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
14	0.00304	0.4469	lmo1187	N/A	-19.26	0.014311	139 -- 172	153 -- 183	ethanolamine utilization protein EutQ	_____________138_______________________________173\n_____________\|_________________________________\|\n5'-UAA...GGUAU____________CC__AU______GA_______AGCAA...UUU-3'\n______________CUAUAUGGCUAA__GA__GAUGAA__AAAAUAA\n______________\|\|\|:\|:\|\|\|:\|\|__\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________GAUGUGCCGGUU__CU__CUACUU__UUUUGUU\n3'-GUU...UACUU____________A___________AC_______UAUUA...GGA-5'\n_____________\|_________________________________\|\n_____________184_______________________________152\n	165 -- 171	154 -- 160	-25.2263 kcal/mol	3.98561 kcal/mol	9.539 kcal/mol	138 173@LB@ \| \|@LB@5'-UAA...GGUAU CC AU GA AGCAA...UUU-3'@LB@ CUAUAUGGCUAA GA GAUGAA AAAAUAA@LB@ \|\|\|:\|:\|\|\|:\|\| \|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ GAUGUGCCGGUU CU CUACUU UUUUGUU@LB@3'-GUU...UACUU A AC UAUUA...GGA-5'@LB@ \| \|@LB@ 184 152@LB@@LB@@LB@Energy -19.26 kcal/mol@LB@Hybridization Energy -25.2263 kcal/mol@LB@Unfolding Energy - mRNA 3.98561 kcal/mol@LB@Unfolding Energy - sRNA 9.539 kcal/mol@LB@@LB@Position - mRNA 139 -- 172@LB@Position - sRNA 153 -- 183@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 154 -- 160@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@
152	0.04001	0.7027	lmo1203	cbiL	-16.49	0.051377	174 -- 199	155 -- 181	cobalt-precorrin-2 C(20)-methyltransferase	_____________173___________________200\n_____________\|_____________________\|\n5'-ACA...CACUG____A________________CGUGG...CAC-3'\n______________CAAU_GAGA_GGGUGAAAACA\n______________\|\|\|\|_\|\|\|\|_\|::\|\|\|\|\|\|\|\|\n______________GUUA_CUCU_CUUACUUUUGU\n3'-GUU...UGCCG_________A___________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________182___________________154\n	193 -- 199	155 -- 161	-18.5314 kcal/mol	4.87195 kcal/mol	0.95817 kcal/mol	173 200@LB@ \| \|@LB@5'-ACA...CACUG A CGUGG...CAC-3'@LB@ CAAU GAGA GGGUGAAAACA@LB@ \|\|\|\| \|\|\|\| \|::\|\|\|\|\|\|\|\|@LB@ GUUA CUCU CUUACUUUUGU@LB@3'-GUU...UGCCG A UUAUU...GGA-5'@LB@ \| \|@LB@ 182 154@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -18.5314 kcal/mol@LB@Unfolding Energy - mRNA 4.87195 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 174 -- 199@LB@Position - sRNA 155 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@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@
130	0.03486	0.6968	lmo1231	N/A	-15.49	0.079293	19 -- 84	118 -- 185	DNA polymerase beta	_____________18___________________85\n_____________\|____________________\|\n5'-UCU...UUGCC__________CU________CGCCA...GCA-3'\n______________CAGUG_GAUG__UGAAAACA\n______________\|\|:\|\|_\|\|\|\|__\|\|\|\|\|\|\|\|\n______________GUUAC_CUAC__ACUUUUGU\n3'-GUU...UGCCG_____U____UU________UUAUU...GGA-5'\n_____________\|____________________\|\n_____________186__________________117\n	46 -- 52	155 -- 161	-18.0743 kcal/mol	4.62758 kcal/mol	0.95817 kcal/mol	18 85@LB@ \| \|@LB@5'-UCU...UUGCC CU CGCCA...GCA-3'@LB@ CAGUG GAUG UGAAAACA@LB@ \|\|:\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUAC CUAC ACUUUUGU@LB@3'-GUU...UGCCG U UU UUAUU...GGA-5'@LB@ \| \|@LB@ 186 117@LB@@LB@@LB@Energy -15.49 kcal/mol@LB@Hybridization Energy -18.0743 kcal/mol@LB@Unfolding Energy - mRNA 4.62758 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 19 -- 84@LB@Position - sRNA 118 -- 185@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 155 -- 161@LB@
188	0.05492	0.7607	lmo1246	N/A	-15.64	0.074442	171 -- 206	183 -- 211	ATP-dependent RNA helicase	_____________170_______________207\n_____________\|_________________\|\n5'-GCC...AUGAU______A__________UGACA...CCU-3'\n______________AUGAGG__AAUGAGGAC\n______________\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UACUCU__UUACUUUUG\n3'-GUU...CCGGU______AC_________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________212_______________182\n	190 -- 196	156 -- 162	-13.5081 kcal/mol	2.39769 kcal/mol	0.922045 kcal/mol	170 207@LB@ \| \|@LB@5'-GCC...AUGAU A UGACA...CCU-3'@LB@ AUGAGG AAUGAGGAC@LB@ \|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UACUCU UUACUUUUG@LB@3'-GUU...CCGGU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 182@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -13.5081 kcal/mol@LB@Unfolding Energy - mRNA 2.39769 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 171 -- 206@LB@Position - sRNA 183 -- 211@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 156 -- 162@LB@
