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
59	0.0137	0.6248	lmo0642	N/A	-14.84	0.103863	179 -- 256	168 -- 213	lmo0642	_____________178________257\n_____________\|__________\|\n5'-UUC...GAUUG__________CAUGA...CAA-3'\n______________GAGAUGAGUG\n______________\|\|\|\|\|\|\|:\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________214________167\n	193 -- 199	161 -- 167	-14.0942 kcal/mol	3.54513 kcal/mol	0.812237 kcal/mol	178 257@LB@ \| \|@LB@5'-UUC...GAUUG CAUGA...CAA-3'@LB@ GAGAUGAGUG@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 214 167@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -14.0942 kcal/mol@LB@Unfolding Energy - mRNA 3.54513 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 179 -- 256@LB@Position - sRNA 168 -- 213@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
118	0.03209	0.6968	lmo0654	N/A	-17.15	0.038336	200 -- 225	156 -- 180	lmo0654	_____________199________________________226\n_____________\|__________________________\|\n5'-GAA...GCGCG_______C______AUUUAA______UAGAA...CAC-3'\n______________UAUGGCC_AUGAGA______GAGAAC\n______________:\|:\|\|\|\|_\|\|\|\|\|\|______\|\|:\|\|\|\n______________GUGCCGG_UACUCU______CUUUUG\n3'-GUU...UUGAU_______U______ACUUA_______UUUAU...GGA-5'\n_____________\|__________________________\|\n_____________181________________________155\n	200 -- 206	174 -- 180	-23.3306 kcal/mol	3.96502 kcal/mol	8.29586 kcal/mol	199 226@LB@ \| \|@LB@5'-GAA...GCGCG C AUUUAA UAGAA...CAC-3'@LB@ UAUGGCC AUGAGA GAGAAC@LB@ :\|:\|\|\|\| \|\|\|\|\|\| \|\|:\|\|\|@LB@ GUGCCGG UACUCU CUUUUG@LB@3'-GUU...UUGAU U ACUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 181 155@LB@@LB@@LB@Energy -17.15 kcal/mol@LB@Hybridization Energy -23.3306 kcal/mol@LB@Unfolding Energy - mRNA 3.96502 kcal/mol@LB@Unfolding Energy - sRNA 8.29586 kcal/mol@LB@@LB@Position - mRNA 200 -- 225@LB@Position - sRNA 156 -- 180@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 174 -- 180@LB@
131	0.03528	0.6968	lmo0788	N/A	-16.25	0.057193	177 -- 197	197 -- 213	lmo0788	_____________176______198\n_____________\|________\|\n5'-AAA...CGAAA________AAAAU...AUU-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________214______196\n	191 -- 197	197 -- 203	-13.9782 kcal/mol	1.18818 kcal/mol	0.386531 kcal/mol	176 198@LB@ \| \|@LB@5'-AAA...CGAAA AAAAU...AUU-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 214 196@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -13.9782 kcal/mol@LB@Unfolding Energy - mRNA 1.18818 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 197 -- 213@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 197 -- 203@LB@
4	0.0009641	0.4469	lmo0851	N/A	-23.35	0.001728	188 -- 220	172 -- 201	lmo0851	_____________187_______________________________221\n_____________\|_________________________________\|\n5'-GGU...AUAGA__________U_______AAAAGAA________CCAAC...UAA-3'\n______________GUGAGGCAUA_ACAUGAA_______GCGGUUAA\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|_______:\|\|\|::\|\|\n______________UACUCCGUAU_UGUACUU_______UGCCGGUU\n3'-GUU...UGCCC__________C_______GAUG___________ACUCU...GGA-5'\n_____________\|_________________________________\|\n_____________202_______________________________171\n	214 -- 220	172 -- 178	-33.261 kcal/mol	3.18896 kcal/mol	13.3764 kcal/mol	187 221@LB@ \| \|@LB@5'-GGU...AUAGA U AAAAGAA CCAAC...UAA-3'@LB@ GUGAGGCAUA ACAUGAA GCGGUUAA@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| :\|\|\|::\|\|@LB@ UACUCCGUAU UGUACUU UGCCGGUU@LB@3'-GUU...UGCCC C GAUG ACUCU...GGA-5'@LB@ \| \|@LB@ 202 171@LB@@LB@@LB@Energy -23.35 kcal/mol@LB@Hybridization Energy -33.261 kcal/mol@LB@Unfolding Energy - mRNA 3.18896 kcal/mol@LB@Unfolding Energy - sRNA 13.3764 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 172 -- 201@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 172 -- 178@LB@
