Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
149	0.01422	0.3104	b0415	ribE	-7.20	0.333957	258 -- 265	4 -- 11	riboflavin synthase beta chain	_____________257______266\n_____________\|________\|\n5'-CGG...CCAUC________CAACA...GUG-3'\n______________GCGCGUUU\n______________\|\|\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	259 -- 265	4 -- 10	-13.1965 kcal/mol	4.83677 kcal/mol	1.15639 kcal/mol	257 266@LB@ \| \|@LB@5'-CGG...CCAUC CAACA...GUG-3'@LB@ GCGCGUUU@LB@ \|\|\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -13.1965 kcal/mol@LB@Unfolding Energy - mRNA 4.83677 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 258 -- 265@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 4 -- 10@LB@
176	0.01748	0.3104	b0435	bolA	-9.78	0.131850	202 -- 220	4 -- 22	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________201_________________221\n_____________\|___________________\|\n5'-UGA...UUUCA________C___A___GA_AGAAG...CCG-3'\n______________UGAUGAUA_GUG_GCG__U\n______________\|\|\|\|:\|:\|_:\|\|_\|\|\|__\|\n______________ACUAUUGU_UAC_CGC__A\n3'-UUU...CUACU________U___G___AG_AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	203 -- 209	15 -- 21	-14.8727 kcal/mol	3.8346 kcal/mol	1.2572 kcal/mol	201 221@LB@ \| \|@LB@5'-UGA...UUUCA C A GA AGAAG...CCG-3'@LB@ UGAUGAUA GUG GCG U@LB@ \|\|\|\|:\|:\| :\|\| \|\|\| \|@LB@ ACUAUUGU UAC CGC A@LB@3'-UUU...CUACU U G AG AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -14.8727 kcal/mol@LB@Unfolding Energy - mRNA 3.8346 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 202 -- 220@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 15 -- 21@LB@
38	0.002512	0.2224	b0436	tig	-7.88	0.265562	192 -- 204	10 -- 21	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________191___________205\n_____________\|_____________\|\n5'-UAC...UUUGA_______A_____AAGUU...UCA-3'\n______________GGUAACA_GAUGC\n______________\|:\|\|\|\|\|_:\|\|\|\|\n______________CUAUUGU_UUACG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	192 -- 198	15 -- 21	-12.2618 kcal/mol	3.15229 kcal/mol	1.23076 kcal/mol	191 205@LB@ \| \|@LB@5'-UAC...UUUGA A AAGUU...UCA-3'@LB@ GGUAACA GAUGC@LB@ \|:\|\|\|\|\| :\|\|\|\|@LB@ CUAUUGU UUACG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.2618 kcal/mol@LB@Unfolding Energy - mRNA 3.15229 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 192 -- 204@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 15 -- 21@LB@
27	0.001549	0.1943	b0440	hupB	-11.81	0.059023	134 -- 149	5 -- 20	HU DNA-binding transcriptional regulator beta subunit	_____________133______________150\n_____________\|________________\|\n5'-CGC...CUGAU_____UGC________CGUAC...CUG-3'\n______________AUAAC___UGCGCGUU\n______________\|\|\|\|\|___\|\|\|\|\|\|\|:\n______________UAUUG___ACGCGCAG\n3'-UUU...ACUAC_____UUU________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	143 -- 149	5 -- 11	-15.9939 kcal/mol	2.93365 kcal/mol	1.24804 kcal/mol	133 150@LB@ \| \|@LB@5'-CGC...CUGAU UGC CGUAC...CUG-3'@LB@ AUAAC UGCGCGUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ UAUUG ACGCGCAG@LB@3'-UUU...ACUAC UUU AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -15.9939 kcal/mol@LB@Unfolding Energy - mRNA 2.93365 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 134 -- 149@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 5 -- 11@LB@
147	0.01411	0.3104	b0441	ppiD	-10.51	0.099467	81 -- 98	3 -- 21	periplasmic folding chaperone has an inactive PPIase domain	_____________80__________________99\n_____________\|___________________\|\n5'-GUA...UAUUC______UUUC_________GUGGG...ACC-3'\n______________GGUGAC_____UGCGUCUU\n______________\|:\|:\|\|_____:\|\|\|\|\|\|\|\n______________CUAUUG_____GCGCAGAA\n3'-UUU...UACUA______UUUAC________AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	92 -- 98	3 -- 9	-17.0331 kcal/mol	5.27038 kcal/mol	1.257 kcal/mol	80 99@LB@ \| \|@LB@5'-GUA...UAUUC UUUC GUGGG...ACC-3'@LB@ GGUGAC UGCGUCUU@LB@ \|:\|:\|\| :\|\|\|\|\|\|\|@LB@ CUAUUG GCGCAGAA@LB@3'-UUU...UACUA UUUAC AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -17.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.27038 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 81 -- 98@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 3 -- 9@LB@
