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
90	0.02372	0.6733	lmo2712	N/A	-17.76	0.029098	218 -- 285	160 -- 210	gluconate kinase	_____________217________286\n_____________\|__________\|\n5'-AGA...AAAAU__________CUGUU...CGA-3'\n______________GCGGGGUGAG\n______________:\|\|\|\|:\|\|\|\|\n______________UGCCCUACUC\n3'-GUU...CGUAU__________CGUAU...GGA-5'\n_____________\|__________\|\n_____________211________159\n	190 -- 196	197 -- 203	-16.6296 kcal/mol	4.31289 kcal/mol	0.38676 kcal/mol	217 286@LB@ \| \|@LB@5'-AGA...AAAAU CUGUU...CGA-3'@LB@ GCGGGGUGAG@LB@ :\|\|\|\|:\|\|\|\|@LB@ UGCCCUACUC@LB@3'-GUU...CGUAU CGUAU...GGA-5'@LB@ \| \|@LB@ 211 159@LB@@LB@@LB@Energy -17.76 kcal/mol@LB@Hybridization Energy -16.6296 kcal/mol@LB@Unfolding Energy - mRNA 4.31289 kcal/mol@LB@Unfolding Energy - sRNA 0.38676 kcal/mol@LB@@LB@Position - mRNA 218 -- 285@LB@Position - sRNA 160 -- 210@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 197 -- 203@LB@
149	0.0387	0.6968	lmo1809	plsX	-16.53	0.050633	188 -- 233	156 -- 203	glycerol-3-phosphate acyltransferase PlsX	_____________187________________234\n_____________\|__________________\|\n5'-ACA...CUGUA____C_____________CACGC...UUC-3'\n______________GAUG_GAUGGGUGGAGAU\n______________:\|\|\|_\|\|\|\|::\|\|:\|:\|:\n______________UUAC_CUACUUACUUUUG\n3'-GUU...GCCGG____U_____________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________204________________155\n	227 -- 233	156 -- 162	-17.4325 kcal/mol	7.3364 kcal/mol	0.941471 kcal/mol	187 234@LB@ \| \|@LB@5'-ACA...CUGUA C CACGC...UUC-3'@LB@ GAUG GAUGGGUGGAGAU@LB@ :\|\|\| \|\|\|\|::\|\|:\|:\|:@LB@ UUAC CUACUUACUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 204 155@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -17.4325 kcal/mol@LB@Unfolding Energy - mRNA 7.3364 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 188 -- 233@LB@Position - sRNA 156 -- 203@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 156 -- 162@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@
95	0.02474	0.6733	lmo2446	N/A	-18.44	0.021161	178 -- 278	95 -- 188	glycosidase	_____________177____________________279\n_____________\|______________________\|\n5'-UGA...AGGAA___________GC_A_______GAAAA...ACG-3'\n______________AGUGAGAUGAA__G_AGAACGA\n______________\|:\|\|\|\|\|\|\|\|\|__\|_\|:\|\|\|:\|\n______________UUACUCUACUU__C_UUUUGUU\n3'-GUU...GCCGG___________A__________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________189____________________94\n	210 -- 216	154 -- 160	-17.9823 kcal/mol	4.45349 kcal/mol	0.959215 kcal/mol	177 279@LB@ \| \|@LB@5'-UGA...AGGAA GC A GAAAA...ACG-3'@LB@ AGUGAGAUGAA G AGAACGA@LB@ \|:\|\|\|\|\|\|\|\|\| \| \|:\|\|\|:\|@LB@ UUACUCUACUU C UUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 189 94@LB@@LB@@LB@Energy -18.44 kcal/mol@LB@Hybridization Energy -17.9823 kcal/mol@LB@Unfolding Energy - mRNA 4.45349 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 178 -- 278@LB@Position - sRNA 95 -- 188@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 154 -- 160@LB@
55	0.01256	0.6043	lmo1725	N/A	-17.74	0.029271	269 -- 300	152 -- 185	GntR family tramscriptional regulator	_____________268______________________________301\n_____________\|________________________________\|\n5'-CAG...CAAAU___________G_______A___A________GU-3'\n______________GAUUACA_GGC_AAUG_GA_GGG_GAGGAUAA\n______________:\|:\|\|\|\|_\|\|\|_\|\|\|\|_\|\|_\|::_\|\|::\|:\|\|\n______________UUGAUGU_CCG_UUAC_CU_CUU_CUUUUGUU\n3'-GUU...UGUAC_______G___G____U__A___A________UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________186______________________________151\n	291 -- 297	155 -- 161	-25.158 kcal/mol	5.52494 kcal/mol	9.66022 kcal/mol	268 301@LB@ \| \|@LB@5'-CAG...CAAAU G A A GU-3'@LB@ GAUUACA GGC AAUG GA GGG GAGGAUAA@LB@ :\|:\|\|\|\| \|\|\| \|\|\|\| \|\| \|:: \|\|::\|:\|\|@LB@ UUGAUGU CCG UUAC CU CUU CUUUUGUU@LB@3'-GUU...UGUAC G G U A A UAUUA...GGA-5'@LB@ \| \|@LB@ 186 151@LB@@LB@@LB@Energy -17.74 kcal/mol@LB@Hybridization Energy -25.158 kcal/mol@LB@Unfolding Energy - mRNA 5.52494 kcal/mol@LB@Unfolding Energy - sRNA 9.66022 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 152 -- 185@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 155 -- 161@LB@
