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
175	0.04975	0.7607	lmo0194	N/A	-16.29	0.056201	181 -- 242	155 -- 212	ABC transporter ATP-binding protein	_____________180________________________243\n_____________\|__________________________\|\n_______5'-AAGA________AAACGAAAAA________AAUUU...AGC-3'\n______________CAAUGGGA__________AGUGAAGA\n______________\|\|\|\|\|:\|\|__________\|:\|\|\|\|:\|\n______________GUUACUCU__________UUACUUUU\n3'-GUU...UGCCG________AC________________GUUUA...GGA-5'\n_____________\|__________________________\|\n_____________213________________________154\n	24 -- 30	157 -- 163	-10.5893 kcal/mol	0.67181 kcal/mol	0.933292 kcal/mol	180 243@LB@ \| \|@LB@ 5'-AAGA AAACGAAAAA AAUUU...AGC-3'@LB@ CAAUGGGA AGUGAAGA@LB@ \|\|\|\|\|:\|\| \|:\|\|\|\|:\|@LB@ GUUACUCU UUACUUUU@LB@3'-GUU...UGCCG AC GUUUA...GGA-5'@LB@ \| \|@LB@ 213 154@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -10.5893 kcal/mol@LB@Unfolding Energy - mRNA 0.67181 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 181 -- 242@LB@Position - sRNA 155 -- 212@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 157 -- 163@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@
15	0.003165	0.4469	lmo0292	N/A	-21.41	0.004857	182 -- 249	155 -- 212	heat-shock protein htrA serine protease	_____________181_____________________________________________________________250\n_____________\|_______________________________________________________________\|\n5'-GAG...GCAGA____AAGGA__________G_G_AAGAAAAGAAUUUA_____AAACAGC______________CGCCG...AAC-3'\n______________GAGG_____AGACAUGGAC_A_A______________AAUGA_______GA_GAAUGAAAGCA\n______________\|\|\|\|_____\|\|\|\|\|\|\|:\|\|_\|_\|______________\|\|\|\|\|_______\|\|_\|\|\|\|\|\|\|\|:\|\|\n______________CUCC_____UCUGUACUUG_U_U______________UUACU_______CU_CUUACUUUUGU\n3'-GUU...CCCUA____GUA____________A_G_GCCGG_______________________A___________UUAUU...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________213_____________________________________________________________154\n	243 -- 249	155 -- 161	-30.3296 kcal/mol	4.19045 kcal/mol	13.9822 kcal/mol	181 250@LB@ \| \|@LB@5'-GAG...GCAGA AAGGA G G AAGAAAAGAAUUUA AAACAGC CGCCG...AAC-3'@LB@ GAGG AGACAUGGAC A A AAUGA GA GAAUGAAAGCA@LB@ \|\|\|\| \|\|\|\|\|\|\|:\|\| \| \| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|:\|\|@LB@ CUCC UCUGUACUUG U U UUACU CU CUUACUUUUGU@LB@3'-GUU...CCCUA GUA A G GCCGG A UUAUU...GGA-5'@LB@ \| \|@LB@ 213 154@LB@@LB@@LB@Energy -21.41 kcal/mol@LB@Hybridization Energy -30.3296 kcal/mol@LB@Unfolding Energy - mRNA 4.19045 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 182 -- 249@LB@Position - sRNA 155 -- 212@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 155 -- 161@LB@
16	0.003215	0.4469	lmo1403	mutS	-20.74	0.006867	183 -- 222	169 -- 209	DNA mismatch repair protein MutS	_____________182________________223\n_____________\|__________________\|\n5'-ACG...UGCUA__________________AGAAG...UGU-3'\n______________UAAUGAGA_GGAUGAAAA\n______________:\|\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________GUUACUCU_CUUACUUUU\n3'-GUU...UGCCG________A_________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________210________________168\n	172 -- 178	157 -- 163	-16.7756 kcal/mol	1.79354 kcal/mol	0.933292 kcal/mol	182 223@LB@ \| \|@LB@5'-ACG...UGCUA AGAAG...UGU-3'@LB@ UAAUGAGA GGAUGAAAA@LB@ :\|\|\|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GUUACUCU CUUACUUUU@LB@3'-GUU...UGCCG A GUUUA...GGA-5'@LB@ \| \|@LB@ 210 168@LB@@LB@@LB@Energy -20.74 kcal/mol@LB@Hybridization Energy -16.7756 kcal/mol@LB@Unfolding Energy - mRNA 1.79354 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 183 -- 222@LB@Position - sRNA 169 -- 209@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 157 -- 163@LB@
