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
81	0.005437	0.2146	b1073	flgB	-5.23	0.286610	229 -- 247	36 -- 53	flagellar component of cell-proximal portion of basal-body rod	_____________228_________________248\n_____________\|___________________\|\n5'-UGA...CUUAC____UCAA___________CAAUC...CCG-3'\n______________GUUU____CAAGAGGCGCU\n______________\|:\|\|____\|\|\|\|\|:\|\|:\|\|\n______________CGAA____GUUCUUCGUGA\n3'-UUU...UUGAA____UUC____________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________35\n	241 -- 247	36 -- 42	-18.0666 kcal/mol	6.73003 kcal/mol	6.10238 kcal/mol	228 248@LB@ \| \|@LB@5'-UGA...CUUAC UCAA CAAUC...CCG-3'@LB@ GUUU CAAGAGGCGCU@LB@ \|:\|\| \|\|\|\|\|:\|\|:\|\|@LB@ CGAA GUUCUUCGUGA@LB@3'-UUU...UUGAA UUC AUUUU...CAA-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -18.0666 kcal/mol@LB@Unfolding Energy - mRNA 6.73003 kcal/mol@LB@Unfolding Energy - sRNA 6.10238 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 36 -- 42@LB@
82	0.005534	0.2146	b1342	ydaN	-6.57	0.141434	180 -- 206	30 -- 54	putative Zn(II) transporter	_____________179_________________________207\n_____________\|___________________________\|\n5'-CGU...AAUAA___G____U_AU_________GU____GCGAU...AUG-3'\n______________UGC_UUGA_G__GGAGGCACU__GGAA\n______________\|\|\|_\|\|:\|_\|__:\|\|:\|\|\|\|\|__::\|\|\n______________ACG_AAUU_C__UCUUCGUGA__UUUU\n3'-UUU...UUUGA__________GU_________AU____UAAGC...CAA-5'\n_____________\|___________________________\|\n_____________55__________________________29\n	194 -- 200	36 -- 42	-19.056 kcal/mol	6.29262 kcal/mol	6.19579 kcal/mol	179 207@LB@ \| \|@LB@5'-CGU...AAUAA G U AU GU GCGAU...AUG-3'@LB@ UGC UUGA G GGAGGCACU GGAA@LB@ \|\|\| \|\|:\| \| :\|\|:\|\|\|\|\| ::\|\|@LB@ ACG AAUU C UCUUCGUGA UUUU@LB@3'-UUU...UUUGA GU AU UAAGC...CAA-5'@LB@ \| \|@LB@ 55 29@LB@@LB@@LB@Energy -6.57 kcal/mol@LB@Hybridization Energy -19.056 kcal/mol@LB@Unfolding Energy - mRNA 6.29262 kcal/mol@LB@Unfolding Energy - sRNA 6.19579 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 30 -- 54@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 36 -- 42@LB@
83	0.005546	0.2146	b0221	fadE	-11.24	0.006780	20 -- 32	37 -- 49	acyl coenzyme A dehydrogenase	_____________19____________33\n_____________\|_____________\|\n5'-GUG...GCCAA_____________GGGCA...GGA-3'\n______________AAGCGAGAAGUAC\n______________\|\|\|\|:\|\|\|\|\|:\|\|\n______________UUCGUUCUUCGUG\n3'-UUU...ACGAA_____________AAUUU...CAA-5'\n_____________\|_____________\|\n_____________50____________36\n	26 -- 32	37 -- 43	-19.9972 kcal/mol	2.7283 kcal/mol	6.03369 kcal/mol	19 33@LB@ \| \|@LB@5'-GUG...GCCAA GGGCA...GGA-3'@LB@ AAGCGAGAAGUAC@LB@ \|\|\|\|:\|\|\|\|\|:\|\|@LB@ UUCGUUCUUCGUG@LB@3'-UUU...ACGAA AAUUU...CAA-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.24 kcal/mol@LB@Hybridization Energy -19.9972 kcal/mol@LB@Unfolding Energy - mRNA 2.7283 kcal/mol@LB@Unfolding Energy - sRNA 6.03369 kcal/mol@LB@@LB@Position - mRNA 20 -- 32@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 37 -- 43@LB@