94	0.02439	0.6733	lmo0952	N/A	-17.21	0.037353	188 -- 223	166 -- 199	lmo0952	_____________187__________________________________224\n_____________\|____________________________________\|\n5'-AAC...AAACG________UU__GAU_____A___AA__________AGUAC...UAA-3'\n______________GAGGCAUA__CA___GAUUA_ACG__CUGGUGAGAU\n______________\|\|\|\|\|\|\|\|__\|\|___:\|:\|\|_\|\|\|__\|:::\|\|\|\|\|\|\n______________CUCCGUAU__GU___UUGAU_UGC__GGUUACUCUA\n3'-GUU...CCCUA________CU__AC______G___C___________CUUAC...GGA-5'\n_____________\|____________________________________\|\n_____________200__________________________________165\n	217 -- 223	166 -- 172	-30.0979 kcal/mol	6.14462 kcal/mol	13.4403 kcal/mol	187 224@LB@ \| \|@LB@5'-AAC...AAACG UU GAU A AA AGUAC...UAA-3'@LB@ GAGGCAUA CA GAUUA ACG CUGGUGAGAU@LB@ \|\|\|\|\|\|\|\| \|\| :\|:\|\| \|\|\| \|:::\|\|\|\|\|\|@LB@ CUCCGUAU GU UUGAU UGC GGUUACUCUA@LB@3'-GUU...CCCUA CU AC G C CUUAC...GGA-5'@LB@ \| \|@LB@ 200 165@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -30.0979 kcal/mol@LB@Unfolding Energy - mRNA 6.14462 kcal/mol@LB@Unfolding Energy - sRNA 13.4403 kcal/mol@LB@@LB@Position - mRNA 188 -- 223@LB@Position - sRNA 166 -- 199@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 166 -- 172@LB@
180	0.05132	0.7607	lmo1643	N/A	-15.34	0.084306	231 -- 286	157 -- 207	lmo1643	_____________230_______________287\n_____________\|_________________\|\n5'-CGA...UAGUA_______GAU_______AGAAG...CUG-3'\n______________AGUGAGG___AUGAAAA\n______________\|:\|\|\|\|:___\|\|\|\|\|\|\|\n______________UUACUCU___UACUUUU\n3'-GUU...GCCGG_______ACU_______GUUUA...GGA-5'\n_____________\|_________________\|\n_____________208_______________156\n	280 -- 286	157 -- 163	-13.3165 kcal/mol	1.24234 kcal/mol	0.930085 kcal/mol	230 287@LB@ \| \|@LB@5'-CGA...UAGUA GAU AGAAG...CUG-3'@LB@ AGUGAGG AUGAAAA@LB@ \|:\|\|\|\|: \|\|\|\|\|\|\|@LB@ UUACUCU UACUUUU@LB@3'-GUU...GCCGG ACU GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -13.3165 kcal/mol@LB@Unfolding Energy - mRNA 1.24234 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 231 -- 286@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 157 -- 163@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@
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@
114	0.02972	0.6968	lmo2166	N/A	-15.48	0.079589	75 -- 119	153 -- 198	lmo2166	_____________74_________________________________________________120\n_____________\|__________________________________________________\|\n5'-GGA...UAUUC___U_____UG___U______CAU________________AA________ACCCA...AAA-3'\n______________AGG_CAUGG__AUG_AACUAC___CGGUCA______UGAA__GAAGACAA\n______________\|\|\|_\|\|\|:\|__\|\|\|_\|\|\|\|\|\|___\|\|\|:\|\|______\|\|\|\|__\|\|\|:\|\|\|\|\n______________UCC_GUAUC__UAC_UUGAUG___GCCGGU______ACUU__CUUUUGUU\n3'-GUU...CCUAC_________UG__________U________UACUCU____A_________UAUUA...GGA-5'\n_____________\|__________________________________________________\|\n_____________199________________________________________________152\n	112 -- 118	154 -- 160	-33.2648 kcal/mol	10.6544 kcal/mol	13.9801 kcal/mol	74 120@LB@ \| \|@LB@5'-GGA...UAUUC U UG U CAU AA ACCCA...AAA-3'@LB@ AGG CAUGG AUG AACUAC CGGUCA UGAA GAAGACAA@LB@ \|\|\| \|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|:\|\| \|\|\|\| \|\|\|:\|\|\|\|@LB@ UCC GUAUC UAC UUGAUG GCCGGU ACUU CUUUUGUU@LB@3'-GUU...CCUAC UG U UACUCU A UAUUA...GGA-5'@LB@ \| \|@LB@ 199 152@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -33.2648 kcal/mol@LB@Unfolding Energy - mRNA 10.6544 kcal/mol@LB@Unfolding Energy - sRNA 13.9801 kcal/mol@LB@@LB@Position - mRNA 75 -- 119@LB@Position - sRNA 153 -- 198@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 154 -- 160@LB@
186	0.05422	0.7607	lmo2356	N/A	-15.92	0.066009	162 -- 205	129 -- 170	lmo2356	_____________161___________________206\n_____________\|_____________________\|\n5'-CUC...AAAGA_______AUUGAU________UUUGA...UUG-3'\n______________GAGAUGA______GUGAGGAU\n______________\|\|\|\|\|\|\|______:\|\|\|::\|:\n______________CUCUACU______UACUUUUG\n3'-GUU...GGUUA_____________________UUUAU...GGA-5'\n_____________\|_____________________\|\n_____________171___________________128\n	176 -- 182	156 -- 162	-14.0636 kcal/mol	2.1522 kcal/mol	0.916023 kcal/mol	161 206@LB@ \| \|@LB@5'-CUC...AAAGA AUUGAU UUUGA...UUG-3'@LB@ GAGAUGA GUGAGGAU@LB@ \|\|\|\|\|\|\| :\|\|\|::\|:@LB@ CUCUACU UACUUUUG@LB@3'-GUU...GGUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 171 128@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -14.0636 kcal/mol@LB@Unfolding Energy - mRNA 2.1522 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 162 -- 205@LB@Position - sRNA 129 -- 170@LB@Position Seed - mRNA 176 -- 182@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)

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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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