150 -- 185@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
158	0.04144	0.7058	lmo1958	fhuB	-14.94	0.099691	191 -- 222	150 -- 181	ferrichrome ABC transporter permease	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GUU...AAGGA_____U__A________A___C___________AAAUG...UCG-3'\n______________ACAUG_GC_GAUG_GAU_AGU_AAAACAGAUAA\n______________\|\|\|:\|_\|\|_:\|\|\|_\|\|\|_\|:\|_\|\|\|\|\|\|:\|\|\|\|\n______________UGUGC_CG_UUAC_CUA_UUA_UUUUGUUUAUU\n3'-GUU...CUUGA________G____U___C___C___________ACUAA...GGA-5'\n_____________\|_________________________________\|\n_____________182_______________________________149\n	214 -- 220	152 -- 158	-22.8664 kcal/mol	3.81003 kcal/mol	11.9534 kcal/mol	190 223@LB@ \| \|@LB@5'-GUU...AAGGA U A A C AAAUG...UCG-3'@LB@ ACAUG GC GAUG GAU AGU AAAACAGAUAA@LB@ \|\|\|:\| \|\| :\|\|\| \|\|\| \|:\| \|\|\|\|\|\|:\|\|\|\|@LB@ UGUGC CG UUAC CUA UUA UUUUGUUUAUU@LB@3'-GUU...CUUGA G U C C ACUAA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -22.8664 kcal/mol@LB@Unfolding Energy - mRNA 3.81003 kcal/mol@LB@Unfolding Energy - sRNA 11.9534 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 152 -- 158@LB@
168	0.04649	0.7403	lmo1875	N/A	-18.37	0.021889	174 -- 204	150 -- 181	ABC transporter ATP-binding protein	_____________173_______________205\n_____________\|_________________\|\n5'-ACA...AACAG__A______________AUGAA...GUU-3'\n______________GA_AUGGAUGGGAAUAA\n______________\|\|_\|\|\|:\|\|\|::\|\|:\|\|\n______________CU_UACUUACUUUUGUU\n3'-GUU...GGUUA__C______________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________182_______________149\n	193 -- 199	155 -- 161	-14.111 kcal/mol	2.1341 kcal/mol	0.933796 kcal/mol	173 205@LB@ \| \|@LB@5'-ACA...AACAG A AUGAA...GUU-3'@LB@ GA AUGGAUGGGAAUAA@LB@ \|\| \|\|\|:\|\|\|::\|\|:\|\|@LB@ CU UACUUACUUUUGUU@LB@3'-GUU...GGUUA C UAUUA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -18.37 kcal/mol@LB@Hybridization Energy -14.111 kcal/mol@LB@Unfolding Energy - mRNA 2.1341 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 174 -- 204@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@LB@
195	0.0561	0.7607	lmo2779	N/A	-14.82	0.104550	1 -- 44	150 -- 181	GTP-binding protein EngD	_____________0____________45\n_____________\|____________\|\n5'-ACG...AGCUU_________U__CUAUU...CGU-3'\n______________AUGAGAUGA_UG\n______________\|\|\|\|\|\|\|\|\|_\|\|\n______________UACUCUACU_AC\n3'-GUU...CCGGU_________U__UUUUG...GGA-5'\n_____________\|____________\|\n_____________182__________149\n	17 -- 23	164 -- 170	-12.8914 kcal/mol	1.66686 kcal/mol	0.818518 kcal/mol	0 45@LB@ \| \|@LB@5'-ACG...AGCUU U CUAUU...CGU-3'@LB@ AUGAGAUGA UG@LB@ \|\|\|\|\|\|\|\|\| \|\|@LB@ UACUCUACU AC@LB@3'-GUU...CCGGU U UUUUG...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -12.8914 kcal/mol@LB@Unfolding Energy - mRNA 1.66686 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 1 -- 44@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 164 -- 170@LB@
