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
8	5.642e-05	0.02272	b2282	nuoH	-5.33	0.272754	189 -- 221	13 -- 44	NADH:ubiquinone oxidoreductase membrane subunit H	_____________188________________________________222\n_____________\|__________________________________\|\n5'-CUC...CUCAA________AACAAU_____G_A__U_________CUGAU...GCU-3'\n______________GGAGGCAC______GAGUU_G_UA_CACC_GGAA\n______________:\|\|:\|\|\|\|______:\|:\|\|_\|_\|\|_\|\|\|\|_\|\|\|\|\n______________UCUUCGUG______UUUAA_C_AU_GUGG_CCUU\n3'-UUU...UUCGU________AAUUU______G_A_______U____UAGAC...CAA-5'\n_____________\|__________________________________\|\n_____________45_________________________________12\n	190 -- 196	37 -- 43	-24.1154 kcal/mol	6.60325 kcal/mol	12.1776 kcal/mol	188 222@LB@ \| \|@LB@5'-CUC...CUCAA AACAAU G A U CUGAU...GCU-3'@LB@ GGAGGCAC GAGUU G UA CACC GGAA@LB@ :\|\|:\|\|\|\| :\|:\|\| \| \|\| \|\|\|\| \|\|\|\|@LB@ UCUUCGUG UUUAA C AU GUGG CCUU@LB@3'-UUU...UUCGU AAUUU G A U UAGAC...CAA-5'@LB@ \| \|@LB@ 45 12@LB@@LB@@LB@Energy -5.33 kcal/mol@LB@Hybridization Energy -24.1154 kcal/mol@LB@Unfolding Energy - mRNA 6.60325 kcal/mol@LB@Unfolding Energy - sRNA 12.1776 kcal/mol@LB@@LB@Position - mRNA 189 -- 221@LB@Position - sRNA 13 -- 44@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 37 -- 43@LB@
9	7.531e-05	0.02695	b0491	fetB	-11.86	0.004271	187 -- 209	25 -- 47	iron export ABC transporter permease; peroxide resistance protein	_____________186_____________________210\n_____________\|_______________________\|\n5'-GCC...GAAAU___________GCUAU___C___CAUAA...AGA-3'\n______________GCAGGAAGCAC_____GAA_UCG\n______________\|\|\|:\|\|\|\|\|\|\|_____:\|\|_\|\|\|\n______________CGUUCUUCGUG_____UUU_AGC\n3'-UUU...GAAUU___________AAUUU___A___AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	191 -- 197	37 -- 43	-22.8314 kcal/mol	4.71887 kcal/mol	6.25056 kcal/mol	186 210@LB@ \| \|@LB@5'-GCC...GAAAU GCUAU C CAUAA...AGA-3'@LB@ GCAGGAAGCAC GAA UCG@LB@ \|\|\|:\|\|\|\|\|\|\| :\|\| \|\|\|@LB@ CGUUCUUCGUG UUU AGC@LB@3'-UUU...GAAUU AAUUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -22.8314 kcal/mol@LB@Unfolding Energy - mRNA 4.71887 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
10	0.0001005	0.03239	b1260	trpA	-10.26	0.013526	184 -- 203	5 -- 22	tryptophan synthase alpha subunit	_____________183__________________204\n_____________\|____________________\|\n5'-GCC...UGAAA____GAG_____________GAACG...CAU-3'\n______________GCAC___GGGAAAUCUGAUG\n______________:\|\|\|___:\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGUG___UCCUUUAGACUAC\n3'-UUU...AGCAA____G_______________ACAA-5'\n_____________\|____________________\|\n_____________23___________________4\n	192 -- 198	10 -- 16	-23.1901 kcal/mol	5.35202 kcal/mol	7.57357 kcal/mol	183 204@LB@ \| \|@LB@5'-GCC...UGAAA GAG GAACG...CAU-3'@LB@ GCAC GGGAAAUCUGAUG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGUG UCCUUUAGACUAC@LB@3'-UUU...AGCAA G ACAA-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -23.1901 kcal/mol@LB@Unfolding Energy - mRNA 5.35202 kcal/mol@LB@Unfolding Energy - sRNA 7.57357 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
11	0.0001294	0.03789	b3687	ibpA	-8.25	0.051487	69 -- 81	26 -- 38	heat shock chaperone	_____________68____________82\n_____________\|_____________\|\n5'-AAC...AUAAG_____________AUUUC...GCU-3'\n______________GCUUGAAAAGUUC\n______________:\|\|\|:\|\|\|\|:\|\|\|\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	75 -- 81	26 -- 32	-13.0918 kcal/mol	3.40592 kcal/mol	1.43364 kcal/mol	68 82@LB@ \| \|@LB@5'-AAC...AUAAG AUUUC...GCU-3'@LB@ GCUUGAAAAGUUC@LB@ :\|\|\|:\|\|\|\|:\|\|\|@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -13.0918 kcal/mol@LB@Unfolding Energy - mRNA 3.40592 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 26 -- 32@LB@
