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
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@
92	0.02404	0.6733	lmo1947	resE	-16.63	0.048416	181 -- 212	141 -- 170	two-component sensor histidine kinas	_____________180_________________213\n_____________\|___________________\|\n5'-AAG...ACCGA_______AUA_________UUGGA...UUU-3'\n______________GGUGAGA___GAUGAAGAU\n______________::\|\|\|\|\|___:\|\|\|\|\|:\|:\n______________UUACUCU___UUACUUUUG\n3'-GUU...GCCGG_______AC__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________171_________________140\n	202 -- 208	156 -- 162	-13.4823 kcal/mol	2.25638 kcal/mol	0.941471 kcal/mol	180 213@LB@ \| \|@LB@5'-AAG...ACCGA AUA UUGGA...UUU-3'@LB@ GGUGAGA GAUGAAGAU@LB@ ::\|\|\|\|\| :\|\|\|\|\|:\|:@LB@ UUACUCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 171 140@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -13.4823 kcal/mol@LB@Unfolding Energy - mRNA 2.25638 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 181 -- 212@LB@Position - sRNA 141 -- 170@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@LB@
165	0.04532	0.7392	lmo2091	argH	-16.36	0.054421	189 -- 262	141 -- 199	argininosuccinate lyase	_____________188_________________263\n_____________\|___________________\|\n5'-UCA...GGUCA_______G__GAG______AAAUC...AAG-3'\n______________UGCCAUU_UA___GGAAGA\n______________\|\|\|\|\|\|\|_\|\|___\|\|\|\|\|\|\n______________ACGGUAA_AU___CCUUCU\n3'-GUU...GAUCA_______G__AA_______ACCUA...GGA-5'\n_____________\|___________________\|\n_____________200_________________140\n	20 -- 26	110 -- 116	-20.7676 kcal/mol	3.64063 kcal/mol	5.20705 kcal/mol	188 263@LB@ \| \|@LB@5'-UCA...GGUCA G GAG AAAUC...AAG-3'@LB@ UGCCAUU UA GGAAGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ ACGGUAA AU CCUUCU@LB@3'-GUU...GAUCA G AA ACCUA...GGA-5'@LB@ \| \|@LB@ 200 140@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -20.7676 kcal/mol@LB@Unfolding Energy - mRNA 3.64063 kcal/mol@LB@Unfolding Energy - sRNA 5.20705 kcal/mol@LB@@LB@Position - mRNA 189 -- 262@LB@Position - sRNA 141 -- 199@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 110 -- 116@LB@
198	0.05669	0.7607	lmo2670	N/A	-16.54	0.050282	118 -- 190	141 -- 216		_____________117_________________191\n_____________\|___________________\|\n5'-AAU...AUUUG_________UACC______UUCAA...UCU-3'\n______________GAUGAGAUG____GGGAAC\n______________:\|\|\|\|\|\|\|\|____\|::\|\|\|\n______________UUACUCUAC____CUUUUG\n3'-GUU...GCCGG_________UUA_______UUUAU...GGA-5'\n_____________\|___________________\|\n_____________217_________________140\n	72 -- 78	165 -- 171	-16.0384 kcal/mol	2.83906 kcal/mol	0.941471 kcal/mol	117 191@LB@ \| \|@LB@5'-AAU...AUUUG UACC UUCAA...UCU-3'@LB@ GAUGAGAUG GGGAAC@LB@ :\|\|\|\|\|\|\|\| \|::\|\|\|@LB@ UUACUCUAC CUUUUG@LB@3'-GUU...GCCGG UUA UUUAU...GGA-5'@LB@ \| \|@LB@ 217 140@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -16.0384 kcal/mol@LB@Unfolding Energy - mRNA 2.83906 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 118 -- 190@LB@Position - sRNA 141 -- 216@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 165 -- 171@LB@
