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	Additional homologs
8	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
20	0.003655	0.4469	lmo1591	argC	-21.66	0.004270	183 -- 240	156 -- 208	N-acetyl-gamma-glutamyl-phosphate reductase		_____________182___________________________________________________________241\n_____________\|_____________________________________________________________\|\n5'-AAA...AUAAU________A________________AGUUUCAAU__U____G___C_______UG______UUGAG...GUU-3'\n______________UAACGGGG_GGGGU_UAGG_AUGAA_________CA_UGGC_CGA_GGGGU_A__GAGGAC\n______________\|\|\|\|\|\|\|:_\|:\|\|:_\|\|\|:_\|\|\|\|\|_________\|\|_:\|\|\|_\|:\|_\|:\|:\|_\|__\|\|::\|\|\n______________AUUGCCCU_CUCCG_AUCU_UACUU_________GU_GCCG_GUU_CUCUA_U__CUUUUG\n3'-GUU...UACGU________A_____U____G_____GAU_________________A_____C_UA______UUUAU...GGA-5'\n_____________\|_____________________________________________________________\|\n_____________209___________________________________________________________155\n	184 -- 190	201 -- 207	-40.8209 kcal/mol	11.7 kcal/mol	18.6528 kcal/mol	182 241@LB@ \| \|@LB@5'-AAA...AUAAU A AGUUUCAAU U G C UG UUGAG...GUU-3'@LB@ UAACGGGG GGGGU UAGG AUGAA CA UGGC CGA GGGGU A GAGGAC@LB@ \|\|\|\|\|\|\|: \|:\|\|: \|\|\|: \|\|\|\|\| \|\| :\|\|\| \|:\| \|:\|:\| \| \|\|::\|\|@LB@ AUUGCCCU CUCCG AUCU UACUU GU GCCG GUU CUCUA U CUUUUG@LB@3'-GUU...UACGU A U G GAU A C UA UUUAU...GGA-5'@LB@ \| \|@LB@ 209 155@LB@@LB@@LB@Energy -21.66 kcal/mol@LB@Hybridization Energy -40.8209 kcal/mol@LB@Unfolding Energy - mRNA 11.7 kcal/mol@LB@Unfolding Energy - sRNA 18.6528 kcal/mol@LB@@LB@Position - mRNA 183 -- 240@LB@Position - sRNA 156 -- 208@LB@Position Seed - mRNA 184 -- 190@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@
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@
15	0.003165	0.4469	lmo0292	N/A	-21.41	0.004857	182 -- 249	155 -- 212	heat-shock protein htrA serine protease		_____________181_____________________________________________________________250\n_____________\|_______________________________________________________________\|\n5'-GAG...GCAGA____AAGGA__________G_G_AAGAAAAGAAUUUA_____AAACAGC______________CGCCG...AAC-3'\n______________GAGG_____AGACAUGGAC_A_A______________AAUGA_______GA_GAAUGAAAGCA\n______________\|\|\|\|_____\|\|\|\|\|\|\|:\|\|_\|_\|______________\|\|\|\|\|_______\|\|_\|\|\|\|\|\|\|\|:\|\|\n______________CUCC_____UCUGUACUUG_U_U______________UUACU_______CU_CUUACUUUUGU\n3'-GUU...CCCUA____GUA____________A_G_GCCGG_______________________A___________UUAUU...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________213_____________________________________________________________154\n	243 -- 249	155 -- 161	-30.3296 kcal/mol	4.19045 kcal/mol	13.9822 kcal/mol	181 250@LB@ \| \|@LB@5'-GAG...GCAGA AAGGA G G AAGAAAAGAAUUUA AAACAGC CGCCG...AAC-3'@LB@ GAGG AGACAUGGAC A A AAUGA GA GAAUGAAAGCA@LB@ \|\|\|\| \|\|\|\|\|\|\|:\|\| \| \| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|:\|\|@LB@ CUCC UCUGUACUUG U U UUACU CU CUUACUUUUGU@LB@3'-GUU...CCCUA GUA A G GCCGG A UUAUU...GGA-5'@LB@ \| \|@LB@ 213 154@LB@@LB@@LB@Energy -21.41 kcal/mol@LB@Hybridization Energy -30.3296 kcal/mol@LB@Unfolding Energy - mRNA 4.19045 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 182 -- 249@LB@Position - sRNA 155 -- 212@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 155 -- 161@LB@
