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
41	0.008795	0.5772	lmo1984	ilvB	-19.06	0.015768	187 -- 229	157 -- 201	acetolactate synthase	_____________186____________________________________________230\n_____________\|______________________________________________\|\n5'-AUU...AAAAA_______G___A______UUG_____A_________CA________AGCGA...ACA-3'\n______________AUGAGGU_AUA_GCGUGA___AUACG__CGA__AGA__AAUGAAAA\n______________\|\|\|\|\|\|:_\|\|\|_:\|:\|\|\|___\|:\|\|\|__\|:\|__\|\|\|__\|\|\|\|\|\|\|\|\n______________UACUCCG_UAU_UGUACU___UGUGC__GUU__UCU__UUACUUUU\n3'-GUU...UGCCC___________C______UGA_____CG___AC___AC________GUUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________202____________________________________________156\n	223 -- 229	157 -- 163	-31.6948 kcal/mol	5.6221 kcal/mol	13.9999 kcal/mol	186 230@LB@ \| \|@LB@5'-AUU...AAAAA G A UUG A CA AGCGA...ACA-3'@LB@ AUGAGGU AUA GCGUGA AUACG CGA AGA AAUGAAAA@LB@ \|\|\|\|\|\|: \|\|\| :\|:\|\|\| \|:\|\|\| \|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UACUCCG UAU UGUACU UGUGC GUU UCU UUACUUUU@LB@3'-GUU...UGCCC C UGA CG AC AC GUUUA...GGA-5'@LB@ \| \|@LB@ 202 156@LB@@LB@@LB@Energy -19.06 kcal/mol@LB@Hybridization Energy -31.6948 kcal/mol@LB@Unfolding Energy - mRNA 5.6221 kcal/mol@LB@Unfolding Energy - sRNA 13.9999 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 157 -- 201@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 157 -- 163@LB@
42	0.009182	0.5883	lmo1767	purM	-18.99	0.016282	211 -- 267	155 -- 213	phosphoribosylaminoimidazole synthetase	_____________210__________________________________________________________________________268\n_____________\|____________________________________________________________________________\|\n5'-GGA...ACAAA___AAU___A_AAA_______UA_UAAA_C____________A______________UCA__U_________C___UCAAA...UAG-3'\n______________UCG___GGC_G___AUGCAUA__G____G_AGGCGUGGACGU_GAA__GC_UGGCUA___AG___AGUGGAA_GCA\n______________\|\|\|___\|\|\|_\|___\|\|\|\|\|\|\|__\|____\|_\|\|\|\|:\|:\|\|\|:\|_\|\|\|__:\|_:\|\|\|:\|___\|\|___\|:\|\|:\|\|_:\|\|\n______________AGC___CCG_C___UACGUAU__C____C_UCCGUAUCUGUA_CUU__UG_GCCGGU___UC___UUACUUU_UGU\n3'-GUU...GUACA___________GGA_______UG_CCUA__________________GA__U______UAC__UAC___________UUAUU...GGA-5'\n_____________\|____________________________________________________________________________\|\n_____________214__________________________________________________________________________154\n	257 -- 263	158 -- 164	-45.9009 kcal/mol	14.0255 kcal/mol	22.2914 kcal/mol	210 268@LB@ \| \|@LB@5'-GGA...ACAAA AAU A AAA UA UAAA C A UCA U C UCAAA...UAG-3'@LB@ UCG GGC G AUGCAUA G G AGGCGUGGACGU GAA GC UGGCUA AG AGUGGAA GCA@LB@ \|\|\| \|\|\| \| \|\|\|\|\|\|\| \| \| \|\|\|\|:\|:\|\|\|:\| \|\|\| :\| :\|\|\|:\| \|\| \|:\|\|:\|\| :\|\|@LB@ AGC CCG C UACGUAU C C UCCGUAUCUGUA CUU UG GCCGGU UC UUACUUU UGU@LB@3'-GUU...GUACA GGA UG CCUA GA U UAC UAC UUAUU...GGA-5'@LB@ \| \|@LB@ 214 154@LB@@LB@@LB@Energy -18.99 kcal/mol@LB@Hybridization Energy -45.9009 kcal/mol@LB@Unfolding Energy - mRNA 14.0255 kcal/mol@LB@Unfolding Energy - sRNA 22.2914 kcal/mol@LB@@LB@Position - mRNA 211 -- 267@LB@Position - sRNA 155 -- 213@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 158 -- 164@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@
44	0.01013	0.599	lmo0022	N/A	-16.20	0.058356	176 -- 261	150 -- 213	PTS fructose transporter subunit IIB	_____________175________________262\n_____________\|__________________\|\n5'-CCG...GUGAU_______A___A______UGAUG...UCA-3'\n______________GAUGGGG_GGA_GAGGAC\n______________:\|\|\|:\|:_\|:\|_\|\|::\|\|\n______________UUACUCU_CUU_CUUUUG\n3'-GUU...GCCGG_______A___A______UUUAU...GGA-5'\n_____________\|__________________\|\n_____________214________________149\n	181 -- 187	167 -- 173	-14.383 kcal/mol	2.57794 kcal/mol	0.941471 kcal/mol	175 262@LB@ \| \|@LB@5'-CCG...GUGAU A A UGAUG...UCA-3'@LB@ GAUGGGG GGA GAGGAC@LB@ :\|\|\|:\|: \|:\| \|\|::\|\|@LB@ UUACUCU CUU CUUUUG@LB@3'-GUU...GCCGG A A UUUAU...GGA-5'@LB@ \| \|@LB@ 214 149@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -14.383 kcal/mol@LB@Unfolding Energy - mRNA 2.57794 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 176 -- 261@LB@Position - sRNA 150 -- 213@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 167 -- 173@LB@
