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@
72	0.01905	0.6733	lmo2074	N/A	-18.09	0.024896	131 -- 158	147 -- 174		_____________130___________________159\n_____________\|_____________________\|\n5'-AUG...GAAAU________A____________AUAAG...CGC-3'\n______________UAAUG_GA_GAAUGGGAACAA\n______________:\|\|\|\|_\|\|_\|\|\|\|\|::\|\|\|\|\|\n______________GUUAC_CU_CUUACUUUUGUU\n3'-GUU...UGCCG_____U__A____________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________175___________________146\n	144 -- 150	154 -- 160	-16.7779 kcal/mol	1.50572 kcal/mol	0.962339 kcal/mol	130 159@LB@ \| \|@LB@5'-AUG...GAAAU A AUAAG...CGC-3'@LB@ UAAUG GA GAAUGGGAACAA@LB@ :\|\|\|\| \|\| \|\|\|\|\|::\|\|\|\|\|@LB@ GUUAC CU CUUACUUUUGUU@LB@3'-GUU...UGCCG U A UAUUA...GGA-5'@LB@ \| \|@LB@ 175 146@LB@@LB@@LB@Energy -18.09 kcal/mol@LB@Hybridization Energy -16.7779 kcal/mol@LB@Unfolding Energy - mRNA 1.50572 kcal/mol@LB@Unfolding Energy - sRNA 0.962339 kcal/mol@LB@@LB@Position - mRNA 131 -- 158@LB@Position - sRNA 147 -- 174@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 154 -- 160@LB@
89	0.02343	0.6733	lmo1651	N/A	-15.38	0.082912	189 -- 217	147 -- 170	ABC transporter ATP-binding protein	_____________188___________________________218\n_____________\|_____________________________\|\n5'-GAA...AGAAG______UAGCA___________UG_____ACAAG...UUC-3'\n______________GGGGUG_____GAUGGAAGCGA__AAUGA\n______________\|:\|:\|\|_____:\|\|\|:\|\|:\|:\|__\|\|\|\|\|\n______________CUCUAC_____UUACUUUUGUU__UUACU\n3'-GUU...GGUUA______________________UA_____AAAAC...GGA-5'\n_____________\|_____________________________\|\n_____________171___________________________146\n	204 -- 210	154 -- 160	-21.1438 kcal/mol	4.28476 kcal/mol	5.93585 kcal/mol	188 218@LB@ \| \|@LB@5'-GAA...AGAAG UAGCA UG ACAAG...UUC-3'@LB@ GGGGUG GAUGGAAGCGA AAUGA@LB@ \|:\|:\|\| :\|\|\|:\|\|:\|:\| \|\|\|\|\|@LB@ CUCUAC UUACUUUUGUU UUACU@LB@3'-GUU...GGUUA UA AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -21.1438 kcal/mol@LB@Unfolding Energy - mRNA 4.28476 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 189 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
100	0.02596	0.6733	lmo2805	N/A	-13.33	0.188364	273 -- 298	147 -- 172	hypothetical secreted protein	_____________272_______________________________________299\n_____________\|_________________________________________\|\n5'-GAA...CAUAC______GG_____AG_____AAAAA________________AAUAG...AAA-3'\n______________AACAGA____UGA__AGUUG____________GAGAUGGAU\n______________\|\|\|\|\|\|____\|\|\|__\|\|\|\|\|____________:\|\|\|\|\|\|\|\|\n______________UUGUCU____ACU__UCAAC____________UUCUACCUA\n3'-GUU...CAGAU______ACAG___GA_____GGUAAGAUAACC_________UGUGG...GGA-5'\n_____________\|_________________________________________\|\n_____________173_______________________________________146\n	211 -- 217	94 -- 100	-22.9496 kcal/mol	2.56346 kcal/mol	9.49359 kcal/mol	272 299@LB@ \| \|@LB@5'-GAA...CAUAC GG AG AAAAA AAUAG...AAA-3'@LB@ AACAGA UGA AGUUG GAGAUGGAU@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUGUCU ACU UCAAC UUCUACCUA@LB@3'-GUU...CAGAU ACAG GA GGUAAGAUAACC UGUGG...GGA-5'@LB@ \| \|@LB@ 173 146@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -22.9496 kcal/mol@LB@Unfolding Energy - mRNA 2.56346 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 147 -- 172@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 94 -- 100@LB@
