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
137	0.01315	0.3087	b2239	glpQ	-7.04	0.107729	242 -- 248	36 -- 42	periplasmic glycerophosphodiester phosphodiesterase	_____________241_____249\n_____________\|_______\|\n5'-CGG...AUGAU_______AUAGU...UCA-3'\n______________GAGCACU\n______________:\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	242 -- 248	36 -- 42	-9.09813 kcal/mol	0.455964 kcal/mol	1.60154 kcal/mol	241 249@LB@ \| \|@LB@5'-CGG...AUGAU AUAGU...UCA-3'@LB@ GAGCACU@LB@ :\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.09813 kcal/mol@LB@Unfolding Energy - mRNA 0.455964 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 242 -- 248@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 36 -- 42@LB@
143	0.01412	0.3181	b0642	leuS	-6.82	0.122159	244 -- 266	37 -- 58	leucyl-tRNA synthetase	_____________243_____________________267\n_____________\|_______________________\|\n5'-AAU...AGUAC_____CA_____A__________ACAUU...AGA-3'\n______________AGCUU__UUGGG_UGAGAAGCGC\n______________\|:\|\|\|__\|\|::\|_::\|\|\|\|\|\|:\|\n______________UUGAA__AAUUC_GUUCUUCGUG\n3'-UUU...CUACU_____CG________________AAUUU...CAA-5'\n_____________\|_______________________\|\n_____________59______________________36\n	260 -- 266	37 -- 43	-20.1861 kcal/mol	7.11823 kcal/mol	6.24354 kcal/mol	243 267@LB@ \| \|@LB@5'-AAU...AGUAC CA A ACAUU...AGA-3'@LB@ AGCUU UUGGG UGAGAAGCGC@LB@ \|:\|\|\| \|\|::\| ::\|\|\|\|\|\|:\|@LB@ UUGAA AAUUC GUUCUUCGUG@LB@3'-UUU...CUACU CG AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.82 kcal/mol@LB@Hybridization Energy -20.1861 kcal/mol@LB@Unfolding Energy - mRNA 7.11823 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 244 -- 266@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 37 -- 43@LB@
171	0.01957	0.3668	b2498	upp	-5.84	0.210430	244 -- 265	42 -- 61	uracil phosphoribosyltransferase	_____________243____________________266\n_____________\|______________________\|\n5'-GGC...CAAGC_______GA___G_________UAUCA...CCG-3'\n______________UGGGACU__UGC_UGAGCAAGA\n______________\|\|::\|\|\|__\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACUUUGA__ACG_AUUCGUUCU\n3'-UUU...GCCCU____________A_________UCGUG...CAA-5'\n_____________\|______________________\|\n_____________62_____________________41\n	259 -- 265	42 -- 48	-21.1169 kcal/mol	8.03919 kcal/mol	7.23689 kcal/mol	243 266@LB@ \| \|@LB@5'-GGC...CAAGC GA G UAUCA...CCG-3'@LB@ UGGGACU UGC UGAGCAAGA@LB@ \|\|::\|\|\| \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACUUUGA ACG AUUCGUUCU@LB@3'-UUU...GCCCU A UCGUG...CAA-5'@LB@ \| \|@LB@ 62 41@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -21.1169 kcal/mol@LB@Unfolding Energy - mRNA 8.03919 kcal/mol@LB@Unfolding Energy - sRNA 7.23689 kcal/mol@LB@@LB@Position - mRNA 244 -- 265@LB@Position - sRNA 42 -- 61@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@LB@
26	0.0007705	0.09021	b3991	thiG	-9.33	0.025562	246 -- 261	25 -- 41	thiamine biosynthesis ThiGH complex subunit	_____________245_______________262\n_____________\|_________________\|\n5'-GCA...UUACC_____A___________CUUCU...CCG-3'\n______________GGCAC__GGGAAAUUCG\n______________:\|\|\|\|__:::\|\|\|\|\|\|\|\n______________UCGUG__UUUUUUAAGC\n3'-UUU...GUUCU_____AA__________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	255 -- 261	25 -- 31	-14.087 kcal/mol	3.10801 kcal/mol	1.64839 kcal/mol	245 262@LB@ \| \|@LB@5'-GCA...UUACC A CUUCU...CCG-3'@LB@ GGCAC GGGAAAUUCG@LB@ :\|\|\|\| :::\|\|\|\|\|\|\|@LB@ UCGUG UUUUUUAAGC@LB@3'-UUU...GUUCU AA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -14.087 kcal/mol@LB@Unfolding Energy - mRNA 3.10801 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 246 -- 261@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 25 -- 31@LB@
152	0.01589	0.3359	b3428	glgP	-3.42	0.610648	252 -- 258	36 -- 42	glycogen phosphorylase	_____________251_____259\n_____________\|_______\|\n5'-CCA...CUCUU_______CUAUC...CGG-3'\n______________AAGCACU\n______________\|\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	252 -- 258	36 -- 42	-8.34293 kcal/mol	3.32239 kcal/mol	1.60154 kcal/mol	251 259@LB@ \| \|@LB@5'-CCA...CUCUU CUAUC...CGG-3'@LB@ AAGCACU@LB@ \|\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -8.34293 kcal/mol@LB@Unfolding Energy - mRNA 3.32239 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 252 -- 258@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 36 -- 42@LB@
