Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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	Additional homologs
71	0.01472	0.6177	b0846	rcdA	-10.28	0.035999	187 -- 195	44 -- 52	transcriptional regulator of csgD and ybiJI; autoregulator		_____________186_______196\n_____________\|_________\|\n5'-GCG...UGCAG_________AUGAC...AAA-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-11.6116 kcal/mol	0.46711 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-GCG...UGCAG AUGAC...AAA-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -11.6116 kcal/mol@LB@Unfolding Energy - mRNA 0.46711 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
76	0.01599	0.6177	b1849	purT	-9.18	0.060248	187 -- 212	25 -- 50	phosphoribosylglycinamide formyltransferase 2		_____________186________________________213\n_____________\|__________________________\|\n5'-UUU...UAAUC______UA______AUGAC_______GGCAC...GUC-3'\n______________AGGGGA__UUCGUU_____GUUAUUA\n______________\|\|:\|\|\|__\|\|\|:\|\|_____:\|\|\|\|\|\|\n______________UCUCCU__AAGUAA_____UAAUAAU\n3'-UUU...CAGUU______UA______AAAAA_______ACGGC...ACA-5'\n_____________\|__________________________\|\n_____________51_________________________24\n	206 -- 212	25 -- 31	-15.1619 kcal/mol	4.88468 kcal/mol	1.09239 kcal/mol	186 213@LB@ \| \|@LB@5'-UUU...UAAUC UA AUGAC GGCAC...GUC-3'@LB@ AGGGGA UUCGUU GUUAUUA@LB@ \|\|:\|\|\| \|\|\|:\|\| :\|\|\|\|\|\|@LB@ UCUCCU AAGUAA UAAUAAU@LB@3'-UUU...CAGUU UA AAAAA ACGGC...ACA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 4.88468 kcal/mol@LB@Unfolding Energy - sRNA 1.09239 kcal/mol@LB@@LB@Position - mRNA 187 -- 212@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 25 -- 31@LB@
92	0.01873	0.6177	b2297	pta	-7.94	0.106741	187 -- 219	22 -- 52	phosphate acetyltransferase		_____________186_______________________________220\n_____________\|_________________________________\|\n5'-CGC...UAACG________UAAAC___GUCCCG___________UGAUC...GUC-3'\n______________AAAGAGGA_____CGU______UAUUAUUAUGC\n______________\|\|\|\|\|\|\|\|_____\|:\|______\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCUCCU_____GUA______AUAAUAAUACG\n3'-UUU...GGCAG________UAAA____AAAAA____________GCAGU...ACA-5'\n_____________\|_________________________________\|\n_____________53________________________________21\n	213 -- 219	22 -- 28	-21.7034 kcal/mol	9.76868 kcal/mol	3.9903 kcal/mol	186 220@LB@ \| \|@LB@5'-CGC...UAACG UAAAC GUCCCG UGAUC...GUC-3'@LB@ AAAGAGGA CGU UAUUAUUAUGC@LB@ \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCU GUA AUAAUAAUACG@LB@3'-UUU...GGCAG UAAA AAAAA GCAGU...ACA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -21.7034 kcal/mol@LB@Unfolding Energy - mRNA 9.76868 kcal/mol@LB@Unfolding Energy - sRNA 3.9903 kcal/mol@LB@@LB@Position - mRNA 187 -- 219@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 22 -- 28@LB@
101	0.01972	0.6177	b3636	rpmG	-7.41	0.136064	187 -- 193	44 -- 50	50S ribosomal subunit protein L33		_____________186_____194\n_____________\|_______\|\n5'-CAC...UACUU_______AUAAA...AAC-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	187 -- 193	44 -- 50	-8.97978 kcal/mol	0.747566 kcal/mol	0.825028 kcal/mol	186 194@LB@ \| \|@LB@5'-CAC...UACUU AUAAA...AAC-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -7.41 kcal/mol@LB@Hybridization Energy -8.97978 kcal/mol@LB@Unfolding Energy - mRNA 0.747566 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
131	0.02569	0.6177	b0848	ybjM	-8.44	0.085177	187 -- 197	44 -- 55	inner membrane protein		_____________186__________198\n_____________\|____________\|\n5'-GAA...GCAGU____________CGAGU...GGG-3'\n______________GUC_AGGAGGAA\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________CAG_UUCUCCUU\n3'-UUU...CCGGG___U________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	191 -- 197	44 -- 50	-13.6185 kcal/mol	4.23971 kcal/mol	0.941432 kcal/mol	186 198@LB@ \| \|@LB@5'-GAA...GCAGU CGAGU...GGG-3'@LB@ GUC AGGAGGAA@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CAG UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -13.6185 kcal/mol@LB@Unfolding Energy - mRNA 4.23971 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 187 -- 197@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
