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
56	0.01257	0.6043	lmo2205	N/A	-16.72	0.046467	190 -- 249	147 -- 203	phosphoglyceromutase	_____________189_____________________250\n_____________\|_______________________\|\n5'-AUG...GCGAA____GAA________________AAUUA...UGG-3'\n______________AAUG___GGAUGAG_GAAGAUGA\n______________\|\|\|\|___:\|\|\|\|\|:_\|\|\|:\|::\|\n______________UUAC___UCUACUU_CUUUUGUU\n3'-GUU...GCCGG______________A________UAUUA...GGA-5'\n_____________\|_______________________\|\n_____________204_____________________146\n	197 -- 203	155 -- 161	-13.1674 kcal/mol	1.25432 kcal/mol	0.959215 kcal/mol	189 250@LB@ \| \|@LB@5'-AUG...GCGAA GAA AAUUA...UGG-3'@LB@ AAUG GGAUGAG GAAGAUGA@LB@ \|\|\|\| :\|\|\|\|\|: \|\|\|:\|::\|@LB@ UUAC UCUACUU CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 204 146@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -13.1674 kcal/mol@LB@Unfolding Energy - mRNA 1.25432 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 147 -- 203@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
181	0.05165	0.7607	lmo2287	N/A	-16.24	0.057456	190 -- 241	154 -- 199	tape-measure	_____________189________________________________________________242\n_____________\|__________________________________________________\|\n5'-UGA...CUGAA________AUAA___AAAA______AG__G_GAACAU_____C_______CAGUA...CAA-3'\n______________AAACAGAU____GUU____GAUUAG__GU_A________GAG_GAUGGAU\n______________\|\|\|\|\|\|\|\|____\|\|:____\|\|:\|\|\|__\|:_\|________\|\|:_\|\|\|\|\|\|\|\n______________UUUGUCUA____CAG____CUGAUC__CG_U________CUU_CUACCUA\n3'-GUU...ACAGA_______________A_________AA__G_AAGAUAAC___________UGUGG...GGA-5'\n_____________\|__________________________________________________\|\n_____________200________________________________________________153\n	207 -- 213	94 -- 100	-23.404 kcal/mol	6.71689 kcal/mol	9.49359 kcal/mol	189 242@LB@ \| \|@LB@5'-UGA...CUGAA AUAA AAAA AG G GAACAU C CAGUA...CAA-3'@LB@ AAACAGAU GUU GAUUAG GU A GAG GAUGGAU@LB@ \|\|\|\|\|\|\|\| \|\|: \|\|:\|\|\| \|: \| \|\|: \|\|\|\|\|\|\|@LB@ UUUGUCUA CAG CUGAUC CG U CUU CUACCUA@LB@3'-GUU...ACAGA A AA G AAGAUAAC UGUGG...GGA-5'@LB@ \| \|@LB@ 200 153@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -23.404 kcal/mol@LB@Unfolding Energy - mRNA 6.71689 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 190 -- 241@LB@Position - sRNA 154 -- 199@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 94 -- 100@LB@
108	0.02743	0.6733	lmo2330	N/A	-16.53	0.050546	195 -- 214	191 -- 207		_____________194_________215\n_____________\|___________\|\n5'-ACG...GAGAA___________CAAGU...UUU-3'\n______________AGCGGGAUGAG\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UUGCCCUACUC\n3'-GUU...ACGUA___________CGUAU...GGA-5'\n_____________\|___________\|\n_____________208_________190\n	199 -- 205	197 -- 203	-18.6004 kcal/mol	2.16538 kcal/mol	0.386761 kcal/mol	194 215@LB@ \| \|@LB@5'-ACG...GAGAA CAAGU...UUU-3'@LB@ AGCGGGAUGAG@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UUGCCCUACUC@LB@3'-GUU...ACGUA CGUAU...GGA-5'@LB@ \| \|@LB@ 208 190@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -18.6004 kcal/mol@LB@Unfolding Energy - mRNA 2.16538 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 195 -- 214@LB@Position - sRNA 191 -- 207@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 197 -- 203@LB@
71	0.01891	0.6733	lmo2349	N/A	-17.22	0.037183	66 -- 119	160 -- 206	amino acid ABC transporter substrate-binding protein	_____________65______________________________________________________________________________________________________________________120\n_____________\|_______________________________________________________________________________________________________________________\|\n5'-ACC...GCACU___A_______CUUCUGCCAGA___________UG_______GA_____A__U__________________UU_______C__UUUU_A_______GA_G___________U_______UUAUG...AAG-3'\n______________GAC_CUUGGAA___________AAACA__UCCA__GUUGCUG__UAUGU_UC__GCGCC________GCGG__AUGAGGU_UA____G_ACAUGAG__A_ACGGC____GA_GUGGGUG\n______________\|\|\|_\|\|:\|:\|\|___________\|\|\|\|\|__\|\|\|\|__\|\|\|\|\|::__:\|\|\|\|_\|\|__\|\|\|\|\|________:\|\|\|__\|\|\|\|\|\|:_\|\|____\|_\|\|\|\|\|\|:__\|_\|\|\|\|\|____\|\|_:\|\|::\|\|\n______________CUG_GAGCUUU___________UUUGU__AGGU__CAACGGU__GUACA_AG__CGCGG________UGCC__UACUCCG_AU____C_UGUACUU__U_UGCCG____CU_UACUUAC\n___3'-GUUUUUUU___C_______A_______________AA____CG_______A_________CC_____AUACGUAU____C________U_______________GA_G_____GUUA__C_______UUUUG...GGA-5'\n_____________\|_______________________________________________________________________________________________________________________\|\n_____________207_____________________________________________________________________________________________________________________159\n	