37	0.007696	0.5562	lmo0551	N/A	-17.72	0.029617	133 -- 210	151 -- 204	lmo0551	_____________132____________211\n_____________\|______________\|\n5'-AGA...UUAAG________G_____AAUUC...CUU-3'\n______________GAGGUGAG_GAAGA\n______________\|\|\|:\|\|\|:_\|\|\|:\|\n______________CUCUACUU_CUUUU\n3'-GUU...GGUUA________A_____GUUUA...GGA-5'\n_____________\|______________\|\n_____________205____________150\n	135 -- 141	163 -- 169	-13.8898 kcal/mol	2.56868 kcal/mol	0.904482 kcal/mol	132 211@LB@ \| \|@LB@5'-AGA...UUAAG G AAUUC...CUU-3'@LB@ GAGGUGAG GAAGA@LB@ \|\|\|:\|\|\|: \|\|\|:\|@LB@ CUCUACUU CUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 205 150@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 2.56868 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 133 -- 210@LB@Position - sRNA 151 -- 204@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 163 -- 169@LB@
83	0.02274	0.6733	lmo1752	N/A	-17.06	0.039898	184 -- 210	151 -- 173	lmo1752	_____________183___________211\n_____________\|_____________\|\n5'-CUA...CAAGA_____________CGAUA...CAG-3'\n______________AAUGAGGUGAAUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\n______________UUACUCUACUUAC\n3'-GUU...GCCGG_____________UUUUG...GGA-5'\n_____________\|_____________\|\n_____________174___________150\n	190 -- 196	161 -- 167	-16.9304 kcal/mol	1.40294 kcal/mol	0.838004 kcal/mol	183 211@LB@ \| \|@LB@5'-CUA...CAAGA CGAUA...CAG-3'@LB@ AAUGAGGUGAAUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|@LB@ UUACUCUACUUAC@LB@3'-GUU...GCCGG UUUUG...GGA-5'@LB@ \| \|@LB@ 174 150@LB@@LB@@LB@Energy -17.06 kcal/mol@LB@Hybridization Energy -16.9304 kcal/mol@LB@Unfolding Energy - mRNA 1.40294 kcal/mol@LB@Unfolding Energy - sRNA 0.838004 kcal/mol@LB@@LB@Position - mRNA 184 -- 210@LB@Position - sRNA 151 -- 173@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 161 -- 167@LB@
134	0.0358	0.6968	lmo2682	kdpA	-15.50	0.078936	69 -- 121	151 -- 202	potassium-transporting ATPase subunit A	_____________68_____________________________________________122\n_____________\|______________________________________________\|\n5'-ACA...UUGGU___AU___UG_____AAGAG______G___________CG______GGGUG...AAA-3'\n______________AGG__UAG__GUGGA_____UACGGU_AA_GGGGUGAA__GAAAAU\n______________\|\|\|__\|\|\|__:\|\|:\|_____:\|\|\|\|:_\|\|_\|:\|:\|\|\|\|__\|\|\|\|\|:\n______________UCC__AUC__UACUU_____GUGCCG_UU_CUCUACUU__CUUUUG\n3'-GUU...CCUAC___GU___UG_____GAU________G__A________A_______UUUAU...GGA-5'\n_____________\|______________________________________________\|\n_____________203____________________________________________150\n	102 -- 108	163 -- 169	-34.0107 kcal/mol	9.08348 kcal/mol	13.9626 kcal/mol	68 122@LB@ \| \|@LB@5'-ACA...UUGGU AU UG AAGAG G CG GGGUG...AAA-3'@LB@ AGG UAG GUGGA UACGGU AA GGGGUGAA GAAAAU@LB@ \|\|\| \|\|\| :\|\|:\| :\|\|\|\|: \|\| \|:\|:\|\|\|\| \|\|\|\|\|:@LB@ UCC AUC UACUU GUGCCG UU CUCUACUU CUUUUG@LB@3'-GUU...CCUAC GU UG GAU G A A UUUAU...GGA-5'@LB@ \| \|@LB@ 203 150@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -34.0107 kcal/mol@LB@Unfolding Energy - mRNA 9.08348 kcal/mol@LB@Unfolding Energy - sRNA 13.9626 kcal/mol@LB@@LB@Position - mRNA 69 -- 121@LB@Position - sRNA 151 -- 202@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 163 -- 169@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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