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
155	0.04112	0.7058	lmo1165	N/A	-16.89	0.043077	88 -- 150	155 -- 206	ethanolamine utilization protein EutE	_____________87_______________________________151\n_____________\|________________________________\|\n5'-AAG...AAUGG____________G___C_______G_______UCCAC...CAA-3'\n______________GGAUUA_GCGGC_GAU_AG_UGGA_GAAGAUA\n______________\|:\|:\|\|_:\|\|\|\|_:\|\|_\|\|_\|\|:\|_\|\|\|:\|:\|\n______________CUUGAU_UGCCG_UUA_UC_ACUU_CUUUUGU\n3'-GUU...CUGUA______G_____G___C__U____A_______UUAUU...GGA-5'\n_____________\|________________________________\|\n_____________207______________________________154\n	144 -- 150	155 -- 161	-24.1777 kcal/mol	5.41964 kcal/mol	9.66922 kcal/mol	87 151@LB@ \| \|@LB@5'-AAG...AAUGG G C G UCCAC...CAA-3'@LB@ GGAUUA GCGGC GAU AG UGGA GAAGAUA@LB@ \|:\|:\|\| :\|\|\|\| :\|\| \|\| \|\|:\| \|\|\|:\|:\|@LB@ CUUGAU UGCCG UUA UC ACUU CUUUUGU@LB@3'-GUU...CUGUA G G C U A UUAUU...GGA-5'@LB@ \| \|@LB@ 207 154@LB@@LB@@LB@Energy -16.89 kcal/mol@LB@Hybridization Energy -24.1777 kcal/mol@LB@Unfolding Energy - mRNA 5.41964 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 88 -- 150@LB@Position - sRNA 155 -- 206@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 155 -- 161@LB@
166	0.04633	0.7403	lmo1152	N/A	-16.33	0.055198	97 -- 188	95 -- 169	PduB protein	_____________96_______________189\n_____________\|________________\|\n5'-GGC...AAGUC________________AAUAA...AAG-3'\n______________AGAUGAGUGA__GCAA\n______________\|\|\|\|\|\|:\|\|\|__:\|\|\|\n______________UCUACUUACU__UGUU\n3'-GUU...GUUAC__________UU____UAUUA...GGA-5'\n_____________\|________________\|\n_____________170______________94\n	100 -- 106	160 -- 166	-13.7881 kcal/mol	2.27776 kcal/mol	0.924402 kcal/mol	96 189@LB@ \| \|@LB@5'-GGC...AAGUC AAUAA...AAG-3'@LB@ AGAUGAGUGA GCAA@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\|@LB@ UCUACUUACU UGUU@LB@3'-GUU...GUUAC UU UAUUA...GGA-5'@LB@ \| \|@LB@ 170 94@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -13.7881 kcal/mol@LB@Unfolding Energy - mRNA 2.27776 kcal/mol@LB@Unfolding Energy - sRNA 0.924402 kcal/mol@LB@@LB@Position - mRNA 97 -- 188@LB@Position - sRNA 95 -- 169@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 160 -- 166@LB@
112	0.029	0.6968	lmo0191	N/A	-14.99	0.097641	103 -- 160	154 -- 212	phospho-beta-glucosidase	_____________102__________161\n_____________\|____________\|\n5'-UGU...CCAUG____________GAACG...CGC-3'\n______________GAGUGAAGGCGA\n______________\|\|:\|\|\|\|::\|:\|\n______________CUUACUUUUGUU\n3'-GUU...CUCUA____________UAUUA...GGA-5'\n_____________\|____________\|\n_____________213__________153\n	148 -- 154	154 -- 160	-12.5182 kcal/mol	1.90916 kcal/mol	0.857742 kcal/mol	102 161@LB@ \| \|@LB@5'-UGU...CCAUG GAACG...CGC-3'@LB@ GAGUGAAGGCGA@LB@ \|\|:\|\|\|\|::\|:\|@LB@ CUUACUUUUGUU@LB@3'-GUU...CUCUA UAUUA...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -12.5182 kcal/mol@LB@Unfolding Energy - mRNA 1.90916 kcal/mol@LB@Unfolding Energy - sRNA 0.857742 kcal/mol@LB@@LB@Position - mRNA 103 -- 160@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 154 -- 160@LB@
