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
168	0.0298	0.5559	b0161	degP	-8.84	0.166335	239 -- 253	75 -- 88	serine endoprotease (protease Do) membrane-associated	_____________238_____________254\n_____________\|_______________\|\n5'-AUU...GCUCU_______G_U_____GUUAU...CGA-3'\n______________GAGUUUA_G_UUGGC\n______________:\|\|\|\|:\|_\|_\|\|\|\|\|\n______________UUCAAGU_C_AACCG\n3'-CGC...GCGUU_______G_______AAAUC...AAG-5'\n_____________\|_______________\|\n_____________89______________74\n	239 -- 245	82 -- 88	-14.9204 kcal/mol	5.56475 kcal/mol	0.515884 kcal/mol	238 254@LB@ \| \|@LB@5'-AUU...GCUCU G U GUUAU...CGA-3'@LB@ GAGUUUA G UUGGC@LB@ :\|\|\|\|:\| \| \|\|\|\|\|@LB@ UUCAAGU C AACCG@LB@3'-CGC...GCGUU G AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -14.9204 kcal/mol@LB@Unfolding Energy - mRNA 5.56475 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 239 -- 253@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 82 -- 88@LB@
173	0.03066	0.5559	b2928	yggC	-11.87	0.049837	290 -- 298	75 -- 83	putative PanK family P-loop kinase	_____________289_______299\n_____________\|_________\|\n5'-GAA...CUGCA_________GG-3'\n______________CAUGUUGGC\n______________\|\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	292 -- 298	75 -- 81	-14.124 kcal/mol	1.76242 kcal/mol	0.492259 kcal/mol	289 299@LB@ \| \|@LB@5'-GAA...CUGCA GG-3'@LB@ CAUGUUGGC@LB@ \|\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -14.124 kcal/mol@LB@Unfolding Energy - mRNA 1.76242 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 290 -- 298@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 75 -- 81@LB@
186	0.03285	0.5559	b1003	yccJ	-7.53	0.270746	41 -- 54	75 -- 88	uncharacterized protein	_____________40_____________55\n_____________\|______________\|\n5'-CCU...UUCAC_________GC___ACGCC...GGU-3'\n______________AGGUUCGCG__GGU\n______________\|:\|\|\|\|:\|\|__\|\|:\n______________UUCAAGUGC__CCG\n3'-CGC...GCGUU_________AA___AAAUC...AAG-5'\n_____________\|______________\|\n_____________89_____________74\n	43 -- 49	80 -- 86	-16.6206 kcal/mol	8.57413 kcal/mol	0.515884 kcal/mol	40 55@LB@ \| \|@LB@5'-CCU...UUCAC GC ACGCC...GGU-3'@LB@ AGGUUCGCG GGU@LB@ \|:\|\|\|\|:\|\| \|\|:@LB@ UUCAAGUGC CCG@LB@3'-CGC...GCGUU AA AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -16.6206 kcal/mol@LB@Unfolding Energy - mRNA 8.57413 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 41 -- 54@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 80 -- 86@LB@
16	0.002981	0.5385	b3428	glgP	-10.45	0.088230	278 -- 289	76 -- 86	glycogen phosphorylase	_____________277__________290\n_____________\|____________\|\n5'-CCA...CUGAU_______A____AAAGG...CGG-3'\n______________GUUUACG_UUGG\n______________\|\|\|:\|\|\|_\|\|\|\|\n______________CAAGUGC_AACC\n3'-CGC...GUUUU____________GAAAU...AAG-5'\n_____________\|____________\|\n_____________87___________75\n	278 -- 284	80 -- 86	-12.981 kcal/mol	2.0211 kcal/mol	0.505081 kcal/mol	