27	0.005046	0.5029	lmo2370	N/A	-21.11	0.005698	252 -- 287	166 -- 205	aminotransferase		_____________251_____________288\n_____________\|_______________\|\n5'-CCU...AUAAU_____C_________AGAAG...UGU-3'\n______________UGAGG_GAAUGAAAG\n______________\|\|\|\|:_\|\|\|\|\|\|\|\|:\n______________ACUCU_CUUACUUUU\n3'-GUU...CGGUU_____A_________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________206_____________165\n	176 -- 182	157 -- 163	-15.2487 kcal/mol	2.36926 kcal/mol	0.905109 kcal/mol	251 288@LB@ \| \|@LB@5'-CCU...AUAAU C AGAAG...UGU-3'@LB@ UGAGG GAAUGAAAG@LB@ \|\|\|\|: \|\|\|\|\|\|\|\|:@LB@ ACUCU CUUACUUUU@LB@3'-GUU...CGGUU A GUUUA...GGA-5'@LB@ \| \|@LB@ 206 165@LB@@LB@@LB@Energy -21.11 kcal/mol@LB@Hybridization Energy -15.2487 kcal/mol@LB@Unfolding Energy - mRNA 2.36926 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 252 -- 287@LB@Position - sRNA 166 -- 205@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 157 -- 163@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@
22	0.003708	0.4469	lmo1689	N/A	-20.94	0.006216	185 -- 218	155 -- 186	A/G-specific adenine glycosylase		_____________184________________________________219\n_____________\|__________________________________\|\n5'-UGA...UAUUA________A__GGAA_______AA________G_CUAAC...CGU-3'\n______________GAAUUACG_GG____AAUGAGA__AAUGAAGA_A\n______________\|\|\|:\|\|\|:_\|\|____\|\|\|\|\|\|\|__\|\|\|\|\|\|:\|_\|\n______________CUUGAUGU_CC____UUACUCU__UUACUUUU_U\n3'-GUU...CUGUA________G__GG_________AC________G_UUAUU...GGA-5'\n_____________\|__________________________________\|\n_____________187________________________________154\n	210 -- 216	157 -- 163	-27.9128 kcal/mol	3.65812 kcal/mol	9.66922 kcal/mol	184 219@LB@ \| \|@LB@5'-UGA...UAUUA A GGAA AA G CUAAC...CGU-3'@LB@ GAAUUACG GG AAUGAGA AAUGAAGA A@LB@ \|\|\|:\|\|\|: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|@LB@ CUUGAUGU CC UUACUCU UUACUUUU U@LB@3'-GUU...CUGUA G GG AC G UUAUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -20.94 kcal/mol@LB@Hybridization Energy -27.9128 kcal/mol@LB@Unfolding Energy - mRNA 3.65812 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 157 -- 163@LB@
9	0.002066	0.4469	lmo0669	N/A	-20.91	0.006284	33 -- 77	156 -- 211	oxidoreductase		_____________32__________________78\n_____________\|___________________\|\n5'-AAU...UAAAG___________________GGGAA...UUC-3'\n______________UAAUGGGG_GGAUGAAAAU\n______________:\|\|\|\|:\|:_\|:\|\|\|\|\|\|\|:\n______________GUUACUCU_CUUACUUUUG\n3'-GUU...UGCCG________A__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________212_________________155\n	71 -- 77	156 -- 162	-16.6504 kcal/mol	2.4241 kcal/mol	0.944687 kcal/mol	32 78@LB@ \| \|@LB@5'-AAU...UAAAG GGGAA...UUC-3'@LB@ UAAUGGGG GGAUGAAAAU@LB@ :\|\|\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ GUUACUCU CUUACUUUUG@LB@3'-GUU...UGCCG A UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -20.91 kcal/mol@LB@Hybridization Energy -16.6504 kcal/mol@LB@Unfolding Energy - mRNA 2.4241 kcal/mol@LB@Unfolding Energy - sRNA 0.944687 kcal/mol@LB@@LB@Position - mRNA 33 -- 77@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 71 -- 77@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@

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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