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
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@
5	0.001245	0.4469	lmo1835	carB	-22.95	0.002153	176 -- 228	154 -- 207	carbamoyl-phosphate synthetase	_____________175____________________________________________________________229\n_____________\|______________________________________________________________\|\n5'-AAA...UGGAA___AUG_______AA_______________________C____AC_C__C__UAUA______AUUCU...CUU-3'\n______________AUG___AAUGGGA__GAGG___AGG_GUGAACUACAUG_CUAA__G_GA_GA____AAAACA\n______________\|\|\|___\|\|:\|\|\|\|__\|\|\|\|___\|\|:_:\|\|\|\|\|\|\|\|\|:\|_\|:\|\|__\|_\|\|_\|\|____\|\|\|\|\|\|\n______________UAC___UUGCCCU__CUCC___UCU_UACUUGAUGUGC_GGUU__C_CU_CU____UUUUGU\n3'-GUU...GCGGA___GUA_______A_____GUA___G____________C____A__U__A__UAC_______UUAUU...GGA-5'\n_____________\|______________________________________________________________\|\n_____________208____________________________________________________________153\n	194 -- 200	180 -- 186	-39.6119 kcal/mol	8.25276 kcal/mol	19.5968 kcal/mol	175 229@LB@ \| \|@LB@5'-AAA...UGGAA AUG AA C AC C C UAUA AUUCU...CUU-3'@LB@ AUG AAUGGGA GAGG AGG GUGAACUACAUG CUAA G GA GA AAAACA@LB@ \|\|\| \|\|:\|\|\|\| \|\|\|\| \|\|: :\|\|\|\|\|\|\|\|\|:\| \|:\|\| \| \|\| \|\| \|\|\|\|\|\|@LB@ UAC UUGCCCU CUCC UCU UACUUGAUGUGC GGUU C CU CU UUUUGU@LB@3'-GUU...GCGGA GUA A GUA G C A U A UAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -39.6119 kcal/mol@LB@Unfolding Energy - mRNA 8.25276 kcal/mol@LB@Unfolding Energy - sRNA 19.5968 kcal/mol@LB@@LB@Position - mRNA 176 -- 228@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 180 -- 186@LB@
6	0.001395	0.4469	lmo2078	N/A	-19.77	0.011149	188 -- 240	154 -- 207		_____________187___________________________________________________________________241\n_____________\|_____________________________________________________________________\|\n5'-GAU...UUUAU_____C______U__________U____UA____________AAUG____A_G________________UUCGA...AGG-3'\n______________UUUGG_GCGUCU_UGU_____GG_AUGA__UGUAGA___GAA____AUGG_C_GGUGAGGU_AAUGGAA\n______________\|\|:\|\|_\|\|\|:\|\|_\|\|:_____\|\|_\|\|\|\|__::\|\|\|\|___\|\|\|____\|:\|\|_\|_::\|\|\|\|:\|_\|\|\|\|:\|\|\n______________AAGCC_CGCGGA_ACG_____CC_UACU__GUAUCU___CUU____UGCC_G_UUACUCUA_UUACUUU\n3'-GUU...AGUAC____________U___UAUUG__C____CC______GUA___GAUG______G________C_______UGUUU...GGA-5'\n_____________\|_____________________________________________________________________\|\n_____________208___________________________________________________________________153\n	200 -- 206	158 -- 164	-46.039 kcal/mol	12.924 kcal/mol	22.2029 kcal/mol	187 241@LB@ \| \|@LB@5'-GAU...UUUAU C U U UA AAUG A G UUCGA...AGG-3'@LB@ UUUGG GCGUCU UGU GG AUGA UGUAGA GAA AUGG C GGUGAGGU AAUGGAA@LB@ \|\|:\|\| \|\|\|:\|\| \|\|: \|\| \|\|\|\| ::\|\|\|\| \|\|\| \|:\|\| \| ::\|\|\|\|:\| \|\|\|\|:\|\|@LB@ AAGCC CGCGGA ACG CC UACU GUAUCU CUU UGCC G UUACUCUA UUACUUU@LB@3'-GUU...AGUAC U UAUUG C CC GUA GAUG G C UGUUU...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -19.77 kcal/mol@LB@Hybridization Energy -46.039 kcal/mol@LB@Unfolding Energy - mRNA 12.924 kcal/mol@LB@Unfolding Energy - sRNA 22.2029 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