45	0.0103	0.599	lmo0066	N/A	-17.00	0.040990	179 -- 207	157 -- 199	toxin	_____________178___________208\n_____________\|_____________\|\n5'-AAA...AGGCC_____________AAGUC...AUU-3'\n______________AGAUGAAUGAAAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCUACUUACUUUU\n3'-GUU...GUUAC_____________GUUUA...GGA-5'\n_____________\|_____________\|\n_____________200___________156\n	201 -- 207	157 -- 163	-14.7839 kcal/mol	1.76886 kcal/mol	0.884237 kcal/mol	178 208@LB@ \| \|@LB@5'-AAA...AGGCC AAGUC...AUU-3'@LB@ AGAUGAAUGAAAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCUACUUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -14.7839 kcal/mol@LB@Unfolding Energy - mRNA 1.76886 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 179 -- 207@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
46	0.01036	0.599	lmo2695	N/A	-19.87	0.010617	150 -- 211	156 -- 209	dihydroxyacetone kinase subunit DhaK	_____________149_________________________________________________________________212\n_____________\|___________________________________________________________________\|\n5'-UUA...UUCUA____A____AAU_____________________UAUAAAGGA____UUU__UC______________UCUUA...CUC-3'\n______________GUAA_GGGA___UGAGGUA_AGA___GGACUAU_________GGUU___UG__AGAUGAA_GAAGAU\n______________:\|\|\|_\|\|\|\|___\|\|\|\|\|:\|_\|\|\|___\|:\|\|\|\|:_________\|\|::___\|\|__\|\|\|\|\|\|\|_\|\|\|:\|:\n______________UAUU_CCCU___ACUCCGU_UCU___CUUGAUG_________CCGG___AC__UCUACUU_CUUUUG\n3'-GUU...AUACG____G______________A___GUA_______UG___________UU____________A______UUUAU...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________210_________________________________________________________________155\n	199 -- 205	163 -- 169	-36.4151 kcal/mol	9.16424 kcal/mol	18.7057 kcal/mol	149 212@LB@ \| \|@LB@5'-UUA...UUCUA A AAU UAUAAAGGA UUU UC UCUUA...CUC-3'@LB@ GUAA GGGA UGAGGUA AGA GGACUAU GGUU UG AGAUGAA GAAGAU@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|\| \|:\|\|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|:\|:@LB@ UAUU CCCU ACUCCGU UCU CUUGAUG CCGG AC UCUACUU CUUUUG@LB@3'-GUU...AUACG G A GUA UG UU A UUUAU...GGA-5'@LB@ \| \|@LB@ 210 155@LB@@LB@@LB@Energy -19.87 kcal/mol@LB@Hybridization Energy -36.4151 kcal/mol@LB@Unfolding Energy - mRNA 9.16424 kcal/mol@LB@Unfolding Energy - sRNA 18.7057 kcal/mol@LB@@LB@Position - mRNA 150 -- 211@LB@Position - sRNA 156 -- 209@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
47	0.01063	0.599	lmo0138	N/A	-20.04	0.009767	146 -- 210	158 -- 213	lmo0138	_____________145_________________________________________________________________________211\n_____________\|___________________________________________________________________________\|\n5'-AAA...AAUGC____G_____U_____UAA_____A____UUCAUUAUU________________A___GCA___A__________UAAAA...GCA-3'\n______________GUGC__AUGC_AUAAU___GGGAU_AGGU_________AUAGACA_GAG__AUG_GGC____GA_AUGAGUGAAA\n______________\|:\|\|__\|\|\|\|_\|\|\|\|:___\|\|\|\|\|_\|\|\|:_________\|\|\|\|\|\|\|_\|\|:__\|::_\|\|\|____\|\|_\|\|\|\|:\|\|\|\|\|\n______________CGCG__UACG_UAUUG___CCCUA_UCCG_________UAUCUGU_CUU__UGU_CCG____CU_UACUUACUUU\n3'-GUU...AAGCC____GA__________________C____________________A___GA___G___GUUA__C__________UGUUU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________214_________________________________________________________________________157\n	