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@
69	0.01791	0.6733	lmo0011	N/A	-18.87	0.017267	48 -- 93	161 -- 209	mevalonate diphosphate decarboxylase	_____________47_________94\n_____________\|__________\|\n5'-AGU...CGGUA__________CAUUA...CCU-3'\n______________GAGGUGGAUG\n______________\|\|\|:\|\|:\|\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________210________160\n	87 -- 93	161 -- 167	-12.2828 kcal/mol	3.75931 kcal/mol	0.812237 kcal/mol	47 94@LB@ \| \|@LB@5'-AGU...CGGUA CAUUA...CCU-3'@LB@ GAGGUGGAUG@LB@ \|\|\|:\|\|:\|\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 210 160@LB@@LB@@LB@Energy -18.87 kcal/mol@LB@Hybridization Energy -12.2828 kcal/mol@LB@Unfolding Energy - mRNA 3.75931 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 48 -- 93@LB@Position - sRNA 161 -- 209@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 161 -- 167@LB@
85	0.0229	0.6733	lmo1788	N/A	-18.82	0.017630	177 -- 227	165 -- 211	transcriptional regulator	_____________176______________________________________________________228\n_____________\|________________________________________________________\|\n5'-UCU...AAAUG_______C______G____AA__G_____AAAA__A____CUGCUUAU________UUCAG...GGC-3'\n______________GAGGUGU_AGAUAU_GAAC__UG_ACGGU____GA_AUGG________GUGGGGAU\n______________\|\|\|\|::\|_\|\|\|:\|\|_\|\|\|\|__\|:_\|\|\|\|:____\|\|_\|\|\|:________:\|\|:::\|:\n______________CUCCGUA_UCUGUA_CUUG__AU_UGCCG____CU_UACU________UACUUUUG\n3'-GUU...CCCUA_______________________G_____GUUA__C____________________UUUAU...GGA-5'\n_____________\|________________________________________________________\|\n_____________212______________________________________________________164\n	238 -- 244	156 -- 162	-32.2408 kcal/mol	14.3369 kcal/mol	13.9689 kcal/mol	176 228@LB@ \| \|@LB@5'-UCU...AAAUG C G AA G AAAA A CUGCUUAU UUCAG...GGC-3'@LB@ GAGGUGU AGAUAU GAAC UG ACGGU GA AUGG GUGGGGAU@LB@ \|\|\|\|::\| \|\|\|:\|\| \|\|\|\| \|: \|\|\|\|: \|\| \|\|\|: :\|\|:::\|:@LB@ CUCCGUA UCUGUA CUUG AU UGCCG CU UACU UACUUUUG@LB@3'-GUU...CCCUA G GUUA C UUUAU...GGA-5'@LB@ \| \|@LB@ 212 164@LB@@LB@@LB@Energy -18.82 kcal/mol@LB@Hybridization Energy -32.2408 kcal/mol@LB@Unfolding Energy - mRNA 14.3369 kcal/mol@LB@Unfolding Energy - sRNA 13.9689 kcal/mol@LB@@LB@Position - mRNA 177 -- 227@LB@Position - sRNA 165 -- 211@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 156 -- 162@LB@
78	0.02097	0.6733	lmo1196	N/A	-18.80	0.017871	157 -- 213	158 -- 203	cobalt-precorrin-6Y C(15)-methyltransferase	_____________156_________________________________________________________214\n_____________\|___________________________________________________________\|\n5'-CCU...AACCA____AA___GCAAAAAAAUAC_________GUAG____G_U__U_______AGA_____UAUUU...AAA-3'\n______________GAGG__GUA____________GAUAUGAAU____UGGU_A_UG_AGAUGAA___UGAAG\n______________\|\|\|\|__:\|\|____________\|\|:\|\|\|\|\|:____:\|\|:_\|_\|\|_\|\|\|\|\|\|\|___\|\|\|\|:\n______________CUCC__UAU____________CUGUACUUG____GCCG_U_AC_UCUACUU___ACUUU\n3'-GUU...CCCUA____G_________________________AUGU____G_U__________________UGUUU...GGA-5'\n_____________\|___________________________________________________________\|\n_____________204_________________________________________________________157\n	