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
43	0.009411	0.5889	lmo0325	N/A	-15.65	0.074138	261 -- 289	174 -- 199	transcriptional regulator	______________261_________________________290\n______________\|___________________________\|\n___________5'-_______AAUACUUAAAAAA________ACGAU...UCG-3'\n______________UGCUAUU_____________GGAAGAUG\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|\|\|\n______________ACGGUAA_____________CCUUCUAC\n3'-GUU...GAUCA_______GAUAA________________CUAUG...GGA-5'\n_____________\|____________________________\|\n_____________200__________________________173\n	22 -- 28	97 -- 103	-16.3216 kcal/mol	2.64423 kcal/mol	5.20765 kcal/mol	261 290@LB@ \| \|@LB@ 5'- AAUACUUAAAAAA ACGAU...UCG-3'@LB@ UGCUAUU GGAAGAUG@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|\|\|@LB@ ACGGUAA CCUUCUAC@LB@3'-GUU...GAUCA GAUAA CUAUG...GGA-5'@LB@ \| \|@LB@ 200 173@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -16.3216 kcal/mol@LB@Unfolding Energy - mRNA 2.64423 kcal/mol@LB@Unfolding Energy - sRNA 5.20765 kcal/mol@LB@@LB@Position - mRNA 261 -- 289@LB@Position - sRNA 174 -- 199@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 97 -- 103@LB@
162	0.04462	0.7375	lmo2840	N/A	-13.73	0.161226	169 -- 225	174 -- 208	sucrose phosphorylase	_____________168____________226\n_____________\|______________\|\n5'-UUU...AUAUU_______UG_____GAAUU...AUA-3'\n______________UAGCGGG__AUGAG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________AUUGCCC__UACUC\n3'-GUU...UACGU______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________209____________173\n	169 -- 175	202 -- 208	-13.6832 kcal/mol	2.78278 kcal/mol	0.386761 kcal/mol	168 226@LB@ \| \|@LB@5'-UUU...AUAUU UG GAAUU...AUA-3'@LB@ UAGCGGG AUGAG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ AUUGCCC UACUC@LB@3'-GUU...UACGU CGUAU...GGA-5'@LB@ \| \|@LB@ 209 173@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -13.6832 kcal/mol@LB@Unfolding Energy - mRNA 2.78278 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 169 -- 225@LB@Position - sRNA 174 -- 208@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 202 -- 208@LB@
199	0.05673	0.7607	lmo0888	N/A	-13.34	0.187096	200 -- 237	174 -- 211		_____________199___________________238\n_____________\|_____________________\|\n5'-AAG...GGCGG_____A__UAU__________ACGCA...AUA-3'\n______________AGUGA_GU___AAUGGAAGCA\n______________\|:\|\|\|_:\|___\|\|\|\|:\|\|:\|\|\n______________UUACU_UA___UUACUUUUGU\n3'-GUU...GCCGG_____C__C____________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________212___________________173\n	32 -- 38	155 -- 161	-11.9538 kcal/mol	2.24583 kcal/mol	0.954976 kcal/mol	199 238@LB@ \| \|@LB@5'-AAG...GGCGG A UAU ACGCA...AUA-3'@LB@ AGUGA GU AAUGGAAGCA@LB@ \|:\|\|\| :\| \|\|\|\|:\|\|:\|\|@LB@ UUACU UA UUACUUUUGU@LB@3'-GUU...GCCGG C C UUAUU...GGA-5'@LB@ \| \|@LB@ 212 173@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -11.9538 kcal/mol@LB@Unfolding Energy - mRNA 2.24583 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 200 -- 237@LB@Position - sRNA 174 -- 211@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 155 -- 161@LB@
