Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
145	0.01066	0.2504	b2153	folE	-11.37	0.162147	44 -- 68	1 -- 21	GTP cyclohydrolase I		_____________43________________________69\n_____________\|_________________________\|\n5'-CUG...UUUUA_____UGCU__U_________C___AAUUA...ACG-3'\n______________ACAUC____GA_GAAAGGCAG_GGC\n______________\|\|\|\|\|____:\|_\|\|\|\|:\|\|\|\|_\|\|\|\n______________UGUAG____UU_CUUUUCGUC_CCG\n3'-UUU...ACCCC___________U_________A___-5'\n_____________\|________________________\|\n_____________22_______________________1\n	58 -- 64	5 -- 11	-23.5216 kcal/mol	10.6442 kcal/mol	1.51103 kcal/mol	43 69@LB@ \| \|@LB@5'-CUG...UUUUA UGCU U C AAUUA...ACG-3'@LB@ ACAUC GA GAAAGGCAG GGC@LB@ \|\|\|\|\| :\| \|\|\|\|:\|\|\|\| \|\|\|@LB@ UGUAG UU CUUUUCGUC CCG@LB@3'-UUU...ACCCC U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -23.5216 kcal/mol@LB@Unfolding Energy - mRNA 10.6442 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 44 -- 68@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@LB@
146	0.01079	0.2504	b2453	eutG	-16.22	0.013596	18 -- 37	1 -- 22	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase		_____________17_____________________38\n_____________\|______________________\|\n5'-GGC...CGCCC_____AUU______________AUUAC...GUC-3'\n______________GGCAU____GAAGGGCAG_GGC\n______________\|:\|\|\|____\|\|\|::\|\|\|\|_\|\|\|\n______________CUGUA____CUUUUCGUC_CCG\n3'-UUU...UACCC_____GUUU_________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	28 -- 34	5 -- 11	-23.1742 kcal/mol	5.41796 kcal/mol	1.54023 kcal/mol	17 38@LB@ \| \|@LB@5'-GGC...CGCCC AUU AUUAC...GUC-3'@LB@ GGCAU GAAGGGCAG GGC@LB@ \|:\|\|\| \|\|\|::\|\|\|\| \|\|\|@LB@ CUGUA CUUUUCGUC CCG@LB@3'-UUU...UACCC GUUU A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -23.1742 kcal/mol@LB@Unfolding Energy - mRNA 5.41796 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 18 -- 37@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
147	0.01091	0.2504	b2720	hycF	-14.84	0.030299	116 -- 133	1 -- 16	formate hydrogenlyase complex iron-sulfur protein		_____________115________________134\n_____________\|__________________\|\n5'-CGA...CGUAA___________AA_____GCCGU...CAG-3'\n______________GAAGAAGAGCA__GUGGU\n______________:\|\|\|\|\|:\|\|\|\|__\|\|\|\|:\n______________UUUCUUUUCGU__CACCG\n3'-UUU...UGUAG__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	120 -- 126	6 -- 12	-19.8629 kcal/mol	3.67538 kcal/mol	1.34555 kcal/mol	115 134@LB@ \| \|@LB@5'-CGA...CGUAA AA GCCGU...CAG-3'@LB@ GAAGAAGAGCA GUGGU@LB@ :\|\|\|\|\|:\|\|\|\| \|\|\|\|:@LB@ UUUCUUUUCGU CACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -19.8629 kcal/mol@LB@Unfolding Energy - mRNA 3.67538 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 116 -- 133@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 6 -- 12@LB@
148	0.01095	0.2504	b0082	rsmH	-17.59	0.005541	130 -- 156	1 -- 25	16S rRNA m(4)C1402 methyltransferase SAM-dependent		_____________129_________________________157\n_____________\|___________________________\|\n5'-UGG...GUCAA__AA________C_C________U___UACCG...GUC-3'\n______________GG__GAUAUCGA_G_AGAGCAGU_GGC\n______________\|\|__\|\|:\|\|\|:\|_\|_\|:\|\|\|\|\|\|_\|\|\|\n______________CC__CUGUAGUU_C_UUUCGUCA_CCG\n3'-UUU...UUUUA__C_________U_U____________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	146 -- 152	4 -- 10	-26.6505 kcal/mol	6.5392 kcal/mol	2.51748 kcal/mol	129 157@LB@ \| \|@LB@5'-UGG...GUCAA AA C C U UACCG...GUC-3'@LB@ GG GAUAUCGA G AGAGCAGU GGC@LB@ \|\| \|\|:\|\|\|:\| \| \|:\|\|\|\|\|\| \|\|\|@LB@ CC CUGUAGUU C UUUCGUCA CCG@LB@3'-UUU...UUUUA C U U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -17.59 kcal/mol@LB@Hybridization Energy -26.6505 kcal/mol@LB@Unfolding Energy - mRNA 6.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 130 -- 156@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 4 -- 10@LB@
