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
161	0.04429	0.7375	lmo0588	N/A	-15.80	0.069486	3 -- 42	156 -- 202	DNA photolyase	_____________2____________43\n_____________\|____________\|\n5'-UUG...CUUAU____________UAUGA...AAG-3'\n______________GUGGAUGAAAGC\n______________:\|\|:\|\|\|\|\|\|:\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________203__________155\n	36 -- 42	156 -- 162	-13.6691 kcal/mol	1.75048 kcal/mol	0.849227 kcal/mol	2 43@LB@ \| \|@LB@5'-UUG...CUUAU UAUGA...AAG-3'@LB@ GUGGAUGAAAGC@LB@ :\|\|:\|\|\|\|\|\|:\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 203 155@LB@@LB@@LB@Energy -15.80 kcal/mol@LB@Hybridization Energy -13.6691 kcal/mol@LB@Unfolding Energy - mRNA 1.75048 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 3 -- 42@LB@Position - sRNA 156 -- 202@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 156 -- 162@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@
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@
164	0.04503	0.7389	lmo2361	N/A	-17.31	0.035661	175 -- 215	153 -- 209		_____________174____________216\n_____________\|______________\|\n5'-CCA...AGGUA_________A____GAGGA...ACC-3'\n______________AUAAUGGGA_GAGG\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|\n______________UAUUGCCCU_CUCC\n3'-GUU...AUACG_________A____GUAUC...GGA-5'\n_____________\|______________\|\n_____________210____________152\n	177 -- 183	201 -- 207	-18.1933 kcal/mol	2.24476 kcal/mol	3.5857 kcal/mol	174 216@LB@ \| \|@LB@5'-CCA...AGGUA A GAGGA...ACC-3'@LB@ AUAAUGGGA GAGG@LB@ \|\|\|\|:\|\|\|\| \|\|\|\|@LB@ UAUUGCCCU CUCC@LB@3'-GUU...AUACG A GUAUC...GGA-5'@LB@ \| \|@LB@ 210 152@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -18.1933 kcal/mol@LB@Unfolding Energy - mRNA 2.24476 kcal/mol@LB@Unfolding Energy - sRNA 3.5857 kcal/mol@LB@@LB@Position - mRNA 175 -- 215@LB@Position - sRNA 153 -- 209@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 201 -- 207@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@
166	0.04633	0.7403	lmo1152	N/A	-16.33	0.055198	97 -- 188	95 -- 169	PduB protein	_____________96_______________189\n_____________\|________________\|\n5'-GGC...AAGUC________________AAUAA...AAG-3'\n______________AGAUGAGUGA__GCAA\n______________\|\|\|\|\|\|:\|\|\|__:\|\|\|\n______________UCUACUUACU__UGUU\n3'-GUU...GUUAC__________UU____UAUUA...GGA-5'\n_____________\|________________\|\n_____________170______________94\n	100 -- 106	160 -- 166	-13.7881 kcal/mol	2.27776 kcal/mol	0.924402 kcal/mol	96 189@LB@ \| \|@LB@5'-GGC...AAGUC AAUAA...AAG-3'@LB@ AGAUGAGUGA GCAA@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\|@LB@ UCUACUUACU UGUU@LB@3'-GUU...GUUAC UU UAUUA...GGA-5'@LB@ \| \|@LB@ 170 94@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -13.7881 kcal/mol@LB@Unfolding Energy - mRNA 2.27776 kcal/mol@LB@Unfolding Energy - sRNA 0.924402 kcal/mol@LB@@LB@Position - mRNA 97 -- 188@LB@Position - sRNA 95 -- 169@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 160 -- 166@LB@
167	0.04638	0.7403	lmo1401	N/A	-16.51	0.050998	149 -- 209	155 -- 204		_____________148________210\n_____________\|__________\|\n5'-AUU...AACAA__________CUAUU...UCA-3'\n______________AAUGAAAAUA\n______________\|\|\|\|\|\|\|\|:\|\n______________UUACUUUUGU\n3'-GUU...UCUAC__________UUAUU...GGA-5'\n_____________\|__________\|\n_____________205________154\n	203 -- 209	155 -- 161	-7.61408 kcal/mol	0.775188 kcal/mol	0.60613 kcal/mol	148 210@LB@ \| \|@LB@5'-AUU...AACAA CUAUU...UCA-3'@LB@ AAUGAAAAUA@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UUACUUUUGU@LB@3'-GUU...UCUAC UUAUU...GGA-5'@LB@ \| \|@LB@ 205 154@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -7.61408 kcal/mol@LB@Unfolding Energy - mRNA 0.775188 kcal/mol@LB@Unfolding Energy - sRNA 0.60613 kcal/mol@LB@@LB@Position - mRNA 149 -- 209@LB@Position - sRNA 155 -- 204@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
168	0.04649	0.7403	lmo1875	N/A	-18.37	0.021889	174 -- 204	150 -- 181	ABC transporter ATP-binding protein	_____________173_______________205\n_____________\|_________________\|\n5'-ACA...AACAG__A______________AUGAA...GUU-3'\n______________GA_AUGGAUGGGAAUAA\n______________\|\|_\|\|\|:\|\|\|::\|\|:\|\|\n______________CU_UACUUACUUUUGUU\n3'-GUU...GGUUA__C______________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________182_______________149\n	193 -- 199	155 -- 161	-14.111 kcal/mol	2.1341 kcal/mol	0.933796 kcal/mol	173 205@LB@ \| \|@LB@5'-ACA...AACAG A AUGAA...GUU-3'@LB@ GA AUGGAUGGGAAUAA@LB@ \|\| \|\|\|:\|\|\|::\|\|:\|\|@LB@ CU UACUUACUUUUGUU@LB@3'-GUU...GGUUA C UAUUA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -18.37 kcal/mol@LB@Hybridization Energy -14.111 kcal/mol@LB@Unfolding Energy - mRNA 2.1341 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 174 -- 204@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@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@
170	0.04745	0.7511	lmo2203	N/A	-15.31	0.085499	133 -- 190	99 -- 165	N-acetylmuramoyl-L-alanine amidase	_____________132___________________________________191\n_____________\|_____________________________________\|\n5'-AUA...AGGUU_________________A________AA_________ACUAA...CAG-3'\n______________AACAGA_____GAC_AG__GCCAUUU__AUUGGGGGA\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UUGUCU_____CUG_UC__CGGUAAG__UAACCUUCU\n3'-GUU...CAGAU______ACAGA___A__AA_______A__________ACCUA...GGA-5'\n_____________\|_____________________________________\|\n_____________166___________________________________98\n	184 -- 190	99 -- 105	-25.8209 kcal/mol	4.57897 kcal/mol	9.42764 kcal/mol	132 191@LB@ \| \|@LB@5'-AUA...AGGUU A AA ACUAA...CAG-3'@LB@ AACAGA GAC AG GCCAUUU AUUGGGGGA@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UUGUCU CUG UC CGGUAAG UAACCUUCU@LB@3'-GUU...CAGAU ACAGA A AA A ACCUA...GGA-5'@LB@ \| \|@LB@ 166 98@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -25.8209 kcal/mol@LB@Unfolding Energy - mRNA 4.57897 kcal/mol@LB@Unfolding Energy - sRNA 9.42764 kcal/mol@LB@@LB@Position - mRNA 133 -- 190@LB@Position - sRNA 99 -- 165@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 99 -- 105@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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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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