107 -- 113	161 -- 167	-71.8793 kcal/mol	29.0166 kcal/mol	34.5254 kcal/mol	65 120@LB@ \| \|@LB@5'-ACC...GCACU A CUUCUGCCAGA UG GA A U UU C UUUU A GA G U UUAUG...AAG-3'@LB@ GAC CUUGGAA AAACA UCCA GUUGCUG UAUGU UC GCGCC GCGG AUGAGGU UA G ACAUGAG A ACGGC GA GUGGGUG@LB@ \|\|\| \|\|:\|:\|\| \|\|\|\|\| \|\|\|\| \|\|\|\|\|:: :\|\|\|\| \|\| \|\|\|\|\| :\|\|\| \|\|\|\|\|\|: \|\| \| \|\|\|\|\|\|: \| \|\|\|\|\| \|\| :\|\|::\|\|@LB@ CUG GAGCUUU UUUGU AGGU CAACGGU GUACA AG CGCGG UGCC UACUCCG AU C UGUACUU U UGCCG CU UACUUAC@LB@ 3'-GUUUUUUU C A AA CG A CC AUACGUAU C U GA G GUUA C UUUUG...GGA-5'@LB@ \| \|@LB@ 207 159@LB@@LB@@LB@Energy -17.22 kcal/mol@LB@Hybridization Energy -71.8793 kcal/mol@LB@Unfolding Energy - mRNA 29.0166 kcal/mol@LB@Unfolding Energy - sRNA 34.5254 kcal/mol@LB@@LB@Position - mRNA 66 -- 119@LB@Position - sRNA 160 -- 206@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 161 -- 167@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@
125	0.03321	0.6968	lmo2357	N/A	-16.59	0.049158	2 -- 27	152 -- 176		_____________1_____________________28\n_____________\|_____________________\|\n_______5'-AGCU___AU________C_______AUCUU...CAC-3'\n______________GAU__GAUGGAUG_AAAACAA\n______________:\|\|__\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUA__CUACUUAC_UUUUGUU\n3'-GUU...GCCGG___CU________________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________177___________________151\n	19 -- 25	154 -- 160	-15.1634 kcal/mol	3.68151 kcal/mol	0.959215 kcal/mol	1 28@LB@ \| \|@LB@ 5'-AGCU AU C AUCUU...CAC-3'@LB@ GAU GAUGGAUG AAAACAA@LB@ :\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UUA CUACUUAC UUUUGUU@LB@3'-GUU...GCCGG CU UAUUA...GGA-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -15.1634 kcal/mol@LB@Unfolding Energy - mRNA 3.68151 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 2 -- 27@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 154 -- 160@LB@
164	0.04503	0.7389	lmo2361	N/A	-17.31	0.035661	175 -- 215	153 -- 209		_____________174____________216\n_____________\|______________\|\n5'-CCA...AGGUA_________A____GAGGA...ACC-3'\n______________AUAAUGGGA_GAGG\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|\n______________UAUUGCCCU_CUCC\n3'-GUU...AUACG_________A____GUAUC...GGA-5'\n_____________\|______________\|\n_____________210____________152\n	177 -- 183	201 -- 207	-18.1933 kcal/mol	2.24476 kcal/mol	3.5857 kcal/mol	174 216@LB@ \| \|@LB@5'-CCA...AGGUA A GAGGA...ACC-3'@LB@ AUAAUGGGA GAGG@LB@ \|\|\|\|:\|\|\|\| \|\|\|\|@LB@ UAUUGCCCU CUCC@LB@3'-GUU...AUACG A GUAUC...GGA-5'@LB@ \| \|@LB@ 210 152@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -18.1933 kcal/mol@LB@Unfolding Energy - mRNA 2.24476 kcal/mol@LB@Unfolding Energy - sRNA 3.5857 kcal/mol@LB@@LB@Position - mRNA 175 -- 215@LB@Position - sRNA 153 -- 209@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 201 -- 207@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@
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@
53	0.0118	0.599	lmo2394	N/A	-15.56	0.076801	20 -- 80	100 -- 170		_____________19_____________________________________81\n_____________\|______________________________________\|\n5'-GGA...UUUUC________GUG___GG____________A_________AUAGU...AAA-3'\n______________GAUAGAUG___GAU________AUUUUG_UGGAGGAUG\n______________:\|:\|\|\|\|\|___\|\|:________\|\|\|:\|:_\|\|\|\|:\|\|\|\|\n______________UUGUCUAC___CUG________UAAGAU_ACCUUCUAC\n3'-GUU...CAGAU________AGA___AUCAACGG______A_________CUAUG...GGA-5'\n_____________\|______________________________________\|\n_____________171____________________________________99\n	189 -- 195	97 -- 103	-26.5698 kcal/mol	4.81204 kcal/mol	9.44565 kcal/mol	19 81@LB@ \| \|@LB@5'-GGA...UUUUC GUG GG A AUAGU...AAA-3'@LB@ GAUAGAUG GAU AUUUUG UGGAGGAUG@LB@ :\|:\|\|\|\|\| \|\|: \|\|\|:\|: \|\|\|\|:\|\|\|\|@LB@ UUGUCUAC CUG UAAGAU ACCUUCUAC@LB@3'-GUU...CAGAU AGA AUCAACGG A CUAUG...GGA-5'@LB@ \| \|@LB@ 171 99@LB@@LB@@LB@Energy -15.56 kcal/mol@LB@Hybridization Energy -26.5698 kcal/mol@LB@Unfolding Energy - mRNA 4.81204 kcal/mol@LB@Unfolding Energy - sRNA 9.44565 kcal/mol@LB@@LB@Position - mRNA 20 -- 80@LB@Position - sRNA 100 -- 170@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 97 -- 103@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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