148	0.02945	0.6177	b0692	potE	-8.42	0.085901	187 -- 195	44 -- 52	putrescine/proton symporter: putrescine/ornithine antiporter		_____________186_______196\n_____________\|_________\|\n5'-UGU...UGUUG_________AAAUU...AGC-3'\n______________AAAGGGGAA\n______________\|\|\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-10.6161 kcal/mol	1.33649 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UGUUG AAAUU...AGC-3'@LB@ AAAGGGGAA@LB@ \|\|\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -10.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.33649 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
152	0.03059	0.6177	b2609	rpsP	-6.70	0.186060	187 -- 203	23 -- 53	30S ribosomal subunit protein S16		_____________186______________________________204\n_____________\|________________________________\|\n5'-UCA...AUUCA__C_____________________________GUAAC...UCG-3'\n______________CA_AAGAGGA_______________UGUUAUG\n______________\|\|_\|\|\|\|\|\|\|_______________\|:\|\|\|\|\|\n______________GU_UUCUCCU_______________AUAAUAC\n3'-UUU...GGGCA__________UAAAGUAAAAAAAUA_______GGCAG...ACA-5'\n_____________\|________________________________\|\n_____________54_______________________________22\n	197 -- 203	23 -- 29	-10.7305 kcal/mol	2.84664 kcal/mol	1.18482 kcal/mol	186 204@LB@ \| \|@LB@5'-UCA...AUUCA C GUAAC...UCG-3'@LB@ CA AAGAGGA UGUUAUG@LB@ \|\| \|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GU UUCUCCU AUAAUAC@LB@3'-UUU...GGGCA UAAAGUAAAAAAAUA GGCAG...ACA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -10.7305 kcal/mol@LB@Unfolding Energy - mRNA 2.84664 kcal/mol@LB@Unfolding Energy - sRNA 1.18482 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 23 -- 29@LB@
188	0.03926	0.6177	b4547	ypfN	-8.44	0.084930	187 -- 194	44 -- 51	putative membrane protein UPF0370 family		_____________186______195\n_____________\|________\|\n5'-UGA...UCUGC________AUAAG...AGA-3'\n______________AAGAGGAA\n______________\|\|\|\|\|\|\|\|\n______________UUCUCCUU\n3'-UUU...GCAGU________AAAGU...ACA-5'\n_____________\|________\|\n_____________52_______43\n	188 -- 194	44 -- 50	-10.245 kcal/mol	0.953219 kcal/mol	0.848077 kcal/mol	186 195@LB@ \| \|@LB@5'-UGA...UCUGC AUAAG...AGA-3'@LB@ AAGAGGAA@LB@ \|\|\|\|\|\|\|\|@LB@ UUCUCCUU@LB@3'-UUU...GCAGU AAAGU...ACA-5'@LB@ \| \|@LB@ 52 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -10.245 kcal/mol@LB@Unfolding Energy - mRNA 0.953219 kcal/mol@LB@Unfolding Energy - sRNA 0.848077 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 44 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
196	0.04084	0.6177	b3137	kbaY	-7.51	0.129887	187 -- 200	37 -- 51	tagatose 6-phosphate aldolase 1 kbaY subunit	b2096	_____________186_____________201\n_____________\|_______________\|\n5'-CAC...GGCAU_______UCG_____AUGAG...CGA-3'\n______________AAGAGGA____CAUU\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________UUCUCCU____GUAA\n3'-UUU...GCAGU_______UAAA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________52______________36\n	187 -- 193	45 -- 51	-11.4071 kcal/mol	2.82588 kcal/mol	1.07049 kcal/mol	186 201@LB@ \| \|@LB@5'-CAC...GGCAU UCG AUGAG...CGA-3'@LB@ AAGAGGA CAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ UUCUCCU GUAA@LB@3'-UUU...GCAGU UAAA AAAAA...ACA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -11.4071 kcal/mol@LB@Unfolding Energy - mRNA 2.82588 kcal/mol@LB@Unfolding Energy - sRNA 1.07049 kcal/mol@LB@@LB@Position - mRNA 187 -- 200@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
25	0.004737	0.5992	b1093	fabG	-11.25	0.022809	188 -- 202	38 -- 52	3-oxoacyl-[acyl-carrier-protein] reductase		_____________187_____________203\n_____________\|_______________\|\n5'-UAC...CUUUA_________AA____GAAUU...UUG-3'\n______________AAAGAGGAA__UCAU\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UUUCUCCUU__AGUA\n3'-UUU...GGCAG_________AA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	190 -- 196	44 -- 50	-14.2885 kcal/mol	1.96871 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-UAC...CUUUA AA GAAUU...UUG-3'@LB@ AAAGAGGAA UCAU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUCCUU AGUA@LB@3'-UUU...GGCAG AA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -14.2885 kcal/mol@LB@Unfolding Energy - mRNA 1.96871 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@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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