199 -- 205	163 -- 169	-30.6214 kcal/mol	5.96601 kcal/mol	13.8965 kcal/mol	156 214@LB@ \| \|@LB@5'-CCU...AACCA AA GCAAAAAAAUAC GUAG G U U AGA UAUUU...AAA-3'@LB@ GAGG GUA GAUAUGAAU UGGU A UG AGAUGAA UGAAG@LB@ \|\|\|\| :\|\| \|\|:\|\|\|\|\|: :\|\|: \| \|\| \|\|\|\|\|\|\| \|\|\|\|:@LB@ CUCC UAU CUGUACUUG GCCG U AC UCUACUU ACUUU@LB@3'-GUU...CCCUA G AUGU G U UGUUU...GGA-5'@LB@ \| \|@LB@ 204 157@LB@@LB@@LB@Energy -18.80 kcal/mol@LB@Hybridization Energy -30.6214 kcal/mol@LB@Unfolding Energy - mRNA 5.96601 kcal/mol@LB@Unfolding Energy - sRNA 13.8965 kcal/mol@LB@@LB@Position - mRNA 157 -- 213@LB@Position - sRNA 158 -- 203@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
31	0.00657	0.5515	lmo1828	N/A	-18.66	0.019040	211 -- 279	154 -- 211		_____________210__________280\n_____________\|____________\|\n5'-AGU...GAAAA____________UUGGG...AAU-3'\n______________GCAUGACGGGAU\n______________\|\|\|\|:\|\|\|\|\|\|\|\n______________CGUAUUGCCCUA\n3'-GUU...GGAUA____________CUCCG...GGA-5'\n_____________\|____________\|\n_____________212__________153\n	216 -- 222	200 -- 206	-19.8213 kcal/mol	2.93239 kcal/mol	6.43166 kcal/mol	210 280@LB@ \| \|@LB@5'-AGU...GAAAA UUGGG...AAU-3'@LB@ GCAUGACGGGAU@LB@ \|\|\|\|:\|\|\|\|\|\|\|@LB@ CGUAUUGCCCUA@LB@3'-GUU...GGAUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -18.66 kcal/mol@LB@Hybridization Energy -19.8213 kcal/mol@LB@Unfolding Energy - mRNA 2.93239 kcal/mol@LB@Unfolding Energy - sRNA 6.43166 kcal/mol@LB@@LB@Position - mRNA 211 -- 279@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 200 -- 206@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@
26	0.004866	0.5029	lmo0682	flgG	-18.63	0.019297	177 -- 239	156 -- 207	flagellar basal body rod protein FlgG	_____________176__________________________________________240\n_____________\|____________________________________________\|\n5'-GAA...ACCAA_______GU_______CGGA__G___________AC____A___GGCAG...UCA-3'\n______________AGA_GUC__UGGCUAG____GC_G_UUUGUUGGA__GGAU_GGA\n______________\|\|\|_\|\|\|__\|\|:\|\|\|\|____\|\|_:_\|:\|:\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UCU_CAG__ACUGAUC____CG_U_AGAUAACCU__UCUA_CCU\n3'-GUU...AUUUG___A____________AA____G_A___________________AUGUG...GGA-5'\n_____________\|____________________________________________\|\n_____________208__________________________________________155\n	171 -- 177	102 -- 108	-30.3451 kcal/mol	11.2986 kcal/mol	9.4836 kcal/mol	176 240@LB@ \| \|@LB@5'-GAA...ACCAA GU CGGA G AC A GGCAG...UCA-3'@LB@ AGA GUC UGGCUAG GC G UUUGUUGGA GGAU GGA@LB@ \|\|\| \|\|\| \|\|:\|\|\|\| \|\| : \|:\|:\|\|\|\|\| :\|\|\| \|\|\|@LB@ UCU CAG ACUGAUC CG U AGAUAACCU UCUA CCU@LB@3'-GUU...AUUUG A AA G A AUGUG...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -30.3451 kcal/mol@LB@Unfolding Energy - mRNA 11.2986 kcal/mol@LB@Unfolding Energy - sRNA 9.4836 kcal/mol@LB@@LB@Position - mRNA 177 -- 239@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 102 -- 108@LB@
