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
75	0.01961	0.6733	lmo0383	N/A	-20.23	0.008871	224 -- 265	150 -- 186	methylmalonate-semialdehyde dehydrogenase	_____________223________________________________________266\n_____________\|__________________________________________\|\n5'-UUC...UUAAA_______AUUG_____G______UC___A_U___________AUAUG...AAG-3'\n______________GAAUUAU____ACGGC_AAUGGG__GAG_G_AAGACAGAUAA\n______________\|\|\|:\|\|:____\|\|\|\|\|_\|\|\|\|:\|__\|\|:_\|_\|\|:\|\|\|:\|\|\|\|\n______________CUUGAUG____UGCCG_UUACUC__CUU_C_UUUUGUUUAUU\n3'-GUU...CUGUA________________G______UA___A_____________ACUAA...GGA-5'\n_____________\|__________________________________________\|\n_____________187________________________________________149\n	257 -- 263	152 -- 158	-34.2826 kcal/mol	8.25616 kcal/mol	13.66 kcal/mol	223 266@LB@ \| \|@LB@5'-UUC...UUAAA AUUG G UC A U AUAUG...AAG-3'@LB@ GAAUUAU ACGGC AAUGGG GAG G AAGACAGAUAA@LB@ \|\|\|:\|\|: \|\|\|\|\| \|\|\|\|:\| \|\|: \| \|\|:\|\|\|:\|\|\|\|@LB@ CUUGAUG UGCCG UUACUC CUU C UUUUGUUUAUU@LB@3'-GUU...CUGUA G UA A ACUAA...GGA-5'@LB@ \| \|@LB@ 187 149@LB@@LB@@LB@Energy -20.23 kcal/mol@LB@Hybridization Energy -34.2826 kcal/mol@LB@Unfolding Energy - mRNA 8.25616 kcal/mol@LB@Unfolding Energy - sRNA 13.66 kcal/mol@LB@@LB@Position - mRNA 224 -- 265@LB@Position - sRNA 150 -- 186@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 152 -- 158@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@
35	0.00718	0.552	lmo0397	N/A	-24.49	0.000911	178 -- 232	160 -- 211		_____________177_________________________________________________________________________233\n_____________\|___________________________________________________________________________\|\n5'-AAU...ACAAA_______AAAAUGAAAGCAAAU_____________G__UU_G______GAG___AU__AA___C___________UAUGA...CGA-3'\n______________CUGUGCG_______________UGGCGGGA___GG_AU__A_AUGAAC___GCA__CG__CGA_GAGAUGA_UGA\n______________\|\|:\|\|\|:_______________\|::\|\|\|\|\|___\|\|_\|\|__\|_\|\|\|\|\|\|___:\|\|__\|\|__\|:\|_\|\|\|\|\|\|\|_\|\|\|\n______________GAUACGU_______________AUUGCCCU___CC_UA__U_UACUUG___UGU__GC__GUU_CUCUACU_ACU\n3'-GUU...CCGCG______________________________ACU__G__UC_G______A_________CG___A_______U___UUUGU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________212_________________________________________________________________________159\n	223 -- 229	164 -- 170	-45.3132 kcal/mol	12.0365 kcal/mol	19.7814 kcal/mol	177 233@LB@ \| \|@LB@5'-AAU...ACAAA AAAAUGAAAGCAAAU G UU G GAG AU AA C UAUGA...CGA-3'@LB@ CUGUGCG UGGCGGGA GG AU A AUGAAC GCA CG CGA GAGAUGA UGA@LB@ \|\|:\|\|\|: \|::\|\|\|\|\| \|\| \|\| \| \|\|\|\|\|\| :\|\| \|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ GAUACGU AUUGCCCU CC UA U UACUUG UGU GC GUU CUCUACU ACU@LB@3'-GUU...CCGCG ACU G UC G A CG A U UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -24.49 kcal/mol@LB@Hybridization Energy -45.3132 kcal/mol@LB@Unfolding Energy - mRNA 12.0365 kcal/mol@LB@Unfolding Energy - sRNA 19.7814 kcal/mol@LB@@LB@Position - mRNA 178 -- 232@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 164 -- 170@LB@
73	0.0193	0.6733	lmo0405	N/A	-18.50	0.020574	154 -- 209	155 -- 199	phosphate transporter	_____________153____________210\n_____________\|______________\|\n5'-GUG...UUAUG________U_____UACGA...CGA-3'\n______________AUGACGGG_AUGAG\n______________\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________UAUUGCCC_UACUC\n3'-GUU...AUACG______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________200____________154\n	50 -- 56	202 -- 208	-16.311 kcal/mol	2.72131 kcal/mol	0.386761 kcal/mol	153 210@LB@ \| \|@LB@5'-GUG...UUAUG U UACGA...CGA-3'@LB@ AUGACGGG AUGAG@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGCCC UACUC@LB@3'-GUU...AUACG CGUAU...GGA-5'@LB@ \| \|@LB@ 200 154@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -16.311 kcal/mol@LB@Unfolding Energy - mRNA 2.72131 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 154 -- 209@LB@Position - sRNA 155 -- 199@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 202 -- 208@LB@
160	0.04276	0.7192	lmo0415	N/A	-19.07	0.015641	183 -- 241	108 -- 171	endo-1 4-beta-xylanase	_____________182_________________________________________________________________242\n_____________\|___________________________________________________________________\|\n5'-UUU...UUUUC_________GU______UAAU____AAA__A____GA______________C_______________CAUUA...AGU-3'\n______________UGAGGUGAG_____GCA____GUGA___UU_GGUG__UUAGAC_____UUU_ACUAGUUGCCAUUCU\n______________\|\|\|\|:\|\|\|:_____:\|\|____:\|\|\|___\|\|_\|\|\|\|__:\|\|:\|\|_____\|:\|_\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACUCUACUU_____UGU____UACU___AA_CCAC__GAUUUG_____AGA_UGAUCAACGGUAAGA\n3'-GUU...CGGUU_________ACUUU___UUAU____A____A____A_______UCUAC___C_______________UAACC...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________172_________________________________________________________________107\n	235 -- 241	108 -- 114	-46.29 kcal/mol	15.9956 kcal/mol	19.2069 kcal/mol	182 242@LB@ \| \|@LB@5'-UUU...UUUUC GU UAAU AAA A GA C CAUUA...AGU-3'@LB@ UGAGGUGAG GCA GUGA UU GGUG UUAGAC UUU ACUAGUUGCCAUUCU@LB@ \|\|\|\|:\|\|\|: :\|\| :\|\|\| \|\| \|\|\|\| :\|\|:\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACUCUACUU UGU UACU AA CCAC GAUUUG AGA UGAUCAACGGUAAGA@LB@3'-GUU...CGGUU ACUUU UUAU A A A UCUAC C UAACC...GGA-5'@LB@ \| \|@LB@ 172 107@LB@@LB@@LB@Energy -19.07 kcal/mol@LB@Hybridization Energy -46.29 kcal/mol@LB@Unfolding Energy - mRNA 15.9956 kcal/mol@LB@Unfolding Energy - sRNA 19.2069 kcal/mol@LB@@LB@Position - mRNA 183 -- 241@LB@Position - sRNA 108 -- 171@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 108 -- 114@LB@
171	0.04778	0.7516	lmo0498	N/A	-14.78	0.106331	152 -- 199	154 -- 211	5-phosphate isomerase	_____________151__________________200\n_____________\|____________________\|\n5'-AUC...AUCAA_______AA___________ACAUG...GUU-3'\n______________GGUGAGA__GGA_GAGGAUA\n______________::\|\|\|\|\|__\|:\|_\|\|::\|:\|\n______________UUACUCU__CUU_CUUUUGU\n3'-GUU...GCCGG_______A____A_______UUAUU...GGA-5'\n_____________\|____________________\|\n_____________212__________________153\n	192 -- 198	155 -- 161	-12.5427 kcal/mol	2.39386 kcal/mol	0.954976 kcal/mol	151 200@LB@ \| \|@LB@5'-AUC...AUCAA AA ACAUG...GUU-3'@LB@ GGUGAGA GGA GAGGAUA@LB@ ::\|\|\|\|\| \|:\| \|\|::\|:\|@LB@ UUACUCU CUU CUUUUGU@LB@3'-GUU...GCCGG A A UUAUU...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -12.5427 kcal/mol@LB@Unfolding Energy - mRNA 2.39386 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 152 -- 199@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 155 -- 161@LB@
138	0.03642	0.6968	lmo0509	prs	-15.18	0.090372	180 -- 241	157 -- 211	phosphoribosyl pyrophosphate synthetase	_____________179____________________________________242\n_____________\|______________________________________\|\n5'-AAC...GAAGA_____G______G__AG_____A_C_____C_______AUGAA...UCC-3'\n______________AAUUA_UAUGGC_GA__GAGAU_G_AAUGG_AGGCAAA\n______________\|\|:\|\|_:\|:\|\|\|_:\|__\|\|\|\|\|_\|_\|\|\|\|:_\|::\|\|\|\|\n______________UUGAU_GUGCCG_UU__CUCUA_C_UUACU_UUUGUUU\n3'-GUU...UGUAC____________G__A______________________AUUAC...GGA-5'\n_____________\|______________________________________\|\n_____________212____________________________________156\n	206 -- 212	153 -- 159	-24.2745 kcal/mol	6.00947 kcal/mol	10.6652 kcal/mol	179 242@LB@ \| \|@LB@5'-AAC...GAAGA G G AG A C C AUGAA...UCC-3'@LB@ AAUUA UAUGGC GA GAGAU G AAUGG AGGCAAA@LB@ \|\|:\|\| :\|:\|\|\| :\| \|\|\|\|\| \| \|\|\|\|: \|::\|\|\|\|@LB@ UUGAU GUGCCG UU CUCUA C UUACU UUUGUUU@LB@3'-GUU...UGUAC G A AUUAC...GGA-5'@LB@ \| \|@LB@ 212 156@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -24.2745 kcal/mol@LB@Unfolding Energy - mRNA 6.00947 kcal/mol@LB@Unfolding Energy - sRNA 10.6652 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 157 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 153 -- 159@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@
37	0.007696	0.5562	lmo0551	N/A	-17.72	0.029617	133 -- 210	151 -- 204	lmo0551	_____________132____________211\n_____________\|______________\|\n5'-AGA...UUAAG________G_____AAUUC...CUU-3'\n______________GAGGUGAG_GAAGA\n______________\|\|\|:\|\|\|:_\|\|\|:\|\n______________CUCUACUU_CUUUU\n3'-GUU...GGUUA________A_____GUUUA...GGA-5'\n_____________\|______________\|\n_____________205____________150\n	135 -- 141	163 -- 169	-13.8898 kcal/mol	2.56868 kcal/mol	0.904482 kcal/mol	132 211@LB@ \| \|@LB@5'-AGA...UUAAG G AAUUC...CUU-3'@LB@ GAGGUGAG GAAGA@LB@ \|\|\|:\|\|\|: \|\|\|:\|@LB@ CUCUACUU CUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 205 150@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 2.56868 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 133 -- 210@LB@Position - sRNA 151 -- 204@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 163 -- 169@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@

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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