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
126	0.03359	0.6968	lmo1599	ccpA	-16.59	0.049230	178 -- 221	146 -- 188	catabolite control protein A	_____________177______________222\n_____________\|________________\|\n5'-UUU...GAAUA__________U_____AUUUA...CAA-3'\n______________GAGAUGAAUG__AACA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________CUCUACUUAC__UUGU\n3'-GUU...GGUUA__________UU____UUAUU...GGA-5'\n_____________\|________________\|\n_____________189______________145\n	201 -- 207	161 -- 167	-17.207 kcal/mol	2.33031 kcal/mol	0.929544 kcal/mol	177 222@LB@ \| \|@LB@5'-UUU...GAAUA U AUUUA...CAA-3'@LB@ GAGAUGAAUG AACA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUCUACUUAC UUGU@LB@3'-GUU...GGUUA UU UUAUU...GGA-5'@LB@ \| \|@LB@ 189 145@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -17.207 kcal/mol@LB@Unfolding Energy - mRNA 2.33031 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 178 -- 221@LB@Position - sRNA 146 -- 188@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@LB@
198	0.05669	0.7607	lmo2670	N/A	-16.54	0.050282	118 -- 190	141 -- 216		_____________117_________________191\n_____________\|___________________\|\n5'-AAU...AUUUG_________UACC______UUCAA...UCU-3'\n______________GAUGAGAUG____GGGAAC\n______________:\|\|\|\|\|\|\|\|____\|::\|\|\|\n______________UUACUCUAC____CUUUUG\n3'-GUU...GCCGG_________UUA_______UUUAU...GGA-5'\n_____________\|___________________\|\n_____________217_________________140\n	72 -- 78	165 -- 171	-16.0384 kcal/mol	2.83906 kcal/mol	0.941471 kcal/mol	117 191@LB@ \| \|@LB@5'-AAU...AUUUG UACC UUCAA...UCU-3'@LB@ GAUGAGAUG GGGAAC@LB@ :\|\|\|\|\|\|\|\| \|::\|\|\|@LB@ UUACUCUAC CUUUUG@LB@3'-GUU...GCCGG UUA UUUAU...GGA-5'@LB@ \| \|@LB@ 217 140@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -16.0384 kcal/mol@LB@Unfolding Energy - mRNA 2.83906 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 118 -- 190@LB@Position - sRNA 141 -- 216@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 165 -- 171@LB@
139	0.03644	0.6968	lmo2566	N/A	-16.54	0.050390	198 -- 240	121 -- 170	lmo2566	_____________197_________________241\n_____________\|___________________\|\n5'-GAA...ACAUA_________AUA_______CCUUA...CAG-3'\n______________GAGAUGAAU___GAAAACA\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUCUACUUA___CUUUUGU\n3'-GUU...GGUUA___________________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________171_________________120\n	210 -- 216	155 -- 161	-17.6586 kcal/mol	1.26524 kcal/mol	0.929544 kcal/mol	197 241@LB@ \| \|@LB@5'-GAA...ACAUA AUA CCUUA...CAG-3'@LB@ GAGAUGAAU GAAAACA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUCUACUUA CUUUUGU@LB@3'-GUU...GGUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 171 120@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 1.26524 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 198 -- 240@LB@Position - sRNA 121 -- 170@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 155 -- 161@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@
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@
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@
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@
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@
156	0.04133	0.7058	lmo1481	holA	-16.45	0.052293	189 -- 224	151 -- 199	DNA polymerase III subunit delta	_____________188_________225\n_____________\|___________\|\n5'-CAA...UGCCA___________GAUAC...UUU-3'\n______________GAAUGGAAACA\n______________\|\|\|\|\|:\|\|\|\|\|\n______________CUUACUUUUGU\n3'-GUU...CUCUA___________UUAUU...GGA-5'\n_____________\|___________\|\n_____________200_________150\n	213 -- 219	156 -- 162	-12.8572 kcal/mol	1.78423 kcal/mol	0.853601 kcal/mol	188 225@LB@ \| \|@LB@5'-CAA...UGCCA GAUAC...UUU-3'@LB@ GAAUGGAAACA@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ CUUACUUUUGU@LB@3'-GUU...CUCUA UUAUU...GGA-5'@LB@ \| \|@LB@ 200 150@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -12.8572 kcal/mol@LB@Unfolding Energy - mRNA 1.78423 kcal/mol@LB@Unfolding Energy - sRNA 0.853601 kcal/mol@LB@@LB@Position - mRNA 189 -- 224@LB@Position - sRNA 151 -- 199@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 156 -- 162@LB@
183	0.0534	0.7607	lmo2583	N/A	-16.44	0.052604	178 -- 212	151 -- 181	DNA-binding response regulator	_____________177___________________________213\n_____________\|_____________________________\|\n5'-UAA...AAAUA_G_____AA______C_____________AACAA...AUG-3'\n______________A_ACGGU__GGUGAG___GGUGAAAAUGA\n______________\|_\|\|\|\|:__::\|\|\|\|___::\|\|\|\|\|\|::\|\n______________U_UGCCG__UUACUC___UUACUUUUGUU\n3'-GUU...CUUGA_G_____G_______UAC___________UAUUA...GGA-5'\n_____________\|_____________________________\|\n_____________182___________________________150\n	197 -- 203	155 -- 161	-21.6156 kcal/mol	3.93053 kcal/mol	8.33518 kcal/mol	177 213@LB@ \| \|@LB@5'-UAA...AAAUA G AA C AACAA...AUG-3'@LB@ A ACGGU GGUGAG GGUGAAAAUGA@LB@ \| \|\|\|\|: ::\|\|\|\| ::\|\|\|\|\|\|::\|@LB@ U UGCCG UUACUC UUACUUUUGUU@LB@3'-GUU...CUUGA G G UAC UAUUA...GGA-5'@LB@ \| \|@LB@ 182 150@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -21.6156 kcal/mol@LB@Unfolding Energy - mRNA 3.93053 kcal/mol@LB@Unfolding Energy - sRNA 8.33518 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 151 -- 181@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@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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