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
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@
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@
44	0.01013	0.599	lmo0022	N/A	-16.20	0.058356	176 -- 261	150 -- 213	PTS fructose transporter subunit IIB	_____________175________________262\n_____________\|__________________\|\n5'-CCG...GUGAU_______A___A______UGAUG...UCA-3'\n______________GAUGGGG_GGA_GAGGAC\n______________:\|\|\|:\|:_\|:\|_\|\|::\|\|\n______________UUACUCU_CUU_CUUUUG\n3'-GUU...GCCGG_______A___A______UUUAU...GGA-5'\n_____________\|__________________\|\n_____________214________________149\n	181 -- 187	167 -- 173	-14.383 kcal/mol	2.57794 kcal/mol	0.941471 kcal/mol	175 262@LB@ \| \|@LB@5'-CCG...GUGAU A A UGAUG...UCA-3'@LB@ GAUGGGG GGA GAGGAC@LB@ :\|\|\|:\|: \|:\| \|\|::\|\|@LB@ UUACUCU CUU CUUUUG@LB@3'-GUU...GCCGG A A UUUAU...GGA-5'@LB@ \| \|@LB@ 214 149@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -14.383 kcal/mol@LB@Unfolding Energy - mRNA 2.57794 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 176 -- 261@LB@Position - sRNA 150 -- 213@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 167 -- 173@LB@
26	0.004866	0.5029	lmo0682	flgG	-18.63	0.019297	177 -- 239	156 -- 207	flagellar basal body rod protein FlgG	_____________176__________________________________________240\n_____________\|____________________________________________\|\n5'-GAA...ACCAA_______GU_______CGGA__G___________AC____A___GGCAG...UCA-3'\n______________AGA_GUC__UGGCUAG____GC_G_UUUGUUGGA__GGAU_GGA\n______________\|\|\|_\|\|\|__\|\|:\|\|\|\|____\|\|_:_\|:\|:\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UCU_CAG__ACUGAUC____CG_U_AGAUAACCU__UCUA_CCU\n3'-GUU...AUUUG___A____________AA____G_A___________________AUGUG...GGA-5'\n_____________\|____________________________________________\|\n_____________208__________________________________________155\n	171 -- 177	102 -- 108	-30.3451 kcal/mol	11.2986 kcal/mol	9.4836 kcal/mol	176 240@LB@ \| \|@LB@5'-GAA...ACCAA GU CGGA G AC A GGCAG...UCA-3'@LB@ AGA GUC UGGCUAG GC G UUUGUUGGA GGAU GGA@LB@ \|\|\| \|\|\| \|\|:\|\|\|\| \|\| : \|:\|:\|\|\|\|\| :\|\|\| \|\|\|@LB@ UCU CAG ACUGAUC CG U AGAUAACCU UCUA CCU@LB@3'-GUU...AUUUG A AA G A AUGUG...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -30.3451 kcal/mol@LB@Unfolding Energy - mRNA 11.2986 kcal/mol@LB@Unfolding Energy - sRNA 9.4836 kcal/mol@LB@@LB@Position - mRNA 177 -- 239@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 102 -- 108@LB@
85	0.0229	0.6733	lmo1788	N/A	-18.82	0.017630	177 -- 227	165 -- 211	transcriptional regulator	_____________176______________________________________________________228\n_____________\|________________________________________________________\|\n5'-UCU...AAAUG_______C______G____AA__G_____AAAA__A____CUGCUUAU________UUCAG...GGC-3'\n______________GAGGUGU_AGAUAU_GAAC__UG_ACGGU____GA_AUGG________GUGGGGAU\n______________\|\|\|\|::\|_\|\|\|:\|\|_\|\|\|\|__\|:_\|\|\|\|:____\|\|_\|\|\|:________:\|\|:::\|:\n______________CUCCGUA_UCUGUA_CUUG__AU_UGCCG____CU_UACU________UACUUUUG\n3'-GUU...CCCUA_______________________G_____GUUA__C____________________UUUAU...GGA-5'\n_____________\|________________________________________________________\|\n_____________212______________________________________________________164\n	238 -- 244	156 -- 162	-32.2408 kcal/mol	14.3369 kcal/mol	13.9689 kcal/mol	176 228@LB@ \| \|@LB@5'-UCU...AAAUG C G AA G AAAA A CUGCUUAU UUCAG...GGC-3'@LB@ GAGGUGU AGAUAU GAAC UG ACGGU GA AUGG GUGGGGAU@LB@ \|\|\|\|::\| \|\|\|:\|\| \|\|\|\| \|: \|\|\|\|: \|\| \|\|\|: :\|\|:::\|:@LB@ CUCCGUA UCUGUA CUUG AU UGCCG CU UACU UACUUUUG@LB@3'-GUU...CCCUA G GUUA C UUUAU...GGA-5'@LB@ \| \|@LB@ 212 164@LB@@LB@@LB@Energy -18.82 kcal/mol@LB@Hybridization Energy -32.2408 kcal/mol@LB@Unfolding Energy - mRNA 14.3369 kcal/mol@LB@Unfolding Energy - sRNA 13.9689 kcal/mol@LB@@LB@Position - mRNA 177 -- 227@LB@Position - sRNA 165 -- 211@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 156 -- 162@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@
