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
181	0.03179	0.5559	b3240	aaeB	-9.50	0.128739	275 -- 287	72 -- 86	p-hydroxybenzoic acid efflux system component	_____________274_____________288\n_____________\|_______________\|\n5'-ACU...GCGCU_______________CACUU...UGG-3'\n______________GUUU__GUUGGCUUU\n______________\|\|\|:__\|\|\|\|\|\|\|\|\|\n______________CAAG__CAACCGAAA\n3'-CGC...GUUUU____UG_________UCAAU...AAG-5'\n_____________\|_______________\|\n_____________87______________71\n	281 -- 287	72 -- 78	-13.8127 kcal/mol	3.79774 kcal/mol	0.514266 kcal/mol	274 288@LB@ \| \|@LB@5'-ACU...GCGCU CACUU...UGG-3'@LB@ GUUU GUUGGCUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ CAAG CAACCGAAA@LB@3'-CGC...GUUUU UG UCAAU...AAG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -13.8127 kcal/mol@LB@Unfolding Energy - mRNA 3.79774 kcal/mol@LB@Unfolding Energy - sRNA 0.514266 kcal/mol@LB@@LB@Position - mRNA 275 -- 287@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 72 -- 78@LB@
182	0.03197	0.5559	b0212	gloB	-7.96	0.231442	50 -- 71	56 -- 75	hydroxyacylglutathione hydrolase	_____________49_____________________72\n_____________\|______________________\|\n5'-UUG...AUACA_______GAACCA_________CUGGC...AGC-3'\n______________UUUUAGU______CGGGUUGAG\n______________:\|\|\|\|\|\|______\|\|:\|\|\|\|\|\|\n______________GAAAUCA______GCUCAACUC\n3'-CGC...CAACC_______AUAA___________UUUGA...AAG-5'\n_____________\|______________________\|\n_____________76_____________________55\n	65 -- 71	56 -- 62	-16.3693 kcal/mol	6.6953 kcal/mol	1.71204 kcal/mol	49 72@LB@ \| \|@LB@5'-UUG...AUACA GAACCA CUGGC...AGC-3'@LB@ UUUUAGU CGGGUUGAG@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GAAAUCA GCUCAACUC@LB@3'-CGC...CAACC AUAA UUUGA...AAG-5'@LB@ \| \|@LB@ 76 55@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -16.3693 kcal/mol@LB@Unfolding Energy - mRNA 6.6953 kcal/mol@LB@Unfolding Energy - sRNA 1.71204 kcal/mol@LB@@LB@Position - mRNA 50 -- 71@LB@Position - sRNA 56 -- 75@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 56 -- 62@LB@
183	0.03203	0.5559	b4484	cpxP	-9.38	0.135070	107 -- 120	71 -- 85	inhibitor of the cpx response; periplasmic adaptor protein	_____________106_____________121\n_____________\|_______________\|\n5'-UAA...AUGAC_______________CACCC...GUG-3'\n______________UUUACGUUG_UUUUA\n______________\|\|:\|\|\|\|\|\|_:\|\|\|\|\n______________AAGUGCAAC_GAAAU\n3'-CGC...UUUUC_________C_____CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	109 -- 115	77 -- 83	-11.4265 kcal/mol	1.48788 kcal/mol	0.560731 kcal/mol	106 121@LB@ \| \|@LB@5'-UAA...AUGAC CACCC...GUG-3'@LB@ UUUACGUUG UUUUA@LB@ \|\|:\|\|\|\|\|\| :\|\|\|\|@LB@ AAGUGCAAC GAAAU@LB@3'-CGC...UUUUC C CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -11.4265 kcal/mol@LB@Unfolding Energy - mRNA 1.48788 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 107 -- 120@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 77 -- 83@LB@
184	0.03259	0.5559	b0811	glnH	-9.61	0.123139	215 -- 230	74 -- 90	glutamine transporter subunit	_____________214________________231\n_____________\|__________________\|\n5'-AUC...GUAUU_______U__________GCACU...CCG-3'\n______________AAAAGUU_CAC__UGGCU\n______________\|\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________UUUUCAA_GUG__ACCGA\n3'-CGC...AGGCG___________CA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	215 -- 221	84 -- 90	-14.2101 kcal/mol	4.07847 kcal/mol	0.517587 kcal/mol	214 231@LB@ \| \|@LB@5'-AUC...GUAUU U GCACU...CCG-3'@LB@ AAAAGUU CAC UGGCU@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUCAA GUG ACCGA@LB@3'-CGC...AGGCG CA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -14.2101 kcal/mol@LB@Unfolding Energy - mRNA 4.07847 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 84 -- 90@LB@
