Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
100	0.01671	0.5385	b3211	yhcC	-9.80	0.114390	283 -- 295	70 -- 82	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________282___________296\n_____________\|_____________\|\n5'-UGC...GCUGC___GC________CUGCC-3'\n______________ACG__GGUUUUAG\n______________\|\|\|__\|\|:\|\|\|\|\|\n______________UGC__CCGAAAUC\n3'-CGC...UCAAG___AA________AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	289 -- 295	70 -- 76	-11.7424 kcal/mol	1.55142 kcal/mol	0.389672 kcal/mol	282 296@LB@ \| \|@LB@5'-UGC...GCUGC GC CUGCC-3'@LB@ ACG GGUUUUAG@LB@ \|\|\| \|\|:\|\|\|\|\|@LB@ UGC CCGAAAUC@LB@3'-CGC...UCAAG AA AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -11.7424 kcal/mol@LB@Unfolding Energy - mRNA 1.55142 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@LB@
175	0.03099	0.5559	b2149	mglA	-9.34	0.136967	92 -- 105	70 -- 84	methyl-galactoside ABC transporter ATPase	_____________91______________106\n_____________\|_______________\|\n5'-CGA...GUACC__________G____AUAAA...AUU-3'\n______________UUAUGUUGGC__UAG\n______________\|:\|:\|\|\|\|\|\|__\|\|\|\n______________AGUGCAACCG__AUC\n3'-CGC...UUUCA__________AA___AAUAA...AAG-5'\n_____________\|_______________\|\n_____________85______________69\n	95 -- 101	75 -- 81	-15.5186 kcal/mol	5.61316 kcal/mol	0.563314 kcal/mol	91 106@LB@ \| \|@LB@5'-CGA...GUACC G AUAAA...AUU-3'@LB@ UUAUGUUGGC UAG@LB@ \|:\|:\|\|\|\|\|\| \|\|\|@LB@ AGUGCAACCG AUC@LB@3'-CGC...UUUCA AA AAUAA...AAG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -15.5186 kcal/mol@LB@Unfolding Energy - mRNA 5.61316 kcal/mol@LB@Unfolding Energy - sRNA 0.563314 kcal/mol@LB@@LB@Position - mRNA 92 -- 105@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 75 -- 81@LB@
189	0.03342	0.5559	b2172	yeiQ	-17.65	0.004645	282 -- 298	70 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________281_______________299\n_____________\|_________________\|\n5'-GAU...GUAUC______U__________AG-3'\n______________GUUCAU_UUGGCUUUGG\n______________\|\|\|\|\|:_\|\|\|\|\|\|\|\|:\|\n______________CAAGUG_AACCGAAAUC\n3'-CGC...GUUUU______C__________AAUAA...AAG-5'\n_____________\|_________________\|\n_____________87________________69\n	292 -- 298	70 -- 76	-21.6632 kcal/mol	3.44897 kcal/mol	0.568254 kcal/mol	281 299@LB@ \| \|@LB@5'-GAU...GUAUC U AG-3'@LB@ GUUCAU UUGGCUUUGG@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|\|:\|@LB@ CAAGUG AACCGAAAUC@LB@3'-CGC...GUUUU C AAUAA...AAG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -17.65 kcal/mol@LB@Hybridization Energy -21.6632 kcal/mol@LB@Unfolding Energy - mRNA 3.44897 kcal/mol@LB@Unfolding Energy - sRNA 0.568254 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 70 -- 76@LB@
200	0.03481	0.5559	b1058	yceO	-9.40	0.133707	85 -- 100	70 -- 85	uncharacterized protein	_____________84_______________101\n_____________\|________________\|\n5'-CCU...UUAAA_______CA_______GGGAA...GAU-3'\n______________UUUGCGU__GUUUUAG\n______________\|\|::\|\|\|__\|:\|\|\|\|\|\n______________AAGUGCA__CGAAAUC\n3'-CGC...UUUUC_______AC_______AAUAA...AAG-5'\n_____________\|________________\|\n_____________86_______________69\n	94 -- 100	70 -- 76	-11.7699 kcal/mol	1.79867 kcal/mol	0.567379 kcal/mol	84 101@LB@ \| \|@LB@5'-CCU...UUAAA CA GGGAA...GAU-3'@LB@ UUUGCGU GUUUUAG@LB@ \|\|::\|\|\| \|:\|\|\|\|\|@LB@ AAGUGCA CGAAAUC@LB@3'-CGC...UUUUC AC AAUAA...AAG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -11.7699 kcal/mol@LB@Unfolding Energy - mRNA 1.79867 kcal/mol@LB@Unfolding Energy - sRNA 0.567379 kcal/mol@LB@@LB@Position - mRNA 85 -- 100@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 70 -- 76@LB@
2	0.0001834	0.3	b2729	hypD	-13.53	0.025234	75 -- 91	71 -- 87	hydrogenase maturation protein	_____________74________________92\n_____________\|_________________\|\n5'-CAG...GUACU___A_____________CCAUG...GCC-3'\n______________GGU_CACGUUGGCUUUG\n______________:\|\|_\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCA_GUGCAACCGAAAU\n3'-CGC...CGUUU___A_____________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	85 -- 91	71 -- 77	-22.1935 kcal/mol	8.09841 kcal/mol	0.562376 kcal/mol	74 92@LB@ \| \|@LB@5'-CAG...GUACU A CCAUG...GCC-3'@LB@ GGU CACGUUGGCUUUG@LB@ :\|\| \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCA GUGCAACCGAAAU@LB@3'-CGC...CGUUU A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.1935 kcal/mol@LB@Unfolding Energy - mRNA 8.09841 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 75 -- 91@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 71 -- 77@LB@
