Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
104	0.01113	0.3575	b2108	yehA	-14.54	0.033608	284 -- 300	56 -- 72	putative fimbrial-like adhesin protein	_____________283_____________300\n_____________\|_______________\|\n5'-GUU...CUGUU___________G____-3'\n______________CAGCACAACUU_GUUG\n______________\|\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________GUCGUGUUGAA_CGAC\n3'-UUU...CGUUG___________G____AGCGC...UAG-5'\n_____________\|________________\|\n_____________73_______________55\n	289 -- 295	61 -- 67	-24.1215 kcal/mol	2.36332 kcal/mol	11.1531 kcal/mol	283 300@LB@ \| \|@LB@5'-GUU...CUGUU G -3'@LB@ CAGCACAACUU GUUG@LB@ \|\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ GUCGUGUUGAA CGAC@LB@3'-UUU...CGUUG G AGCGC...UAG-5'@LB@ \| \|@LB@ 73 55@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -24.1215 kcal/mol@LB@Unfolding Energy - mRNA 2.36332 kcal/mol@LB@Unfolding Energy - sRNA 11.1531 kcal/mol@LB@@LB@Position - mRNA 284 -- 300@LB@Position - sRNA 56 -- 72@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 61 -- 67@LB@
139	0.01488	0.3575	b2167	fruA	-12.05	0.108648	223 -- 242	167 -- 187	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________222___________________243\n_____________\|_____________________\|\n5'-CGC...UAUUG_________________G___CGCGC...AAA-3'\n______________ACGCUAAU_CUCGGUCA_GCA\n______________\|\|:\|:\|\|\|_\|\|\|:\|\|\|\|_:\|\|\n______________UGUGGUUA_GAGUCAGU_UGU\n3'-UUU...UAAAA________U________G___ACUAC...UAG-5'\n_____________\|_____________________\|\n_____________188___________________166\n	232 -- 238	171 -- 177	-25.758 kcal/mol	6.7352 kcal/mol	5.05492 kcal/mol	222 243@LB@ \| \|@LB@5'-CGC...UAUUG G CGCGC...AAA-3'@LB@ ACGCUAAU CUCGGUCA GCA@LB@ \|\|:\|:\|\|\| \|\|\|:\|\|\|\| :\|\|@LB@ UGUGGUUA GAGUCAGU UGU@LB@3'-UUU...UAAAA U G ACUAC...UAG-5'@LB@ \| \|@LB@ 188 166@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -25.758 kcal/mol@LB@Unfolding Energy - mRNA 6.7352 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 223 -- 242@LB@Position - sRNA 167 -- 187@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 171 -- 177@LB@
176	0.01994	0.3812	b2170	setB	-11.80	0.122017	181 -- 237	58 -- 116	lactose/glucose efflux system	_____________180____________238\n_____________\|______________\|\n5'-GCU...GAUCG______________AACUC...UGC-3'\n______________AC_CAG_CAUGCAU\n______________\|\|_\|\|\|_\|\|::\|\|\|\n______________UG_GUC_GUGUGUA\n3'-UUU...GGUUA__A___A_______CUACG...UAG-5'\n_____________\|______________\|\n_____________117____________57\n	200 -- 206	166 -- 172	-10.2756 kcal/mol	1.89616 kcal/mol	0.604817 kcal/mol	180 238@LB@ \| \|@LB@5'-GCU...GAUCG AACUC...UGC-3'@LB@ AC CAG CAUGCAU@LB@ \|\| \|\|\| \|\|::\|\|\|@LB@ UG GUC GUGUGUA@LB@3'-UUU...GGUUA A A CUACG...UAG-5'@LB@ \| \|@LB@ 117 57@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -10.2756 kcal/mol@LB@Unfolding Energy - mRNA 1.89616 kcal/mol@LB@Unfolding Energy - sRNA 0.604817 kcal/mol@LB@@LB@Position - mRNA 181 -- 237@LB@Position - sRNA 58 -- 116@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 166 -- 172@LB@
