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
107	0.02737	0.6733	lmo1575	N/A	-17.23	0.037041	80 -- 118	156 -- 205		_____________79______119\n_____________\|_______\|\n5'-GUA...UCACA_______C-3'\n______________AAUGGGG\n______________\|\|:\|\|\|:\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________206_____155\n	293 -- 299	201 -- 207	-8.20946 kcal/mol	0.611387 kcal/mol	0.326294 kcal/mol	79 119@LB@ \| \|@LB@5'-GUA...UCACA C-3'@LB@ AAUGGGG@LB@ \|\|:\|\|\|:@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 206 155@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -8.20946 kcal/mol@LB@Unfolding Energy - mRNA 0.611387 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 80 -- 118@LB@Position - sRNA 156 -- 205@LB@Position Seed - mRNA 293 -- 299@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@
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@
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@
126	0.03359	0.6968	lmo1599	ccpA	-16.59	0.049230	178 -- 221	146 -- 188	catabolite control protein A	_____________177______________222\n_____________\|________________\|\n5'-UUU...GAAUA__________U_____AUUUA...CAA-3'\n______________GAGAUGAAUG__AACA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________CUCUACUUAC__UUGU\n3'-GUU...GGUUA__________UU____UUAUU...GGA-5'\n_____________\|________________\|\n_____________189______________145\n	201 -- 207	161 -- 167	-17.207 kcal/mol	2.33031 kcal/mol	0.929544 kcal/mol	177 222@LB@ \| \|@LB@5'-UUU...GAAUA U AUUUA...CAA-3'@LB@ GAGAUGAAUG AACA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUCUACUUAC UUGU@LB@3'-GUU...GGUUA UU UUAUU...GGA-5'@LB@ \| \|@LB@ 189 145@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -17.207 kcal/mol@LB@Unfolding Energy - mRNA 2.33031 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 178 -- 221@LB@Position - sRNA 146 -- 188@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@LB@
194	0.05602	0.7607	lmo1602	N/A	-15.08	0.094256	153 -- 204	160 -- 207		_____________152_______________________________________205\n_____________\|_________________________________________\|\n5'-UUU...ACUCA_________AAAA___________A_____U____A_____UAGUA...CAA-3'\n______________GGGUAUAGA____GGA__AUAUGG__GGUG_GGAU_GAUGA\n______________:\|\|:\|\|\|\|\|____\|:\|__\|:\|:\|\|__::\|\|_:\|\|\|_:\|\|\|\|\n______________UCCGUAUCU____CUU__UGUGCC__UUAC_UCUA_UUACU\n3'-GUU...CCUAC_________GUA____GA______GG_________C_____UUUGU...GGA-5'\n_____________\|_________________________________________\|\n_____________208_______________________________________159\n	168 -- 174	191 -- 197	-27.2651 kcal/mol	6.9826 kcal/mol	13.8637 kcal/mol	152 205@LB@ \| \|@LB@5'-UUU...ACUCA AAAA A U A UAGUA...CAA-3'@LB@ GGGUAUAGA GGA AUAUGG GGUG GGAU GAUGA@LB@ :\|\|:\|\|\|\|\| \|:\| \|:\|:\|\| ::\|\| :\|\|\| :\|\|\|\|@LB@ UCCGUAUCU CUU UGUGCC UUAC UCUA UUACU@LB@3'-GUU...CCUAC GUA GA GG C UUUGU...GGA-5'@LB@ \| \|@LB@ 208 159@LB@@LB@@LB@Energy -15.08 kcal/mol@LB@Hybridization Energy -27.2651 kcal/mol@LB@Unfolding Energy - mRNA 6.9826 kcal/mol@LB@Unfolding Energy - sRNA 13.8637 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 160 -- 207@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 191 -- 197@LB@
