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
21	0.003699	0.4469	lmo2681	kdpB	-18.50	0.020601	185 -- 204	154 -- 173	potassium-transporting ATPase subunit B	_____________184__________________205\n_____________\|____________________\|\n5'-GCA...UUUCA____________________UGGAA...AUG-3'\n______________AAUGAGGUGAAUGGAAAUGA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|\n______________UUACUCUACUUACUUUUGUU\n3'-GUU...GCCGG____________________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________153\n	197 -- 203	155 -- 161	-22.9313 kcal/mol	3.41 kcal/mol	0.959215 kcal/mol	184 205@LB@ \| \|@LB@5'-GCA...UUUCA UGGAA...AUG-3'@LB@ AAUGAGGUGAAUGGAAAUGA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|@LB@ UUACUCUACUUACUUUUGUU@LB@3'-GUU...GCCGG UAUUA...GGA-5'@LB@ \| \|@LB@ 174 153@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -22.9313 kcal/mol@LB@Unfolding Energy - mRNA 3.41 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 154 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@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@
23	0.00382	0.4469	lmo1572	accA	-20.61	0.007329	192 -- 226	157 -- 188	acetyl-CoA carboxylase carboxyltransferase subunit alpha	_____________191______________________________________________________________________________227\n_____________\|________________________________________________________________________________\|\n5'-AGG...UUUAA__AU______GAAA__A____GA_____________A__UG__________________G___________AUU______ACCGA...CCA-3'\n______________GC__UCAUGU____GC_CCUG___GUAG_GGGGUGA_GU_______________AUGGC_AAUGAGAUGGA___UGAGAA\n______________\|\|__\|\|\|\|\|\|____\|\|_\|\|\|:___:\|\|:_\|\|\|:\|\|\|_\|:_______________\|:\|\|\|_\|\|\|\|\|\|\|\|\|:\|___\|\|\|:\|\|\n______________CG__AGUACA____CG_GGAU___UAUU_CCCUACU_CG_______________UGCCG_UUACUCUACUU___ACUUUU\n3'-GUU...CGCAA__GU______AGCC__C____ACG____G_______C__UAUCUGUACUUGAUG_____G____________________GUUUA...GGA-5'\n_____________\|________________________________________________________________________________\|\n_____________189______________________________________________________________________________156\n	211 -- 217	163 -- 169	-59.1532 kcal/mol	18.9584 kcal/mol	22.6787 kcal/mol	191 227@LB@ \| \|@LB@5'-AGG...UUUAA AU GAAA A GA A UG G AUU ACCGA...CCA-3'@LB@ GC UCAUGU GC CCUG GUAG GGGGUGA GU AUGGC AAUGAGAUGGA UGAGAA@LB@ \|\| \|\|\|\|\|\| \|\| \|\|\|: :\|\|: \|\|\|:\|\|\| \|: \|:\|\|\| \|\|\|\|\|\|\|\|\|:\| \|\|\|:\|\|@LB@ CG AGUACA CG GGAU UAUU CCCUACU CG UGCCG UUACUCUACUU ACUUUU@LB@3'-GUU...CGCAA GU AGCC C ACG G C UAUCUGUACUUGAUG G GUUUA...GGA-5'@LB@ \| \|@LB@ 189 156@LB@@LB@@LB@Energy -20.61 kcal/mol@LB@Hybridization Energy -59.1532 kcal/mol@LB@Unfolding Energy - mRNA 18.9584 kcal/mol@LB@Unfolding Energy - sRNA 22.6787 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 157 -- 188@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@LB@