29	0.005218	0.5385	b3433	asd	-11.22	0.064904	208 -- 219	71 -- 82	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________207__________220\n_____________\|____________\|\n5'-UCA...GAAAA____________UCGGC...UCU-3'\n______________AUGUUGGUUUUA\n______________\|:\|\|\|\|\|:\|\|\|\|\n______________UGCAACCGAAAU\n3'-CGC...UCAAG____________CAAUA...AAG-5'\n_____________\|____________\|\n_____________83___________70\n	213 -- 219	71 -- 77	-13.9075 kcal/mol	2.30708 kcal/mol	0.38228 kcal/mol	207 220@LB@ \| \|@LB@5'-UCA...GAAAA UCGGC...UCU-3'@LB@ AUGUUGGUUUUA@LB@ \|:\|\|\|\|\|:\|\|\|\|@LB@ UGCAACCGAAAU@LB@3'-CGC...UCAAG CAAUA...AAG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -13.9075 kcal/mol@LB@Unfolding Energy - mRNA 2.30708 kcal/mol@LB@Unfolding Energy - sRNA 0.38228 kcal/mol@LB@@LB@Position - mRNA 208 -- 219@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 71 -- 77@LB@
31	0.005384	0.5385	b0159	mtn	-14.65	0.015942	9 -- 52	71 -- 108	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	_____________8____________________________________________53\n_____________\|____________________________________________\|\n___5'-GAUACGCC__C____G__CUC_A____________UC_______C_______ACGCC...UCU-3'\n______________CG_GAUC_CU___G_AGAUCCGCAGGA__UCAUGUU_GGUUUUA\n______________\|\|_\|\|\|\|_\|\|___\|_\|\|\|\|\|\|\|\|\|::\|__\|\|\|:\|\|\|_\|\|:\|\|\|\|\n______________GC_CUAG_GA___C_UCUAGGCGUUUU__AGUGCAA_CCGAAAU\n__________3'-C__________C________________CA_______________CAAUA...AAG-5'\n_____________\|____________________________________________\|\n_____________109__________________________________________70\n	46 -- 52	71 -- 77	-39.2779 kcal/mol	12.7007 kcal/mol	11.9275 kcal/mol	8 53@LB@ \| \|@LB@ 5'-GAUACGCC C G CUC A UC C ACGCC...UCU-3'@LB@ CG GAUC CU G AGAUCCGCAGGA UCAUGUU GGUUUUA@LB@ \|\| \|\|\|\| \|\| \| \|\|\|\|\|\|\|\|\|::\| \|\|\|:\|\|\| \|\|:\|\|\|\|@LB@ GC CUAG GA C UCUAGGCGUUUU AGUGCAA CCGAAAU@LB@ 3'-C C CA CAAUA...AAG-5'@LB@ \| \|@LB@ 109 70@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -39.2779 kcal/mol@LB@Unfolding Energy - mRNA 12.7007 kcal/mol@LB@Unfolding Energy - sRNA 11.9275 kcal/mol@LB@@LB@Position - mRNA 9 -- 52@LB@Position - sRNA 71 -- 108@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 71 -- 77@LB@
37	0.006912	0.5385	b3693	dgoK	-11.15	0.066742	227 -- 259	71 -- 102	2-oxo-3-deoxygalactonate kinase	_____________226________________________________260\n_____________\|__________________________________\|\n5'-CAG...AUUGA_________GAC___UCUG_____CC________UCAGG...CAG-3'\n______________CUGGGGAUC___CAA_____CGCG__UGGCUUUA\n______________\|\|\|\|:\|\|\|\|___\|\|\|_____\|:\|\|__\|\|\|\|\|\|\|\|\n______________GACCUCUAG___GUU_____GUGC__ACCGAAAU\n____3'-CGCCUAG_________GC____UUCAA____A_________CAAUA...AAG-5'\n_____________\|__________________________________\|\n_____________103________________________________70\n	253 -- 259	71 -- 77	-30.6737 kcal/mol	7.60256 kcal/mol	11.9219 kcal/mol	226 260@LB@ \| \|@LB@5'-CAG...AUUGA GAC UCUG CC UCAGG...CAG-3'@LB@ CUGGGGAUC CAA CGCG UGGCUUUA@LB@ \|\|\|\|:\|\|\|\| \|\|\| \|:\|\| \|\|\|\|\|\|\|\|@LB@ GACCUCUAG GUU GUGC ACCGAAAU@LB@ 3'-CGCCUAG GC UUCAA A CAAUA...AAG-5'@LB@ \| \|@LB@ 103 70@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -30.6737 kcal/mol@LB@Unfolding Energy - mRNA 7.60256 kcal/mol@LB@Unfolding Energy - sRNA 11.9219 kcal/mol@LB@@LB@Position - mRNA 227 -- 259@LB@Position - sRNA 71 -- 102@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 71 -- 77@LB@
49	0.01016	0.5385	b3354	yheU	-13.31	0.027656	105 -- 118	71 -- 84	UPF0270 family protein	_____________104____________119\n_____________\|______________\|\n5'-CUG...GGCGG______________UUGGC...GUA-3'\n______________UCAUGUUGGCUUUA\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGAAAU\n3'-CGC...UUUCA______________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	112 -- 118	71 -- 77	-20.4483 kcal/mol	6.58199 kcal/mol	0.5567 kcal/mol	104 119@LB@ \| \|@LB@5'-CUG...GGCGG UUGGC...GUA-3'@LB@ UCAUGUUGGCUUUA@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGAAAU@LB@3'-CGC...UUUCA CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -20.4483 kcal/mol@LB@Unfolding Energy - mRNA 6.58199 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 105 -- 118@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 71 -- 77@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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