84	0.005596	0.2146	b4065	yjcE	-5.39	0.265673	197 -- 210	9 -- 22	putative cation/proton antiporter	_____________196____________211\n_____________\|______________\|\n5'-UAU...AGGGA____AU________UCUUC...UGC-3'\n______________ACGC__GGAAAUCU\n______________\|\|:\|__\|\|\|\|\|\|\|\|\n______________UGUG__CCUUUAGA\n3'-UUU...AGCAA____GU________CUACACAA-5'\n_____________\|______________\|\n_____________23_____________8\n	203 -- 209	10 -- 16	-15.8377 kcal/mol	2.89158 kcal/mol	7.5588 kcal/mol	196 211@LB@ \| \|@LB@5'-UAU...AGGGA AU UCUUC...UGC-3'@LB@ ACGC GGAAAUCU@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ UGUG CCUUUAGA@LB@3'-UUU...AGCAA GU CUACACAA-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.8377 kcal/mol@LB@Unfolding Energy - mRNA 2.89158 kcal/mol@LB@Unfolding Energy - sRNA 7.5588 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 10 -- 16@LB@
85	0.005692	0.2157	b4052	dnaB	-8.38	0.047402	89 -- 103	26 -- 40	replicative DNA helicase	_____________88______________104\n_____________\|_______________\|\n5'-UGC...CCACC_______U_______AAUUC...CGG-3'\n______________GUGCUUG_GAAAUUC\n______________\|::\|\|\|:_:\|\|\|\|\|\|\n______________CGUGAAU_UUUUAAG\n3'-UUU...UUCUU_______U_______CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	97 -- 103	26 -- 32	-13.045 kcal/mol	3.01413 kcal/mol	1.64811 kcal/mol	88 104@LB@ \| \|@LB@5'-UGC...CCACC U AAUUC...CGG-3'@LB@ GUGCUUG GAAAUUC@LB@ \|::\|\|\|: :\|\|\|\|\|\|@LB@ CGUGAAU UUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -13.045 kcal/mol@LB@Unfolding Energy - mRNA 3.01413 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 89 -- 103@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 26 -- 32@LB@
86	0.005829	0.217	b2399	yfeD	-9.44	0.023742	136 -- 182	13 -- 56	DUF1323 family putative DNA-binding protein	_____________135______________________________________________183\n_____________\|________________________________________________\|\n5'-UGA...ACAUC_______CU________G_A___UC____________ACGC_______UUCGC...GGA-3'\n______________CUUGCUU__GCGGGAAG_G_UUA__GGAUU_GUUACA____UUAGGGA\n______________\|\|\|\|\|\|\|__\|\|::\|\|\|\|_:_\|\|\|__::\|\|\|_\|\|\|\|\|\|____::\|\|\|:\|\n______________GAACGAA__CGUUCUUC_U_AAU__UUUAA_CAAUGU____GGUCCUU\n3'-UUU...ACUUU_______UU________G_G___UU_____G_________________UAGAC...CAA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________12\n	146 -- 152	40 -- 46	-35.8501 kcal/mol	12.5789 kcal/mol	13.8302 kcal/mol	135 183@LB@ \| \|@LB@5'-UGA...ACAUC CU G A UC ACGC UUCGC...GGA-3'@LB@ CUUGCUU GCGGGAAG G UUA GGAUU GUUACA UUAGGGA@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\| : \|\|\| ::\|\|\| \|\|\|\|\|\| ::\|\|\|:\|@LB@ GAACGAA CGUUCUUC U AAU UUUAA CAAUGU GGUCCUU@LB@3'-UUU...ACUUU UU G G UU G UAGAC...CAA-5'@LB@ \| \|@LB@ 57 12@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -35.8501 kcal/mol@LB@Unfolding Energy - mRNA 12.5789 kcal/mol@LB@Unfolding Energy - sRNA 13.8302 kcal/mol@LB@@LB@Position - mRNA 136 -- 182@LB@Position - sRNA 13 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 40 -- 46@LB@
87	0.005861	0.217	b3083	higB	-4.01	0.492619	220 -- 233	28 -- 42	mRNA interferase toxin of the HigB-HigA toxin-antitoxin system	_____________219_____________234\n_____________\|_______________\|\n5'-GCA...UCAAA_______________GCUGC...GAU-3'\n______________AAGCAUU_GAAAGAU\n______________\|\|\|\|\|:\|_:\|\|\|:\|\|\n______________UUCGUGA_UUUUUUA\n3'-UUU...CGUUC_______A_______AGCAA...CAA-5'\n_____________\|_______________\|\n_____________43______________27\n	220 -- 226	36 -- 42	-9.16043 kcal/mol	3.51035 kcal/mol	1.63711 kcal/mol	219 234@LB@ \| \|@LB@5'-GCA...UCAAA GCUGC...GAU-3'@LB@ AAGCAUU GAAAGAU@LB@ \|\|\|\|\|:\| :\|\|\|:\|\|@LB@ UUCGUGA UUUUUUA@LB@3'-UUU...CGUUC A AGCAA...CAA-5'@LB@ \| \|@LB@ 43 27@LB@@LB@@LB@Energy -4.01 kcal/mol@LB@Hybridization Energy -9.16043 kcal/mol@LB@Unfolding Energy - mRNA 3.51035 kcal/mol@LB@Unfolding Energy - sRNA 1.63711 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 28 -- 42@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 36 -- 42@LB@