12	0.0001753	0.04706	b3676	yidH	-12.46	0.002725	279 -- 300	7 -- 26	DUF202 family inner membrane protein	_____________278___________________300\n_____________\|_____________________\|\n5'-GCC...GGAUC___AC__________UU_____-3'\n______________CGU__UGCACUAGGA__UCUGG\n______________\|\|\|__\|:\|\|\|:\|\|\|\|__\|\|\|\|:\n______________GCA__AUGUGGUCCU__AGACU\n3'-UUU...UUUAA_______________UU_____ACACAA-5'\n_____________\|______________________\|\n_____________27_____________________6\n	286 -- 292	15 -- 21	-23.8048 kcal/mol	2.98352 kcal/mol	8.36616 kcal/mol	278 300@LB@ \| \|@LB@5'-GCC...GGAUC AC UU -3'@LB@ CGU UGCACUAGGA UCUGG@LB@ \|\|\| \|:\|\|\|:\|\|\|\| \|\|\|\|:@LB@ GCA AUGUGGUCCU AGACU@LB@3'-UUU...UUUAA UU ACACAA-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -23.8048 kcal/mol@LB@Unfolding Energy - mRNA 2.98352 kcal/mol@LB@Unfolding Energy - sRNA 8.36616 kcal/mol@LB@@LB@Position - mRNA 279 -- 300@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 15 -- 21@LB@
13	0.0002543	0.06302	b3583	sgbE	-8.82	0.035786	171 -- 191	39 -- 61	L-ribulose-5-phosphate 4-epimerase	_____________170_____________________192\n_____________\|_______________________\|\n5'-CAA...UGGAU__________GUAU_________UGGAU...ACG-3'\n______________UGAAGC__GC____GCAGGAGGC\n______________\|\|\|\|:\|__\|\|____\|\|\|:\|\|:\|\|\n______________ACUUUG__CG____CGUUCUUCG\n3'-UUU...GCCCU______AA__AAUU_________UGAAU...CAA-5'\n_____________\|_______________________\|\n_____________62______________________38\n	185 -- 191	39 -- 45	-21.2799 kcal/mol	5.20492 kcal/mol	7.25518 kcal/mol	170 192@LB@ \| \|@LB@5'-CAA...UGGAU GUAU UGGAU...ACG-3'@LB@ UGAAGC GC GCAGGAGGC@LB@ \|\|\|\|:\| \|\| \|\|\|:\|\|:\|\|@LB@ ACUUUG CG CGUUCUUCG@LB@3'-UUU...GCCCU AA AAUU UGAAU...CAA-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 5.20492 kcal/mol@LB@Unfolding Energy - sRNA 7.25518 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 39 -- 45@LB@
14	0.0002995	0.06692	b4195	ulaC	-9.74	0.019405	182 -- 212	24 -- 54	L-ascorbate-specific enzyme IIA component of PTS	_____________181_______________________________213\n_____________\|_________________________________\|\n5'-GCG...CAGGA___G__________C____CAU_______A___GAUUC...UGG-3'\n______________UGU__AAGUAAGGA_GCGC____GAAAUU_CGU\n______________\|\|:__\|\|\|:\|\|\|:\|_\|\|:\|____:\|\|\|\|\|_\|\|\|\n______________ACG__UUCGUUCUU_CGUG____UUUUAA_GCA\n3'-UUU...UUUGA___AA______________AAUU__________AUGUG...CAA-5'\n_____________\|_________________________________\|\n_____________55________________________________23\n	187 -- 193	42 -- 48	-22.0137 kcal/mol	6.00518 kcal/mol	6.26866 kcal/mol	181 213@LB@ \| \|@LB@5'-GCG...CAGGA G C CAU A GAUUC...UGG-3'@LB@ UGU AAGUAAGGA GCGC GAAAUU CGU@LB@ \|\|: \|\|\|:\|\|\|:\| \|\|:\| :\|\|\|\|\| \|\|\|@LB@ ACG UUCGUUCUU CGUG UUUUAA GCA@LB@3'-UUU...UUUGA AA AAUU AUGUG...CAA-5'@LB@ \| \|@LB@ 55 23@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -22.0137 kcal/mol@LB@Unfolding Energy - mRNA 6.00518 kcal/mol@LB@Unfolding Energy - sRNA 6.26866 kcal/mol@LB@@LB@Position - mRNA 182 -- 212@LB@Position - sRNA 24 -- 54@LB@Position Seed - mRNA 187 -- 193@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@
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@
18	0.0004863	0.08107	b2217	rcsB	-10.91	0.008593	172 -- 193	39 -- 59	response regulator in two-component regulatory system with RcsC and YojN	_____________171____________________194\n_____________\|______________________\|\n5'-AAC...GUCAA_________GU_______U___CUAUU...GCG-3'\n______________GAGCUUGCU__AGCAAGG_AGC\n______________:\|:\|\|\|\|\|\|__\|\|\|\|\|\|:_\|\|\|\n______________UUUGAACGA__UCGUUCU_UCG\n3'-UUU...CCUAC_________AU___________UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	183 -- 189	42 -- 48	-25.4912 kcal/mol	8.43277 kcal/mol	6.15149 kcal/mol	171 194@LB@ \| \|@LB@5'-AAC...GUCAA GU U CUAUU...GCG-3'@LB@ GAGCUUGCU AGCAAGG AGC@LB@ :\|:\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ UUUGAACGA UCGUUCU UCG@LB@3'-UUU...CCUAC AU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -25.4912 kcal/mol@LB@Unfolding Energy - mRNA 8.43277 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 42 -- 48@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)

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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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