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
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@
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@
33	0.006763	0.5515	lmo1941	N/A	-21.42	0.004845	223 -- 286	154 -- 207		_____________222___________________________________________________________________287\n_____________\|_____________________________________________________________________\|\n5'-UAG...AGAAA_______AUACGAAGAACC___UGAUUAU________UU___AA_________________UC______UGAAC...UGU-3'\n______________AACGGGA____________GGC_______GACAUGAG__CUG___GGCCA___AGAUGAAU___AACAA\n______________\|\|\|\|\|\|\|____________\|\|\|_______\|\|\|\|\|\|\|:__\|\|:___\|\|\|\|\|___\|\|\|\|\|\|\|\|___\|\|\|\|\|\n______________UUGCCCU____________CCG_______CUGUACUU__GAU___CCGGU___UCUACUUA___UUGUU\n3'-GUU...ACGUA_______ACU____________UAU_________________GUG_____UAC________CUU_____UAUUA...GGA-5'\n_____________\|_____________________________________________________________________\|\n_____________208___________________________________________________________________153\n	273 -- 279	162 -- 168	-39.5283 kcal/mol	10.6608 kcal/mol	18.6655 kcal/mol	222 287@LB@ \| \|@LB@5'-UAG...AGAAA AUACGAAGAACC UGAUUAU UU AA UC UGAAC...UGU-3'@LB@ AACGGGA GGC GACAUGAG CUG GGCCA AGAUGAAU AACAA@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGCCCU CCG CUGUACUU GAU CCGGU UCUACUUA UUGUU@LB@3'-GUU...ACGUA ACU UAU GUG UAC CUU UAUUA...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -21.42 kcal/mol@LB@Hybridization Energy -39.5283 kcal/mol@LB@Unfolding Energy - mRNA 10.6608 kcal/mol@LB@Unfolding Energy - sRNA 18.6655 kcal/mol@LB@@LB@Position - mRNA 223 -- 286@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 162 -- 168@LB@
34	0.007076	0.552	lmo2678	N/A	-19.30	0.013995	184 -- 246	155 -- 207	XRE family transcriptional regulator	_____________183__________________________________________________________247\n_____________\|____________________________________________________________\|\n5'-GAA...AGACG____AG_____AA______A__AA______U___CUAAUUGUGGA__________U____UCAGU...AAG-3'\n______________GAGG__AUGGA__AUGAAC_GC__GCGGCU_GUG___________AGAUGAA_GA_GGCA\n______________\|\|\|\|__\|\|:\|\|__\|\|\|\|\|\|_:\|__:\|\|\|\|:_:\|\|___________\|\|\|\|\|\|\|_\|\|_::\|\|\n______________CUCC__UAUCU__UACUUG_UG__UGCCGG_UAC___________UCUACUU_CU_UUGU\n3'-GUU...CCCUA____G______G_______A__________U_____________________A__U____UUAUU...GGA-5'\n_____________\|____________________________________________________________\|\n_____________208__________________________________________________________154\n	233 -- 239	163 -- 169	-37.3867 kcal/mol	12.1272 kcal/mol	13.9822 kcal/mol	183 247@LB@ \| \|@LB@5'-GAA...AGACG AG AA A AA U CUAAUUGUGGA U UCAGU...AAG-3'@LB@ GAGG AUGGA AUGAAC GC GCGGCU GUG AGAUGAA GA GGCA@LB@ \|\|\|\| \|\|:\|\| \|\|\|\|\|\| :\| :\|\|\|\|: :\|\| \|\|\|\|\|\|\| \|\| ::\|\|@LB@ CUCC UAUCU UACUUG UG UGCCGG UAC UCUACUU CU UUGU@LB@3'-GUU...CCCUA G G A U A U UUAUU...GGA-5'@LB@ \| \|@LB@ 208 154@LB@@LB@@LB@Energy -19.30 kcal/mol@LB@Hybridization Energy -37.3867 kcal/mol@LB@Unfolding Energy - mRNA 12.1272 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 184 -- 246@LB@Position - sRNA 155 -- 207@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 163 -- 169@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@