277 290@LB@ \| \|@LB@5'-CCA...CUGAU A AAAGG...CGG-3'@LB@ GUUUACG UUGG@LB@ \|\|\|:\|\|\| \|\|\|\|@LB@ CAAGUGC AACC@LB@3'-CGC...GUUUU GAAAU...AAG-5'@LB@ \| \|@LB@ 87 75@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -12.981 kcal/mol@LB@Unfolding Energy - mRNA 2.0211 kcal/mol@LB@Unfolding Energy - sRNA 0.505081 kcal/mol@LB@@LB@Position - mRNA 278 -- 289@LB@Position - sRNA 76 -- 86@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 80 -- 86@LB@
36	0.006672	0.5385	b3956	ppc	-10.31	0.093393	270 -- 282	76 -- 88	phosphoenolpyruvate carboxylase	_____________269___________283\n_____________\|_____________\|\n5'-CUU...CCAUC___GA________GAGAA...AAC-3'\n______________AAG__UGCGUUGG\n______________\|\|\|__::\|\|\|\|\|\|\n______________UUC__GUGCAACC\n3'-CGC...GCGUU___AA________GAAAU...AAG-5'\n_____________\|_____________\|\n_____________89____________75\n	276 -- 282	76 -- 82	-12.0501 kcal/mol	1.22517 kcal/mol	0.512479 kcal/mol	269 283@LB@ \| \|@LB@5'-CUU...CCAUC GA GAGAA...AAC-3'@LB@ AAG UGCGUUGG@LB@ \|\|\| ::\|\|\|\|\|\|@LB@ UUC GUGCAACC@LB@3'-CGC...GCGUU AA GAAAU...AAG-5'@LB@ \| \|@LB@ 89 75@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -12.0501 kcal/mol@LB@Unfolding Energy - mRNA 1.22517 kcal/mol@LB@Unfolding Energy - sRNA 0.512479 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 76 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 76 -- 82@LB@
3	0.0006202	0.5173	b3310	rplN	-11.54	0.056896	6 -- 16	77 -- 87	50S ribosomal subunit protein L14	_____________5___________17\n_____________\|___________\|\n______5'-ACGCU___________UAGAG...CAG-3'\n______________GGUUCGCGUUG\n______________:\|\|\|\|:\|\|\|\|\|\n______________UCAAGUGCAAC\n3'-CGC...CGUUU___________CGAAA...AAG-5'\n_____________\|___________\|\n_____________88__________76\n	10 -- 16	77 -- 83	-15.9171 kcal/mol	3.86869 kcal/mol	0.505155 kcal/mol	5 17@LB@ \| \|@LB@ 5'-ACGCU UAGAG...CAG-3'@LB@ GGUUCGCGUUG@LB@ :\|\|\|\|:\|\|\|\|\|@LB@ UCAAGUGCAAC@LB@3'-CGC...CGUUU CGAAA...AAG-5'@LB@ \| \|@LB@ 88 76@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -15.9171 kcal/mol@LB@Unfolding Energy - mRNA 3.86869 kcal/mol@LB@Unfolding Energy - sRNA 0.505155 kcal/mol@LB@@LB@Position - mRNA 6 -- 16@LB@Position - sRNA 77 -- 87@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 77 -- 83@LB@
24	0.00428	0.5385	b0090	murG	-10.85	0.075280	191 -- 203	77 -- 89	N-acetylglucosaminyl transferase	_____________190___________204\n_____________\|_____________\|\n5'-AUU...UGUAC__________A__AGUGG...GUU-3'\n______________GAGGUUCACG_UG\n______________:\|:\|\|\|\|\|\|\|_\|\|\n______________UUUCAAGUGC_AC\n3'-CGC...GGCGU__________A__CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	194 -- 200	80 -- 86	-14.5499 kcal/mol	3.18923 kcal/mol	0.510111 kcal/mol	190 204@LB@ \| \|@LB@5'-AUU...UGUAC A AGUGG...GUU-3'@LB@ GAGGUUCACG UG@LB@ :\|:\|\|\|\|\|\|\| \|\|@LB@ UUUCAAGUGC AC@LB@3'-CGC...GGCGU A CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -14.5499 kcal/mol@LB@Unfolding Energy - mRNA 3.18923 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 80 -- 86@LB@