20	0.003655	0.4469	lmo1591	argC	-21.66	0.004270	183 -- 240	156 -- 208	N-acetyl-gamma-glutamyl-phosphate reductase	_____________182___________________________________________________________241\n_____________\|_____________________________________________________________\|\n5'-AAA...AUAAU________A________________AGUUUCAAU__U____G___C_______UG______UUGAG...GUU-3'\n______________UAACGGGG_GGGGU_UAGG_AUGAA_________CA_UGGC_CGA_GGGGU_A__GAGGAC\n______________\|\|\|\|\|\|\|:_\|:\|\|:_\|\|\|:_\|\|\|\|\|_________\|\|_:\|\|\|_\|:\|_\|:\|:\|_\|__\|\|::\|\|\n______________AUUGCCCU_CUCCG_AUCU_UACUU_________GU_GCCG_GUU_CUCUA_U__CUUUUG\n3'-GUU...UACGU________A_____U____G_____GAU_________________A_____C_UA______UUUAU...GGA-5'\n_____________\|_____________________________________________________________\|\n_____________209___________________________________________________________155\n	184 -- 190	201 -- 207	-40.8209 kcal/mol	11.7 kcal/mol	18.6528 kcal/mol	182 241@LB@ \| \|@LB@5'-AAA...AUAAU A AGUUUCAAU U G C UG UUGAG...GUU-3'@LB@ UAACGGGG GGGGU UAGG AUGAA CA UGGC CGA GGGGU A GAGGAC@LB@ \|\|\|\|\|\|\|: \|:\|\|: \|\|\|: \|\|\|\|\| \|\| :\|\|\| \|:\| \|:\|:\| \| \|\|::\|\|@LB@ AUUGCCCU CUCCG AUCU UACUU GU GCCG GUU CUCUA U CUUUUG@LB@3'-GUU...UACGU A U G GAU A C UA UUUAU...GGA-5'@LB@ \| \|@LB@ 209 155@LB@@LB@@LB@Energy -21.66 kcal/mol@LB@Hybridization Energy -40.8209 kcal/mol@LB@Unfolding Energy - mRNA 11.7 kcal/mol@LB@Unfolding Energy - sRNA 18.6528 kcal/mol@LB@@LB@Position - mRNA 183 -- 240@LB@Position - sRNA 156 -- 208@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 201 -- 207@LB@
25	0.004689	0.5029	lmo1584	N/A	-20.33	0.008463	183 -- 211	169 -- 209		_____________182___________212\n_____________\|_____________\|\n5'-GAA...GGCGC_____________AAAUG...CUG-3'\n______________ACAUGGCUAAUGA\n______________\|\|\|:\|\|\|:\|\|\|\|\|\n______________UGUGCCGGUUACU\n3'-GUU...CUUGA_____________CUACU...GGA-5'\n_____________\|_____________\|\n_____________210___________168\n	205 -- 211	169 -- 175	-19.4521 kcal/mol	2.17631 kcal/mol	6.15322 kcal/mol	182 212@LB@ \| \|@LB@5'-GAA...GGCGC AAAUG...CUG-3'@LB@ ACAUGGCUAAUGA@LB@ \|\|\|:\|\|\|:\|\|\|\|\|@LB@ UGUGCCGGUUACU@LB@3'-GUU...CUUGA CUACU...GGA-5'@LB@ \| \|@LB@ 210 168@LB@@LB@@LB@Energy -20.33 kcal/mol@LB@Hybridization Energy -19.4521 kcal/mol@LB@Unfolding Energy - mRNA 2.17631 kcal/mol@LB@Unfolding Energy - sRNA 6.15322 kcal/mol@LB@@LB@Position - mRNA 183 -- 211@LB@Position - sRNA 169 -- 209@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 169 -- 175@LB@
160	0.04276	0.7192	lmo0415	N/A	-19.07	0.015641	183 -- 241	108 -- 171	endo-1 4-beta-xylanase	_____________182_________________________________________________________________242\n_____________\|___________________________________________________________________\|\n5'-UUU...UUUUC_________GU______UAAU____AAA__A____GA______________C_______________CAUUA...AGU-3'\n______________UGAGGUGAG_____GCA____GUGA___UU_GGUG__UUAGAC_____UUU_ACUAGUUGCCAUUCU\n______________\|\|\|\|:\|\|\|:_____:\|\|____:\|\|\|___\|\|_\|\|\|\|__:\|\|:\|\|_____\|:\|_\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACUCUACUU_____UGU____UACU___AA_CCAC__GAUUUG_____AGA_UGAUCAACGGUAAGA\n3'-GUU...CGGUU_________ACUUU___UUAU____A____A____A_______UCUAC___C_______________UAACC...