11	0.002745	0.4469	lmo0197	N/A	-21.05	0.005861	175 -- 258	154 -- 211	regulatory protein SpoVG	_____________174__________________259\n_____________\|____________________\|\n5'-UUA...AAACU_______A____________UUGCU...AUA-3'\n______________GAUG_GA_GAAUGAGAGCGA\n______________:\|\|\|_\|\|_\|\|\|\|\|\|:\|:\|:\|\n______________UUAC_CU_CUUACUUUUGUU\n3'-GUU...GCCGG____U__A____________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________212__________________153\n	252 -- 258	154 -- 160	-17.4227 kcal/mol	2.96559 kcal/mol	0.959215 kcal/mol	174 259@LB@ \| \|@LB@5'-UUA...AAACU A UUGCU...AUA-3'@LB@ GAUG GA GAAUGAGAGCGA@LB@ :\|\|\| \|\| \|\|\|\|\|\|:\|:\|:\|@LB@ UUAC CU CUUACUUUUGUU@LB@3'-GUU...GCCGG U A UAUUA...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -21.05 kcal/mol@LB@Hybridization Energy -17.4227 kcal/mol@LB@Unfolding Energy - mRNA 2.96559 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 175 -- 258@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 154 -- 160@LB@
12	0.002933	0.4469	lmo1952	lysA	-19.68	0.011630	182 -- 245	154 -- 213	diaminopimelate decarboxylase	_____________181___________________________________________________________246\n_____________\|_____________________________________________________________\|\n5'-UUG...CUAUA_____AAGG______U__________________A______UG___ACA_______U____GCAGA...CGC-3'\n______________AUGUA____UGGGAU__GGCGU_GACGU___UUG_ACGGCU___GA___AUGAAUG_AAAU\n______________\|\|\|:\|____:\|\|\|\|\|__\|\|\|:\|_\|\|\|:\|___:\|:_\|\|\|\|\|:___\|\|___\|\|\|\|\|\|\|_\|\|\|:\n______________UACGU____GCCCUA__CCGUA_CUGUA___GAU_UGCCGG___CU___UACUUAC_UUUG\n3'-GUU...GCGGA_____AUU_______CU_____U_____CUU___G______UUA__C_________U____UUUAU...GGA-5'\n_____________\|_____________________________________________________________\|\n_____________214___________________________________________________________153\n	225 -- 231	161 -- 167	-39.877 kcal/mol	10.395 kcal/mol	19.5834 kcal/mol	181 246@LB@ \| \|@LB@5'-UUG...CUAUA AAGG U A UG ACA U GCAGA...CGC-3'@LB@ AUGUA UGGGAU GGCGU GACGU UUG ACGGCU GA AUGAAUG AAAU@LB@ \|\|\|:\| :\|\|\|\|\| \|\|\|:\| \|\|\|:\| :\|: \|\|\|\|\|: \|\| \|\|\|\|\|\|\| \|\|\|:@LB@ UACGU GCCCUA CCGUA CUGUA GAU UGCCGG CU UACUUAC UUUG@LB@3'-GUU...GCGGA AUU CU U CUU G UUA C U UUUAU...GGA-5'@LB@ \| \|@LB@ 214 153@LB@@LB@@LB@Energy -19.68 kcal/mol@LB@Hybridization Energy -39.877 kcal/mol@LB@Unfolding Energy - mRNA 10.395 kcal/mol@LB@Unfolding Energy - sRNA 19.5834 kcal/mol@LB@@LB@Position - mRNA 182 -- 245@LB@Position - sRNA 154 -- 213@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 161 -- 167@LB@
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@
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@
31	0.00657	0.5515	lmo1828	N/A	-18.66	0.019040	211 -- 279	154 -- 211		_____________210__________280\n_____________\|____________\|\n5'-AGU...GAAAA____________UUGGG...AAU-3'\n______________GCAUGACGGGAU\n______________\|\|\|\|:\|\|\|\|\|\|\|\n______________CGUAUUGCCCUA\n3'-GUU...GGAUA____________CUCCG...GGA-5'\n_____________\|____________\|\n_____________212__________153\n	216 -- 222	200 -- 206	-19.8213 kcal/mol	2.93239 kcal/mol	6.43166 kcal/mol	210 280@LB@ \| \|@LB@5'-AGU...GAAAA UUGGG...AAU-3'@LB@ GCAUGACGGGAU@LB@ \|\|\|\|:\|\|\|\|\|\|\|@LB@ CGUAUUGCCCUA@LB@3'-GUU...GGAUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -18.66 kcal/mol@LB@Hybridization Energy -19.8213 kcal/mol@LB@Unfolding Energy - mRNA 2.93239 kcal/mol@LB@Unfolding Energy - sRNA 6.43166 kcal/mol@LB@@LB@Position - mRNA 211 -- 279@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 200 -- 206@LB@