132	0.03532	0.6968	lmo1773	purB	-14.78	0.106383	9 -- 45	147 -- 186	adenylosuccinate lyase	_____________8___________________________46\n_____________\|___________________________\|\n5'-AUA...AUGUU____CU_____________________AUUAU...CUU-3'\n______________GAUG__GUGAAU__AAACAAAUGGUGA\n______________:\|\|\|__:\|\|\|\|\|__\|\|\|\|\|\|\|\|::\|\|\|\n______________UUAC__UACUUA__UUUGUUUAUUACU\n3'-GUU...GCCGG____UC______CU_____________AAAAC...GGA-5'\n_____________\|___________________________\|\n_____________187_________________________146\n	33 -- 39	153 -- 159	-18.9825 kcal/mol	5.01078 kcal/mol	5.96192 kcal/mol	8 46@LB@ \| \|@LB@5'-AUA...AUGUU CU AUUAU...CUU-3'@LB@ GAUG GUGAAU AAACAAAUGGUGA@LB@ :\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|\|::\|\|\|@LB@ UUAC UACUUA UUUGUUUAUUACU@LB@3'-GUU...GCCGG UC CU AAAAC...GGA-5'@LB@ \| \|@LB@ 187 146@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -18.9825 kcal/mol@LB@Unfolding Energy - mRNA 5.01078 kcal/mol@LB@Unfolding Energy - sRNA 5.96192 kcal/mol@LB@@LB@Position - mRNA 9 -- 45@LB@Position - sRNA 147 -- 186@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 153 -- 159@LB@
140	0.0365	0.6968	lmo1717	N/A	-17.46	0.033387	195 -- 217	147 -- 170		_____________194______________________218\n_____________\|________________________\|\n5'-UAG...AGUAG____C___________________AACAC...AAA-3'\n______________GAGA__GAUGAAAAUGGAUAGUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|:::\|\|\|:\|\|\|\n______________CUCU__UUACUUUUGUUUAUUACU\n3'-GUU...GGUUA____AC__________________AAAAC...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	203 -- 209	155 -- 161	-21.6361 kcal/mol	2.67158 kcal/mol	5.93585 kcal/mol	194 218@LB@ \| \|@LB@5'-UAG...AGUAG C AACAC...AAA-3'@LB@ GAGA GAUGAAAAUGGAUAGUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|:::\|\|\|:\|\|\|@LB@ CUCU UUACUUUUGUUUAUUACU@LB@3'-GUU...GGUUA AC AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -21.6361 kcal/mol@LB@Unfolding Energy - mRNA 2.67158 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 195 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
145	0.03765	0.6968	lmo0134	N/A	-12.36	0.267504	193 -- 220	147 -- 170		_____________192__________________________221\n_____________\|____________________________\|\n5'-GGG...AGGAG_____UA_______UAUAA_________AAAUA...UUA-3'\n______________GAGAU__AAUGGAA_____AAAUGGUGA\n______________\|\|\|\|\|__\|\|\|\|:\|\|_____\|\|\|\|::\|\|\|\n______________CUCUA__UUACUUU_____UUUAUUACU\n3'-GUU...GGUUA_____C________UG____________AAAAC...GGA-5'\n_____________\|____________________________\|\n_____________171__________________________146\n	200 -- 206	158 -- 164	-15.5721 kcal/mol	1.73331 kcal/mol	5.93585 kcal/mol	192 221@LB@ \| \|@LB@5'-GGG...AGGAG UA UAUAA AAAUA...UUA-3'@LB@ GAGAU AAUGGAA AAAUGGUGA@LB@ \|\|\|\|\| \|\|\|\|:\|\| \|\|\|\|::\|\|\|@LB@ CUCUA UUACUUU UUUAUUACU@LB@3'-GUU...GGUUA C UG AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -15.5721 kcal/mol@LB@Unfolding Energy - mRNA 1.73331 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 193 -- 220@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