24	0.004153	0.4656	lmo1386	N/A	-22.14	0.003328	2 -- 37	155 -- 186	DNA translocase	_____________1____________________________________38\n_____________\|____________________________________\|\n__________5'-G___G________G__AAGCU______CAC_______CCGCA...UUA-3'\n______________GAA_UACGCGGC_GA_____GAUGAA___GAAAACA\n______________\|\|\|_\|\|\|:\|\|\|\|_:\|_____\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUU_AUGUGCCG_UU_____CUACUU___CUUUUGU\n3'-GUU...CUGUA___G________G__ACU________A_________UUAUU...GGA-5'\n_____________\|____________________________________\|\n_____________187__________________________________154\n	31 -- 37	155 -- 161	-32.0969 kcal/mol	6.67763 kcal/mol	9.66922 kcal/mol	1 38@LB@ \| \|@LB@ 5'-G G G AAGCU CAC CCGCA...UUA-3'@LB@ GAA UACGCGGC GA GAUGAA GAAAACA@LB@ \|\|\| \|\|\|:\|\|\|\| :\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUU AUGUGCCG UU CUACUU CUUUUGU@LB@3'-GUU...CUGUA G G ACU A UUAUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -22.14 kcal/mol@LB@Hybridization Energy -32.0969 kcal/mol@LB@Unfolding Energy - mRNA 6.67763 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 2 -- 37@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 155 -- 161@LB@
25	0.004689	0.5029	lmo1584	N/A	-20.33	0.008463	183 -- 211	169 -- 209		_____________182___________212\n_____________\|_____________\|\n5'-GAA...GGCGC_____________AAAUG...CUG-3'\n______________ACAUGGCUAAUGA\n______________\|\|\|:\|\|\|:\|\|\|\|\|\n______________UGUGCCGGUUACU\n3'-GUU...CUUGA_____________CUACU...GGA-5'\n_____________\|_____________\|\n_____________210___________168\n	205 -- 211	169 -- 175	-19.4521 kcal/mol	2.17631 kcal/mol	6.15322 kcal/mol	182 212@LB@ \| \|@LB@5'-GAA...GGCGC AAAUG...CUG-3'@LB@ ACAUGGCUAAUGA@LB@ \|\|\|:\|\|\|:\|\|\|\|\|@LB@ UGUGCCGGUUACU@LB@3'-GUU...CUUGA CUACU...GGA-5'@LB@ \| \|@LB@ 210 168@LB@@LB@@LB@Energy -20.33 kcal/mol@LB@Hybridization Energy -19.4521 kcal/mol@LB@Unfolding Energy - mRNA 2.17631 kcal/mol@LB@Unfolding Energy - sRNA 6.15322 kcal/mol@LB@@LB@Position - mRNA 183 -- 211@LB@Position - sRNA 169 -- 209@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 169 -- 175@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@
27	0.005046	0.5029	lmo2370	N/A	-21.11	0.005698	252 -- 287	166 -- 205	aminotransferase	_____________251_____________288\n_____________\|_______________\|\n5'-CCU...AUAAU_____C_________AGAAG...UGU-3'\n______________UGAGG_GAAUGAAAG\n______________\|\|\|\|:_\|\|\|\|\|\|\|\|:\n______________ACUCU_CUUACUUUU\n3'-GUU...CGGUU_____A_________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________206_____________165\n	176 -- 182	157 -- 163	-15.2487 kcal/mol	2.36926 kcal/mol	0.905109 kcal/mol	251 288@LB@ \| \|@LB@5'-CCU...AUAAU C AGAAG...UGU-3'@LB@ UGAGG GAAUGAAAG@LB@ \|\|\|\|: \|\|\|\|\|\|\|\|:@LB@ ACUCU CUUACUUUU@LB@3'-GUU...CGGUU A GUUUA...GGA-5'@LB@ \| \|@LB@ 206 165@LB@@LB@@LB@Energy -21.11 kcal/mol@LB@Hybridization Energy -15.2487 kcal/mol@LB@Unfolding Energy - mRNA 2.36926 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 252 -- 287@LB@Position - sRNA 166 -- 205@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 157 -- 163@LB@
