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
52	0.01176	0.599	lmo0302	N/A	-19.32	0.013869	143 -- 287	107 -- 220	lmo0302	_____________142________________288\n_____________\|__________________\|\n5'-CGA...CAUAG_________A__U_____AAAAA...AUA-3'\n______________GAGAUGAAU_GA_GAUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|_:\|::\|\n______________CUCUACUUA_CU_UUGUU\n3'-GUU...GGUUA____________U_____UAUUA...GGA-5'\n_____________\|__________________\|\n_____________221________________106\n	189 -- 195	162 -- 168	-14.2485 kcal/mol	1.08239 kcal/mol	0.933796 kcal/mol	142 288@LB@ \| \|@LB@5'-CGA...CAUAG A U AAAAA...AUA-3'@LB@ GAGAUGAAU GA GAUGA@LB@ \|\|\|\|\|\|\|\|\| \|\| :\|::\|@LB@ CUCUACUUA CU UUGUU@LB@3'-GUU...GGUUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 221 106@LB@@LB@@LB@Energy -19.32 kcal/mol@LB@Hybridization Energy -14.2485 kcal/mol@LB@Unfolding Energy - mRNA 1.08239 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 143 -- 287@LB@Position - sRNA 107 -- 220@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 162 -- 168@LB@
160	0.04276	0.7192	lmo0415	N/A	-19.07	0.015641	183 -- 241	108 -- 171	endo-1 4-beta-xylanase	_____________182_________________________________________________________________242\n_____________\|___________________________________________________________________\|\n5'-UUU...UUUUC_________GU______UAAU____AAA__A____GA______________C_______________CAUUA...AGU-3'\n______________UGAGGUGAG_____GCA____GUGA___UU_GGUG__UUAGAC_____UUU_ACUAGUUGCCAUUCU\n______________\|\|\|\|:\|\|\|:_____:\|\|____:\|\|\|___\|\|_\|\|\|\|__:\|\|:\|\|_____\|:\|_\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACUCUACUU_____UGU____UACU___AA_CCAC__GAUUUG_____AGA_UGAUCAACGGUAAGA\n3'-GUU...CGGUU_________ACUUU___UUAU____A____A____A_______UCUAC___C_______________UAACC...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________172_________________________________________________________________107\n	235 -- 241	108 -- 114	-46.29 kcal/mol	15.9956 kcal/mol	19.2069 kcal/mol	182 242@LB@ \| \|@LB@5'-UUU...UUUUC GU UAAU AAA A GA C CAUUA...AGU-3'@LB@ UGAGGUGAG GCA GUGA UU GGUG UUAGAC UUU ACUAGUUGCCAUUCU@LB@ \|\|\|\|:\|\|\|: :\|\| :\|\|\| \|\| \|\|\|\| :\|\|:\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACUCUACUU UGU UACU AA CCAC GAUUUG AGA UGAUCAACGGUAAGA@LB@3'-GUU...CGGUU ACUUU UUAU A A A UCUAC C UAACC...GGA-5'@LB@ \| \|@LB@ 172 107@LB@@LB@@LB@Energy -19.07 kcal/mol@LB@Hybridization Energy -46.29 kcal/mol@LB@Unfolding Energy - mRNA 15.9956 kcal/mol@LB@Unfolding Energy - sRNA 19.2069 kcal/mol@LB@@LB@Position - mRNA 183 -- 241@LB@Position - sRNA 108 -- 171@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 108 -- 114@LB@
1	1.731e-05	0.04657	lmo1883	N/A	-26.54	0.000269	199 -- 265	114 -- 169	chitinase	_____________198_________________________________________________________________266\n_____________\|___________________________________________________________________\|\n5'-GCG...AAAGU________G_________________GG___UU_____UU__UUUUAGUU____CGG______GG__AUUUG...ACG-3'\n______________AGAUGAAU_GAAAACAAGUAAUGGUU__UGG__UGUCU__AC________GGUG___GACUGG__GC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|\|:\|\|\|\|\|:\|\|__\|\|\|__\|\|\|\|\|__\|\|________\|:\|\|___\|\|\|\|:\|__\|\|\n______________UCUACUUA_CUUUUGUUUAUUACUAA__ACC__ACAGA__UG________CUAC___CUGAUC__CG\n3'-GUU...GUUAC__________________________A___________UU__U___________AGA______AA__GUAAG...