68	0.01752	0.6733	lmo0547	N/A	-17.81	0.028341	205 -- 246	175 -- 207	DeoR family transcriptional regulator	_____________204_________________247\n_____________\|___________________\|\n5'-AGA...AAUGA_______A___AA____G_UAUGG...CUA-3'\n______________AAUGGGA_GAA__AAGA_A\n______________\|\|\|\|:\|\|_\|\|\|__\|\|:\|_\|\n______________UUACUCU_CUU__UUUU_U\n3'-GUU...GCCGG_______A___AC____G_UUAUU...GGA-5'\n_____________\|___________________\|\n_____________208_________________174\n	205 -- 211	167 -- 173	-10.1256 kcal/mol	0.951731 kcal/mol	0.954976 kcal/mol	204 247@LB@ \| \|@LB@5'-AGA...AAUGA A AA G UAUGG...CUA-3'@LB@ AAUGGGA GAA AAGA A@LB@ \|\|\|\|:\|\| \|\|\| \|\|:\| \|@LB@ UUACUCU CUU UUUU U@LB@3'-GUU...GCCGG A AC G UUAUU...GGA-5'@LB@ \| \|@LB@ 208 174@LB@@LB@@LB@Energy -17.81 kcal/mol@LB@Hybridization Energy -10.1256 kcal/mol@LB@Unfolding Energy - mRNA 0.951731 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 205 -- 246@LB@Position - sRNA 175 -- 207@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 167 -- 173@LB@
129	0.03464	0.6968	lmo0756	N/A	-20.18	0.009099	160 -- 214	175 -- 223	ABC transporter ATP-binding protein	_____________159__________215\n_____________\|____________\|\n5'-AGU...AUAGA_______G____AGAAG...UUU-3'\n______________GACGGGA_GGGG\n______________:\|\|\|\|\|\|_\|:\|\|\n______________UUGCCCU_CUCC\n3'-GUU...ACGUA_______A____GUAUC...GGA-5'\n_____________\|____________\|\n_____________224__________174\n	181 -- 187	201 -- 207	-16.8336 kcal/mol	1.76926 kcal/mol	3.58567 kcal/mol	159 215@LB@ \| \|@LB@5'-AGU...AUAGA G AGAAG...UUU-3'@LB@ GACGGGA GGGG@LB@ :\|\|\|\|\|\| \|:\|\|@LB@ UUGCCCU CUCC@LB@3'-GUU...ACGUA A GUAUC...GGA-5'@LB@ \| \|@LB@ 224 174@LB@@LB@@LB@Energy -20.18 kcal/mol@LB@Hybridization Energy -16.8336 kcal/mol@LB@Unfolding Energy - mRNA 1.76926 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 160 -- 214@LB@Position - sRNA 175 -- 223@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 201 -- 207@LB@
190	0.0551	0.7607	lmo0641	N/A	-14.65	0.112053	196 -- 245	175 -- 211	heavy metal-transporting ATPase	_____________195_____________________246\n_____________\|_______________________\|\n5'-AUU...GAGCA______AA__U____________GAAUU...ACU-3'\n______________UAAUGA__GA_UGGAUGAAG_CA\n______________:\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\|:_\|\|\n______________GUUACU__CU_ACUUACUUU_GU\n3'-GUU...UGCCG____________________U__UUAUU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________174\n	212 -- 218	158 -- 164	-12.4633 kcal/mol	2.08827 kcal/mol	0.95817 kcal/mol	195 246@LB@ \| \|@LB@5'-AUU...GAGCA AA U GAAUU...ACU-3'@LB@ UAAUGA GA UGGAUGAAG CA@LB@ :\|\|\|\|\| \|\| \|\|:\|\|\|\|\|: \|\|@LB@ GUUACU CU ACUUACUUU GU@LB@3'-GUU...UGCCG U UUAUU...GGA-5'@LB@ \| \|@LB@ 212 174@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -12.4633 kcal/mol@LB@Unfolding Energy - mRNA 2.08827 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 196 -- 245@LB@Position - sRNA 175 -- 211@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 158 -- 164@LB@
