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
182	0.05242	0.7607	lmo2028	N/A	-14.74	0.108099	169 -- 210	158 -- 185		_____________168_________211\n_____________\|___________\|\n5'-CUU...AUUAU___________UUUAU...AAC-3'\n______________GAUGGAUGGAA\n______________\|\|\|\|:\|\|\|:\|\|\n______________CUACUUACUUU\n3'-GUU...UUACU___________UGUUU...GGA-5'\n_____________\|___________\|\n_____________186_________157\n	204 -- 210	158 -- 164	-12.4441 kcal/mol	2.18802 kcal/mol	0.806249 kcal/mol	168 211@LB@ \| \|@LB@5'-CUU...AUUAU UUUAU...AAC-3'@LB@ GAUGGAUGGAA@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ CUACUUACUUU@LB@3'-GUU...UUACU UGUUU...GGA-5'@LB@ \| \|@LB@ 186 157@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.4441 kcal/mol@LB@Unfolding Energy - mRNA 2.18802 kcal/mol@LB@Unfolding Energy - sRNA 0.806249 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 158 -- 185@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
113	0.02939	0.6968	lmo0232	clpC	-17.21	0.037249	171 -- 212	159 -- 202	endopeptidase Clp ATP-binding chain C	_____________170___________________________________________213\n_____________\|_____________________________________________\|\n5'-AUU...UAAAU________U__C____A___GGAA__AA___________UU____CGAUU...AUA-3'\n______________GAUGAGGC_UA_GAUA_GGA____AC___CAAUGA__UG__UGGA\n______________\|\|\|\|\|\|\|\|_\|\|_\|\|:\|_\|:\|____\|\|___\|\|\|\|\|\|__\|\|__\|\|:\|\n______________CUACUCCG_AU_CUGU_CUU____UG___GUUACU__AC__ACUU\n3'-GUU...UUGCC________U_______A___GAUG__CCG______CU__UU____UUGUU...GGA-5'\n_____________\|_____________________________________________\|\n_____________203___________________________________________158\n	172 -- 178	195 -- 201	-28.9894 kcal/mol	4.99237 kcal/mol	13.9304 kcal/mol	170 213@LB@ \| \|@LB@5'-AUU...UAAAU U C A GGAA AA UU CGAUU...AUA-3'@LB@ GAUGAGGC UA GAUA GGA AC CAAUGA UG UGGA@LB@ \|\|\|\|\|\|\|\| \|\| \|\|:\| \|:\| \|\| \|\|\|\|\|\| \|\| \|\|:\|@LB@ CUACUCCG AU CUGU CUU UG GUUACU AC ACUU@LB@3'-GUU...UUGCC U A GAUG CCG CU UU UUGUU...GGA-5'@LB@ \| \|@LB@ 203 158@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.9894 kcal/mol@LB@Unfolding Energy - mRNA 4.99237 kcal/mol@LB@Unfolding Energy - sRNA 13.9304 kcal/mol@LB@@LB@Position - mRNA 171 -- 212@LB@Position - sRNA 159 -- 202@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 195 -- 201@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@
10	0.002311	0.4469	lmo2106	N/A	-20.89	0.006356	172 -- 222	159 -- 207		_____________171__________________________________________________223\n_____________\|____________________________________________________\|\n5'-AGU...UAAUA_______AC__CAA______G_____AAA____U__UUAA_______G____UUAUA...AUG-3'\n______________AAUGGGA__AG___CAUAGA_GUGAA____AUG_CU____AGAUGAA_UGGA\n______________\|\|:\|\|\|\|__\|\|___\|\|\|\|\|\|_:\|\|\|\|____\|:\|_\|:____\|\|\|\|\|\|\|_\|\|:\|\n______________UUGCCCU__UC___GUAUCU_UACUU____UGC_GG____UCUACUU_ACUU\n3'-GUU...ACGUA_______AC__C________G_____GAUG___C__UUAC____________UUGUU...GGA-5'\n_____________\|____________________________________________________\|\n_____________208__________________________________________________158\n	211 -- 217	163 -- 169	-34.9864 kcal/mol	6.68059 kcal/mol	18.5724 kcal/mol	171 223@LB@ \| \|@LB@5'-AGU...UAAUA AC CAA G AAA U UUAA G UUAUA...AUG-3'@LB@ AAUGGGA AG CAUAGA GUGAA AUG CU AGAUGAA UGGA@LB@ \|\|:\|\|\|\| \|\| \|\|\|\|\|\| :\|\|\|\| \|:\| \|: \|\|\|\|\|\|\| \|\|:\|@LB@ UUGCCCU UC GUAUCU UACUU UGC GG UCUACUU ACUU@LB@3'-GUU...ACGUA AC C G GAUG C UUAC UUGUU...GGA-5'@LB@ \| \|@LB@ 208 158@LB@@LB@@LB@Energy -20.89 kcal/mol@LB@Hybridization Energy -34.9864 kcal/mol@LB@Unfolding Energy - mRNA 6.68059 kcal/mol@LB@Unfolding Energy - sRNA 18.5724 kcal/mol@LB@@LB@Position - mRNA 172 -- 222@LB@Position - sRNA 159 -- 207@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@LB@