149	0.01096	0.2504	b3230	rpsI	-12.23	0.111717	165 -- 205	1 -- 34	30S ribosomal subunit protein S9		_____________164_______________________________________206\n_____________\|_________________________________________\|\n5'-GUG...AGCAA_______UUCUU______UAAUC____UUAU_____A____UGAAA...GUU-3'\n______________CCGCAAG_____GACAUC_____GGGA____AGGCA_UGGC\n______________\|\|:\|\|\|:_____\|\|\|\|\|\|_____:\|:\|____\|:\|\|\|_\|\|\|\|\n______________GGUGUUU_____CUGUAG_____UCUU____UUCGU_ACCG\n3'-UUU...CCCGA_______UACCC______UU________________C____-5'\n_____________\|________________________________________\|\n_____________35_______________________________________1\n	165 -- 171	28 -- 34	-26.3465 kcal/mol	9.84752 kcal/mol	4.26884 kcal/mol	164 206@LB@ \| \|@LB@5'-GUG...AGCAA UUCUU UAAUC UUAU A UGAAA...GUU-3'@LB@ CCGCAAG GACAUC GGGA AGGCA UGGC@LB@ \|\|:\|\|\|: \|\|\|\|\|\| :\|:\| \|:\|\|\| \|\|\|\|@LB@ GGUGUUU CUGUAG UCUU UUCGU ACCG@LB@3'-UUU...CCCGA UACCC UU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -26.3465 kcal/mol@LB@Unfolding Energy - mRNA 9.84752 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 28 -- 34@LB@
152	0.01123	0.2504	b1872	torZ	-17.40	0.006326	76 -- 107	1 -- 34	trimethylamine N-oxide reductase system III catalytic subunit	b0997 b3551	_____________75___________________________________108\n_____________\|____________________________________\|\n5'-ACG...CAUUG___AA_________________CC_________A__GAAAA...AGA-3'\n______________CCA__GGAAUGGGGGCA_CGAA____AGCA_UG_GC\n______________\|\|\|__::\|\|\|\|\|\|\|:\|\|_\|:\|\|____\|\|\|\|_\|\|_\|\|\n______________GGU__UUUUACCCCUGU_GUUU____UCGU_AC_CG\n3'-UUU...CCCGA___G_____________A____CUUU____C_____-5'\n_____________\|___________________________________\|\n_____________35__________________________________1\n	86 -- 92	19 -- 25	-29.6219 kcal/mol	7.95271 kcal/mol	4.26884 kcal/mol	75 108@LB@ \| \|@LB@5'-ACG...CAUUG AA CC A GAAAA...AGA-3'@LB@ CCA GGAAUGGGGGCA CGAA AGCA UG GC@LB@ \|\|\| ::\|\|\|\|\|\|\|:\|\| \|:\|\| \|\|\|\| \|\| \|\|@LB@ GGU UUUUACCCCUGU GUUU UCGU AC CG@LB@3'-UUU...CCCGA G A CUUU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -29.6219 kcal/mol@LB@Unfolding Energy - mRNA 7.95271 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 76 -- 107@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 19 -- 25@LB@
153	0.01124	0.2504	b0414	ribD	-14.78	0.031370	153 -- 170	1 -- 22	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase		_____________152____________________171\n_____________\|______________________\|\n5'-AAA...UCGAA____________UU________GAAGA...AAG-3'\n______________GAUAUCAAAGAA______UGGC\n______________\|\|:\|\|\|\|\|\|\|\|\|______\|\|\|\|\n______________CUGUAGUUUCUU______ACCG\n3'-UUU...UACCC____________UUCGUC____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	158 -- 164	11 -- 17	-19.3666 kcal/mol	3.04735 kcal/mol	1.54023 kcal/mol	152 171@LB@ \| \|@LB@5'-AAA...UCGAA UU GAAGA...AAG-3'@LB@ GAUAUCAAAGAA UGGC@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUU ACCG@LB@3'-UUU...UACCC UUCGUC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -19.3666 kcal/mol@LB@Unfolding Energy - mRNA 3.04735 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 153 -- 170@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 11 -- 17@LB@