89	0.009028	0.3104	b0529	folD	-8.62	0.203566	239 -- 251	4 -- 17	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase	_____________238____________252\n_____________\|______________\|\n5'-CAA...GCGCA______________GAAGU...CAC-3'\n______________GCAGGUGCGC_UCU\n______________:\|\|::\|\|\|\|\|_\|\|\|\n______________UGUUUACGCG_AGA\n3'-UUU...ACUAU__________C___AAG-5'\n_____________\|______________\|\n_____________18_____________3\n	242 -- 248	8 -- 14	-17.587 kcal/mol	7.73476 kcal/mol	1.22888 kcal/mol	238 252@LB@ \| \|@LB@5'-CAA...GCGCA GAAGU...CAC-3'@LB@ GCAGGUGCGC UCU@LB@ :\|\|::\|\|\|\|\| \|\|\|@LB@ UGUUUACGCG AGA@LB@3'-UUU...ACUAU C AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -17.587 kcal/mol@LB@Unfolding Energy - mRNA 7.73476 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 239 -- 251@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 8 -- 14@LB@
22	0.001004	0.1545	b0583	entD	-18.10	0.004183	41 -- 63	1 -- 22	phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex	_____________40______________________64\n_____________\|_______________________\|\n5'-AUA...CAGAU__U____A___________G___AUGCC...UGC-3'\n______________UG_UGAC_AAGUGCGCGUC_UUC\n______________\|\|_\|:\|\|_\|\|:\|\|\|\|\|\|\|\|_\|\|\|\n______________AC_AUUG_UUUACGCGCAG_AAG\n3'-UUU...CUACU__U________________A___-5'\n_____________\|______________________\|\n_____________23_____________________1\n	53 -- 59	5 -- 11	-24.6004 kcal/mol	5.24265 kcal/mol	1.25963 kcal/mol	40 64@LB@ \| \|@LB@5'-AUA...CAGAU U A G AUGCC...UGC-3'@LB@ UG UGAC AAGUGCGCGUC UUC@LB@ \|\| \|:\|\| \|\|:\|\|\|\|\|\|\|\| \|\|\|@LB@ AC AUUG UUUACGCGCAG AAG@LB@3'-UUU...CUACU U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -24.6004 kcal/mol@LB@Unfolding Energy - mRNA 5.24265 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 41 -- 63@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
45	0.00309	0.2325	b0584	fepA	-13.78	0.026215	91 -- 106	1 -- 17	ferrienterobactin outer membrane transporter	_____________90________________107\n_____________\|_________________\|\n5'-GAA...CAACU___C_____________AGGAU...ACG-3'\n______________GCA__UGCGUGUCUUUC\n______________:\|\|__\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__ACGCGCAGAAAG\n3'-UUU...ACUAU___UU____________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.1338 kcal/mol	6.10916 kcal/mol	1.23994 kcal/mol	90 107@LB@ \| \|@LB@5'-GAA...CAACU C AGGAU...ACG-3'@LB@ GCA UGCGUGUCUUUC@LB@ :\|\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU ACGCGCAGAAAG@LB@3'-UUU...ACUAU UU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -21.1338 kcal/mol@LB@Unfolding Energy - mRNA 6.10916 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 91 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@LB@
180	0.01774	0.3104	b0593	entC	-14.03	0.023631	112 -- 128	4 -- 19	isochorismate synthase 1	_____________111_______________129\n_____________\|_________________\|\n5'-GGC...AGAGU_____U___________GCUUU...CAG-3'\n______________UGACA_AGUGCGCGUUU\n______________\|:\|\|\|_\|:\|\|\|\|\|\|\|:\|\n______________AUUGU_UUACGCGCAGA\n3'-UUU...CUACU_________________AAG-5'\n_____________\|_________________\|\n_____________20________________3\n	122 -- 128	4 -- 10	-18.4725 kcal/mol	3.19872 kcal/mol	1.2406 kcal/mol	111 129@LB@ \| \|@LB@5'-GGC...AGAGU U GCUUU...CAG-3'@LB@ UGACA AGUGCGCGUUU@LB@ \|:\|\|\| \|:\|\|\|\|\|\|\|:\|@LB@ AUUGU UUACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -18.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.19872 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 112 -- 128@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 4 -- 10@LB@
47	0.003448	0.2484	b0614	citX	-10.13	0.115098	76 -- 91	4 -- 17	apo-citrate lyase phosphoribosyl-dephospho-CoA transferase	_____________75_______________92\n_____________\|________________\|\n5'-UUA...GCUGC____AC__________GCUGA...UCA-3'\n______________GCGA__GUGCGCGUCU\n______________:\|:\|__:\|\|\|\|\|\|\|\|\|\n______________UGUU__UACGCGCAGA\n3'-UUU...ACUAU________________AAG-5'\n_____________\|________________\|\n_____________18_______________3\n	85 -- 91	4 -- 10	-19.1919 kcal/mol	7.83057 kcal/mol	1.22888 kcal/mol	75 92@LB@ \| \|@LB@5'-UUA...GCUGC AC GCUGA...UCA-3'@LB@ GCGA GUGCGCGUCU@LB@ :\|:\| :\|\|\|\|\|\|\|\|\|@LB@ UGUU UACGCGCAGA@LB@3'-UUU...ACUAU AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -19.1919 kcal/mol@LB@Unfolding Energy - mRNA 7.83057 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 76 -- 91@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 4 -- 10@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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