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
171	0.04778	0.7516	lmo0498	N/A	-14.78	0.106331	152 -- 199	154 -- 211	5-phosphate isomerase	_____________151__________________200\n_____________\|____________________\|\n5'-AUC...AUCAA_______AA___________ACAUG...GUU-3'\n______________GGUGAGA__GGA_GAGGAUA\n______________::\|\|\|\|\|__\|:\|_\|\|::\|:\|\n______________UUACUCU__CUU_CUUUUGU\n3'-GUU...GCCGG_______A____A_______UUAUU...GGA-5'\n_____________\|____________________\|\n_____________212__________________153\n	192 -- 198	155 -- 161	-12.5427 kcal/mol	2.39386 kcal/mol	0.954976 kcal/mol	151 200@LB@ \| \|@LB@5'-AUC...AUCAA AA ACAUG...GUU-3'@LB@ GGUGAGA GGA GAGGAUA@LB@ ::\|\|\|\|\| \|:\| \|\|::\|:\|@LB@ UUACUCU CUU CUUUUGU@LB@3'-GUU...GCCGG A A UUAUU...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -12.5427 kcal/mol@LB@Unfolding Energy - mRNA 2.39386 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 152 -- 199@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 155 -- 161@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@
173	0.04847	0.7539	lmo1143	N/A	-15.38	0.082828	238 -- 287	171 -- 211	PduT protein	_____________237_______________________________288\n_____________\|_________________________________\|\n5'-GUG...GCAUC______GUC____C__U____AAA_________UCGGA...UUU-3'\n______________GAGGCG___GAUA_GA_GCUA___GCGGCCAAU\n______________\|\|\|\|\|:___\|\|:\|_\|\|_:\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUCCGU___CUGU_CU_UGAU___UGCCGGUUA\n3'-GUU...CCCUA______AU_____A_______G___________CUCUA...GGA-5'\n_____________\|_________________________________\|\n_____________212_______________________________170\n	281 -- 287	171 -- 177	-30.6178 kcal/mol	10.0561 kcal/mol	13.341 kcal/mol	237 288@LB@ \| \|@LB@5'-GUG...GCAUC GUC C U AAA UCGGA...UUU-3'@LB@ GAGGCG GAUA GA GCUA GCGGCCAAU@LB@ \|\|\|\|\|: \|\|:\| \|\| :\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUCCGU CUGU CU UGAU UGCCGGUUA@LB@3'-GUU...CCCUA AU A G CUCUA...GGA-5'@LB@ \| \|@LB@ 212 170@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -30.6178 kcal/mol@LB@Unfolding Energy - mRNA 10.0561 kcal/mol@LB@Unfolding Energy - sRNA 13.341 kcal/mol@LB@@LB@Position - mRNA 238 -- 287@LB@Position - sRNA 171 -- 211@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 171 -- 177@LB@
174	0.04903	0.7583	lmo1615	trmB	-12.39	0.264018	169 -- 243	157 -- 213	tRNA (guanine-N(7)-)-methyltransferase	_____________168________________244\n_____________\|__________________\|\n5'-AAU...AAGAU_________U__A_____AUGCG...AAG-3'\n______________GAUGAGGUG_AA_GAAAG\n______________:\|\|\|\|\|:\|\|_\|\|_\|\|\|\|:\n______________UUACUCUAC_UU_CUUUU\n3'-GUU...GCCGG____________A_____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________214________________156\n	185 -- 191	165 -- 171	-13.3606 kcal/mol	4.29808 kcal/mol	0.930085 kcal/mol	168 244@LB@ \| \|@LB@5'-AAU...AAGAU U A AUGCG...AAG-3'@LB@ GAUGAGGUG AA GAAAG@LB@ :\|\|\|\|\|:\|\| \|\| \|\|\|\|:@LB@ UUACUCUAC UU CUUUU@LB@3'-GUU...GCCGG A GUUUA...GGA-5'@LB@ \| \|@LB@ 214 156@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -13.3606 kcal/mol@LB@Unfolding Energy - mRNA 4.29808 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 169 -- 243@LB@Position - sRNA 157 -- 213@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 165 -- 171@LB@
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@
176	0.04979	0.7607	lmo1340	N/A	-16.63	0.048446	193 -- 216	151 -- 177		_____________192_____________217\n_____________\|_______________\|\n5'-UGC...UUGGA_______________AAAAU...CUG-3'\n______________GGCCA__GAGAUGAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CCGGU__CUCUACUU\n3'-GUU...AUGUG_____UA________ACUUU...GGA-5'\n_____________\|_______________\|\n_____________178_____________150\n	199 -- 205	163 -- 169	-19.0992 kcal/mol	1.80937 kcal/mol	7.44208 kcal/mol	192 217@LB@ \| \|@LB@5'-UGC...UUGGA AAAAU...CUG-3'@LB@ GGCCA GAGAUGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCGGU CUCUACUU@LB@3'-GUU...AUGUG UA ACUUU...GGA-5'@LB@ \| \|@LB@ 178 150@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -19.0992 kcal/mol@LB@Unfolding Energy - mRNA 1.80937 kcal/mol@LB@Unfolding Energy - sRNA 7.44208 kcal/mol@LB@@LB@Position - mRNA 193 -- 216@LB@Position - sRNA 151 -- 177@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
