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
80	0.01709	0.6177	b2498	upp	-4.70	0.418803	173 -- 195	44 -- 70	uracil phosphoribosyltransferase		_____________172_________________________196\n_____________\|___________________________\|\n5'-GGC...UUUUU___G___________C_______A___AGAGU...CCG-3'\n______________UGU_GCU____GCCC_UCAAAGG_GAA\n______________\|:\|_\|\|\|____\|\|\|\|_\|\|\|\|\|\|:_\|\|\|\n______________AUA_CGA____CGGG_AGUUUCU_CUU\n3'-UUU...CGGUU___G___UAAC____C_______C___AAAGU...ACA-5'\n_____________\|___________________________\|\n_____________71__________________________43\n	185 -- 191	48 -- 54	-22.3772 kcal/mol	6.37003 kcal/mol	11.3101 kcal/mol	172 196@LB@ \| \|@LB@5'-GGC...UUUUU G C A AGAGU...CCG-3'@LB@ UGU GCU GCCC UCAAAGG GAA@LB@ \|:\| \|\|\| \|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ AUA CGA CGGG AGUUUCU CUU@LB@3'-UUU...CGGUU G UAAC C C AAAGU...ACA-5'@LB@ \| \|@LB@ 71 43@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -22.3772 kcal/mol@LB@Unfolding Energy - mRNA 6.37003 kcal/mol@LB@Unfolding Energy - sRNA 11.3101 kcal/mol@LB@@LB@Position - mRNA 173 -- 195@LB@Position - sRNA 44 -- 70@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 48 -- 54@LB@
38	0.007716	0.6129	b0480	ushA	-6.97	0.165152	186 -- 197	45 -- 55	bifunctional UDP-sugar hydrolase/5'-nucleotidase		_____________185__________198\n_____________\|____________\|\n5'-AGG...AUCAG_________A__AGUAU...AAA-3'\n______________GUCAGGGAG_GA\n______________\|\|\|\|::\|\|\|_\|\|\n______________CAGUUUCUC_CU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	188 -- 194	47 -- 53	-13.3467 kcal/mol	5.44454 kcal/mol	0.930875 kcal/mol	185 198@LB@ \| \|@LB@5'-AGG...AUCAG A AGUAU...AAA-3'@LB@ GUCAGGGAG GA@LB@ \|\|\|\|::\|\|\| \|\|@LB@ CAGUUUCUC CU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -13.3467 kcal/mol@LB@Unfolding Energy - mRNA 5.44454 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
43	0.008509	0.6129	b4322	uxuA	-11.91	0.016653	184 -- 195	44 -- 55	mannonate hydrolase		_____________183__________196\n_____________\|____________\|\n5'-CAU...ACUAU__G_________AAAUC...AUA-3'\n______________GU_AAAGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CA_UUUCUCCUU\n3'-UUU...CCGGG__G_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-15.5118 kcal/mol	2.65561 kcal/mol	0.941432 kcal/mol	183 196@LB@ \| \|@LB@5'-CAU...ACUAU G AAAUC...AUA-3'@LB@ GU AAAGAGGAA@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CA UUUCUCCUU@LB@3'-UUU...CCGGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -15.5118 kcal/mol@LB@Unfolding Energy - mRNA 2.65561 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
27	0.005027	0.5992	b3745	viaA	-10.46	0.033099	243 -- 253	42 -- 52	stimulator of RavA ATPase activity; von Willebrand factor domain protein		_____________242_________254\n_____________\|___________\|\n5'-ACG...UCAGC___________GAUCG...CGG-3'\n______________GAAGAGGGAUU\n______________:\|\|\|\|\|\|:\|\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	247 -- 253	42 -- 48	-12.7293 kcal/mol	1.40033 kcal/mol	0.866923 kcal/mol	242 254@LB@ \| \|@LB@5'-ACG...UCAGC GAUCG...CGG-3'@LB@ GAAGAGGGAUU@LB@ :\|\|\|\|\|\|:\|\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -12.7293 kcal/mol@LB@Unfolding Energy - mRNA 1.40033 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 243 -- 253@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 42 -- 48@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@