18	0.003504	0.4469	lmo0129	N/A	-18.06	0.025228	187 -- 226	176 -- 203	N-acetylmuramoyl-L-alanine amidase	_____________186____________227\n_____________\|______________\|\n5'-UUU...GUCAG______________AAAAC...AAC-3'\n______________GAGA_GGAUGAGGA\n______________\|\|\|\|_\|:\|\|\|\|::\|\n______________CUCU_CUUACUUUU\n3'-GUU...GGUUA____A_________GUUUA...GGA-5'\n_____________\|______________\|\n_____________204____________175\n	189 -- 195	157 -- 163	-12.9517 kcal/mol	0.542108 kcal/mol	0.904482 kcal/mol	186 227@LB@ \| \|@LB@5'-UUU...GUCAG AAAAC...AAC-3'@LB@ GAGA GGAUGAGGA@LB@ \|\|\|\| \|:\|\|\|\|::\|@LB@ CUCU CUUACUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 204 175@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -12.9517 kcal/mol@LB@Unfolding Energy - mRNA 0.542108 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 187 -- 226@LB@Position - sRNA 176 -- 203@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 157 -- 163@LB@
76	0.01998	0.6733	lmo1751	N/A	-17.90	0.027246	260 -- 292	176 -- 211	Uncharacterized RNA methyltransferase lmo1751	_____________259______________293\n_____________\|________________\|\n5'-GAA...GGCAA____CUU_________UCCCU...CAU-3'\n______________GGGA____UGGAAGCA\n______________\|:\|\|____\|\|:\|\|:\|\|\n______________CUCU____ACUUUUGU\n3'-GUU...GGUUA____ACUU________UUAUU...GGA-5'\n_____________\|________________\|\n_____________212______________175\n	203 -- 209	155 -- 161	-10.7582 kcal/mol	2.48877 kcal/mol	0.929544 kcal/mol	259 293@LB@ \| \|@LB@5'-GAA...GGCAA CUU UCCCU...CAU-3'@LB@ GGGA UGGAAGCA@LB@ \|:\|\| \|\|:\|\|:\|\|@LB@ CUCU ACUUUUGU@LB@3'-GUU...GGUUA ACUU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 175@LB@@LB@@LB@Energy -17.90 kcal/mol@LB@Hybridization Energy -10.7582 kcal/mol@LB@Unfolding Energy - mRNA 2.48877 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 260 -- 292@LB@Position - sRNA 176 -- 211@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
87	0.02294	0.6733	lmo2765	N/A	-17.07	0.039744	188 -- 213	176 -- 199	PTS cellbiose transporter subunit IIA	_____________187_________________214\n_____________\|___________________\|\n5'-UUA...UAGAC________A__________GUUAU...AUU-3'\n______________AUGA_AUG_AAUGGAAACA\n______________\|\|\|\|_\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________UACU_UAC_UUACUUUUGU\n3'-GUU...CCGGU____C______________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________200_________________175\n	212 -- 218	155 -- 161	-13.3886 kcal/mol	2.47541 kcal/mol	0.935542 kcal/mol	187 214@LB@ \| \|@LB@5'-UUA...UAGAC A GUUAU...AUU-3'@LB@ AUGA AUG AAUGGAAACA@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UACU UAC UUACUUUUGU@LB@3'-GUU...CCGGU C UUAUU...GGA-5'@LB@ \| \|@LB@ 200 175@LB@@LB@@LB@Energy -17.07 kcal/mol@LB@Hybridization Energy -13.3886 kcal/mol@LB@Unfolding Energy - mRNA 2.47541 kcal/mol@LB@Unfolding Energy - sRNA 0.935542 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 176 -- 199@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@LB@
36	0.007609	0.5562	lmo0649	N/A	-18.52	0.020396	192 -- 219	177 -- 204	transcriptional regulator	_____________191______220\n_____________\|________\|\n5'-UUU...AACGA________CAUGG...GUA-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______176\n	193 -- 199	197 -- 203	-13.9784 kcal/mol	1.5957 kcal/mol	0.386531 kcal/mol	191 220@LB@ \| \|@LB@5'-UUU...AACGA CAUGG...GUA-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 176@LB@@LB@@LB@Energy -18.52 kcal/mol@LB@Hybridization Energy -13.9784 kcal/mol@LB@Unfolding Energy - mRNA 1.5957 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 192 -- 219@LB@Position - sRNA 177 -- 204@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 197 -- 203@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching