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@
87	0.02294	0.6733	lmo2765	N/A	-17.07	0.039744	188 -- 213	176 -- 199	PTS cellbiose transporter subunit IIA	_____________187_________________214\n_____________\|___________________\|\n5'-UUA...UAGAC________A__________GUUAU...AUU-3'\n______________AUGA_AUG_AAUGGAAACA\n______________\|\|\|\|_\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________UACU_UAC_UUACUUUUGU\n3'-GUU...CCGGU____C______________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________200_________________175\n	212 -- 218	155 -- 161	-13.3886 kcal/mol	2.47541 kcal/mol	0.935542 kcal/mol	187 214@LB@ \| \|@LB@5'-UUA...UAGAC A GUUAU...AUU-3'@LB@ AUGA AUG AAUGGAAACA@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UACU UAC UUACUUUUGU@LB@3'-GUU...CCGGU C UUAUU...GGA-5'@LB@ \| \|@LB@ 200 175@LB@@LB@@LB@Energy -17.07 kcal/mol@LB@Hybridization Energy -13.3886 kcal/mol@LB@Unfolding Energy - mRNA 2.47541 kcal/mol@LB@Unfolding Energy - sRNA 0.935542 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 176 -- 199@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@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@
133	0.03548	0.6968	lmo2772	N/A	-15.87	0.067267	191 -- 210	179 -- 199	PTS beta-glucoside transporter subunit IIABC	_____________190__________________211\n_____________\|____________________\|\n5'-GCG...UUUAG____AU______________AAUCA...AAU-3'\n______________GAGG__UAG_CAUGGACUAC\n______________\|\|\|\|__\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________CUCC__AUC_GUACUUGAUG\n3'-GUU...CCCUA____GU___U__________UGCCG...GGA-5'\n_____________\|____________________\|\n_____________200__________________178\n	203 -- 209	180 -- 186	-24.3176 kcal/mol	4.09739 kcal/mol	10.4768 kcal/mol	190 211@LB@ \| \|@LB@5'-GCG...UUUAG AU AAUCA...AAU-3'@LB@ GAGG UAG CAUGGACUAC@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ CUCC AUC GUACUUGAUG@LB@3'-GUU...CCCUA GU U UGCCG...GGA-5'@LB@ \| \|@LB@ 200 178@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 4.09739 kcal/mol@LB@Unfolding Energy - sRNA 10.4768 kcal/mol@LB@@LB@Position - mRNA 191 -- 210@LB@Position - sRNA 179 -- 199@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 180 -- 186@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@
28	0.005366	0.5157	lmo2793	N/A	-19.39	0.013418	199 -- 253	121 -- 174	lmo2793	_____________198__________________254\n_____________\|____________________\|\n5'-AAA...UGUAG_________UUU________AUUGG...GUU-3'\n______________CAGUGAGGU___UGAAGAUA\n______________\|\|:\|\|\|\|:\|___\|\|\|\|:\|:\|\n______________GUUACUCUA___ACUUUUGU\n3'-GUU...UGCCG_________CUU________UUAUU...GGA-5'\n_____________\|____________________\|\n_____________175__________________120\n	212 -- 218	155 -- 161	-16.7389 kcal/mol	5.68665 kcal/mol	0.95817 kcal/mol	198 254@LB@ \| \|@LB@5'-AAA...UGUAG UUU AUUGG...GUU-3'@LB@ CAGUGAGGU UGAAGAUA@LB@ \|\|:\|\|\|\|:\| \|\|\|\|:\|:\|@LB@ GUUACUCUA ACUUUUGU@LB@3'-GUU...UGCCG CUU UUAUU...GGA-5'@LB@ \| \|@LB@ 175 120@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -16.7389 kcal/mol@LB@Unfolding Energy - mRNA 5.68665 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 199 -- 253@LB@Position - sRNA 121 -- 174@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@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@