124	0.02431	0.6177	b2044	wcaL	-7.42	0.135034	145 -- 156	45 -- 56	putative glycosyl transferase		_____________144__________157\n_____________\|____________\|\n5'-GGG...GUGAG_______C____AUGCA...AGA-3'\n______________CGUCAGA_AGGA\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________GCAGUUU_UCCU\n3'-UUU...ACCGG_______C____UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	145 -- 151	50 -- 56	-12.5799 kcal/mol	4.21745 kcal/mol	0.938337 kcal/mol	144 157@LB@ \| \|@LB@5'-GGG...GUGAG C AUGCA...AGA-3'@LB@ CGUCAGA AGGA@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ GCAGUUU UCCU@LB@3'-UUU...ACCGG C UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -12.5799 kcal/mol@LB@Unfolding Energy - mRNA 4.21745 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 145 -- 156@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
54	0.01118	0.6177	b0127	yadG	-7.27	0.144346	282 -- 299	40 -- 55	putative ABC transporter ATPase		_____________281________________300\n_____________\|__________________\|\n5'-UGU...UGCAG_______C___U______U-3'\n______________GUCGAAG_GGG_GAUUUU\n______________\|\|\|:\|\|\|_:\|\|_:\|\|\|\|:\n______________CAGUUUC_UCC_UUAAAG\n3'-UUU...CCGGG__________________UAAAA...ACA-5'\n_____________\|__________________\|\n_____________56_________________39\n	282 -- 288	49 -- 55	-13.6497 kcal/mol	5.35692 kcal/mol	1.01784 kcal/mol	281 300@LB@ \| \|@LB@5'-UGU...UGCAG C U U-3'@LB@ GUCGAAG GGG GAUUUU@LB@ \|\|\|:\|\|\| :\|\| :\|\|\|\|:@LB@ CAGUUUC UCC UUAAAG@LB@3'-UUU...CCGGG UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -13.6497 kcal/mol@LB@Unfolding Energy - mRNA 5.35692 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 49 -- 55@LB@
129	0.02539	0.6177	b0129	yadI	-10.21	0.037333	124 -- 136	40 -- 52	putative PTS Enzyme IIA		_____________123___________137\n_____________\|_____________\|\n5'-CUG...UUGGG_____________GACGG...UGA-3'\n______________GGAGAGGAGUUUU\n______________::\|\|\|\|\|\|:\|\|\|:\n______________UUUCUCCUUAAAG\n3'-UUU...GGCAG_____________UAAAA...ACA-5'\n_____________\|_____________\|\n_____________53____________39\n	130 -- 136	40 -- 46	-14.8894 kcal/mol	3.74683 kcal/mol	0.936082 kcal/mol	123 137@LB@ \| \|@LB@5'-CUG...UUGGG GACGG...UGA-3'@LB@ GGAGAGGAGUUUU@LB@ ::\|\|\|\|\|\|:\|\|\|:@LB@ UUUCUCCUUAAAG@LB@3'-UUU...GGCAG UAAAA...ACA-5'@LB@ \| \|@LB@ 53 39@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -14.8894 kcal/mol@LB@Unfolding Energy - mRNA 3.74683 kcal/mol@LB@Unfolding Energy - sRNA 0.936082 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 40 -- 52@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 40 -- 46@LB@
110	0.02234	0.6177	b0141	yadN	-8.72	0.074917	179 -- 189	37 -- 47	putative fimbrial-like adhesin protein		_____________178_________190\n_____________\|___________\|\n5'-UUA...CUAAU___________AAAGG...GUG-3'\n______________GGAAUUUUAUU\n______________\|\|\|\|\|\|\|:\|\|\|\n______________CCUUAAAGUAA\n3'-UUU...UUUCU___________AAAAA...ACA-5'\n_____________\|___________\|\n_____________48__________36\n	183 -- 189	37 -- 43	-11.1734 kcal/mol	1.41261 kcal/mol	1.04525 kcal/mol	178 190@LB@ \| \|@LB@5'-UUA...CUAAU AAAGG...GUG-3'@LB@ GGAAUUUUAUU@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ CCUUAAAGUAA@LB@3'-UUU...UUUCU AAAAA...ACA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1734 kcal/mol@LB@Unfolding Energy - mRNA 1.41261 kcal/mol@LB@Unfolding Energy - sRNA 1.04525 kcal/mol@LB@@LB@Position - mRNA 179 -- 189@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 37 -- 43@LB@
168	0.03398	0.6177	b0321	yahG	-8.56	0.080369	183 -- 192	44 -- 53	DUF1116 family protein	b4572	_____________182________193\n_____________\|__________\|\n5'-AUC...AUCUG__________GAAGC...AAC-3'\n______________CAAAGGGGAG\n______________\|\|\|\|\|:\|\|\|:\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	186 -- 192	44 -- 50	-12.9704 kcal/mol	3.47901 kcal/mol	0.927997 kcal/mol	182 193@LB@ \| \|@LB@5'-AUC...AUCUG GAAGC...AAC-3'@LB@ CAAAGGGGAG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.9704 kcal/mol@LB@Unfolding Energy - mRNA 3.47901 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 183 -- 192@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 44 -- 50@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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