36	0.007609	0.5562	lmo0649	N/A	-18.52	0.020396	192 -- 219	177 -- 204	transcriptional regulator	_____________191______220\n_____________\|________\|\n5'-UUU...AACGA________CAUGG...GUA-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______176\n	193 -- 199	197 -- 203	-13.9784 kcal/mol	1.5957 kcal/mol	0.386531 kcal/mol	191 220@LB@ \| \|@LB@5'-UUU...AACGA CAUGG...GUA-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 176@LB@@LB@@LB@Energy -18.52 kcal/mol@LB@Hybridization Energy -13.9784 kcal/mol@LB@Unfolding Energy - mRNA 1.5957 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 192 -- 219@LB@Position - sRNA 177 -- 204@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 197 -- 203@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@
38	0.007855	0.5562	lmo1229	N/A	-18.27	0.022927	193 -- 228	147 -- 186		_____________192_______________________________________229\n_____________\|_________________________________________\|\n5'-AUU...AGGAG___U_________A________________UA_________CAACA...GCG-3'\n______________GAA_UUACGUGGC_AAUGAGA_____GAAA__AAGUAGUGA\n______________\|\|\|_:\|\|\|::\|\|\|_\|\|\|\|\|\|\|_____\|\|\|\|__\|\|:\|\|:\|\|\|\n______________CUU_GAUGUGCCG_UUACUCU_____CUUU__UUUAUUACU\n3'-GUU...CUGUA_____________G_______ACUUA____UG_________AAAAC...GGA-5'\n_____________\|_________________________________________\|\n_____________187_______________________________________146\n	207 -- 213	167 -- 173	-29.0601 kcal/mol	3.84241 kcal/mol	14.4129 kcal/mol	192 229@LB@ \| \|@LB@5'-AUU...AGGAG U A UA CAACA...GCG-3'@LB@ GAA UUACGUGGC AAUGAGA GAAA AAGUAGUGA@LB@ \|\|\| :\|\|\|::\|\|\| \|\|\|\|\|\|\| \|\|\|\| \|\|:\|\|:\|\|\|@LB@ CUU GAUGUGCCG UUACUCU CUUU UUUAUUACU@LB@3'-GUU...CUGUA G ACUUA UG AAAAC...GGA-5'@LB@ \| \|@LB@ 187 146@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -29.0601 kcal/mol@LB@Unfolding Energy - mRNA 3.84241 kcal/mol@LB@Unfolding Energy - sRNA 14.4129 kcal/mol@LB@@LB@Position - mRNA 193 -- 228@LB@Position - sRNA 147 -- 186@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 167 -- 173@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@
40	0.00848	0.5705	lmo2399	N/A	-21.52	0.004592	127 -- 195	156 -- 207		_____________126_________________________________________________________________196\n_____________\|___________________________________________________________________\|\n5'-AUU...UCGAC_________GU_______CUUGUGGUUUAAAC____AGA____G__UAGA______A___G______GCUAA...CUG-3'\n______________GGUGAGGCA__GGCG_GA______________GCUA___ACGG_UA____AUGGGG_GAA_GAGGAU\n______________\|:\|\|\|\|\|\|\|__\|:\|:_\|\|______________:\|\|\|___\|\|\|\|_:\|____\|\|\|:\|:_\|\|\|_\|\|::\|:\n______________CUACUCCGU__CUGU_CU______________UGAU___UGCC_GU____UACUCU_CUU_CUUUUG\n3'-GUU...UUGCC_________AU____A____________________G______G____________A___A______UUUAU...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________208_________________________________________________________________155\n	132 -- 138	194 -- 200	-37.8581 kcal/mol	11.6457 kcal/mol	14.014 kcal/mol	126 196@LB@ \| \|@LB@5'-AUU...UCGAC GU CUUGUGGUUUAAAC AGA G UAGA A G GCUAA...CUG-3'@LB@ GGUGAGGCA GGCG GA GCUA ACGG UA AUGGGG GAA GAGGAU@LB@ \|:\|\|\|\|\|\|\| \|:\|: \|\| :\|\|\| \|\|\|\| :\| \|\|\|:\|: \|\|\| \|\|::\|:@LB@ CUACUCCGU CUGU CU UGAU UGCC GU UACUCU CUU CUUUUG@LB@3'-GUU...UUGCC AU A G G A A UUUAU...GGA-5'@LB@ \| \|@LB@ 208 155@LB@@LB@@LB@Energy -21.52 kcal/mol@LB@Hybridization Energy -37.8581 kcal/mol@LB@Unfolding Energy - mRNA 11.6457 kcal/mol@LB@Unfolding Energy - sRNA 14.014 kcal/mol@LB@@LB@Position - mRNA 127 -- 195@LB@Position - sRNA 156 -- 207@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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