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
121	0.03234	0.6968	lmo0198	glmU	-15.85	0.067914	228 -- 259	153 -- 184	bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase	_____________227______________________________260\n_____________\|________________________________\|\n5'-UAC...UGCUU_____________GGCACAC________U___AACUU...UGG-3'\n______________GCUGC_UGGCCAA_______GGAUGAAA_CAA\n______________:\|\|:\|_:\|\|\|\|\|\|_______\|:\|\|\|\|\|\|_\|\|\|\n______________UGAUG_GCCGGUU_______CUUACUUU_GUU\n3'-GUU...GUACU_____U_______ACUCUA_________U___UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________185______________________________152\n	248 -- 254	158 -- 164	-25.2592 kcal/mol	7.21839 kcal/mol	9.59579 kcal/mol	227 260@LB@ \| \|@LB@5'-UAC...UGCUU GGCACAC U AACUU...UGG-3'@LB@ GCUGC UGGCCAA GGAUGAAA CAA@LB@ :\|\|:\| :\|\|\|\|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGAUG GCCGGUU CUUACUUU GUU@LB@3'-GUU...GUACU U ACUCUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 185 152@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -25.2592 kcal/mol@LB@Unfolding Energy - mRNA 7.21839 kcal/mol@LB@Unfolding Energy - sRNA 9.59579 kcal/mol@LB@@LB@Position - mRNA 228 -- 259@LB@Position - sRNA 153 -- 184@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 158 -- 164@LB@
161	0.04429	0.7375	lmo0588	N/A	-15.80	0.069486	3 -- 42	156 -- 202	DNA photolyase	_____________2____________43\n_____________\|____________\|\n5'-UUG...CUUAU____________UAUGA...AAG-3'\n______________GUGGAUGAAAGC\n______________:\|\|:\|\|\|\|\|\|:\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________203__________155\n	36 -- 42	156 -- 162	-13.6691 kcal/mol	1.75048 kcal/mol	0.849227 kcal/mol	2 43@LB@ \| \|@LB@5'-UUG...CUUAU UAUGA...AAG-3'@LB@ GUGGAUGAAAGC@LB@ :\|\|:\|\|\|\|\|\|:\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 203 155@LB@@LB@@LB@Energy -15.80 kcal/mol@LB@Hybridization Energy -13.6691 kcal/mol@LB@Unfolding Energy - mRNA 1.75048 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 3 -- 42@LB@Position - sRNA 156 -- 202@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 156 -- 162@LB@
147	0.03815	0.6968	lmo0655	N/A	-15.78	0.070044	227 -- 290	154 -- 212	phosphoprotein phosphatase	_____________226_____________291\n_____________\|_______________\|\n______5'-AACAA______UU_______CCACA...UUG-3'\n______________GAGA_G__UGAAGAC\n______________\|\|\|\|_\|__\|\|\|\|:\|\|\n______________CUCU_C__ACUUUUG\n3'-GUU...GGUUA____A_UU_______UUUAU...GGA-5'\n_____________\|_______________\|\n_____________213_____________153\n	13 -- 19	156 -- 162	-12.8457 kcal/mol	3.32795 kcal/mol	0.916023 kcal/mol	226 291@LB@ \| \|@LB@ 5'-AACAA UU CCACA...UUG-3'@LB@ GAGA G UGAAGAC@LB@ \|\|\|\| \| \|\|\|\|:\|\|@LB@ CUCU C ACUUUUG@LB@3'-GUU...GGUUA A UU UUUAU...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -12.8457 kcal/mol@LB@Unfolding Energy - mRNA 3.32795 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 227 -- 290@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 156 -- 162@LB@
39	0.008114	0.5599	lmo0390	N/A	-15.77	0.070471	151 -- 193	167 -- 211	uracil-DNA glycosylase	_____________150________194\n_____________\|__________\|\n5'-UCG...ACUGA__________AUUAA...AUG-3'\n______________GACGGGA_GA\n______________:\|\|\|\|\|\|_\|\|\n______________UUGCCCU_CU\n3'-GUU...ACGUA_______A__CCGUA...GGA-5'\n_____________\|__________\|\n_____________212________166\n	185 -- 191	201 -- 207	-12.4012 kcal/mol	0.989391 kcal/mol	0.374399 kcal/mol	150 194@LB@ \| \|@LB@5'-UCG...ACUGA AUUAA...AUG-3'@LB@ GACGGGA GA@LB@ :\|\|\|\|\|\| \|\|@LB@ UUGCCCU CU@LB@3'-GUU...ACGUA A CCGUA...GGA-5'@LB@ \| \|@LB@ 212 166@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -12.4012 kcal/mol@LB@Unfolding Energy - mRNA 0.989391 kcal/mol@LB@Unfolding Energy - sRNA 0.374399 kcal/mol@LB@@LB@Position - mRNA 151 -- 193@LB@Position - sRNA 167 -- 211@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 201 -- 207@LB@
