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
63	0.01551	0.6624	lmo2613	rplO	-17.63	0.030853	185 -- 213	177 -- 203	50S ribosomal protein L15	_____________184______214\n_____________\|________\|\n5'-AAU...AUUCG________UCACU...GCG-3'\n______________UGGGAUGA\n______________:\|\|\|\|\|\|\|\n______________GCCCUACU\n3'-GUU...GUAUU________CCGUA...GGA-5'\n_____________\|________\|\n_____________204______176\n	98 -- 104	198 -- 204	-11.9514 kcal/mol	5.35707 kcal/mol	0.374397 kcal/mol	184 214@LB@ \| \|@LB@5'-AAU...AUUCG UCACU...GCG-3'@LB@ UGGGAUGA@LB@ :\|\|\|\|\|\|\|@LB@ GCCCUACU@LB@3'-GUU...GUAUU CCGUA...GGA-5'@LB@ \| \|@LB@ 204 176@LB@@LB@@LB@Energy -17.63 kcal/mol@LB@Hybridization Energy -11.9514 kcal/mol@LB@Unfolding Energy - mRNA 5.35707 kcal/mol@LB@Unfolding Energy - sRNA 0.374397 kcal/mol@LB@@LB@Position - mRNA 185 -- 213@LB@Position - sRNA 177 -- 203@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 198 -- 204@LB@
66	0.01668	0.6733	lmo0959	N/A	-18.16	0.024105	185 -- 212	177 -- 206	undacaprenyl-phosphate N-acetylglucosaminyltransferase	_____________184________________213\n_____________\|__________________\|\n5'-GAA...AAGUA_____________A____AUUUG...CAG-3'\n______________UAAUGAGAUGAGU_AAAA\n______________:\|\|\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________GUUACUCUACUUA_UUUU\n3'-GUU...UGCCG_____________C____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________207________________176\n	169 -- 175	162 -- 168	-15.497 kcal/mol	1.5517 kcal/mol	0.933292 kcal/mol	184 213@LB@ \| \|@LB@5'-GAA...AAGUA A AUUUG...CAG-3'@LB@ UAAUGAGAUGAGU AAAA@LB@ :\|\|\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GUUACUCUACUUA UUUU@LB@3'-GUU...UGCCG C GUUUA...GGA-5'@LB@ \| \|@LB@ 207 176@LB@@LB@@LB@Energy -18.16 kcal/mol@LB@Hybridization Energy -15.497 kcal/mol@LB@Unfolding Energy - mRNA 1.5517 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 185 -- 212@LB@Position - sRNA 177 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 162 -- 168@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@
197	0.05638	0.7607	lmo0344	N/A	-15.66	0.073858	267 -- 298	182 -- 211	short chain dehydrogenase	_____________266______299\n_____________\|________\|\n5'-CAG...CAGCA________UGGUA...UUU-3'\n______________AGCGGGAU\n______________\|:\|\|\|\|\|\|\n______________UUGCCCUA\n3'-GUU...ACGUA________CUCCG...GGA-5'\n_____________\|________\|\n_____________212______181\n	271 -- 277	200 -- 206	-11.8444 kcal/mol	1.0403 kcal/mol	0.330969 kcal/mol	266 299@LB@ \| \|@LB@5'-CAG...CAGCA UGGUA...UUU-3'@LB@ AGCGGGAU@LB@ \|:\|\|\|\|\|\|@LB@ UUGCCCUA@LB@3'-GUU...ACGUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 181@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.8444 kcal/mol@LB@Unfolding Energy - mRNA 1.0403 kcal/mol@LB@Unfolding Energy - sRNA 0.330969 kcal/mol@LB@@LB@Position - mRNA 267 -- 298@LB@Position - sRNA 182 -- 211@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 200 -- 206@LB@
127	0.03392	0.6968	lmo2096	N/A	-16.75	0.045974	122 -- 137	183 -- 198	PTS galacticol transporter subunit IIC	_____________121___________________138\n_____________\|_____________________\|\n5'-UAG...UUUCU____A__C_____________GAAGA...UGA-3'\n______________UAAC_GG_AUG_GGCAUGGAC\n______________\|\|\|\|_\|\|_\|\|\|_\|\|\|\|\|:\|\|\|\n______________AUUG_CC_UAC_CCGUAUCUG\n3'-GUU...UACGU____C______U_________UACUU...GGA-5'\n_____________\|_____________________\|\n_____________199___________________182\n	129 -- 135	191 -- 197	-23.3255 kcal/mol	4.68556 kcal/mol	9.82628 kcal/mol	121 138@LB@ \| \|@LB@5'-UAG...UUUCU A C GAAGA...UGA-3'@LB@ UAAC GG AUG GGCAUGGAC@LB@ \|\|\|\| \|\| \|\|\| \|\|\|\|\|:\|\|\|@LB@ AUUG CC UAC CCGUAUCUG@LB@3'-GUU...UACGU C U UACUU...GGA-5'@LB@ \| \|@LB@ 199 182@LB@@LB@@LB@Energy -16.75 kcal/mol@LB@Hybridization Energy -23.3255 kcal/mol@LB@Unfolding Energy - mRNA 4.68556 kcal/mol@LB@Unfolding Energy - sRNA 9.82628 kcal/mol@LB@@LB@Position - mRNA 122 -- 137@LB@Position - sRNA 183 -- 198@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 191 -- 197@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@