35	0.00718	0.552	lmo0397	N/A	-24.49	0.000911	178 -- 232	160 -- 211		_____________177_________________________________________________________________________233\n_____________\|___________________________________________________________________________\|\n5'-AAU...ACAAA_______AAAAUGAAAGCAAAU_____________G__UU_G______GAG___AU__AA___C___________UAUGA...CGA-3'\n______________CUGUGCG_______________UGGCGGGA___GG_AU__A_AUGAAC___GCA__CG__CGA_GAGAUGA_UGA\n______________\|\|:\|\|\|:_______________\|::\|\|\|\|\|___\|\|_\|\|__\|_\|\|\|\|\|\|___:\|\|__\|\|__\|:\|_\|\|\|\|\|\|\|_\|\|\|\n______________GAUACGU_______________AUUGCCCU___CC_UA__U_UACUUG___UGU__GC__GUU_CUCUACU_ACU\n3'-GUU...CCGCG______________________________ACU__G__UC_G______A_________CG___A_______U___UUUGU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________212_________________________________________________________________________159\n	223 -- 229	164 -- 170	-45.3132 kcal/mol	12.0365 kcal/mol	19.7814 kcal/mol	177 233@LB@ \| \|@LB@5'-AAU...ACAAA AAAAUGAAAGCAAAU G UU G GAG AU AA C UAUGA...CGA-3'@LB@ CUGUGCG UGGCGGGA GG AU A AUGAAC GCA CG CGA GAGAUGA UGA@LB@ \|\|:\|\|\|: \|::\|\|\|\|\| \|\| \|\| \| \|\|\|\|\|\| :\|\| \|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ GAUACGU AUUGCCCU CC UA U UACUUG UGU GC GUU CUCUACU ACU@LB@3'-GUU...CCGCG ACU G UC G A CG A U UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -24.49 kcal/mol@LB@Hybridization Energy -45.3132 kcal/mol@LB@Unfolding Energy - mRNA 12.0365 kcal/mol@LB@Unfolding Energy - sRNA 19.7814 kcal/mol@LB@@LB@Position - mRNA 178 -- 232@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 164 -- 170@LB@
95	0.02474	0.6733	lmo2446	N/A	-18.44	0.021161	178 -- 278	95 -- 188	glycosidase	_____________177____________________279\n_____________\|______________________\|\n5'-UGA...AGGAA___________GC_A_______GAAAA...ACG-3'\n______________AGUGAGAUGAA__G_AGAACGA\n______________\|:\|\|\|\|\|\|\|\|\|__\|_\|:\|\|\|:\|\n______________UUACUCUACUU__C_UUUUGUU\n3'-GUU...GCCGG___________A__________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________189____________________94\n	210 -- 216	154 -- 160	-17.9823 kcal/mol	4.45349 kcal/mol	0.959215 kcal/mol	177 279@LB@ \| \|@LB@5'-UGA...AGGAA GC A GAAAA...ACG-3'@LB@ AGUGAGAUGAA G AGAACGA@LB@ \|:\|\|\|\|\|\|\|\|\| \| \|:\|\|\|:\|@LB@ UUACUCUACUU C UUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 189 94@LB@@LB@@LB@Energy -18.44 kcal/mol@LB@Hybridization Energy -17.9823 kcal/mol@LB@Unfolding Energy - mRNA 4.45349 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 178 -- 278@LB@Position - sRNA 95 -- 188@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 154 -- 160@LB@
110	0.02752	0.6733	lmo0057	N/A	-17.32	0.035592	178 -- 213	150 -- 185		_____________177_________________214\n_____________\|___________________\|\n5'-AAA...GCGGG_______CA__________AAGUA...AAG-3'\n______________AGUGGGA__UGAAUGAAGA\n______________\|:\|\|:\|\|__\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__ACUUACUUUU\n3'-GUU...GCCGG___________________GUUUA...GGA-5'\n_____________\|___________________\|\n_____________186_________________149\n	201 -- 207	157 -- 163	-16.939 kcal/mol	2.5385 kcal/mol	0.930085 kcal/mol	177 214@LB@ \| \|@LB@5'-AAA...GCGGG CA AAGUA...AAG-3'@LB@ AGUGGGA UGAAUGAAGA@LB@ \|:\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU ACUUACUUUU@LB@3'-GUU...GCCGG GUUUA...GGA-5'@LB@ \| \|@LB@ 186 149@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -16.939 kcal/mol@LB@Unfolding Energy - mRNA 2.5385 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 178 -- 213@LB@Position - sRNA 150 -- 185@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@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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