88	0.006209	0.2266	b1643	ydhI	-11.55	0.005389	141 -- 153	28 -- 40	DUF1656 family putative inner membrane efflux pump associated protein	_____________140___________154\n_____________\|_____________\|\n5'-UUU...UUUUC_____________AUUUA...GAU-3'\n______________GCACUUAAAGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUUUUA\n3'-UUU...UUCUU_____________AGCAA...CAA-5'\n_____________\|_____________\|\n_____________41____________27\n	144 -- 150	31 -- 37	-15.2864 kcal/mol	2.10141 kcal/mol	1.63611 kcal/mol	140 154@LB@ \| \|@LB@5'-UUU...UUUUC AUUUA...GAU-3'@LB@ GCACUUAAAGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -15.2864 kcal/mol@LB@Unfolding Energy - mRNA 2.10141 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 141 -- 153@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 31 -- 37@LB@
89	0.006302	0.2266	b3208	mtgA	-4.90	0.336213	28 -- 47	28 -- 47	biosynthetic peptidoglycan transglycosylase	_____________27____________________48\n_____________\|_____________________\|\n5'-UUG...AUACC____________GG_______GGGCG...UGU-3'\n______________GC_AGAAGUGCU__AAGAGAU\n______________\|\|_\|\|\|\|\|::\|\|__\|\|:\|:\|\|\n______________CG_UCUUCGUGA__UUUUUUA\n3'-UUU...GAAUU__U_________A________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________48____________________27\n	32 -- 38	36 -- 42	-15.6239 kcal/mol	4.50128 kcal/mol	6.22212 kcal/mol	27 48@LB@ \| \|@LB@5'-UUG...AUACC GG GGGCG...UGU-3'@LB@ GC AGAAGUGCU AAGAGAU@LB@ \|\| \|\|\|\|\|::\|\| \|\|:\|:\|\|@LB@ CG UCUUCGUGA UUUUUUA@LB@3'-UUU...GAAUU U A AGCAA...CAA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -4.90 kcal/mol@LB@Hybridization Energy -15.6239 kcal/mol@LB@Unfolding Energy - mRNA 4.50128 kcal/mol@LB@Unfolding Energy - sRNA 6.22212 kcal/mol@LB@@LB@Position - mRNA 28 -- 47@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 36 -- 42@LB@
90	0.006331	0.2266	b1710	btuE	-7.57	0.078405	256 -- 270	25 -- 39	glutathione peroxidase	_____________255_____________271\n_____________\|_______________\|\n5'-GCA...GACCA____G__________CCGGU...UCG-3'\n______________CGCU_GAGAAGUUCG\n______________\|:\|\|_:\|:\|\|:\|\|\|\|\n______________GUGA_UUUUUUAAGC\n3'-UUU...UCUUC____A__________AAUGU...CAA-5'\n_____________\|_______________\|\n_____________40______________24\n	264 -- 270	25 -- 31	-13.949 kcal/mol	4.72897 kcal/mol	1.64678 kcal/mol	255 271@LB@ \| \|@LB@5'-GCA...GACCA G CCGGU...UCG-3'@LB@ CGCU GAGAAGUUCG@LB@ \|:\|\| :\|:\|\|:\|\|\|\|@LB@ GUGA UUUUUUAAGC@LB@3'-UUU...UCUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -13.949 kcal/mol@LB@Unfolding Energy - mRNA 4.72897 kcal/mol@LB@Unfolding Energy - sRNA 1.64678 kcal/mol@LB@@LB@Position - mRNA 256 -- 270@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 25 -- 31@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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