108	0.02743	0.6733	lmo2330	N/A	-16.53	0.050546	195 -- 214	191 -- 207		_____________194_________215\n_____________\|___________\|\n5'-ACG...GAGAA___________CAAGU...UUU-3'\n______________AGCGGGAUGAG\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UUGCCCUACUC\n3'-GUU...ACGUA___________CGUAU...GGA-5'\n_____________\|___________\|\n_____________208_________190\n	199 -- 205	197 -- 203	-18.6004 kcal/mol	2.16538 kcal/mol	0.386761 kcal/mol	194 215@LB@ \| \|@LB@5'-ACG...GAGAA CAAGU...UUU-3'@LB@ AGCGGGAUGAG@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UUGCCCUACUC@LB@3'-GUU...ACGUA CGUAU...GGA-5'@LB@ \| \|@LB@ 208 190@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -18.6004 kcal/mol@LB@Unfolding Energy - mRNA 2.16538 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 195 -- 214@LB@Position - sRNA 191 -- 207@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 197 -- 203@LB@
141	0.03665	0.6968	lmo1798	N/A	-14.74	0.108024	280 -- 295	194 -- 209		_____________279_______296\n_____________\|_________\|\n5'-GAU...CACUU_________AAUGG...GUU-3'\n______________AUAACGGGA\n______________\|\|\|\|\|\|\|\|\|\n______________UAUUGCCCU\n3'-GUU...AUACG_________ACUCC...GGA-5'\n_____________\|_________\|\n_____________210_______193\n	282 -- 288	201 -- 207	-12.5707 kcal/mol	0.27177 kcal/mol	0.374318 kcal/mol	279 296@LB@ \| \|@LB@5'-GAU...CACUU AAUGG...GUU-3'@LB@ AUAACGGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UAUUGCCCU@LB@3'-GUU...AUACG ACUCC...GGA-5'@LB@ \| \|@LB@ 210 193@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.5707 kcal/mol@LB@Unfolding Energy - mRNA 0.27177 kcal/mol@LB@Unfolding Energy - sRNA 0.374318 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 194 -- 209@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 201 -- 207@LB@
169	0.04649	0.7403	lmo0268	N/A	-16.22	0.057928	275 -- 284	195 -- 204	phosphoglycerate mutase	_____________274________285\n_____________\|__________\|\n5'-ACC...AUGCA__________GAUUC...UUG-3'\n______________GGGAUGGGGC\n______________\|\|\|\|\|\|:\|\|\|\n______________CCCUACUCCG\n3'-GUU...UAUUG__________UAUCU...GGA-5'\n_____________\|__________\|\n_____________205________194\n	278 -- 284	195 -- 201	-19.94 kcal/mol	1.96731 kcal/mol	6.55531 kcal/mol	274 285@LB@ \| \|@LB@5'-ACC...AUGCA GAUUC...UUG-3'@LB@ GGGAUGGGGC@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CCCUACUCCG@LB@3'-GUU...UAUUG UAUCU...GGA-5'@LB@ \| \|@LB@ 205 194@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -19.94 kcal/mol@LB@Unfolding Energy - mRNA 1.96731 kcal/mol@LB@Unfolding Energy - sRNA 6.55531 kcal/mol@LB@@LB@Position - mRNA 275 -- 284@LB@Position - sRNA 195 -- 204@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 195 -- 201@LB@
131	0.03528	0.6968	lmo0788	N/A	-16.25	0.057193	177 -- 197	197 -- 213	lmo0788	_____________176______198\n_____________\|________\|\n5'-AAA...CGAAA________AAAAU...AUU-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________214______196\n	191 -- 197	197 -- 203	-13.9782 kcal/mol	1.18818 kcal/mol	0.386531 kcal/mol	176 198@LB@ \| \|@LB@5'-AAA...CGAAA AAAAU...AUU-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 214 196@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -13.9782 kcal/mol@LB@Unfolding Energy - mRNA 1.18818 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 197 -- 213@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 197 -- 203@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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