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________170_________________________________________________________________113\n	210 -- 216	153 -- 159	-51.3221 kcal/mol	15.9506 kcal/mol	18.5045 kcal/mol	198 266@LB@ \| \|@LB@5'-GCG...AAAGU G GG UU UU UUUUAGUU CGG GG AUUUG...ACG-3'@LB@ AGAUGAAU GAAAACAAGUAAUGGUU UGG UGUCU AC GGUG GACUGG GC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|:\|\|\|\|\|:\|\| \|\|\| \|\|\|\|\| \|\| \|:\|\| \|\|\|\|:\| \|\|@LB@ UCUACUUA CUUUUGUUUAUUACUAA ACC ACAGA UG CUAC CUGAUC CG@LB@3'-GUU...GUUAC A UU U AGA AA GUAAG...GGA-5'@LB@ \| \|@LB@ 170 113@LB@@LB@@LB@Energy -26.54 kcal/mol@LB@Hybridization Energy -51.3221 kcal/mol@LB@Unfolding Energy - mRNA 15.9506 kcal/mol@LB@Unfolding Energy - sRNA 18.5045 kcal/mol@LB@@LB@Position - mRNA 199 -- 265@LB@Position - sRNA 114 -- 169@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 153 -- 159@LB@
130	0.03486	0.6968	lmo1231	N/A	-15.49	0.079293	19 -- 84	118 -- 185	DNA polymerase beta	_____________18___________________85\n_____________\|____________________\|\n5'-UCU...UUGCC__________CU________CGCCA...GCA-3'\n______________CAGUG_GAUG__UGAAAACA\n______________\|\|:\|\|_\|\|\|\|__\|\|\|\|\|\|\|\|\n______________GUUAC_CUAC__ACUUUUGU\n3'-GUU...UGCCG_____U____UU________UUAUU...GGA-5'\n_____________\|____________________\|\n_____________186__________________117\n	46 -- 52	155 -- 161	-18.0743 kcal/mol	4.62758 kcal/mol	0.95817 kcal/mol	18 85@LB@ \| \|@LB@5'-UCU...UUGCC CU CGCCA...GCA-3'@LB@ CAGUG GAUG UGAAAACA@LB@ \|\|:\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUAC CUAC ACUUUUGU@LB@3'-GUU...UGCCG U UU UUAUU...GGA-5'@LB@ \| \|@LB@ 186 117@LB@@LB@@LB@Energy -15.49 kcal/mol@LB@Hybridization Energy -18.0743 kcal/mol@LB@Unfolding Energy - mRNA 4.62758 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 19 -- 84@LB@Position - sRNA 118 -- 185@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 155 -- 161@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@
124	0.03258	0.6968	lmo1611	N/A	-17.32	0.035574	130 -- 182	121 -- 173	aminopeptidase	_____________129_______________________183\n_____________\|_________________________\|\n5'-CAU...AGAGA_______C___C_____________AUUUG...UUG-3'\n______________AGUGAGG_GAG_GGAAACGGAUAAU\n______________\|:\|\|\|\|:_\|\|:_\|:\|\|\|\|::\|\|\|\|\|\n______________UUACUCU_CUU_CUUUUGUUUAUUA\n3'-GUU...GCCGG_______A___A_____________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________174_______________________120\n	143 -- 149	154 -- 160	-22.8649 kcal/mol	4.94187 kcal/mol	5.58154 kcal/mol	129 183@LB@ \| \|@LB@5'-CAU...AGAGA C C AUUUG...UUG-3'@LB@ AGUGAGG GAG GGAAACGGAUAAU@LB@ \|:\|\|\|\|: \|\|: \|:\|\|\|\|::\|\|\|\|\|@LB@ UUACUCU CUU CUUUUGUUUAUUA@LB@3'-GUU...GCCGG A A CUAAA...GGA-5'@LB@ \| \|@LB@ 174 120@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -22.8649 kcal/mol@LB@Unfolding Energy - mRNA 4.94187 kcal/mol@LB@Unfolding Energy - sRNA 5.58154 kcal/mol@LB@@LB@Position - mRNA 130 -- 182@LB@Position - sRNA 121 -- 173@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 154 -- 160@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@