54	0.01218	0.6043	lmo0065	N/A	-17.22	0.037093	77 -- 100	146 -- 171	lmo0065	_____________76_________________________101\n_____________\|__________________________\|\n5'-GUA...GCAUU____________________U_____UGGUA...CUA-3'\n______________UGAGAUG___GAAGACAAAU_AAUGA\n______________\|\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|_\|\|\|\|\|\n______________ACUCUAC___CUUUUGUUUA_UUACU\n3'-GUU...CGGUU_______UUA________________AAAAC...GGA-5'\n_____________\|__________________________\|\n_____________172________________________145\n	87 -- 93	152 -- 158	-20.9762 kcal/mol	2.94176 kcal/mol	5.93625 kcal/mol	76 101@LB@ \| \|@LB@5'-GUA...GCAUU U UGGUA...CUA-3'@LB@ UGAGAUG GAAGACAAAU AAUGA@LB@ \|\|\|\|\|\|\| \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ ACUCUAC CUUUUGUUUA UUACU@LB@3'-GUU...CGGUU UUA AAAAC...GGA-5'@LB@ \| \|@LB@ 172 145@LB@@LB@@LB@Energy -17.22 kcal/mol@LB@Hybridization Energy -20.9762 kcal/mol@LB@Unfolding Energy - mRNA 2.94176 kcal/mol@LB@Unfolding Energy - sRNA 5.93625 kcal/mol@LB@@LB@Position - mRNA 77 -- 100@LB@Position - sRNA 146 -- 171@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 152 -- 158@LB@
60	0.01449	0.6412	lmo0835	N/A	-17.67	0.030280	187 -- 229	146 -- 187	peptidoglycan binding protein	_____________186______________________________________________230\n_____________\|________________________________________________\|\n5'-UUU...UAUGA_____UUGGAGGA____________UAAA____U____A_________UAACU...CAG-3'\n______________GAACU________AUGGUCAGUGAG____AAUG_AAAA_AAAUAGUGA\n______________\|\|\|\|\|________\|:\|\|:\|\|:\|\|\|\|____\|\|\|\|_\|\|\|\|_\|\|\|\|\|:\|\|\|\n______________CUUGA________UGCCGGUUACUC____UUAC_UUUU_UUUAUUACU\n3'-GUU...CUGUA_____UG__________________UAC__________G_________AAAAC...GGA-5'\n_____________\|________________________________________________\|\n_____________188______________________________________________145\n	199 -- 205	168 -- 174	-31.6389 kcal/mol	7.07372 kcal/mol	14.4129 kcal/mol	186 230@LB@ \| \|@LB@5'-UUU...UAUGA UUGGAGGA UAAA U A UAACU...CAG-3'@LB@ GAACU AUGGUCAGUGAG AAUG AAAA AAAUAGUGA@LB@ \|\|\|\|\| \|:\|\|:\|\|:\|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CUUGA UGCCGGUUACUC UUAC UUUU UUUAUUACU@LB@3'-GUU...CUGUA UG UAC G AAAAC...GGA-5'@LB@ \| \|@LB@ 188 145@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -31.6389 kcal/mol@LB@Unfolding Energy - mRNA 7.07372 kcal/mol@LB@Unfolding Energy - sRNA 14.4129 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 146 -- 187@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 168 -- 174@LB@
80	0.02141	0.6733	lmo1147	N/A	-19.90	0.010431	143 -- 214	146 -- 207	cobalamin biosynthesis protein CopB	_____________142____________________________________________________________________215\n_____________\|______________________________________________________________________\|\n5'-UAU...AUUUG_______AUUUUUA________A____AUC____UGU_______A_______GAAUGGAC__________UGAUG...CAA-3'\n______________AGCGGGA_______GGGGC_UA_ACGU___GGAU___UACGCGG__AAUGAG________AUGAGUGAAA\n______________\|:\|\|\|\|\|_______\|:\|\|\|_\|\|_\|\|:\|___\|:\|:___\|\|\|:\|\|\|__\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|\|\n______________UUGCCCU_______CUCCG_AU_UGUA___CUUG___AUGUGCC__UUACUC________UACUUACUUU\n3'-GUU...ACGUA_______A___________U__C_____________________GG________________________UGUUU...GGA-5'\n_____________\|______________________________________________________________________\|\n_____________208____________________________________________________________________145\n	