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
109	0.02227	0.6177	b4040	ubiA	-8.97	0.066674	182 -- 194	44 -- 55	p-hydroxybenzoate octaprenyltransferase		_____________181___________195\n_____________\|_____________\|\n5'-AGC...CCGUU__A_U________AAAAA...UAU-3'\n______________GU_C_AAGAGGAA\n______________\|\|_\|_\|\|\|\|\|\|\|\|\n______________CA_G_UUCUCCUU\n3'-UUU...CCGGG____U________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	188 -- 194	44 -- 50	-10.7786 kcal/mol	0.870226 kcal/mol	0.941432 kcal/mol	181 195@LB@ \| \|@LB@5'-AGC...CCGUU A U AAAAA...UAU-3'@LB@ GU C AAGAGGAA@LB@ \|\| \| \|\|\|\|\|\|\|\|@LB@ CA G UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -10.7786 kcal/mol@LB@Unfolding Energy - mRNA 0.870226 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
115	0.02287	0.6177	b3621	waaC	-10.02	0.040839	179 -- 191	44 -- 55	ADP-heptose:LPS heptosyl transferase I		_____________178___________192\n_____________\|_____________\|\n5'-UUG...CUAUU____C________GCCUG...UUG-3'\n______________GUUA_AAGAGGAA\n______________\|\|:\|_\|\|\|\|\|\|\|\|\n______________CAGU_UUCUCCUU\n3'-UUU...CCGGG_____________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	185 -- 191	44 -- 50	-12.6771 kcal/mol	1.72007 kcal/mol	0.941432 kcal/mol	178 192@LB@ \| \|@LB@5'-UUG...CUAUU C GCCUG...UUG-3'@LB@ GUUA AAGAGGAA@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ CAGU UUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.6771 kcal/mol@LB@Unfolding Energy - mRNA 1.72007 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 179 -- 191@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 44 -- 50@LB@
120	0.02398	0.6177	b0283	paoD	-10.02	0.040757	188 -- 198	44 -- 54	moco insertion factor for PaoABC aldehyde oxidoreductase		_____________187_________199\n_____________\|___________\|\n5'-AGG...GUGGU___________CAAUG...AGG-3'\n______________UUAAGGAGGAA\n______________\|:\|\|:\|\|\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	192 -- 198	44 -- 50	-12.5456 kcal/mol	1.58604 kcal/mol	0.939671 kcal/mol	187 199@LB@ \| \|@LB@5'-AGG...GUGGU CAAUG...AGG-3'@LB@ UUAAGGAGGAA@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.5456 kcal/mol@LB@Unfolding Energy - mRNA 1.58604 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 188 -- 198@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
123	0.02427	0.6177	b4485	ytfR	-5.89	0.261942	32 -- 42	44 -- 54	putative sugar ABC transporter ATPase		_____________31__________43\n_____________\|___________\|\n5'-CCU...AAGAA_______A___GAAAA...GCC-3'\n______________UUAGAGA_GAA\n______________\|:\|:\|\|\|_\|\|\|\n______________AGUUUCU_CUU\n3'-UUU...CGGGC_______C___AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	32 -- 38	48 -- 54	-7.06152 kcal/mol	0.22708 kcal/mol	0.939671 kcal/mol	31 43@LB@ \| \|@LB@5'-CCU...AAGAA A GAAAA...GCC-3'@LB@ UUAGAGA GAA@LB@ \|:\|:\|\|\| \|\|\|@LB@ AGUUUCU CUU@LB@3'-UUU...CGGGC C AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -5.89 kcal/mol@LB@Hybridization Energy -7.06152 kcal/mol@LB@Unfolding Energy - mRNA 0.22708 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 32 -- 42@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 48 -- 54@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@
139	0.02683	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
147	0.02922	0.6177	b3836	tatA	-6.91	0.169904	186 -- 195	44 -- 53	TatABCE protein translocation system subunit		_____________185________196\n_____________\|__________\|\n5'-CUA...UCUAC__C_______CAUGU...GUG-3'\n______________CA_AGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_UCUCCUU\n3'-UUU...GGGCA__U_______AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-10.6779 kcal/mol	2.84312 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-CUA...UCUAC C CAUGU...GUG-3'@LB@ CA AGAGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU UCUCCUU@LB@3'-UUU...GGGCA U AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -10.6779 kcal/mol@LB@Unfolding Energy - mRNA 2.84312 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@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@
149	0.03014	0.6177	b4470	yhaM	-8.71	0.074988	251 -- 260	44 -- 54	putative L-serine dehydratase alpha chain		_____________250_________261\n_____________\|___________\|\n5'-UGU...GCCGU___________GUAAA...UGG-3'\n______________UC_AGGAGGAA\n______________\|\|_\|:\|\|\|\|\|\|\n______________AG_UUCUCCUU\n3'-UUU...CGGGC__U________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	254 -- 260	44 -- 50	-10.8529 kcal/mol	1.19981 kcal/mol	0.939671 kcal/mol	250 261@LB@ \| \|@LB@5'-UGU...GCCGU GUAAA...UGG-3'@LB@ UC AGGAGGAA@LB@ \|\| \|:\|\|\|\|\|\|@LB@ AG UUCUCCUU@LB@3'-UUU...CGGGC U AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -10.8529 kcal/mol@LB@Unfolding Energy - mRNA 1.19981 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 251 -- 260@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 44 -- 50@LB@
159	0.0318	0.6177	b2532	trmJ	-7.64	0.122614	101 -- 114	44 -- 55	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent		_____________100____________115\n_____________\|______________\|\n5'-CGU...UGGAU________AC____AAACG...UGU-3'\n______________GUUAAAGA__GGGA\n______________\|\|:\|\|\|\|\|__\|\|:\|\n______________CAGUUUCU__CCUU\n3'-UUU...CCGGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________56_____________43\n	102 -- 108	48 -- 54	-10.9175 kcal/mol	2.33739 kcal/mol	0.941432 kcal/mol	100 115@LB@ \| \|@LB@5'-CGU...UGGAU AC AAACG...UGU-3'@LB@ GUUAAAGA GGGA@LB@ \|\|:\|\|\|\|\| \|\|:\|@LB@ CAGUUUCU CCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -10.9175 kcal/mol@LB@Unfolding Energy - mRNA 2.33739 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 48 -- 54@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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