186	0.05422	0.7607	lmo2356	N/A	-15.92	0.066009	162 -- 205	129 -- 170	lmo2356	_____________161___________________206\n_____________\|_____________________\|\n5'-CUC...AAAGA_______AUUGAU________UUUGA...UUG-3'\n______________GAGAUGA______GUGAGGAU\n______________\|\|\|\|\|\|\|______:\|\|\|::\|:\n______________CUCUACU______UACUUUUG\n3'-GUU...GGUUA_____________________UUUAU...GGA-5'\n_____________\|_____________________\|\n_____________171___________________128\n	176 -- 182	156 -- 162	-14.0636 kcal/mol	2.1522 kcal/mol	0.916023 kcal/mol	161 206@LB@ \| \|@LB@5'-CUC...AAAGA AUUGAU UUUGA...UUG-3'@LB@ GAGAUGA GUGAGGAU@LB@ \|\|\|\|\|\|\| :\|\|\|::\|:@LB@ CUCUACU UACUUUUG@LB@3'-GUU...GGUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 171 128@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -14.0636 kcal/mol@LB@Unfolding Energy - mRNA 2.1522 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 162 -- 205@LB@Position - sRNA 129 -- 170@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 156 -- 162@LB@
116	0.03152	0.6968	lmo1963	N/A	-17.16	0.038227	218 -- 258	130 -- 166		_____________217___________________________________________259\n_____________\|_____________________________________________\|\n5'-ACA...CACAU_________AAC________A__GUC___U___________U___GGUGA...UCC-3'\n______________UGAAUGGAA___GCGAAUAA_GA___UGG_UGUUUGGGCAG_UGU\n______________\|\|\|\|\|\|:\|\|___:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|:\|:::\|\|\|_\|\|\|\n______________ACUUACUUU___UGUUUAUU_CU___ACC_ACAGAUUUGUC_ACA\n3'-GUU...ACUCU____________________A__AAA_______________U___GACUG...GGA-5'\n_____________\|_____________________________________________\|\n_____________167___________________________________________129\n	220 -- 226	158 -- 164	-34.7415 kcal/mol	9.15867 kcal/mol	13.701 kcal/mol	217 259@LB@ \| \|@LB@5'-ACA...CACAU AAC A GUC U U GGUGA...UCC-3'@LB@ UGAAUGGAA GCGAAUAA GA UGG UGUUUGGGCAG UGU@LB@ \|\|\|\|\|\|:\|\| :\|:\|\|\|\|\| \|\| \|\|\| \|\|\|:\|:::\|\|\| \|\|\|@LB@ ACUUACUUU UGUUUAUU CU ACC ACAGAUUUGUC ACA@LB@3'-GUU...ACUCU A AAA U GACUG...GGA-5'@LB@ \| \|@LB@ 167 129@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.7415 kcal/mol@LB@Unfolding Energy - mRNA 9.15867 kcal/mol@LB@Unfolding Energy - sRNA 13.701 kcal/mol@LB@@LB@Position - mRNA 218 -- 258@LB@Position - sRNA 130 -- 166@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 158 -- 164@LB@
128	0.03459	0.6968	lmo1993	pdp	-15.44	0.080912	179 -- 212	139 -- 174	pyrimidine-nucleoside phosphorylase	_____________178_________________213\n_____________\|___________________\|\n5'-AUU...GAAAG____A___GA_________GGUGG...UUC-3'\n______________GGUG_AGA__AAUGAGAAU\n______________::\|\|_\|\|\|__\|\|\|\|\|:\|\|:\n______________UUAC_UCU__UUACUUUUG\n3'-GUU...GCCGG________AC_________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________175_________________138\n	202 -- 208	156 -- 162	-13.005 kcal/mol	2.24337 kcal/mol	0.941471 kcal/mol	178 213@LB@ \| \|@LB@5'-AUU...GAAAG A GA GGUGG...UUC-3'@LB@ GGUG AGA AAUGAGAAU@LB@ ::\|\| \|\|\| \|\|\|\|\|:\|\|:@LB@ UUAC UCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -13.005 kcal/mol@LB@Unfolding Energy - mRNA 2.24337 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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