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
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@
169	0.04649	0.7403	lmo0268	N/A	-16.22	0.057928	275 -- 284	195 -- 204	phosphoglycerate mutase	_____________274________285\n_____________\|__________\|\n5'-ACC...AUGCA__________GAUUC...UUG-3'\n______________GGGAUGGGGC\n______________\|\|\|\|\|\|:\|\|\|\n______________CCCUACUCCG\n3'-GUU...UAUUG__________UAUCU...GGA-5'\n_____________\|__________\|\n_____________205________194\n	278 -- 284	195 -- 201	-19.94 kcal/mol	1.96731 kcal/mol	6.55531 kcal/mol	274 285@LB@ \| \|@LB@5'-ACC...AUGCA GAUUC...UUG-3'@LB@ GGGAUGGGGC@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CCCUACUCCG@LB@3'-GUU...UAUUG UAUCU...GGA-5'@LB@ \| \|@LB@ 205 194@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -19.94 kcal/mol@LB@Unfolding Energy - mRNA 1.96731 kcal/mol@LB@Unfolding Energy - sRNA 6.55531 kcal/mol@LB@@LB@Position - mRNA 275 -- 284@LB@Position - sRNA 195 -- 204@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 195 -- 201@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@
91	0.02389	0.6733	lmo2425	N/A	-16.15	0.059838	240 -- 263	146 -- 170	glycine cleavage system protein H	_____________239______________264\n_____________\|________________\|\n5'-CGA...AACAC________________GACGA...AUC-3'\n______________GA_AUGGGUGAAAGCA\n______________\|\|_\|\|\|::\|\|\|\|\|:\|\|\n______________CU_UACUUACUUUUGU\n3'-GUU...GGUUA__C_____________UUAUU...GGA-5'\n_____________\|________________\|\n_____________171______________145\n	248 -- 254	155 -- 161	-15.1065 kcal/mol	3.08859 kcal/mol	0.929544 kcal/mol	239 264@LB@ \| \|@LB@5'-CGA...AACAC GACGA...AUC-3'@LB@ GA AUGGGUGAAAGCA@LB@ \|\| \|\|\|::\|\|\|\|\|:\|\|@LB@ CU UACUUACUUUUGU@LB@3'-GUU...GGUUA C UUAUU...GGA-5'@LB@ \| \|@LB@ 171 145@LB@@LB@@LB@Energy -16.15 kcal/mol@LB@Hybridization Energy -15.1065 kcal/mol@LB@Unfolding Energy - mRNA 3.08859 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 240 -- 263@LB@Position - sRNA 146 -- 170@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 155 -- 161@LB@
98	0.02549	0.6733	lmo2155	N/A	-16.07	0.061955	240 -- 298	157 -- 207	ribonucleotide-diphosphate reductase subunit alpha	_____________239________299\n_____________\|__________\|\n5'-UAU...UAAAA__________AACAG...AAA-3'\n______________GACGGGG_GA\n______________:\|\|\|\|\|:_\|\|\n______________UUGCCCU_CU\n3'-GUU...ACGUA_______A__CCGUA...GGA-5'\n_____________\|__________\|\n_____________208________156\n	240 -- 246	201 -- 207	-11.5149 kcal/mol	1.00175 kcal/mol	0.374399 kcal/mol	239 299@LB@ \| \|@LB@5'-UAU...UAAAA AACAG...AAA-3'@LB@ GACGGGG GA@LB@ :\|\|\|\|\|: \|\|@LB@ UUGCCCU CU@LB@3'-GUU...ACGUA A CCGUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -16.07 kcal/mol@LB@Hybridization Energy -11.5149 kcal/mol@LB@Unfolding Energy - mRNA 1.00175 kcal/mol@LB@Unfolding Energy - sRNA 0.374399 kcal/mol@LB@@LB@Position - mRNA 240 -- 298@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 201 -- 207@LB@