204 -- 210	158 -- 164	-47.7003 kcal/mol	15.2802 kcal/mol	21.9717 kcal/mol	145 211@LB@ \| \|@LB@5'-AAA...AAUGC G U UAA A UUCAUUAUU A GCA A UAAAA...GCA-3'@LB@ GUGC AUGC AUAAU GGGAU AGGU AUAGACA GAG AUG GGC GA AUGAGUGAAA@LB@ \|:\|\| \|\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|: \|\|\|\|\|\|\| \|\|: \|:: \|\|\| \|\| \|\|\|\|:\|\|\|\|\|@LB@ CGCG UACG UAUUG CCCUA UCCG UAUCUGU CUU UGU CCG CU UACUUACUUU@LB@3'-GUU...AAGCC GA C A GA G GUUA C UGUUU...GGA-5'@LB@ \| \|@LB@ 214 157@LB@@LB@@LB@Energy -20.04 kcal/mol@LB@Hybridization Energy -47.7003 kcal/mol@LB@Unfolding Energy - mRNA 15.2802 kcal/mol@LB@Unfolding Energy - sRNA 21.9717 kcal/mol@LB@@LB@Position - mRNA 146 -- 210@LB@Position - sRNA 158 -- 213@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
48	0.01096	0.599	lmo0184	N/A	-18.00	0.026009	159 -- 211	157 -- 203	oligo-1 6-glucosidase	_____________158_____212\n_____________\|_______\|\n5'-ACG...ACAAG_______AUUUA...GAA-3'\n______________GGCGGGA\n______________::\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________204_____156\n	185 -- 191	201 -- 207	-10.9952 kcal/mol	1.94403 kcal/mol	0.326294 kcal/mol	158 212@LB@ \| \|@LB@5'-ACG...ACAAG AUUUA...GAA-3'@LB@ GGCGGGA@LB@ ::\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 204 156@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -10.9952 kcal/mol@LB@Unfolding Energy - mRNA 1.94403 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 159 -- 211@LB@Position - sRNA 157 -- 203@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 201 -- 207@LB@
49	0.01139	0.599	lmo0181	N/A	-18.25	0.023109	147 -- 168	157 -- 179	sugar ABC transporter substrate-binding protein	_____________146________________169\n_____________\|__________________\|\n5'-AAG...AAUGG_______CG_________AAUAA...UUA-3'\n______________CAAUGAG__GAAUGAAAG\n______________\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\|:\n______________GUUACUC__CUUACUUUU\n3'-GUU...UGCCG_______UA_________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________180________________156\n	162 -- 168	157 -- 163	-17.3464 kcal/mol	2.46271 kcal/mol	0.933292 kcal/mol	146 169@LB@ \| \|@LB@5'-AAG...AAUGG CG AAUAA...UUA-3'@LB@ CAAUGAG GAAUGAAAG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|:@LB@ GUUACUC CUUACUUUU@LB@3'-GUU...UGCCG UA GUUUA...GGA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -18.25 kcal/mol@LB@Hybridization Energy -17.3464 kcal/mol@LB@Unfolding Energy - mRNA 2.46271 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 147 -- 168@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 157 -- 163@LB@
50	0.01167	0.599	lmo0850	N/A	-18.65	0.019190	166 -- 190	141 -- 165		_____________165________________________191\n_____________\|__________________________\|\n5'-UGG...AAAGA____AAAAUAAAAA____________AUUUU...AAU-3'\n______________GAGA__________GAAUGAAAACAA\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCU__________CUUACUUUUGUU\n3'-GUU...GGUUA____A_____________________UAUUA...GGA-5'\n_____________\|__________________________\|\n_____________166________________________140\n	171 -- 177	154 -- 160	-14.3235 kcal/mol	1.0644 kcal/mol	0.933796 kcal/mol	165 191@LB@ \| \|@LB@5'-UGG...AAAGA AAAAUAAAAA AUUUU...AAU-3'@LB@ GAGA GAAUGAAAACAA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCU CUUACUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 166 140@LB@@LB@@LB@Energy -18.65 kcal/mol@LB@Hybridization Energy -14.3235 kcal/mol@LB@Unfolding Energy - mRNA 1.0644 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 166 -- 190@LB@Position - sRNA 141 -- 165@LB@Position Seed - mRNA 171 -- 177@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)

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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