Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
109	0.009396	0.2693	b1958	yedI	-10.22	0.013950	83 -- 110	33 -- 54	DUF808 family inner membrane protein	_____________82_____________________________111\n_____________\|______________________________\|\n5'-AAA...CAUUC______________AUAUAAUU________UUGUU...CCG-3'\n______________UGCU__GGCGAGAG________GCACUUGA\n______________\|\|\|\|__:\|\|:\|\|\|:________\|\|\|\|\|\|:\|\n______________ACGA__UCGUUCUU________CGUGAAUU\n3'-UUU...UUUGA____AU________________________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________55_____________________________32\n	104 -- 110	33 -- 39	-21.3805 kcal/mol	4.98239 kcal/mol	6.17798 kcal/mol	82 111@LB@ \| \|@LB@5'-AAA...CAUUC AUAUAAUU UUGUU...CCG-3'@LB@ UGCU GGCGAGAG GCACUUGA@LB@ \|\|\|\| :\|\|:\|\|\|: \|\|\|\|\|\|:\|@LB@ ACGA UCGUUCUU CGUGAAUU@LB@3'-UUU...UUUGA AU UUUUA...CAA-5'@LB@ \| \|@LB@ 55 32@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 4.98239 kcal/mol@LB@Unfolding Energy - sRNA 6.17798 kcal/mol@LB@@LB@Position - mRNA 83 -- 110@LB@Position - sRNA 33 -- 54@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 33 -- 39@LB@
17	0.0004446	0.08107	b1976	mtfA	-9.25	0.026966	241 -- 268	36 -- 59	anti-repressor for DgsA(Mlc)	_____________240___________________________269\n_____________\|_____________________________\|\n5'-AUA...ACAUC________CCUUCCCU_____________AUCGA...AAC-3'\n______________AAAC_UGC________GGCAGGAAGCACU\n______________\|\|\|\|_\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|\n______________UUUG_ACG________UCGUUCUUCGUGA\n3'-UUU...CCUAC____A___AAU__________________AUUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________35\n	262 -- 268	36 -- 42	-23.9855 kcal/mol	8.48573 kcal/mol	6.24948 kcal/mol	240 269@LB@ \| \|@LB@5'-AUA...ACAUC CCUUCCCU AUCGA...AAC-3'@LB@ AAAC UGC GGCAGGAAGCACU@LB@ \|\|\|\| \|\|\| :\|\|\|:\|\|\|\|\|\|\|\|@LB@ UUUG ACG UCGUUCUUCGUGA@LB@3'-UUU...CCUAC A AAU AUUUU...CAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.9855 kcal/mol@LB@Unfolding Energy - mRNA 8.48573 kcal/mol@LB@Unfolding Energy - sRNA 6.24948 kcal/mol@LB@@LB@Position - mRNA 241 -- 268@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 36 -- 42@LB@
97	0.007216	0.239	b2021	hisC	-5.42	0.261518	59 -- 66	37 -- 44	histidinol-phosphate aminotransferase	_____________58_______67\n_____________\|________\|\n5'-GUU...UUUCC________AUGAC...GGC-3'\n______________AGAAGCGC\n______________\|\|\|\|\|\|:\|\n______________UCUUCGUG\n3'-UUU...UUCGU________AAUUU...CAA-5'\n_____________\|________\|\n_____________45_______36\n	60 -- 66	37 -- 43	-11.6623 kcal/mol	1.85203 kcal/mol	4.39141 kcal/mol	58 67@LB@ \| \|@LB@5'-GUU...UUUCC AUGAC...GGC-3'@LB@ AGAAGCGC@LB@ \|\|\|\|\|\|:\|@LB@ UCUUCGUG@LB@3'-UUU...UUCGU AAUUU...CAA-5'@LB@ \| \|@LB@ 45 36@LB@@LB@@LB@Energy -5.42 kcal/mol@LB@Hybridization Energy -11.6623 kcal/mol@LB@Unfolding Energy - mRNA 1.85203 kcal/mol@LB@Unfolding Energy - sRNA 4.39141 kcal/mol@LB@@LB@Position - mRNA 59 -- 66@LB@Position - sRNA 37 -- 44@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 37 -- 43@LB@
111	0.009564	0.2693	b2040	rfbD	-5.00	0.321114	87 -- 99	24 -- 42	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________86__________________100\n_____________\|___________________\|\n5'-GAU...UUUGA___________________AAAAC...CUA-3'\n______________GAGCG______GGAUUCGU\n______________:\|\|\|:______::\|\|\|\|\|\|\n______________UUCGU______UUUAAGCA\n3'-UUU...CGUUC_____GAAUUU________AUGUG...CAA-5'\n_____________\|___________________\|\n_____________43__________________23\n	93 -- 99	24 -- 30	-9.51502 kcal/mol	2.86783 kcal/mol	1.64896 kcal/mol	86 100@LB@ \| \|@LB@5'-GAU...UUUGA AAAAC...CUA-3'@LB@ GAGCG GGAUUCGU@LB@ :\|\|\|: ::\|\|\|\|\|\|@LB@ UUCGU UUUAAGCA@LB@3'-UUU...CGUUC GAAUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.00 kcal/mol@LB@Hybridization Energy -9.51502 kcal/mol@LB@Unfolding Energy - mRNA 2.86783 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 87 -- 99@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 24 -- 30@LB@
33	0.001071	0.1045	b2058	wcaB	-10.41	0.012241	46 -- 64	25 -- 42	putative acyl transferase	_____________45__________________65\n_____________\|___________________\|\n5'-ACC...ACCGC______AA___C_______ACCGC...AGA-3'\n______________AAGCAC__AGA_AAAUUCG\n______________\|\|\|\|\|\|__\|:\|_\|\|\|\|\|\|\|\n______________UUCGUG__UUU_UUUAAGC\n3'-UUU...CGUUC______AA___________AAUGU...CAA-5'\n_____________\|___________________\|\n_____________43__________________24\n	58 -- 64	25 -- 31	-12.8013 kcal/mol	0.745291 kcal/mol	1.64855 kcal/mol	45 65@LB@ \| \|@LB@5'-ACC...ACCGC AA C ACCGC...AGA-3'@LB@ AAGCAC AGA AAAUUCG@LB@ \|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ UUCGUG UUU UUUAAGC@LB@3'-UUU...CGUUC AA AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -12.8013 kcal/mol@LB@Unfolding Energy - mRNA 0.745291 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 46 -- 64@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 25 -- 31@LB@