204 -- 210	158 -- 164	-42.8674 kcal/mol	12.3523 kcal/mol	18.5828 kcal/mol	142 215@LB@ \| \|@LB@5'-UAU...AUUUG AUUUUUA A AUC UGU A GAAUGGAC UGAUG...CAA-3'@LB@ AGCGGGA GGGGC UA ACGU GGAU UACGCGG AAUGAG AUGAGUGAAA@LB@ \|:\|\|\|\|\| \|:\|\|\| \|\| \|\|:\| \|:\|: \|\|\|:\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UUGCCCU CUCCG AU UGUA CUUG AUGUGCC UUACUC UACUUACUUU@LB@3'-GUU...ACGUA A U C GG UGUUU...GGA-5'@LB@ \| \|@LB@ 208 145@LB@@LB@@LB@Energy -19.90 kcal/mol@LB@Hybridization Energy -42.8674 kcal/mol@LB@Unfolding Energy - mRNA 12.3523 kcal/mol@LB@Unfolding Energy - sRNA 18.5828 kcal/mol@LB@@LB@Position - mRNA 143 -- 214@LB@Position - sRNA 146 -- 207@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
91	0.02389	0.6733	lmo2425	N/A	-16.15	0.059838	240 -- 263	146 -- 170	glycine cleavage system protein H	_____________239______________264\n_____________\|________________\|\n5'-CGA...AACAC________________GACGA...AUC-3'\n______________GA_AUGGGUGAAAGCA\n______________\|\|_\|\|\|::\|\|\|\|\|:\|\|\n______________CU_UACUUACUUUUGU\n3'-GUU...GGUUA__C_____________UUAUU...GGA-5'\n_____________\|________________\|\n_____________171______________145\n	248 -- 254	155 -- 161	-15.1065 kcal/mol	3.08859 kcal/mol	0.929544 kcal/mol	239 264@LB@ \| \|@LB@5'-CGA...AACAC GACGA...AUC-3'@LB@ GA AUGGGUGAAAGCA@LB@ \|\| \|\|\|::\|\|\|\|\|:\|\|@LB@ CU UACUUACUUUUGU@LB@3'-GUU...GGUUA C UUAUU...GGA-5'@LB@ \| \|@LB@ 171 145@LB@@LB@@LB@Energy -16.15 kcal/mol@LB@Hybridization Energy -15.1065 kcal/mol@LB@Unfolding Energy - mRNA 3.08859 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 240 -- 263@LB@Position - sRNA 146 -- 170@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 155 -- 161@LB@
126	0.03359	0.6968	lmo1599	ccpA	-16.59	0.049230	178 -- 221	146 -- 188	catabolite control protein A	_____________177______________222\n_____________\|________________\|\n5'-UUU...GAAUA__________U_____AUUUA...CAA-3'\n______________GAGAUGAAUG__AACA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________CUCUACUUAC__UUGU\n3'-GUU...GGUUA__________UU____UUAUU...GGA-5'\n_____________\|________________\|\n_____________189______________145\n	201 -- 207	161 -- 167	-17.207 kcal/mol	2.33031 kcal/mol	0.929544 kcal/mol	177 222@LB@ \| \|@LB@5'-UUU...GAAUA U AUUUA...CAA-3'@LB@ GAGAUGAAUG AACA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUCUACUUAC UUGU@LB@3'-GUU...GGUUA UU UUAUU...GGA-5'@LB@ \| \|@LB@ 189 145@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -17.207 kcal/mol@LB@Unfolding Energy - mRNA 2.33031 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 178 -- 221@LB@Position - sRNA 146 -- 188@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@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@

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)

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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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