96	0.02498	0.6733	lmo1278	clpQ	-17.33	0.035430	185 -- 216	173 -- 203	ATP-dependent protease peptidase subunit	_____________184_____217\n_____________\|_______\|\n5'-AAA...UCAAC_______AAAAG...UGA-3'\n______________AUGACGG\n______________\|\|:\|\|\|\|\n______________UAUUGCC\n3'-GUU...AUACG_______CUACU...GGA-5'\n_____________\|_______\|\n_____________204_____172\n	238 -- 244	203 -- 209	-8.20287 kcal/mol	1.40847 kcal/mol	0.374301 kcal/mol	184 217@LB@ \| \|@LB@5'-AAA...UCAAC AAAAG...UGA-3'@LB@ AUGACGG@LB@ \|\|:\|\|\|\|@LB@ UAUUGCC@LB@3'-GUU...AUACG CUACU...GGA-5'@LB@ \| \|@LB@ 204 172@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -8.20287 kcal/mol@LB@Unfolding Energy - mRNA 1.40847 kcal/mol@LB@Unfolding Energy - sRNA 0.374301 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 173 -- 203@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 203 -- 209@LB@
163	0.04467	0.7375	lmo1286	parE	-16.49	0.051436	172 -- 223	160 -- 211	DNA topoisomerase IV subunit B	_____________171____________________________224\n_____________\|______________________________\|\n5'-CUU...AAUCA______UAA__________AU_________UUUUA...UAC-3'\n______________GCUAGU___UGCUAUUCUG____AAGGUGG\n______________:\|\|\|\|\|___\|\|\|:\|\|\|\|\|:____\|\|\|:\|\|\|\n______________UGAUCA___ACGGUAAGAU____UUCUACC\n3'-GUU...CAGAC___________________AACC_______UAUGU...GGA-5'\n_____________\|______________________________\|\n_____________212____________________________159\n	135 -- 141	96 -- 102	-24.989 kcal/mol	7.49229 kcal/mol	9.10061 kcal/mol	171 224@LB@ \| \|@LB@5'-CUU...AAUCA UAA AU UUUUA...UAC-3'@LB@ GCUAGU UGCUAUUCUG AAGGUGG@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|: \|\|\|:\|\|\|@LB@ UGAUCA ACGGUAAGAU UUCUACC@LB@3'-GUU...CAGAC AACC UAUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -24.989 kcal/mol@LB@Unfolding Energy - mRNA 7.49229 kcal/mol@LB@Unfolding Energy - sRNA 9.10061 kcal/mol@LB@@LB@Position - mRNA 172 -- 223@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 96 -- 102@LB@
104	0.02699	0.6733	lmo1327	rbfA	-16.36	0.054483	188 -- 240	157 -- 199	ribosome-binding factor A	_____________187________________241\n_____________\|__________________\|\n5'-ACA...CGUGU_______CA_________AAGAA...CUG-3'\n______________CAGUGAG___AAUGAAAA\n______________\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\n______________GUUACUC___UUACUUUU\n3'-GUU...UGCCG_______UAC________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________200________________156\n	234 -- 240	157 -- 163	-12.7883 kcal/mol	2.00785 kcal/mol	0.933292 kcal/mol	187 241@LB@ \| \|@LB@5'-ACA...CGUGU CA AAGAA...CUG-3'@LB@ CAGUGAG AAUGAAAA@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUACUC UUACUUUU@LB@3'-GUU...UGCCG UAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -12.7883 kcal/mol@LB@Unfolding Energy - mRNA 2.00785 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 157 -- 163@LB@
176	0.04979	0.7607	lmo1340	N/A	-16.63	0.048446	193 -- 216	151 -- 177		_____________192_____________217\n_____________\|_______________\|\n5'-UGC...UUGGA_______________AAAAU...CUG-3'\n______________GGCCA__GAGAUGAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CCGGU__CUCUACUU\n3'-GUU...AUGUG_____UA________ACUUU...GGA-5'\n_____________\|_______________\|\n_____________178_____________150\n	199 -- 205	163 -- 169	-19.0992 kcal/mol	1.80937 kcal/mol	7.44208 kcal/mol	192 217@LB@ \| \|@LB@5'-UGC...UUGGA AAAAU...CUG-3'@LB@ GGCCA GAGAUGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCGGU CUCUACUU@LB@3'-GUU...AUGUG UA ACUUU...GGA-5'@LB@ \| \|@LB@ 178 150@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -19.0992 kcal/mol@LB@Unfolding Energy - mRNA 1.80937 kcal/mol@LB@Unfolding Energy - sRNA 7.44208 kcal/mol@LB@@LB@Position - mRNA 193 -- 216@LB@Position - sRNA 151 -- 177@LB@Position Seed - mRNA 199 -- 205@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)

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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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