96	0.007122	0.239	b2060	wzc	-5.51	0.249431	285 -- 291	37 -- 43	colanic acid production tyrosine-protein kinase; autokinase; Ugd phosphorylase	_____________284_____292\n_____________\|_______\|\n5'-GAA...UCAUU_______GCUGG...GGG-3'\n______________GAAGCGC\n______________\|\|\|\|\|:\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	285 -- 291	37 -- 43	-9.9751 kcal/mol	0.803081 kcal/mol	3.6595 kcal/mol	284 292@LB@ \| \|@LB@5'-GAA...UCAUU GCUGG...GGG-3'@LB@ GAAGCGC@LB@ \|\|\|\|\|:\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -5.51 kcal/mol@LB@Hybridization Energy -9.9751 kcal/mol@LB@Unfolding Energy - mRNA 0.803081 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 285 -- 291@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 37 -- 43@LB@
4	1.769e-05	0.01424	b2105	rcnR	-7.88	0.065143	12 -- 26	36 -- 49	transcriptional repressor of rcnA	_____________11______________27\n_____________\|_______________\|\n5'-UGA...GCACC________U______GGGGA...ACG-3'\n______________AAGUAAGA_GGCGCU\n______________\|\|\|:\|\|\|\|_:\|\|:\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	13 -- 19	42 -- 48	-15.6635 kcal/mol	1.75127 kcal/mol	6.03645 kcal/mol	11 27@LB@ \| \|@LB@5'-UGA...GCACC U GGGGA...ACG-3'@LB@ AAGUAAGA GGCGCU@LB@ \|\|\|:\|\|\|\| :\|\|:\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -15.6635 kcal/mol@LB@Unfolding Energy - mRNA 1.75127 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 12 -- 26@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 42 -- 48@LB@
15	0.0003116	0.06692	b2149	mglA	-7.01	0.109495	281 -- 289	33 -- 41	methyl-galactoside ABC transporter ATPase	_____________280_______290\n_____________\|_________\|\n5'-CGA...GUUAA_________UAACG...AUU-3'\n______________GGCACUUGA\n______________:\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	283 -- 289	33 -- 39	-11.227 kcal/mol	2.59529 kcal/mol	1.6188 kcal/mol	280 290@LB@ \| \|@LB@5'-CGA...GUUAA UAACG...AUU-3'@LB@ GGCACUUGA@LB@ :\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.227 kcal/mol@LB@Unfolding Energy - mRNA 2.59529 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 281 -- 289@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 33 -- 39@LB@
153	0.016	0.3359	b2167	fruA	-4.10	0.476180	191 -- 199	37 -- 45	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________190_______200\n_____________\|_________\|\n5'-CGC...AGCAG_________AAUGA...AAA-3'\n______________GAGAGGCAU\n______________:\|\|\|:\|\|\|:\n______________UUCUUCGUG\n3'-UUU...AUUCG_________AAUUU...CAA-5'\n_____________\|_________\|\n_____________46________36\n	193 -- 199	37 -- 43	-10.9543 kcal/mol	1.97714 kcal/mol	4.8783 kcal/mol	190 200@LB@ \| \|@LB@5'-CGC...AGCAG AAUGA...AAA-3'@LB@ GAGAGGCAU@LB@ :\|\|\|:\|\|\|:@LB@ UUCUUCGUG@LB@3'-UUU...AUUCG AAUUU...CAA-5'@LB@ \| \|@LB@ 46 36@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -10.9543 kcal/mol@LB@Unfolding Energy - mRNA 1.97714 kcal/mol@LB@Unfolding Energy - sRNA 4.8783 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 37 -- 45@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
148	0.01496	0.3255	b2202	napC	-5.47	0.254772	189 -- 211	26 -- 46	quinol dehydrogenase electron source for NapAB	_____________188_____________________212\n_____________\|_______________________\|\n5'-ACG...GGAAA_______U____A__________UGACC...GUU-3'\n______________UAAGAGG_UAUU_UGGGAAAUUC\n______________:\|\|\|\|:\|_:\|:\|_\|:::\|\|\|\|\|\|\n______________GUUCUUC_GUGA_AUUUUUUAAG\n3'-UUU...AAUUC_______________________CAAUG...CAA-5'\n_____________\|_______________________\|\n_____________47______________________25\n	205 -- 211	26 -- 32	-14.2639 kcal/mol	2.66276 kcal/mol	6.13041 kcal/mol	188 212@LB@ \| \|@LB@5'-ACG...GGAAA U A UGACC...GUU-3'@LB@ UAAGAGG UAUU UGGGAAAUUC@LB@ :\|\|\|\|:\| :\|:\| \|:::\|\|\|\|\|\|@LB@ GUUCUUC GUGA AUUUUUUAAG@LB@3'-UUU...AAUUC CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -14.2639 kcal/mol@LB@Unfolding Energy - mRNA 2.66276 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 26 -- 32@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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service.

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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