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________172_________________________________________________________________107\n	235 -- 241	108 -- 114	-46.29 kcal/mol	15.9956 kcal/mol	19.2069 kcal/mol	182 242@LB@ \| \|@LB@5'-UUU...UUUUC GU UAAU AAA A GA C CAUUA...AGU-3'@LB@ UGAGGUGAG GCA GUGA UU GGUG UUAGAC UUU ACUAGUUGCCAUUCU@LB@ \|\|\|\|:\|\|\|: :\|\| :\|\|\| \|\| \|\|\|\| :\|\|:\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACUCUACUU UGU UACU AA CCAC GAUUUG AGA UGAUCAACGGUAAGA@LB@3'-GUU...CGGUU ACUUU UUAU A A A UCUAC C UAACC...GGA-5'@LB@ \| \|@LB@ 172 107@LB@@LB@@LB@Energy -19.07 kcal/mol@LB@Hybridization Energy -46.29 kcal/mol@LB@Unfolding Energy - mRNA 15.9956 kcal/mol@LB@Unfolding Energy - sRNA 19.2069 kcal/mol@LB@@LB@Position - mRNA 183 -- 241@LB@Position - sRNA 108 -- 171@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 108 -- 114@LB@
34	0.007076	0.552	lmo2678	N/A	-19.30	0.013995	184 -- 246	155 -- 207	XRE family transcriptional regulator	_____________183__________________________________________________________247\n_____________\|____________________________________________________________\|\n5'-GAA...AGACG____AG_____AA______A__AA______U___CUAAUUGUGGA__________U____UCAGU...AAG-3'\n______________GAGG__AUGGA__AUGAAC_GC__GCGGCU_GUG___________AGAUGAA_GA_GGCA\n______________\|\|\|\|__\|\|:\|\|__\|\|\|\|\|\|_:\|__:\|\|\|\|:_:\|\|___________\|\|\|\|\|\|\|_\|\|_::\|\|\n______________CUCC__UAUCU__UACUUG_UG__UGCCGG_UAC___________UCUACUU_CU_UUGU\n3'-GUU...CCCUA____G______G_______A__________U_____________________A__U____UUAUU...GGA-5'\n_____________\|____________________________________________________________\|\n_____________208__________________________________________________________154\n	233 -- 239	163 -- 169	-37.3867 kcal/mol	12.1272 kcal/mol	13.9822 kcal/mol	183 247@LB@ \| \|@LB@5'-GAA...AGACG AG AA A AA U CUAAUUGUGGA U UCAGU...AAG-3'@LB@ GAGG AUGGA AUGAAC GC GCGGCU GUG AGAUGAA GA GGCA@LB@ \|\|\|\| \|\|:\|\| \|\|\|\|\|\| :\| :\|\|\|\|: :\|\| \|\|\|\|\|\|\| \|\| ::\|\|@LB@ CUCC UAUCU UACUUG UG UGCCGG UAC UCUACUU CU UUGU@LB@3'-GUU...CCCUA G G A U A U UUAUU...GGA-5'@LB@ \| \|@LB@ 208 154@LB@@LB@@LB@Energy -19.30 kcal/mol@LB@Hybridization Energy -37.3867 kcal/mol@LB@Unfolding Energy - mRNA 12.1272 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 184 -- 246@LB@Position - sRNA 155 -- 207@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 163 -- 169@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@
111	0.02805	0.6801	lmo2841	N/A	-15.50	0.078879	184 -- 209	152 -- 178	sucrose phosphorylase	_____________183_______________________210\n_____________\|_________________________\|\n5'-UUU...AGGUA_____U__C____UUAA________CUUUC...AAC-3'\n______________AAUGA_GA_GAAU____GAAAACGA\n______________\|\|\|\|\|_\|\|_\|\|\|\|____\|\|\|\|\|\|:\|\n______________UUACU_CU_CUUA____CUUUUGUU\n3'-GUU...GCCGG________A________________UAUUA...GGA-5'\n_____________\|_________________________\|\n_____________179_______________________151\n	215 -- 221	154 -- 160	-12.3618 kcal/mol	2.60591 kcal/mol	0.959215 kcal/mol	183 210@LB@ \| \|@LB@5'-UUU...AGGUA U C UUAA CUUUC...AAC-3'@LB@ AAUGA GA GAAU GAAAACGA@LB@ \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UUACU CU CUUA CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 179 151@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -12.3618 kcal/mol@LB@Unfolding Energy - mRNA 2.60591 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 152 -- 178@LB@Position Seed - mRNA 215 -- 221@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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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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