195	0.0561	0.7607	lmo2779	N/A	-14.82	0.104550	1 -- 44	150 -- 181	GTP-binding protein EngD	_____________0____________45\n_____________\|____________\|\n5'-ACG...AGCUU_________U__CUAUU...CGU-3'\n______________AUGAGAUGA_UG\n______________\|\|\|\|\|\|\|\|\|_\|\|\n______________UACUCUACU_AC\n3'-GUU...CCGGU_________U__UUUUG...GGA-5'\n_____________\|____________\|\n_____________182__________149\n	17 -- 23	164 -- 170	-12.8914 kcal/mol	1.66686 kcal/mol	0.818518 kcal/mol	0 45@LB@ \| \|@LB@5'-ACG...AGCUU U CUAUU...CGU-3'@LB@ AUGAGAUGA UG@LB@ \|\|\|\|\|\|\|\|\| \|\|@LB@ UACUCUACU AC@LB@3'-GUU...CCGGU U UUUUG...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -12.8914 kcal/mol@LB@Unfolding Energy - mRNA 1.66686 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 1 -- 44@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 164 -- 170@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@
190	0.0551	0.7607	lmo0641	N/A	-14.65	0.112053	196 -- 245	175 -- 211	heavy metal-transporting ATPase	_____________195_____________________246\n_____________\|_______________________\|\n5'-AUU...GAGCA______AA__U____________GAAUU...ACU-3'\n______________UAAUGA__GA_UGGAUGAAG_CA\n______________:\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\|:_\|\|\n______________GUUACU__CU_ACUUACUUU_GU\n3'-GUU...UGCCG____________________U__UUAUU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________174\n	212 -- 218	158 -- 164	-12.4633 kcal/mol	2.08827 kcal/mol	0.95817 kcal/mol	195 246@LB@ \| \|@LB@5'-AUU...GAGCA AA U GAAUU...ACU-3'@LB@ UAAUGA GA UGGAUGAAG CA@LB@ :\|\|\|\|\| \|\| \|\|:\|\|\|\|\|: \|\|@LB@ GUUACU CU ACUUACUUU GU@LB@3'-GUU...UGCCG U UUAUU...GGA-5'@LB@ \| \|@LB@ 212 174@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -12.4633 kcal/mol@LB@Unfolding Energy - mRNA 2.08827 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 196 -- 245@LB@Position - sRNA 175 -- 211@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 158 -- 164@LB@
101	0.026	0.6733	lmo2768	N/A	-17.52	0.032492	230 -- 251	161 -- 179	hypothetical membrane protein	_____________229__________252\n_____________\|____________\|\n5'-UUA...GUAAU____________CUUUU...UAA-3'\n______________AUGAGAUGGAUG\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________UACUCUACUUAC\n3'-GUU...CCGGU____________UUUUG...GGA-5'\n_____________\|____________\|\n_____________180__________160\n	245 -- 251	161 -- 167	-15.292 kcal/mol	2.52317 kcal/mol	0.818518 kcal/mol	229 252@LB@ \| \|@LB@5'-UUA...GUAAU CUUUU...UAA-3'@LB@ AUGAGAUGGAUG@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ UACUCUACUUAC@LB@3'-GUU...CCGGU UUUUG...GGA-5'@LB@ \| \|@LB@ 180 160@LB@@LB@@LB@Energy -17.52 kcal/mol@LB@Hybridization Energy -15.292 kcal/mol@LB@Unfolding Energy - mRNA 2.52317 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 230 -- 251@LB@Position - sRNA 161 -- 179@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 161 -- 167@LB@
100	0.02596	0.6733	lmo2805	N/A	-13.33	0.188364	273 -- 298	147 -- 172	hypothetical secreted protein	_____________272_______________________________________299\n_____________\|_________________________________________\|\n5'-GAA...CAUAC______GG_____AG_____AAAAA________________AAUAG...AAA-3'\n______________AACAGA____UGA__AGUUG____________GAGAUGGAU\n______________\|\|\|\|\|\|____\|\|\|__\|\|\|\|\|____________:\|\|\|\|\|\|\|\|\n______________UUGUCU____ACU__UCAAC____________UUCUACCUA\n3'-GUU...CAGAU______ACAG___GA_____GGUAAGAUAACC_________UGUGG...GGA-5'\n_____________\|_________________________________________\|\n_____________173_______________________________________146\n	211 -- 217	94 -- 100	-22.9496 kcal/mol	2.56346 kcal/mol	9.49359 kcal/mol	272 299@LB@ \| \|@LB@5'-GAA...CAUAC GG AG AAAAA AAUAG...AAA-3'@LB@ AACAGA UGA AGUUG GAGAUGGAU@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUGUCU ACU UCAAC UUCUACCUA@LB@3'-GUU...CAGAU ACAG GA GGUAAGAUAACC UGUGG...GGA-5'@LB@ \| \|@LB@ 173 146@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -22.9496 kcal/mol@LB@Unfolding Energy - mRNA 2.56346 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 147 -- 172@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 94 -- 100@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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