154	0.01125	0.2504	b3412	bioH	-12.84	0.084220	262 -- 288	1 -- 28	pimeloyl-ACP methyl ester carboxylesterase		_____________261__________________________289\n_____________\|____________________________\|\n5'-GGC...GCACG_________UGAAUGCC___________GUUGC...ACG-3'\n______________GAUGGGGAC________GAAGU_GUGGC\n______________:\|\|\|\|\|\|\|\|________:\|\|\|:_\|\|\|\|\|\n______________UUACCCCUG________UUUCG_CACCG\n3'-UUU...GUGUU_________UAGUUUCU_____U_____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	264 -- 270	20 -- 26	-27.647 kcal/mol	12.2839 kcal/mol	2.519 kcal/mol	261 289@LB@ \| \|@LB@5'-GGC...GCACG UGAAUGCC GUUGC...ACG-3'@LB@ GAUGGGGAC GAAGU GUGGC@LB@ :\|\|\|\|\|\|\|\| :\|\|\|: \|\|\|\|\|@LB@ UUACCCCUG UUUCG CACCG@LB@3'-UUU...GUGUU UAGUUUCU U -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -27.647 kcal/mol@LB@Unfolding Energy - mRNA 12.2839 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 262 -- 288@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 20 -- 26@LB@
156	0.01139	0.2504	b0197	metQ	-9.46	0.330846	169 -- 205	1 -- 33	DL-methionine transporter subunit		_____________168_____________________________________206\n_____________\|_______________________________________\|\n5'-GUG...UUCAA_____CAUAAAUA___________GAAUAA_________GUUCA...UUA-3'\n______________CACAA_________AUUGAAGAAG______GGUA_UGGC\n______________\|\|\|\|\|_________\|\|::\|\|\|\|\|:______:\|:\|_\|\|\|\|\n______________GUGUU_________UAGUUUCUUU______UCGU_ACCG\n3'-UUU...CCGAG_____UUACCCCUG____________________C____-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	185 -- 191	10 -- 16	-16.9822 kcal/mol	4.44131 kcal/mol	3.07861 kcal/mol	168 206@LB@ \| \|@LB@5'-GUG...UUCAA CAUAAAUA GAAUAA GUUCA...UUA-3'@LB@ CACAA AUUGAAGAAG GGUA UGGC@LB@ \|\|\|\|\| \|\|::\|\|\|\|\|: :\|:\| \|\|\|\|@LB@ GUGUU UAGUUUCUUU UCGU ACCG@LB@3'-UUU...CCGAG UUACCCCUG C -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -16.9822 kcal/mol@LB@Unfolding Energy - mRNA 4.44131 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 169 -- 205@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 10 -- 16@LB@
157	0.0114	0.2504	b3833	ubiE	-14.57	0.035245	198 -- 236	1 -- 30	bifunctional 2-octaprenyl-6-methoxy-1 4-benzoquinone methylase/ S-adenosylmethionine:2-DMK methyltransferase		_____________197_____________________________________237\n_____________\|_______________________________________\|\n5'-ACA...GCAUU_______U____AA____C______CGAC___CUU____UUUCA...CAU-3'\n______________GAGAUGG_GGAU__GUCA_AAGAAA____GCA___UGGU\n______________:\|:\|\|\|\|_\|\|\|:__:\|\|\|_\|\|\|\|\|\|____\|\|\|___\|\|\|:\n______________UUUUACC_CCUG__UAGU_UUCUUU____CGU___ACCG\n3'-UUU...AGGUG_________________________U______C______-5'\n_____________\|______________________________________\|\n_____________31_____________________________________1\n	198 -- 204	24 -- 30	-23.6374 kcal/mol	6.55293 kcal/mol	2.51911 kcal/mol	197 237@LB@ \| \|@LB@5'-ACA...GCAUU U AA C CGAC CUU UUUCA...CAU-3'@LB@ GAGAUGG GGAU GUCA AAGAAA GCA UGGU@LB@ :\|:\|\|\|\| \|\|\|: :\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|:@LB@ UUUUACC CCUG UAGU UUCUUU CGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -23.6374 kcal/mol@LB@Unfolding Energy - mRNA 6.55293 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 236@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@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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