159	0.04218	0.7139	lmo1454	rpoD	-16.27	0.056776	172 -- 217	153 -- 211	RNA polymerase sigma factor RpoD	_____________171_______________218\n_____________\|_________________\|\n5'-AGA...GUUAA___G________U____UAAUA...UAA-3'\n______________ACA_CGGCCAAU_GGAU\n______________\|\|\|_\|\|\|\|\|\|\|\|_:\|\|\|\n______________UGU_GCCGGUUA_UCUA\n3'-GUU...CUUGA____________C____CUUAC...GGA-5'\n_____________\|_________________\|\n_____________212_______________152\n	92 -- 98	171 -- 177	-19.258 kcal/mol	2.66151 kcal/mol	6.2749 kcal/mol	171 218@LB@ \| \|@LB@5'-AGA...GUUAA G U UAAUA...UAA-3'@LB@ ACA CGGCCAAU GGAU@LB@ \|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGU GCCGGUUA UCUA@LB@3'-GUU...CUUGA C CUUAC...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -16.27 kcal/mol@LB@Hybridization Energy -19.258 kcal/mol@LB@Unfolding Energy - mRNA 2.66151 kcal/mol@LB@Unfolding Energy - sRNA 6.2749 kcal/mol@LB@@LB@Position - mRNA 172 -- 217@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 171 -- 177@LB@
163	0.04467	0.7375	lmo1286	parE	-16.49	0.051436	172 -- 223	160 -- 211	DNA topoisomerase IV subunit B	_____________171____________________________224\n_____________\|______________________________\|\n5'-CUU...AAUCA______UAA__________AU_________UUUUA...UAC-3'\n______________GCUAGU___UGCUAUUCUG____AAGGUGG\n______________:\|\|\|\|\|___\|\|\|:\|\|\|\|\|:____\|\|\|:\|\|\|\n______________UGAUCA___ACGGUAAGAU____UUCUACC\n3'-GUU...CAGAC___________________AACC_______UAUGU...GGA-5'\n_____________\|______________________________\|\n_____________212____________________________159\n	135 -- 141	96 -- 102	-24.989 kcal/mol	7.49229 kcal/mol	9.10061 kcal/mol	171 224@LB@ \| \|@LB@5'-CUU...AAUCA UAA AU UUUUA...UAC-3'@LB@ GCUAGU UGCUAUUCUG AAGGUGG@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|: \|\|\|:\|\|\|@LB@ UGAUCA ACGGUAAGAU UUCUACC@LB@3'-GUU...CAGAC AACC UAUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -24.989 kcal/mol@LB@Unfolding Energy - mRNA 7.49229 kcal/mol@LB@Unfolding Energy - sRNA 9.10061 kcal/mol@LB@@LB@Position - mRNA 172 -- 223@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 96 -- 102@LB@
74	0.01955	0.6733	lmo0190	ipk	-17.49	0.032930	174 -- 210	154 -- 192	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	_____________173_______________________________________211\n_____________\|_________________________________________\|\n5'-AUA...AAAAG____UU_________GA___________AA___________GCAUU...CAA-3'\n______________AGAU__UGAAC_GCG__GGCCA___AGA__AAUGAAAAUAA\n______________\|\|\|:__\|\|\|\|\|_:\|:__\|\|\|\|\|___\|\|\|__\|\|\|\|\|\|\|\|:\|\|\n______________UCUG__ACUUG_UGU__CCGGU___UCU__UUACUUUUGUU\n3'-GUU...CCGUA____U______A___G______UAC___AC___________UAUUA...GGA-5'\n_____________\|_________________________________________\|\n_____________193_______________________________________153\n	204 -- 210	154 -- 160	-28.6344 kcal/mol	5.15958 kcal/mol	12.1365 kcal/mol	173 211@LB@ \| \|@LB@5'-AUA...AAAAG UU GA AA GCAUU...CAA-3'@LB@ AGAU UGAAC GCG GGCCA AGA AAUGAAAAUAA@LB@ \|\|\|: \|\|\|\|\| :\|: \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ UCUG ACUUG UGU CCGGU UCU UUACUUUUGUU@LB@3'-GUU...CCGUA U A G UAC AC UAUUA...GGA-5'@LB@ \| \|@LB@ 193 153@LB@@LB@@LB@Energy -17.49 kcal/mol@LB@Hybridization Energy -28.6344 kcal/mol@LB@Unfolding Energy - mRNA 5.15958 kcal/mol@LB@Unfolding Energy - sRNA 12.1365 kcal/mol@LB@@LB@Position - mRNA 174 -- 210@LB@Position - sRNA 154 -- 192@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