177	0.05015	0.7607	lmo1905	cca	-16.43	0.052746	154 -- 208	160 -- 211	tRNA CCA-pyrophosphorylase	_____________153_______________209\n_____________\|_________________\|\n5'-UUA...AGGAG______CA_________CGUUU...UGC-3'\n______________CGAUGA__GAUGAAUGA\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________GUUACU__CUACUUACU\n3'-GUU...UGCCG_________________UUUGU...GGA-5'\n_____________\|_________________\|\n_____________212_______________159\n	202 -- 208	160 -- 166	-15.3935 kcal/mol	2.32419 kcal/mol	0.846187 kcal/mol	153 209@LB@ \| \|@LB@5'-UUA...AGGAG CA CGUUU...UGC-3'@LB@ CGAUGA GAUGAAUGA@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUUACU CUACUUACU@LB@3'-GUU...UGCCG UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -15.3935 kcal/mol@LB@Unfolding Energy - mRNA 2.32419 kcal/mol@LB@Unfolding Energy - sRNA 0.846187 kcal/mol@LB@@LB@Position - mRNA 154 -- 208@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 160 -- 166@LB@
178	0.05066	0.7607	lmo0216	N/A	-18.27	0.022949	55 -- 114	166 -- 213		_____________54__________________________________________________________________________________115\n_____________\|___________________________________________________________________________________\|\n5'-GCG...UCCAA__AAU______A______A__A___G__________UUUCCUUGUUUUU___CUA______A______U___U____A_____UUUGU...CGG-3'\n______________GC_____UGUU___GUGC_CU_GUG_GUGGCGGGAU_____________GCA___AGAUAU_AAUUAC_CGG_CCAA__AGAU\n______________\|\|_____\|\|\|\|___\|:\|\|_\|\|_:\|\|_:\|::\|\|\|\|\|\|_____________\|\|\|___\|\|\|:\|\|_\|\|:\|\|\|_\|\|\|_\|\|\|\|__\|\|\|\|\n______________CG_____ACAA___CGCG_GA_UAC_UAUUGCCCUA_____________CGU___UCUGUA_UUGAUG_GCC_GGUU__UCUA\n3'-GUU...CGCAA__GUAGU____GCC___________G__________CUC_____________A________C______U________AC____CUUAC...GGA-5'\n_____________\|___________________________________________________________________________________\|\n_____________214_________________________________________________________________________________165\n	62 -- 68	200 -- 206	-50.1796 kcal/mol	16.7648 kcal/mol	22.1647 kcal/mol	54 115@LB@ \| \|@LB@5'-GCG...UCCAA AAU A A A G UUUCCUUGUUUUU CUA A U U A UUUGU...CGG-3'@LB@ GC UGUU GUGC CU GUG GUGGCGGGAU GCA AGAUAU AAUUAC CGG CCAA AGAU@LB@ \|\| \|\|\|\| \|:\|\| \|\| :\|\| :\|::\|\|\|\|\|\| \|\|\| \|\|\|:\|\| \|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|@LB@ CG ACAA CGCG GA UAC UAUUGCCCUA CGU UCUGUA UUGAUG GCC GGUU UCUA@LB@3'-GUU...CGCAA GUAGU GCC G CUC A C U AC CUUAC...GGA-5'@LB@ \| \|@LB@ 214 165@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -50.1796 kcal/mol@LB@Unfolding Energy - mRNA 16.7648 kcal/mol@LB@Unfolding Energy - sRNA 22.1647 kcal/mol@LB@@LB@Position - mRNA 55 -- 114@LB@Position - sRNA 166 -- 213@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 200 -- 206@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@
180	0.05132	0.7607	lmo1643	N/A	-15.34	0.084306	231 -- 286	157 -- 207	lmo1643	_____________230_______________287\n_____________\|_________________\|\n5'-CGA...UAGUA_______GAU_______AGAAG...CUG-3'\n______________AGUGAGG___AUGAAAA\n______________\|:\|\|\|\|:___\|\|\|\|\|\|\|\n______________UUACUCU___UACUUUU\n3'-GUU...GCCGG_______ACU_______GUUUA...GGA-5'\n_____________\|_________________\|\n_____________208_______________156\n	280 -- 286	157 -- 163	-13.3165 kcal/mol	1.24234 kcal/mol	0.930085 kcal/mol	230 287@LB@ \| \|@LB@5'-CGA...UAGUA GAU AGAAG...CUG-3'@LB@ AGUGAGG AUGAAAA@LB@ \|:\|\|\|\|: \|\|\|\|\|\|\|@LB@ UUACUCU UACUUUU@LB@3'-GUU...GCCGG ACU GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -13.3165 kcal/mol@LB@Unfolding Energy - mRNA 1.24234 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 231 -- 286@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 280 -- 286@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)

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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