124	0.03258	0.6968	lmo1611	N/A	-17.32	0.035574	130 -- 182	121 -- 173	aminopeptidase	_____________129_______________________183\n_____________\|_________________________\|\n5'-CAU...AGAGA_______C___C_____________AUUUG...UUG-3'\n______________AGUGAGG_GAG_GGAAACGGAUAAU\n______________\|:\|\|\|\|:_\|\|:_\|:\|\|\|\|::\|\|\|\|\|\n______________UUACUCU_CUU_CUUUUGUUUAUUA\n3'-GUU...GCCGG_______A___A_____________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________174_______________________120\n	143 -- 149	154 -- 160	-22.8649 kcal/mol	4.94187 kcal/mol	5.58154 kcal/mol	129 183@LB@ \| \|@LB@5'-CAU...AGAGA C C AUUUG...UUG-3'@LB@ AGUGAGG GAG GGAAACGGAUAAU@LB@ \|:\|\|\|\|: \|\|: \|:\|\|\|\|::\|\|\|\|\|@LB@ UUACUCU CUU CUUUUGUUUAUUA@LB@3'-GUU...GCCGG A A CUAAA...GGA-5'@LB@ \| \|@LB@ 174 120@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -22.8649 kcal/mol@LB@Unfolding Energy - mRNA 4.94187 kcal/mol@LB@Unfolding Energy - sRNA 5.58154 kcal/mol@LB@@LB@Position - mRNA 130 -- 182@LB@Position - sRNA 121 -- 173@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 154 -- 160@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@
106	0.02722	0.6733	lmo1616	N/A	-15.61	0.075454	67 -- 108	167 -- 211		_____________66______________________109\n_____________\|_______________________\|\n5'-AAG...AUAAC_____U_____GACU________AGGGC...UUU-3'\n______________GAACA_AUGUU____UGACUAGU\n______________:\|\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\|\n______________UUUGU_UACAG____ACUGAUCA\n3'-GUU...ACAGA_____C_________________ACGGU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________166\n	90 -- 96	117 -- 123	-17.5219 kcal/mol	5.32799 kcal/mol	5.058 kcal/mol	66 109@LB@ \| \|@LB@5'-AAG...AUAAC U GACU AGGGC...UUU-3'@LB@ GAACA AUGUU UGACUAGU@LB@ :\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UUUGU UACAG ACUGAUCA@LB@3'-GUU...ACAGA C ACGGU...GGA-5'@LB@ \| \|@LB@ 212 166@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -17.5219 kcal/mol@LB@Unfolding Energy - mRNA 5.32799 kcal/mol@LB@Unfolding Energy - sRNA 5.058 kcal/mol@LB@@LB@Position - mRNA 67 -- 108@LB@Position - sRNA 167 -- 211@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 117 -- 123@LB@
185	0.05367	0.7607	lmo1631	trpD	-14.92	0.100424	142 -- 163	148 -- 170	anthranilate phosphoribosyltransferase	_____________141__________________164\n_____________\|____________________\|\n5'-UUC...UACGA____CG______________GAAAA...AAA-3'\n______________AUGA__GAAAACAAAUGAUG\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UACU__CUUUUGUUUAUUAC\n3'-GUU...UACUC____UA______________UAAAA...GGA-5'\n_____________\|____________________\|\n_____________171__________________147\n	153 -- 159	152 -- 158	-19.3831 kcal/mol	2.89443 kcal/mol	5.80116 kcal/mol	141 164@LB@ \| \|@LB@5'-UUC...UACGA CG GAAAA...AAA-3'@LB@ AUGA GAAAACAAAUGAUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UACU CUUUUGUUUAUUAC@LB@3'-GUU...UACUC UA UAAAA...GGA-5'@LB@ \| \|@LB@ 171 147@LB@@LB@@LB@Energy -14.92 kcal/mol@LB@Hybridization Energy -19.3831 kcal/mol@LB@Unfolding Energy - mRNA 2.89443 kcal/mol@LB@Unfolding Energy - sRNA 5.80116 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 148 -- 170@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 152 -- 158@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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