162	0.04462	0.7375	lmo2840	N/A	-13.73	0.161226	169 -- 225	174 -- 208	sucrose phosphorylase	_____________168____________226\n_____________\|______________\|\n5'-UUU...AUAUU_______UG_____GAAUU...AUA-3'\n______________UAGCGGG__AUGAG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________AUUGCCC__UACUC\n3'-GUU...UACGU______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________209____________173\n	169 -- 175	202 -- 208	-13.6832 kcal/mol	2.78278 kcal/mol	0.386761 kcal/mol	168 226@LB@ \| \|@LB@5'-UUU...AUAUU UG GAAUU...AUA-3'@LB@ UAGCGGG AUGAG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ AUUGCCC UACUC@LB@3'-GUU...UACGU CGUAU...GGA-5'@LB@ \| \|@LB@ 209 173@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -13.6832 kcal/mol@LB@Unfolding Energy - mRNA 2.78278 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 169 -- 225@LB@Position - sRNA 174 -- 208@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 202 -- 208@LB@
111	0.02805	0.6801	lmo2841	N/A	-15.50	0.078879	184 -- 209	152 -- 178	sucrose phosphorylase	_____________183_______________________210\n_____________\|_________________________\|\n5'-UUU...AGGUA_____U__C____UUAA________CUUUC...AAC-3'\n______________AAUGA_GA_GAAU____GAAAACGA\n______________\|\|\|\|\|_\|\|_\|\|\|\|____\|\|\|\|\|\|:\|\n______________UUACU_CU_CUUA____CUUUUGUU\n3'-GUU...GCCGG________A________________UAUUA...GGA-5'\n_____________\|_________________________\|\n_____________179_______________________151\n	215 -- 221	154 -- 160	-12.3618 kcal/mol	2.60591 kcal/mol	0.959215 kcal/mol	183 210@LB@ \| \|@LB@5'-UUU...AGGUA U C UUAA CUUUC...AAC-3'@LB@ AAUGA GA GAAU GAAAACGA@LB@ \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UUACU CU CUUA CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 179 151@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -12.3618 kcal/mol@LB@Unfolding Energy - mRNA 2.60591 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 152 -- 178@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 154 -- 160@LB@
191	0.0551	0.7607	lmo2853	N/A	-14.70	0.110014	201 -- 241	156 -- 201		_____________200_______________________________________________242\n_____________\|_________________________________________________\|\n5'-GGU...AGAAA________________________AA___U___ACGU____________UAUCC...UUC-3'\n______________GUGAG____AGAUAU_AACUGCGC__GGC_CAA_____UGAA__GAAGC\n______________:\|\|\|\|____\|\|\|:\|\|_\|\|\|\|:\|:\|__\|\|\|_\|\|\|_____\|\|\|\|__:\|\|:\|\n______________UACUC____UCUGUA_UUGAUGUG__CCG_GUU_____ACUU__UUUUG\n3'-GUU...UGCCC_____CGUA______C_________________ACUCU____AC_____UUUAU...GGA-5'\n_____________\|_________________________________________________\|\n_____________202_______________________________________________155\n	213 -- 219	178 -- 184	-28.7711 kcal/mol	7.06239 kcal/mol	14.0114 kcal/mol	200 242@LB@ \| \|@LB@5'-GGU...AGAAA AA U ACGU UAUCC...UUC-3'@LB@ GUGAG AGAUAU AACUGCGC GGC CAA UGAA GAAGC@LB@ :\|\|\|\| \|\|\|:\|\| \|\|\|\|:\|:\| \|\|\| \|\|\| \|\|\|\| :\|\|:\|@LB@ UACUC UCUGUA UUGAUGUG CCG GUU ACUU UUUUG@LB@3'-GUU...UGCCC CGUA C ACUCU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 202 155@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -28.7711 kcal/mol@LB@Unfolding Energy - mRNA 7.06239 kcal/mol@LB@Unfolding Energy - sRNA 14.0114 kcal/mol@LB@@LB@Position - mRNA 201 -- 241@LB@Position - sRNA 156 -- 201@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 178 -- 184@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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