185	0.03283	0.5559	b1937	fliE	-12.05	0.046361	209 -- 229	14 -- 35	flagellar basal-body component	_____________208____________________230\n_____________\|______________________\|\n5'-CUG...UCAGC___A_______AUU________UAUCA...GUU-3'\n______________GAU__CAGGGG___GAAGGGGU\n______________\|\|:__\|\|:\|\|\|___:\|\|\|:\|\|\|\n______________CUG__GUUCCC___UUUCUCCA\n3'-CGC...CGUCA___AA______AAU________CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	223 -- 229	14 -- 20	-20.5154 kcal/mol	5.13678 kcal/mol	3.33183 kcal/mol	208 230@LB@ \| \|@LB@5'-CUG...UCAGC A AUU UAUCA...GUU-3'@LB@ GAU CAGGGG GAAGGGGU@LB@ \|\|: \|\|:\|\|\| :\|\|\|:\|\|\|@LB@ CUG GUUCCC UUUCUCCA@LB@3'-CGC...CGUCA AA AAU CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -20.5154 kcal/mol@LB@Unfolding Energy - mRNA 5.13678 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 209 -- 229@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 14 -- 20@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@
187	0.03332	0.5559	b2019	hisG	-10.76	0.077976	170 -- 191	15 -- 34	ATP phosphoribosyltransferase	_____________169____________________192\n_____________\|______________________\|\n5'-UUU...AUAAC_G_____ACA____U_______AAUAA...AUC-3'\n______________G_UUCAG___GGUU_AAAGAGG\n______________:_\|\|\|\|:___\|\|\|\|_\|\|\|\|\|\|\|\n______________U_AAGUU___CCAA_UUUCUCC\n3'-CGC...GUCAC_G_____C______U_______ACGGC...AAG-5'\n_____________\|______________________\|\n_____________35_____________________14\n	185 -- 191	15 -- 21	-17.0816 kcal/mol	2.9882 kcal/mol	3.33044 kcal/mol	169 192@LB@ \| \|@LB@5'-UUU...AUAAC G ACA U AAUAA...AUC-3'@LB@ G UUCAG GGUU AAAGAGG@LB@ : \|\|\|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ U AAGUU CCAA UUUCUCC@LB@3'-CGC...GUCAC G C U ACGGC...AAG-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -17.0816 kcal/mol@LB@Unfolding Energy - mRNA 2.9882 kcal/mol@LB@Unfolding Energy - sRNA 3.33044 kcal/mol@LB@@LB@Position - mRNA 170 -- 191@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 15 -- 21@LB@
188	0.03339	0.5559	b3232	zapE	-6.91	0.336884	267 -- 282	15 -- 35	divisome ATPase	_____________266____________________283\n_____________\|______________________\|\n5'-AGG...CCGAC___G__________________CCGUC...AAA-3'\n______________GAC_UUCA______AAAAGAGG\n______________\|\|\|_\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CUG_AAGU______UUUUCUCC\n3'-CGC...CGUCA________UCCCAA________ACGGC...AAG-5'\n_____________\|______________________\|\n_____________36_____________________14\n	276 -- 282	15 -- 21	-13.3674 kcal/mol	3.12995 kcal/mol	3.33058 kcal/mol	266 283@LB@ \| \|@LB@5'-AGG...CCGAC G CCGUC...AAA-3'@LB@ GAC UUCA AAAAGAGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUG AAGU UUUUCUCC@LB@3'-CGC...CGUCA UCCCAA ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -13.3674 kcal/mol@LB@Unfolding Energy - mRNA 3.12995 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 267 -- 282@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 15 -- 21@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@
190	0.03345	0.5559	b4090	rpiB	-6.75	0.355761	259 -- 286	57 -- 78	ribose 5-phosphate isomerase B/allose 6-phosphate isomerase	_____________258__________________________287\n_____________\|____________________________\|\n5'-AAC...AAUAG____ACA________AGCG___C_____AGUGA...AAG-3'\n______________UGGC___UUUAGUUG____UGG_GUUGA\n______________\|\|\|\|___\|\|\|\|\|\|\|:____:\|:_\|\|\|\|\|\n______________ACCG___AAAUCAAU____GCU_CAACU\n3'-CGC...GUGCA_______________AA___________CUUUG...AAG-5'\n_____________\|____________________________\|\n_____________79___________________________56\n	267 -- 273	67 -- 73	-15.2709 kcal/mol	7.30632 kcal/mol	1.21856 kcal/mol	258 287@LB@ \| \|@LB@5'-AAC...AAUAG ACA AGCG C AGUGA...AAG-3'@LB@ UGGC UUUAGUUG UGG GUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|: :\|: \|\|\|\|\|@LB@ ACCG AAAUCAAU GCU CAACU@LB@3'-CGC...GUGCA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 79 56@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -15.2709 kcal/mol@LB@Unfolding Energy - mRNA 7.30632 kcal/mol@LB@Unfolding Energy - sRNA 1.21856 kcal/mol@LB@@LB@Position - mRNA 259 -- 286@LB@Position - sRNA 57 -- 78@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 67 -- 73@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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