42	0.003683	0.2912	b2221	atoD	-14.87	0.028783	141 -- 155	6 -- 19	acetyl-CoA:acetoacetyl-CoA transferase alpha subunit	_____________140_____________156\n_____________\|_______________\|\n5'-UAU...AUUCU_____U_________AUUGC...CCC-3'\n______________GGCAC_CCCCUUGCU\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________CCGUG_GGGGAACGA\n3'-UUU...GUACC_______________AGUAG-5'\n_____________\|_______________\|\n_____________20______________5\n	149 -- 155	6 -- 12	-27.0081 kcal/mol	4.79018 kcal/mol	8.30673 kcal/mol	140 156@LB@ \| \|@LB@5'-UAU...AUUCU U AUUGC...CCC-3'@LB@ GGCAC CCCCUUGCU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCGUG GGGGAACGA@LB@3'-UUU...GUACC AGUAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0081 kcal/mol@LB@Unfolding Energy - mRNA 4.79018 kcal/mol@LB@Unfolding Energy - sRNA 8.30673 kcal/mol@LB@@LB@Position - mRNA 141 -- 155@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 6 -- 12@LB@
181	0.0209	0.3833	b2233	yfaL	-9.66	0.317681	275 -- 285	50 -- 60	adhesin	_____________274______________286\n_____________\|________________\|\n5'-UAU...UCUCU___AA__G________CGGUC...CAU-3'\n______________GCU__CG_UGUCGCGG\n______________:\|\|__\|\|_\|\|\|\|\|\|\|\|\n______________UGA__GC_ACAGCGCC\n3'-UUU...CGUGU___A___G________AUUUU...UAG-5'\n_____________\|________________\|\n_____________61_______________49\n	279 -- 285	50 -- 56	-20.2435 kcal/mol	4.65708 kcal/mol	6.1451 kcal/mol	274 286@LB@ \| \|@LB@5'-UAU...UCUCU AA G CGGUC...CAU-3'@LB@ GCU CG UGUCGCGG@LB@ :\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UGA GC ACAGCGCC@LB@3'-UUU...CGUGU A G AUUUU...UAG-5'@LB@ \| \|@LB@ 61 49@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -20.2435 kcal/mol@LB@Unfolding Energy - mRNA 4.65708 kcal/mol@LB@Unfolding Energy - sRNA 6.1451 kcal/mol@LB@@LB@Position - mRNA 275 -- 285@LB@Position - sRNA 50 -- 60@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 50 -- 56@LB@
69	0.006739	0.3286	b2265	menF	-9.03	0.410924	65 -- 108	52 -- 101	isochorismate synthase 2	_____________64__________109\n_____________\|___________\|\n5'-ACU...CGGGU___________CUUUC...CUC-3'\n______________UAUCGAUAUUC\n______________:\|:\|:\|\|\|:\|\|\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________102_________51\n	285 -- 291	176 -- 182	-9.38108 kcal/mol	0.14396 kcal/mol	3.38772 kcal/mol	64 109@LB@ \| \|@LB@5'-ACU...CGGGU CUUUC...CUC-3'@LB@ UAUCGAUAUUC@LB@ :\|:\|:\|\|\|:\|\|@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 102 51@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -9.38108 kcal/mol@LB@Unfolding Energy - mRNA 0.14396 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 65 -- 108@LB@Position - sRNA 52 -- 101@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 176 -- 182@LB@
185	0.02128	0.3833	b2276	nuoN	-8.72	0.461673	62 -- 81	196 -- 211	NADH:ubiquinone oxidoreductase membrane subunit N	_____________61______________82\n_____________\|_______________\|\n5'-GUA...UAUGA__________U____GUGCU...AUC-3'\n______________UC_CUGUUGC_GGUG\n______________\|\|_\|\|\|\|:\|\|_\|\|\|:\n______________AG_GACAGCG_CCAU\n3'-UUU...GUUGA__C____________UUUAU...UAG-5'\n_____________\|_______________\|\n_____________212_____________195\n	69 -- 75	52 -- 58	-15.8669 kcal/mol	5.2118 kcal/mol	5.88061 kcal/mol	61 82@LB@ \| \|@LB@5'-GUA...UAUGA U GUGCU...AUC-3'@LB@ UC CUGUUGC GGUG@LB@ \|\| \|\|\|\|:\|\| \|\|\|:@LB@ AG GACAGCG CCAU@LB@3'-UUU...GUUGA C UUUAU...UAG-5'@LB@ \| \|@LB@ 212 195@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -15.8669 kcal/mol@LB@Unfolding Energy - mRNA 5.2118 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 196 -- 211@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 52 -- 58@LB@