33	0.006763	0.5515	lmo1941	N/A	-21.42	0.004845	223 -- 286	154 -- 207		_____________222___________________________________________________________________287\n_____________\|_____________________________________________________________________\|\n5'-UAG...AGAAA_______AUACGAAGAACC___UGAUUAU________UU___AA_________________UC______UGAAC...UGU-3'\n______________AACGGGA____________GGC_______GACAUGAG__CUG___GGCCA___AGAUGAAU___AACAA\n______________\|\|\|\|\|\|\|____________\|\|\|_______\|\|\|\|\|\|\|:__\|\|:___\|\|\|\|\|___\|\|\|\|\|\|\|\|___\|\|\|\|\|\n______________UUGCCCU____________CCG_______CUGUACUU__GAU___CCGGU___UCUACUUA___UUGUU\n3'-GUU...ACGUA_______ACU____________UAU_________________GUG_____UAC________CUU_____UAUUA...GGA-5'\n_____________\|_____________________________________________________________________\|\n_____________208___________________________________________________________________153\n	273 -- 279	162 -- 168	-39.5283 kcal/mol	10.6608 kcal/mol	18.6655 kcal/mol	222 287@LB@ \| \|@LB@5'-UAG...AGAAA AUACGAAGAACC UGAUUAU UU AA UC UGAAC...UGU-3'@LB@ AACGGGA GGC GACAUGAG CUG GGCCA AGAUGAAU AACAA@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGCCCU CCG CUGUACUU GAU CCGGU UCUACUUA UUGUU@LB@3'-GUU...ACGUA ACU UAU GUG UAC CUU UAUUA...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -21.42 kcal/mol@LB@Hybridization Energy -39.5283 kcal/mol@LB@Unfolding Energy - mRNA 10.6608 kcal/mol@LB@Unfolding Energy - sRNA 18.6655 kcal/mol@LB@@LB@Position - mRNA 223 -- 286@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 162 -- 168@LB@
62	0.01477	0.6412	lmo1163	N/A	-15.96	0.064740	175 -- 219	154 -- 212	carbon dioxide concentrating mechanism protein	_____________174_________________________________________________________220\n_____________\|___________________________________________________________\|\n5'-UAG...AAUAU____GU______A______GU_____UAUGUU______A____________________CAGGA...AUG-3'\n______________UGCA__GCGGGA__AGGCA__GACGU______UAUGGC______________AAAAUAA\n______________\|\|\|\|__:\|\|\|\|\|__\|\|\|\|\|__\|\|\|:\|______:\|:\|\|\|______________\|\|\|\|:\|\|\n______________ACGU__UGCCCU__UCCGU__CUGUA______GUGCCG______________UUUUGUU\n3'-GUU...CGGAU____AU______AC_____AU_____CUUGAU______GUUACUCUACUUAC_______UAUUA...GGA-5'\n_____________\|___________________________________________________________\|\n_____________213_________________________________________________________153\n	213 -- 219	154 -- 160	-36.6169 kcal/mol	12.1656 kcal/mol	19.5998 kcal/mol	174 220@LB@ \| \|@LB@5'-UAG...AAUAU GU A GU UAUGUU A CAGGA...AUG-3'@LB@ UGCA GCGGGA AGGCA GACGU UAUGGC AAAAUAA@LB@ \|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|\|\|:\| :\|:\|\|\| \|\|\|\|:\|\|@LB@ ACGU UGCCCU UCCGU CUGUA GUGCCG UUUUGUU@LB@3'-GUU...CGGAU AU AC AU CUUGAU GUUACUCUACUUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.96 kcal/mol@LB@Hybridization Energy -36.6169 kcal/mol@LB@Unfolding Energy - mRNA 12.1656 kcal/mol@LB@Unfolding Energy - sRNA 19.5998 kcal/mol@LB@@LB@Position - mRNA 175 -- 219@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 213 -- 219@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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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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