19	0.003536	0.4469	lmo0321	N/A	-22.74	0.002408	114 -- 157	167 -- 207		_____________113____________________________________________158\n_____________\|______________________________________________\|\n5'-AUU...UGUUA________UA____G_AC__________GGA_____U_________AUGUU...AGG-3'\n______________AGCGGGAU__GAGG_A__UAGGUA_GAA____ACGG_CUAAUGAGA\n______________\|:\|\|\|\|\|\|__\|\|\|\|_\|__\|\|\|::\|_\|\|\|____\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________UUGCCCUA__CUCC_U__AUCUGU_CUU____UGCC_GGUUACUCU\n3'-GUU...ACGUA______________G_________A___GAUG______________ACUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________208____________________________________________166\n	151 -- 157	167 -- 173	-39.7249 kcal/mol	9.73371 kcal/mol	18.0488 kcal/mol	113 158@LB@ \| \|@LB@5'-AUU...UGUUA UA G AC GGA U AUGUU...AGG-3'@LB@ AGCGGGAU GAGG A UAGGUA GAA ACGG CUAAUGAGA@LB@ \|:\|\|\|\|\|\| \|\|\|\| \| \|\|\|::\| \|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ UUGCCCUA CUCC U AUCUGU CUU UGCC GGUUACUCU@LB@3'-GUU...ACGUA G A GAUG ACUUA...GGA-5'@LB@ \| \|@LB@ 208 166@LB@@LB@@LB@Energy -22.74 kcal/mol@LB@Hybridization Energy -39.7249 kcal/mol@LB@Unfolding Energy - mRNA 9.73371 kcal/mol@LB@Unfolding Energy - sRNA 18.0488 kcal/mol@LB@@LB@Position - mRNA 114 -- 157@LB@Position - sRNA 167 -- 207@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 167 -- 173@LB@
32	0.006611	0.5515	lmo1649	N/A	-18.63	0.019340	118 -- 153	171 -- 207	lmo1649	_____________117_____________________________________________________________154\n_____________\|_______________________________________________________________\|\n5'-GUA...UGUUA_______AGUAAU__UA______CG__________A_____UC__A_____G___________UACAA...AAA-3'\n______________CAUCGUG______GU__CU_UGC__GAUGGG_UGA_GCAUA__CG_G_ACU_ACGCGGCCAGU\n______________\|\|\|\|:\|\|______\|:__\|\|_\|\|\|__:\|:\|\|\|_\|\|\|_\|\|\|\|\|__\|:_\|_\|\|\|_\|\|:\|\|\|\|\|\|:\|\n______________GUAGUAC______CG__GA_ACG__UUGCCC_ACU_CGUAU__GU_C_UGA_UGUGCCGGUUA\n3'-GUU...CAACG_______AAGCC___CG__U___UA______U___C_____CU__A_U_______________CUCUA...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________208_____________________________________________________________170\n	147 -- 153	171 -- 177	-50.2657 kcal/mol	18.2787 kcal/mol	22.0434 kcal/mol	117 154@LB@ \| \|@LB@5'-GUA...UGUUA AGUAAU UA CG A UC A G UACAA...AAA-3'@LB@ CAUCGUG GU CU UGC GAUGGG UGA GCAUA CG G ACU ACGCGGCCAGU@LB@ \|\|\|\|:\|\| \|: \|\| \|\|\| :\|:\|\|\| \|\|\| \|\|\|\|\| \|: \| \|\|\| \|\|:\|\|\|\|\|\|:\|@LB@ GUAGUAC CG GA ACG UUGCCC ACU CGUAU GU C UGA UGUGCCGGUUA@LB@3'-GUU...CAACG AAGCC CG U UA U C CU A U CUCUA...GGA-5'@LB@ \| \|@LB@ 208 170@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -50.2657 kcal/mol@LB@Unfolding Energy - mRNA 18.2787 kcal/mol@LB@Unfolding Energy - sRNA 22.0434 kcal/mol@LB@@LB@Position - mRNA 118 -- 153@LB@Position - sRNA 171 -- 207@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 171 -- 177@LB@