51	0.01052	0.5385	b0751	pnuC	-11.84	0.050492	77 -- 89	77 -- 89	nicotinamide riboside transporter	_____________76____________90\n_____________\|_____________\|\n5'-CGC...AUCAC_____________AUGAA...GGU-3'\n______________GAGGUUCAUGUUG\n______________:\|:\|\|\|\|\|:\|\|\|\|\n______________UUUCAAGUGCAAC\n3'-CGC...GGCGU_____________CGAAA...AAG-5'\n_____________\|_____________\|\n_____________90____________76\n	83 -- 89	77 -- 83	-16.9239 kcal/mol	4.57656 kcal/mol	0.510111 kcal/mol	76 90@LB@ \| \|@LB@5'-CGC...AUCAC AUGAA...GGU-3'@LB@ GAGGUUCAUGUUG@LB@ :\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUCAAGUGCAAC@LB@3'-CGC...GGCGU CGAAA...AAG-5'@LB@ \| \|@LB@ 90 76@LB@@LB@@LB@Energy -11.84 kcal/mol@LB@Hybridization Energy -16.9239 kcal/mol@LB@Unfolding Energy - mRNA 4.57656 kcal/mol@LB@Unfolding Energy - sRNA 0.510111 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 77 -- 89@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 77 -- 83@LB@
157	0.02703	0.5559	b3221	yhcH	-9.14	0.148013	119 -- 127	77 -- 85	DUF386 family protein cupin superfamily	_____________118_______128\n_____________\|_________\|\n5'-AUC...GGCAU_________AUUUA...AAG-3'\n______________UUCAUGUUG\n______________\|\|\|\|:\|\|\|\|\n______________AAGUGCAAC\n3'-CGC...UUUUC_________CGAAA...AAG-5'\n_____________\|_________\|\n_____________86________76\n	121 -- 127	77 -- 83	-10.7393 kcal/mol	1.16925 kcal/mol	0.427568 kcal/mol	118 128@LB@ \| \|@LB@5'-AUC...GGCAU AUUUA...AAG-3'@LB@ UUCAUGUUG@LB@ \|\|\|\|:\|\|\|\|@LB@ AAGUGCAAC@LB@3'-CGC...UUUUC CGAAA...AAG-5'@LB@ \| \|@LB@ 86 76@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.16925 kcal/mol@LB@Unfolding Energy - sRNA 0.427568 kcal/mol@LB@@LB@Position - mRNA 119 -- 127@LB@Position - sRNA 77 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 77 -- 83@LB@
194	0.03409	0.5559	b1836	yebV	-7.98	0.229830	12 -- 23	77 -- 87	uncharacterized protein	_____________11___________24\n_____________\|____________\|\n5'-CCA...GGAUU________A___AAAAA...CUG-3'\n______________GGUUCGCG_UUG\n______________:\|\|\|\|:\|\|_\|\|\|\n______________UCAAGUGC_AAC\n3'-CGC...CGUUU____________CGAAA...AAG-5'\n_____________\|____________\|\n_____________88___________76\n	13 -- 19	80 -- 86	-12.5297 kcal/mol	4.04369 kcal/mol	0.505155 kcal/mol	11 24@LB@ \| \|@LB@5'-CCA...GGAUU A AAAAA...CUG-3'@LB@ GGUUCGCG UUG@LB@ :\|\|\|\|:\|\| \|\|\|@LB@ UCAAGUGC AAC@LB@3'-CGC...CGUUU CGAAA...AAG-5'@LB@ \| \|@LB@ 88 76@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -12.5297 kcal/mol@LB@Unfolding Energy - mRNA 4.04369 kcal/mol@LB@Unfolding Energy - sRNA 0.505155 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 77 -- 87@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 80 -- 86@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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