133	0.01432	0.3575	b2342	fadI	-11.00	0.176527	78 -- 109	125 -- 153	beta-ketoacyl-CoA thiolase anaerobic subunit	_____________77________________________________110\n_____________\|_________________________________\|\n5'-UCC...UCUCU__UU_____CUCUC________UAGC_______UUCCC...AUG-3'\n______________UC__CUUUU_____UGU_GUCA____UCCCACU\n______________\|\|__\|\|\|\|:_____\|\|:_\|\|\|\|____\|\|\|\|\|\|\|\n______________AG__GAAAG_____ACG_CAGU____AGGGUGA\n3'-UUU...CGUUC__UU_____UCUUA___C_______________CGUAG...UAG-5'\n_____________\|_________________________________\|\n_____________154_______________________________124\n	103 -- 109	125 -- 131	-19.0317 kcal/mol	1.6674 kcal/mol	9.91012 kcal/mol	77 110@LB@ \| \|@LB@5'-UCC...UCUCU UU CUCUC UAGC UUCCC...AUG-3'@LB@ UC CUUUU UGU GUCA UCCCACU@LB@ \|\| \|\|\|\|: \|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ AG GAAAG ACG CAGU AGGGUGA@LB@3'-UUU...CGUUC UU UCUUA C CGUAG...UAG-5'@LB@ \| \|@LB@ 154 124@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0317 kcal/mol@LB@Unfolding Energy - mRNA 1.6674 kcal/mol@LB@Unfolding Energy - sRNA 9.91012 kcal/mol@LB@@LB@Position - mRNA 78 -- 109@LB@Position - sRNA 125 -- 153@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 125 -- 131@LB@
106	0.01145	0.3575	b2350	gtrA	-11.86	0.119007	4 -- 25	148 -- 167	CPS-53 (KpLE1) prophage; bactoprenol-linked glucose translocase/flippase	_____________3_____________26\n_____________\|_____________\|\n5'-GAA...UGUAU__AU_________ACAAACC-3'\n______________CU__GUCGCGCAU\n______________\|\|__\|\|\|:\|:\|\|\|\n______________GA__CAGUGUGUA\n3'-UUU...GUUAU__GU_________CUACG...UAG-5'\n_____________\|_____________\|\n_____________168___________147\n	287 -- 293	166 -- 172	-13.6011 kcal/mol	2.0532 kcal/mol	0.604639 kcal/mol	3 26@LB@ \| \|@LB@5'-GAA...UGUAU AU ACAAACC-3'@LB@ CU GUCGCGCAU@LB@ \|\| \|\|\|:\|:\|\|\|@LB@ GA CAGUGUGUA@LB@3'-UUU...GUUAU GU CUACG...UAG-5'@LB@ \| \|@LB@ 168 147@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -13.6011 kcal/mol@LB@Unfolding Energy - mRNA 2.0532 kcal/mol@LB@Unfolding Energy - sRNA 0.604639 kcal/mol@LB@@LB@Position - mRNA 4 -- 25@LB@Position - sRNA 148 -- 167@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 166 -- 172@LB@
97	0.01056	0.3575	b2372	yfdV	-22.84	0.000764	17 -- 36	167 -- 186	putative transporter	_____________16___________________37\n_____________\|____________________\|\n5'-UUC...UUAAC____________________AACCG...CUC-3'\n______________CACCGGUAUUCAGUCGCGCA\n______________\|\|\|\|::\|\|:\|\|\|\|\|\|:\|:\|\|\n______________GUGGUUAUGAGUCAGUGUGU\n3'-UUU...AAAAU____________________ACUAC...UAG-5'\n_____________\|____________________\|\n_____________187__________________166\n	30 -- 36	167 -- 173	-32.2779 kcal/mol	2.6891 kcal/mol	5.05466 kcal/mol	16 37@LB@ \| \|@LB@5'-UUC...UUAAC AACCG...CUC-3'@LB@ CACCGGUAUUCAGUCGCGCA@LB@ \|\|\|\|::\|\|:\|\|\|\|\|\|:\|:\|\|@LB@ GUGGUUAUGAGUCAGUGUGU@LB@3'-UUU...AAAAU ACUAC...UAG-5'@LB@ \| \|@LB@ 187 166@LB@@LB@@LB@Energy -22.84 kcal/mol@LB@Hybridization Energy -32.2779 kcal/mol@LB@Unfolding Energy - mRNA 2.6891 kcal/mol@LB@Unfolding Energy - sRNA 5.05466 kcal/mol@LB@@LB@Position - mRNA 17 -- 36@LB@Position - sRNA 167 -- 186@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 167 -- 173@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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