198	0.05669	0.7607	lmo2670	N/A	-16.54	0.050282	118 -- 190	141 -- 216		_____________117_________________191\n_____________\|___________________\|\n5'-AAU...AUUUG_________UACC______UUCAA...UCU-3'\n______________GAUGAGAUG____GGGAAC\n______________:\|\|\|\|\|\|\|\|____\|::\|\|\|\n______________UUACUCUAC____CUUUUG\n3'-GUU...GCCGG_________UUA_______UUUAU...GGA-5'\n_____________\|___________________\|\n_____________217_________________140\n	72 -- 78	165 -- 171	-16.0384 kcal/mol	2.83906 kcal/mol	0.941471 kcal/mol	117 191@LB@ \| \|@LB@5'-AAU...AUUUG UACC UUCAA...UCU-3'@LB@ GAUGAGAUG GGGAAC@LB@ :\|\|\|\|\|\|\|\| \|::\|\|\|@LB@ UUACUCUAC CUUUUG@LB@3'-GUU...GCCGG UUA UUUAU...GGA-5'@LB@ \| \|@LB@ 217 140@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -16.0384 kcal/mol@LB@Unfolding Energy - mRNA 2.83906 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 118 -- 190@LB@Position - sRNA 141 -- 216@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 165 -- 171@LB@
103	0.02634	0.6733	lmo2183	N/A	-17.72	0.029644	120 -- 189	95 -- 172	ferrichrome ABC transporter permease	_____________119_______________190\n_____________\|_________________\|\n5'-AGA...UGUGU____UU___________UUAUU...UCC-3'\n______________AUGA__UGGAUGAAAAU\n______________\|\|\|\|__\|\|:\|\|\|\|\|\|\|:\n______________UACU__ACUUACUUUUG\n3'-GUU...CCGGU____CU___________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________173_______________94\n	130 -- 136	156 -- 162	-14.4355 kcal/mol	3.54286 kcal/mol	0.922045 kcal/mol	119 190@LB@ \| \|@LB@5'-AGA...UGUGU UU UUAUU...UCC-3'@LB@ AUGA UGGAUGAAAAU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ UACU ACUUACUUUUG@LB@3'-GUU...CCGGU CU UUUAU...GGA-5'@LB@ \| \|@LB@ 173 94@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -14.4355 kcal/mol@LB@Unfolding Energy - mRNA 3.54286 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 120 -- 189@LB@Position - sRNA 95 -- 172@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 156 -- 162@LB@
127	0.03392	0.6968	lmo2096	N/A	-16.75	0.045974	122 -- 137	183 -- 198	PTS galacticol transporter subunit IIC	_____________121___________________138\n_____________\|_____________________\|\n5'-UAG...UUUCU____A__C_____________GAAGA...UGA-3'\n______________UAAC_GG_AUG_GGCAUGGAC\n______________\|\|\|\|_\|\|_\|\|\|_\|\|\|\|\|:\|\|\|\n______________AUUG_CC_UAC_CCGUAUCUG\n3'-GUU...UACGU____C______U_________UACUU...GGA-5'\n_____________\|_____________________\|\n_____________199___________________182\n	129 -- 135	191 -- 197	-23.3255 kcal/mol	4.68556 kcal/mol	9.82628 kcal/mol	121 138@LB@ \| \|@LB@5'-UAG...UUUCU A C GAAGA...UGA-3'@LB@ UAAC GG AUG GGCAUGGAC@LB@ \|\|\|\| \|\| \|\|\| \|\|\|\|\|:\|\|\|@LB@ AUUG CC UAC CCGUAUCUG@LB@3'-GUU...UACGU C U UACUU...GGA-5'@LB@ \| \|@LB@ 199 182@LB@@LB@@LB@Energy -16.75 kcal/mol@LB@Hybridization Energy -23.3255 kcal/mol@LB@Unfolding Energy - mRNA 4.68556 kcal/mol@LB@Unfolding Energy - sRNA 9.82628 kcal/mol@LB@@LB@Position - mRNA 122 -- 137@LB@Position - sRNA 183 -- 198@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 191 -- 197@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@
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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