117	0.03157	0.6968	lmo0079	N/A	-15.68	0.073126	244 -- 277	156 -- 185	lmo0079	_____________243________________________________278\n_____________\|__________________________________\|\n5'-UCG...AUACC_________CAA_______ACCAG___G______UAUCC...CCG-3'\n______________AGCUACGUG___CCAAUGA_____GAA_GAAAAC\n______________\|:\|\|\|\|::\|___\|\|\|\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\n______________UUGAUGUGC___GGUUACU_____CUU_CUUUUG\n3'-GUU...UGUAC_________C_________CUA_____A______UUUAU...GGA-5'\n_____________\|__________________________________\|\n_____________186________________________________155\n	256 -- 262	169 -- 175	-22.638 kcal/mol	3.99376 kcal/mol	9.64492 kcal/mol	243 278@LB@ \| \|@LB@5'-UCG...AUACC CAA ACCAG G UAUCC...CCG-3'@LB@ AGCUACGUG CCAAUGA GAA GAAAAC@LB@ \|:\|\|\|\|::\| \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UUGAUGUGC GGUUACU CUU CUUUUG@LB@3'-GUU...UGUAC C CUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 186 155@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -22.638 kcal/mol@LB@Unfolding Energy - mRNA 3.99376 kcal/mol@LB@Unfolding Energy - sRNA 9.64492 kcal/mol@LB@@LB@Position - mRNA 244 -- 277@LB@Position - sRNA 156 -- 185@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 169 -- 175@LB@
146	0.03799	0.6968	lmo1526	N/A	-15.66	0.073786	160 -- 215	153 -- 207		_____________159____________________216\n_____________\|______________________\|\n5'-AUG...AGGAG____AAACA____A________AGUAC...UAA-3'\n______________GAGA_____UGAA_GAAAAUAA\n______________\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|\n______________CUCU_____ACUU_CUUUUGUU\n3'-GUU...GGUUA_____________A________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________208____________________152\n	208 -- 214	154 -- 160	-11.4679 kcal/mol	1.00795 kcal/mol	0.933796 kcal/mol	159 216@LB@ \| \|@LB@5'-AUG...AGGAG AAACA A AGUAC...UAA-3'@LB@ GAGA UGAA GAAAAUAA@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|@LB@ CUCU ACUU CUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 208 152@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.4679 kcal/mol@LB@Unfolding Energy - mRNA 1.00795 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 160 -- 215@LB@Position - sRNA 153 -- 207@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 154 -- 160@LB@
197	0.05638	0.7607	lmo0344	N/A	-15.66	0.073858	267 -- 298	182 -- 211	short chain dehydrogenase	_____________266______299\n_____________\|________\|\n5'-CAG...CAGCA________UGGUA...UUU-3'\n______________AGCGGGAU\n______________\|:\|\|\|\|\|\|\n______________UUGCCCUA\n3'-GUU...ACGUA________CUCCG...GGA-5'\n_____________\|________\|\n_____________212______181\n	271 -- 277	200 -- 206	-11.8444 kcal/mol	1.0403 kcal/mol	0.330969 kcal/mol	266 299@LB@ \| \|@LB@5'-CAG...CAGCA UGGUA...UUU-3'@LB@ AGCGGGAU@LB@ \|:\|\|\|\|\|\|@LB@ UUGCCCUA@LB@3'-GUU...ACGUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 181@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.8444 kcal/mol@LB@Unfolding Energy - mRNA 1.0403 kcal/mol@LB@Unfolding Energy - sRNA 0.330969 kcal/mol@LB@@LB@Position - mRNA 267 -- 298@LB@Position - sRNA 182 -- 211@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 200 -- 206@LB@
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@
188	0.05492	0.7607	lmo1246	N/A	-15.64	0.074442	171 -- 206	183 -- 211	ATP-dependent RNA helicase	_____________170_______________207\n_____________\|_________________\|\n5'-GCC...AUGAU______A__________UGACA...CCU-3'\n______________AUGAGG__AAUGAGGAC\n______________\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UACUCU__UUACUUUUG\n3'-GUU...CCGGU______AC_________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________212_______________182\n	190 -- 196	156 -- 162	-13.5081 kcal/mol	2.39769 kcal/mol	0.922045 kcal/mol	170 207@LB@ \| \|@LB@5'-GCC...AUGAU A UGACA...CCU-3'@LB@ AUGAGG AAUGAGGAC@LB@ \|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UACUCU UUACUUUUG@LB@3'-GUU...CCGGU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 182@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -13.5081 kcal/mol@LB@Unfolding Energy - mRNA 2.39769 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 171 -- 206@LB@Position - sRNA 183 -- 211@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 156 -- 162@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@

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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