28	0.005366	0.5157	lmo2793	N/A	-19.39	0.013418	199 -- 253	121 -- 174	lmo2793	_____________198__________________254\n_____________\|____________________\|\n5'-AAA...UGUAG_________UUU________AUUGG...GUU-3'\n______________CAGUGAGGU___UGAAGAUA\n______________\|\|:\|\|\|\|:\|___\|\|\|\|:\|:\|\n______________GUUACUCUA___ACUUUUGU\n3'-GUU...UGCCG_________CUU________UUAUU...GGA-5'\n_____________\|____________________\|\n_____________175__________________120\n	212 -- 218	155 -- 161	-16.7389 kcal/mol	5.68665 kcal/mol	0.95817 kcal/mol	198 254@LB@ \| \|@LB@5'-AAA...UGUAG UUU AUUGG...GUU-3'@LB@ CAGUGAGGU UGAAGAUA@LB@ \|\|:\|\|\|\|:\| \|\|\|\|:\|:\|@LB@ GUUACUCUA ACUUUUGU@LB@3'-GUU...UGCCG CUU UUAUU...GGA-5'@LB@ \| \|@LB@ 175 120@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -16.7389 kcal/mol@LB@Unfolding Energy - mRNA 5.68665 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 199 -- 253@LB@Position - sRNA 121 -- 174@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@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@
30	0.00607	0.5445	lmo0619	N/A	-20.15	0.009257	186 -- 283	154 -- 223	lmo0619	_____________185_____________________________________________________________________________________________________284\n_____________\|_______________________________________________________________________________________________________\|\n5'-UAU...AACAG_____G__GC____CUU___________AAAAAG_____AGUAAAUUACUUCA_______AAAAAAGCGACCAAUU_________GUAUUA____________GGCGG...CAA-3'\n______________UCGGG_GU____GC___AU_GGAUGGGG______AGACA______________UGAAUUA________________UAC_GCCAA_______GAUGAAAACGA\n______________\|\|\|\|\|_\|:____\|\|___\|:_\|\|\|\|\|:\|\|______\|\|\|\|\|______________\|\|\|\|:\|\|________________:\|\|_\|\|\|\|\|_______:\|\|\|\|\|\|\|\|:\|\n______________AGCCC_CG____CG___UG_CCUACUCC______UCUGU______________ACUUGAU________________GUG_CGGUU_______UUACUUUUGUU\n3'-GUU...GUACA_____G__GAUA__UAU__C________GUA________________________________________________C_____ACUCUAC___________UAUUA...GGA-5'\n_____________\|_______________________________________________________________________________________________________\|\n_____________224_____________________________________________________________________________________________________153\n	277 -- 283	154 -- 160	-48.8019 kcal/mol	13.571 kcal/mol	22.2956 kcal/mol	185 284@LB@ \| \|@LB@5'-UAU...AACAG G GC CUU AAAAAG AGUAAAUUACUUCA AAAAAAGCGACCAAUU GUAUUA GGCGG...CAA-3'@LB@ UCGGG GU GC AU GGAUGGGG AGACA UGAAUUA UAC GCCAA GAUGAAAACGA@LB@ \|\|\|\|\| \|: \|\| \|: \|\|\|\|\|:\|\| \|\|\|\|\| \|\|\|\|:\|\| :\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ AGCCC CG CG UG CCUACUCC UCUGU ACUUGAU GUG CGGUU UUACUUUUGUU@LB@3'-GUU...GUACA G GAUA UAU C GUA C ACUCUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 224 153@LB@@LB@@LB@Energy -20.15 kcal/mol@LB@Hybridization Energy -48.8019 kcal/mol@LB@Unfolding Energy - mRNA 13.571 kcal/mol@LB@Unfolding Energy - sRNA 22.2956 kcal/mol@LB@@LB@Position - mRNA 186 -- 283@LB@Position - sRNA 154 -- 223@LB@Position Seed - mRNA 277 -- 283@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

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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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