23	0.000685	0.09021	b3780	rhlB	-7.99	0.060609	254 -- 278	29 -- 60	ATP-dependent RNA helicase	_____________253______________________________279\n_____________\|________________________________\|\n5'-UCG...CAUCC____G_________________C_________AAAGG...CGC-3'\n______________GAAG_UUGU_______AGAAGC_CUUGAAAAA\n______________\|\|\|:_\|\|\|:_______\|\|\|\|\|\|_\|\|\|:\|\|\|\|\|\n______________CUUU_AACG_______UCUUCG_GAAUUUUUU\n3'-UUU...CCCUA____G____AAUUCGU______U_________AAGCA...CAA-5'\n_____________\|________________________________\|\n_____________61_______________________________28\n	270 -- 276	31 -- 37	-19.7636 kcal/mol	5.50064 kcal/mol	6.27092 kcal/mol	253 279@LB@ \| \|@LB@5'-UCG...CAUCC G C AAAGG...CGC-3'@LB@ GAAG UUGU AGAAGC CUUGAAAAA@LB@ \|\|\|: \|\|\|: \|\|\|\|\|\| \|\|\|:\|\|\|\|\|@LB@ CUUU AACG UCUUCG GAAUUUUUU@LB@3'-UUU...CCCUA G AAUUCGU U AAGCA...CAA-5'@LB@ \| \|@LB@ 61 28@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -19.7636 kcal/mol@LB@Unfolding Energy - mRNA 5.50064 kcal/mol@LB@Unfolding Energy - sRNA 6.27092 kcal/mol@LB@@LB@Position - mRNA 254 -- 278@LB@Position - sRNA 29 -- 60@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 31 -- 37@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@
142	0.01375	0.3119	b4166	queG	-9.76	0.019130	257 -- 284	36 -- 60	epoxyqueuosine reductase cobalamine-stimulated; queosine biosynthesis	_____________256__________________________285\n_____________\|____________________________\|\n5'-CGC...GGGCU______GG____UC______U_______ACCGA...UCA-3'\n______________GGAACU__GCUU__AGCAGG_AGGUAUU\n______________\|:\|\|\|\|__\|\|\|\|__\|\|\|\|:\|_\|:\|:\|:\|\n______________CUUUGA__CGAA__UCGUUC_UUCGUGA\n3'-UUU...CCCUA______A_____U_______________AUUUU...CAA-5'\n_____________\|____________________________\|\n_____________61___________________________35\n	278 -- 284	36 -- 42	-22.8123 kcal/mol	6.80174 kcal/mol	6.24973 kcal/mol	256 285@LB@ \| \|@LB@5'-CGC...GGGCU GG UC U ACCGA...UCA-3'@LB@ GGAACU GCUU AGCAGG AGGUAUU@LB@ \|:\|\|\|\| \|\|\|\| \|\|\|\|:\| \|:\|:\|:\|@LB@ CUUUGA CGAA UCGUUC UUCGUGA@LB@3'-UUU...CCCUA A U AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -22.8123 kcal/mol@LB@Unfolding Energy - mRNA 6.80174 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 257 -- 284@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 36 -- 42@LB@
136	0.01308	0.3087	b0131	panD	-6.12	0.181240	260 -- 282	17 -- 40	aspartate 1-decarboxylase	_____________259______________________283\n_____________\|________________________\|\n5'-AUU...GACCU_____AU_________________UUGAC...UUG-3'\n______________GCACU__GAAGGUUC_UUGCGCCA\n______________\|\|\|\|\|__:\|\|::\|\|\|_\|\|:\|:\|\|\|\n______________CGUGA__UUUUUAAG_AAUGUGGU\n3'-UUU...UUCUU_____AU________C________CCUUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________16\n	268 -- 274	26 -- 32	-23.1255 kcal/mol	7.80932 kcal/mol	9.19627 kcal/mol	259 283@LB@ \| \|@LB@5'-AUU...GACCU AU UUGAC...UUG-3'@LB@ GCACU GAAGGUUC UUGCGCCA@LB@ \|\|\|\|\| :\|\|::\|\|\| \|\|:\|:\|\|\|@LB@ CGUGA UUUUUAAG AAUGUGGU@LB@3'-UUU...UUCUU AU C CCUUU...CAA-5'@LB@ \| \|@LB@ 41 16@LB@@LB@@LB@Energy -6.12 kcal/mol@LB@Hybridization Energy -23.1255 kcal/mol@LB@Unfolding Energy - mRNA 7.80932 kcal/mol@LB@Unfolding Energy - sRNA 9.19627 kcal/mol@LB@@LB@Position - mRNA 260 -- 282@LB@Position - sRNA 17 -- 40@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 26 -- 32@LB@
144	0.01453	0.3231	b3614	yibQ	-4.49	0.404320	261 -- 267	34 -- 40	putative polysaccharide deacetylase	_____________260_____268\n_____________\|_______\|\n5'-UGG...CCCCC_______CUGGC...UUG-3'\n______________GUACUUG\n______________\|:\|\|\|\|:\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	261 -- 267	34 -- 40	-7.10274 kcal/mol	0.998159 kcal/mol	1.61352 kcal/mol	260 268@LB@ \| \|@LB@5'-UGG...CCCCC CUGGC...UUG-3'@LB@ GUACUUG@LB@ \|:\|\|\|\|:@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -4.49 kcal/mol@LB@Hybridization Energy -7.10274 kcal/mol@LB@Unfolding Energy - mRNA 0.998159 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 261 -- 267@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 34 -- 40@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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