184	0.05355	0.7607	lmo2119	N/A	-15.99	0.064071	3 -- 81	95 -- 171		_____________2_________________________82\n_____________\|_________________________\|\n_________5'-CU______U______GU__________AUUAC...CCA-3'\n______________UGGGAU_AGUGAA__GACAGAUAGU\n______________\|\|:\|\|\|_\|:\|\|\|\|__:\|\|\|:\|\|\|:\|\n______________ACUCUA_UUACUU__UUGUUUAUUA\n3'-GUU...CGGUU______C__________________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________172_______________________94\n	18 -- 24	152 -- 158	-18.6088 kcal/mol	3.83703 kcal/mol	5.55637 kcal/mol	2 82@LB@ \| \|@LB@ 5'-CU U GU AUUAC...CCA-3'@LB@ UGGGAU AGUGAA GACAGAUAGU@LB@ \|\|:\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|:\|@LB@ ACUCUA UUACUU UUGUUUAUUA@LB@3'-GUU...CGGUU C CUAAA...GGA-5'@LB@ \| \|@LB@ 172 94@LB@@LB@@LB@Energy -15.99 kcal/mol@LB@Hybridization Energy -18.6088 kcal/mol@LB@Unfolding Energy - mRNA 3.83703 kcal/mol@LB@Unfolding Energy - sRNA 5.55637 kcal/mol@LB@@LB@Position - mRNA 3 -- 81@LB@Position - sRNA 95 -- 171@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 152 -- 158@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@
179	0.05074	0.7607	lmo1598	tyrS	-15.93	0.065557	245 -- 292	152 -- 211	tyrosyl-tRNA synthetase	_____________244_______________293\n_____________\|_________________\|\n5'-UAG...AAAAG____AU___________AUAUU...UGU-3'\n______________GAGA__GAUGAAAAUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|::\|\n______________CUCU__UUACUUUUGUU\n3'-GUU...GGUUA____AC___________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________212_______________151\n	197 -- 203	155 -- 161	-12.3519 kcal/mol	1.69495 kcal/mol	0.933796 kcal/mol	244 293@LB@ \| \|@LB@5'-UAG...AAAAG AU AUAUU...UGU-3'@LB@ GAGA GAUGAAAAUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|::\|@LB@ CUCU UUACUUUUGUU@LB@3'-GUU...GGUUA AC UAUUA...GGA-5'@LB@ \| \|@LB@ 212 151@LB@@LB@@LB@Energy -15.93 kcal/mol@LB@Hybridization Energy -12.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.69495 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 245 -- 292@LB@Position - sRNA 152 -- 211@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@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@
133	0.03548	0.6968	lmo2772	N/A	-15.87	0.067267	191 -- 210	179 -- 199	PTS beta-glucoside transporter subunit IIABC	_____________190__________________211\n_____________\|____________________\|\n5'-GCG...UUUAG____AU______________AAUCA...AAU-3'\n______________GAGG__UAG_CAUGGACUAC\n______________\|\|\|\|__\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________CUCC__AUC_GUACUUGAUG\n3'-GUU...CCCUA____GU___U__________UGCCG...GGA-5'\n_____________\|____________________\|\n_____________200__________________178\n	203 -- 209	180 -- 186	-24.3176 kcal/mol	4.09739 kcal/mol	10.4768 kcal/mol	190 211@LB@ \| \|@LB@5'-GCG...UUUAG AU AAUCA...AAU-3'@LB@ GAGG UAG CAUGGACUAC@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ CUCC AUC GUACUUGAUG@LB@3'-GUU...CCCUA GU U UGCCG...GGA-5'@LB@ \| \|@LB@ 200 178@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 4.09739 kcal/mol@LB@Unfolding Energy - sRNA 10.4768 kcal/mol@LB@@LB@Position - mRNA 191 -- 210@LB@Position - sRNA 179 -- 199@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 180 -- 186@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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