152	0.04001	0.7027	lmo1203	cbiL	-16.49	0.051377	174 -- 199	155 -- 181	cobalt-precorrin-2 C(20)-methyltransferase	_____________173___________________200\n_____________\|_____________________\|\n5'-ACA...CACUG____A________________CGUGG...CAC-3'\n______________CAAU_GAGA_GGGUGAAAACA\n______________\|\|\|\|_\|\|\|\|_\|::\|\|\|\|\|\|\|\|\n______________GUUA_CUCU_CUUACUUUUGU\n3'-GUU...UGCCG_________A___________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________182___________________154\n	193 -- 199	155 -- 161	-18.5314 kcal/mol	4.87195 kcal/mol	0.95817 kcal/mol	173 200@LB@ \| \|@LB@5'-ACA...CACUG A CGUGG...CAC-3'@LB@ CAAU GAGA GGGUGAAAACA@LB@ \|\|\|\| \|\|\|\| \|::\|\|\|\|\|\|\|\|@LB@ GUUA CUCU CUUACUUUUGU@LB@3'-GUU...UGCCG A UUAUU...GGA-5'@LB@ \| \|@LB@ 182 154@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -18.5314 kcal/mol@LB@Unfolding Energy - mRNA 4.87195 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 174 -- 199@LB@Position - sRNA 155 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@LB@
168	0.04649	0.7403	lmo1875	N/A	-18.37	0.021889	174 -- 204	150 -- 181	ABC transporter ATP-binding protein	_____________173_______________205\n_____________\|_________________\|\n5'-ACA...AACAG__A______________AUGAA...GUU-3'\n______________GA_AUGGAUGGGAAUAA\n______________\|\|_\|\|\|:\|\|\|::\|\|:\|\|\n______________CU_UACUUACUUUUGUU\n3'-GUU...GGUUA__C______________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________182_______________149\n	193 -- 199	155 -- 161	-14.111 kcal/mol	2.1341 kcal/mol	0.933796 kcal/mol	173 205@LB@ \| \|@LB@5'-ACA...AACAG A AUGAA...GUU-3'@LB@ GA AUGGAUGGGAAUAA@LB@ \|\| \|\|\|:\|\|\|::\|\|:\|\|@LB@ CU UACUUACUUUUGUU@LB@3'-GUU...GGUUA C UAUUA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -18.37 kcal/mol@LB@Hybridization Energy -14.111 kcal/mol@LB@Unfolding Energy - mRNA 2.1341 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 174 -- 204@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@LB@
11	0.002745	0.4469	lmo0197	N/A	-21.05	0.005861	175 -- 258	154 -- 211	regulatory protein SpoVG	_____________174__________________259\n_____________\|____________________\|\n5'-UUA...AAACU_______A____________UUGCU...AUA-3'\n______________GAUG_GA_GAAUGAGAGCGA\n______________:\|\|\|_\|\|_\|\|\|\|\|\|:\|:\|:\|\n______________UUAC_CU_CUUACUUUUGUU\n3'-GUU...GCCGG____U__A____________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________212__________________153\n	252 -- 258	154 -- 160	-17.4227 kcal/mol	2.96559 kcal/mol	0.959215 kcal/mol	174 259@LB@ \| \|@LB@5'-UUA...AAACU A UUGCU...AUA-3'@LB@ GAUG GA GAAUGAGAGCGA@LB@ :\|\|\| \|\| \|\|\|\|\|\|:\|:\|:\|@LB@ UUAC CU CUUACUUUUGUU@LB@3'-GUU...GCCGG U A UAUUA...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -21.05 kcal/mol@LB@Hybridization Energy -17.4227 kcal/mol@LB@Unfolding Energy - mRNA 2.96559 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 175 -- 258@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 154 -- 160@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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