172	0.04804	0.7516	lmo0111	N/A	-17.34	0.035270	180 -- 204	147 -- 170	lmo0111	_____________179______________________205\n_____________\|________________________\|\n5'-AAU...AUAGA____A_A________G________GGACU...CAG-3'\n______________GAGG_G_AAUGAGAA_GGAUGAUG\n______________\|\|\|:_\|_\|\|\|\|\|:\|\|_::\|\|:\|\|\|\n______________CUCU_C_UUACUUUU_UUUAUUAC\n3'-GUU...GGUUA____A__________G________UAAAA...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	188 -- 194	157 -- 163	-20.9699 kcal/mol	2.01501 kcal/mol	5.93381 kcal/mol	179 205@LB@ \| \|@LB@5'-AAU...AUAGA A A G GGACU...CAG-3'@LB@ GAGG G AAUGAGAA GGAUGAUG@LB@ \|\|\|: \| \|\|\|\|\|:\|\| ::\|\|:\|\|\|@LB@ CUCU C UUACUUUU UUUAUUAC@LB@3'-GUU...GGUUA A G UAAAA...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.34 kcal/mol@LB@Hybridization Energy -20.9699 kcal/mol@LB@Unfolding Energy - mRNA 2.01501 kcal/mol@LB@Unfolding Energy - sRNA 5.93381 kcal/mol@LB@@LB@Position - mRNA 180 -- 204@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 157 -- 163@LB@
185	0.05367	0.7607	lmo1631	trpD	-14.92	0.100424	142 -- 163	148 -- 170	anthranilate phosphoribosyltransferase	_____________141__________________164\n_____________\|____________________\|\n5'-UUC...UACGA____CG______________GAAAA...AAA-3'\n______________AUGA__GAAAACAAAUGAUG\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UACU__CUUUUGUUUAUUAC\n3'-GUU...UACUC____UA______________UAAAA...GGA-5'\n_____________\|____________________\|\n_____________171__________________147\n	153 -- 159	152 -- 158	-19.3831 kcal/mol	2.89443 kcal/mol	5.80116 kcal/mol	141 164@LB@ \| \|@LB@5'-UUC...UACGA CG GAAAA...AAA-3'@LB@ AUGA GAAAACAAAUGAUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UACU CUUUUGUUUAUUAC@LB@3'-GUU...UACUC UA UAAAA...GGA-5'@LB@ \| \|@LB@ 171 147@LB@@LB@@LB@Energy -14.92 kcal/mol@LB@Hybridization Energy -19.3831 kcal/mol@LB@Unfolding Energy - mRNA 2.89443 kcal/mol@LB@Unfolding Energy - sRNA 5.80116 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 148 -- 170@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 152 -- 158@LB@
64	0.01603	0.6733	lmo0131	N/A	-19.25	0.014339	193 -- 248	149 -- 204		_____________192____________________________________________________249\n_____________\|______________________________________________________\|\n5'-UGU...AAAAG____G_____G______AUCUCGA______AAAU________C___UAG_____AUAGU...UCG-3'\n______________GAGG_AUA_A_AUGGAU_______GCACGG____AUGGGAUG_GAU___GAGAA\n______________\|\|\|\|_\|\|\|_\|_\|\|\|:\|:_______:\|\|\|\|\|____\|\|\|:\|\|\|\|_:\|\|___\|\|:\|\|\n______________CUCC_UAU_U_UACUUG_______UGUGCC____UACUCUAC_UUA___CUUUU\n3'-GUU...CCCUA____G___C_G______A____________GGU_____________________GUUUA...GGA-5'\n_____________\|______________________________________________________\|\n_____________205____________________________________________________148\n	225 -- 231	165 -- 171	-32.0138 kcal/mol	8.31689 kcal/mol	13.9574 kcal/mol	192 249@LB@ \| \|@LB@5'-UGU...AAAAG G G AUCUCGA AAAU C UAG AUAGU...UCG-3'@LB@ GAGG AUA A AUGGAU GCACGG AUGGGAUG GAU GAGAA@LB@ \|\|\|\| \|\|\| \| \|\|\|:\|: :\|\|\|\|\| \|\|\|:\|\|\|\| :\|\| \|\|:\|\|@LB@ CUCC UAU U UACUUG UGUGCC UACUCUAC UUA CUUUU@LB@3'-GUU...CCCUA G C G A GGU GUUUA...GGA-5'@LB@ \| \|@LB@ 205 148@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -32.0138 kcal/mol@LB@Unfolding Energy - mRNA 8.31689 kcal/mol@LB@Unfolding Energy - sRNA 13.9574 kcal/mol@LB@@LB@Position - mRNA 193 -- 248@LB@Position - sRNA 149 -- 204@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 165 -- 171@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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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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