32	0.006611	0.5515	lmo1649	N/A	-18.63	0.019340	118 -- 153	171 -- 207	lmo1649	_____________117_____________________________________________________________154\n_____________\|_______________________________________________________________\|\n5'-GUA...UGUUA_______AGUAAU__UA______CG__________A_____UC__A_____G___________UACAA...AAA-3'\n______________CAUCGUG______GU__CU_UGC__GAUGGG_UGA_GCAUA__CG_G_ACU_ACGCGGCCAGU\n______________\|\|\|\|:\|\|______\|:__\|\|_\|\|\|__:\|:\|\|\|_\|\|\|_\|\|\|\|\|__\|:_\|_\|\|\|_\|\|:\|\|\|\|\|\|:\|\n______________GUAGUAC______CG__GA_ACG__UUGCCC_ACU_CGUAU__GU_C_UGA_UGUGCCGGUUA\n3'-GUU...CAACG_______AAGCC___CG__U___UA______U___C_____CU__A_U_______________CUCUA...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________208_____________________________________________________________170\n	147 -- 153	171 -- 177	-50.2657 kcal/mol	18.2787 kcal/mol	22.0434 kcal/mol	117 154@LB@ \| \|@LB@5'-GUA...UGUUA AGUAAU UA CG A UC A G UACAA...AAA-3'@LB@ CAUCGUG GU CU UGC GAUGGG UGA GCAUA CG G ACU ACGCGGCCAGU@LB@ \|\|\|\|:\|\| \|: \|\| \|\|\| :\|:\|\|\| \|\|\| \|\|\|\|\| \|: \| \|\|\| \|\|:\|\|\|\|\|\|:\|@LB@ GUAGUAC CG GA ACG UUGCCC ACU CGUAU GU C UGA UGUGCCGGUUA@LB@3'-GUU...CAACG AAGCC CG U UA U C CU A U CUCUA...GGA-5'@LB@ \| \|@LB@ 208 170@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -50.2657 kcal/mol@LB@Unfolding Energy - mRNA 18.2787 kcal/mol@LB@Unfolding Energy - sRNA 22.0434 kcal/mol@LB@@LB@Position - mRNA 118 -- 153@LB@Position - sRNA 171 -- 207@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 171 -- 177@LB@
61	0.01458	0.6412	lmo2589	N/A	-18.59	0.019740	180 -- 258	153 -- 210	TetR family transcriptional regulator	_____________179__________259\n_____________\|____________\|\n5'-ACU...AACAG____________UGUUU...CUG-3'\n______________AAC_GGGUGGGG\n______________\|\|\|_\|\|:\|\|:\|\|\n______________UUG_CCUACUCC\n3'-GUU...ACGUA___C________GUAUC...GGA-5'\n_____________\|____________\|\n_____________211__________152\n	186 -- 192	197 -- 203	-13.3669 kcal/mol	1.19489 kcal/mol	3.58567 kcal/mol	179 259@LB@ \| \|@LB@5'-ACU...AACAG UGUUU...CUG-3'@LB@ AAC GGGUGGGG@LB@ \|\|\| \|\|:\|\|:\|\|@LB@ UUG CCUACUCC@LB@3'-GUU...ACGUA C GUAUC...GGA-5'@LB@ \| \|@LB@ 211 152@LB@@LB@@LB@Energy -18.59 kcal/mol@LB@Hybridization Energy -13.3669 kcal/mol@LB@Unfolding Energy - mRNA 1.19489 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 180 -- 258@LB@Position - sRNA 153 -- 210@LB@Position Seed - mRNA 186 -- 192@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

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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

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