Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
132	0.005751	0.146	b2294	yfbU	-8.39	0.309344	3 -- 25	24 -- 50	UPF0304 family protein	_____________2______________________________26\n_____________\|______________________________\|\n_________5'-GC____________________GGU_______CCCGU...AAA-3'\n______________AGGAG______UCUGG_ACA___GUUGGCA\n______________\|\|\|\|\|______:\|\|\|\|_\|\|\|___\|:\|:\|\|\|\n______________UCCUC______GGACC_UGU___CGAUCGU\n3'-UUU...CCGAU_____CACCAA_____A_____________AAAAU...UCG-5'\n_____________\|______________________________\|\n_____________51_____________________________23\n	19 -- 25	24 -- 30	-20.5947 kcal/mol	7.58762 kcal/mol	4.6134 kcal/mol	2 26@LB@ \| \|@LB@ 5'-GC GGU CCCGU...AAA-3'@LB@ AGGAG UCUGG ACA GUUGGCA@LB@ \|\|\|\|\| :\|\|\|\| \|\|\| \|:\|:\|\|\|@LB@ UCCUC GGACC UGU CGAUCGU@LB@3'-UUU...CCGAU CACCAA A AAAAU...UCG-5'@LB@ \| \|@LB@ 51 23@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -20.5947 kcal/mol@LB@Unfolding Energy - mRNA 7.58762 kcal/mol@LB@Unfolding Energy - sRNA 4.6134 kcal/mol@LB@@LB@Position - mRNA 3 -- 25@LB@Position - sRNA 24 -- 50@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 24 -- 30@LB@
133	0.005817	0.146	b3461	rpoH	-7.67	0.391921	235 -- 243	24 -- 32	RNA polymerase sigma 32 (sigma H) factor	_____________234_______244\n_____________\|_________\|\n5'-GGA...AGCCC_________ACCUG...AGG-3'\n______________CAGUUGGCA\n______________\|\|\|:\|:\|\|\|\n______________GUCGAUCGU\n3'-UUU...ACCAU_________AAAAU...UCG-5'\n_____________\|_________\|\n_____________33________23\n	237 -- 243	24 -- 30	-13.04 kcal/mol	3.94405 kcal/mol	1.424 kcal/mol	234 244@LB@ \| \|@LB@5'-GGA...AGCCC ACCUG...AGG-3'@LB@ CAGUUGGCA@LB@ \|\|\|:\|:\|\|\|@LB@ GUCGAUCGU@LB@3'-UUU...ACCAU AAAAU...UCG-5'@LB@ \| \|@LB@ 33 23@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 3.94405 kcal/mol@LB@Unfolding Energy - sRNA 1.424 kcal/mol@LB@@LB@Position - mRNA 235 -- 243@LB@Position - sRNA 24 -- 32@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 24 -- 30@LB@
134	0.005847	0.146	b0065	yabI	-9.48	0.206647	266 -- 290	24 -- 46	DedA family inner membrane protein	_____________265_______________________291\n_____________\|_________________________\|\n5'-UGA...GUGUU_____CC_______AGUC_______CUGGU...GUU-3'\n______________GGUGG__UUUCUGG____GCUGGCG\n______________\|\|\|\|\|__\|\|:\|\|\|\|____\|\|\|:\|\|:\n______________CCACC__AAGGACC____CGAUCGU\n3'-UUU...UUCCU______________AUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	284 -- 290	24 -- 30	-26.6068 kcal/mol	12.5692 kcal/mol	4.55813 kcal/mol	265 291@LB@ \| \|@LB@5'-UGA...GUGUU CC AGUC CUGGU...GUU-3'@LB@ GGUGG UUUCUGG GCUGGCG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|\|:\|\|:@LB@ CCACC AAGGACC CGAUCGU@LB@3'-UUU...UUCCU AUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -26.6068 kcal/mol@LB@Unfolding Energy - mRNA 12.5692 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
141	0.006623	0.1579	b1992	cobS	-16.13	0.004945	167 -- 192	24 -- 49	cobalamin synthase	_____________166_________________________193\n_____________\|___________________________\|\n5'-GAG...AGUAU__CU_________G_____UGG_____AAAAU...GUA-3'\n______________GG__GGUGGUUUC_GGUAU____AGUA\n______________\|\|__\|\|\|\|\|\|\|:\|_\|\|\|\|:____\|\|:\|\n______________CC__CCACCAAGG_CCAUG____UCGU\n3'-UUU...CGAUU__U__________A_____UCGA____AAAAU...UCG-5'\n_____________\|___________________________\|\n_____________50__________________________23\n	173 -- 179	38 -- 44	-26.3933 kcal/mol	5.70356 kcal/mol	4.5591 kcal/mol	166 193@LB@ \| \|@LB@5'-GAG...AGUAU CU G UGG AAAAU...GUA-3'@LB@ GG GGUGGUUUC GGUAU AGUA@LB@ \|\| \|\|\|\|\|\|\|:\| \|\|\|\|: \|\|:\|@LB@ CC CCACCAAGG CCAUG UCGU@LB@3'-UUU...CGAUU U A UCGA AAAAU...UCG-5'@LB@ \| \|@LB@ 50 23@LB@@LB@@LB@Energy -16.13 kcal/mol@LB@Hybridization Energy -26.3933 kcal/mol@LB@Unfolding Energy - mRNA 5.70356 kcal/mol@LB@Unfolding Energy - sRNA 4.5591 kcal/mol@LB@@LB@Position - mRNA 167 -- 192@LB@Position - sRNA 24 -- 49@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 38 -- 44@LB@
152	0.007594	0.1679	b3992	thiF	-12.60	0.047865	3 -- 22	24 -- 47	adenylyltransferase modifies ThiS C-terminus	_____________2________________________23\n_____________\|________________________\|\n_________5'-GC_____________A__________CGGCA...UUA-3'\n______________AGG_GG___CUGG_ACAGCUGGCA\n______________\|\|\|_\|\|___\|\|\|\|_\|\|\|\|\|\|:\|\|\|\n______________UCC_CC___GACC_UGUCGAUCGU\n3'-UUU...AUUCC___A__AAG____A__________AAAAU...UCG-5'\n_____________\|________________________\|\n_____________48_______________________23\n	16 -- 22	24 -- 30	-27.3128 kcal/mol	10.1529 kcal/mol	4.55893 kcal/mol	2 23@LB@ \| \|@LB@ 5'-GC A CGGCA...UUA-3'@LB@ AGG GG CUGG ACAGCUGGCA@LB@ \|\|\| \|\| \|\|\|\| \|\|\|\|\|\|:\|\|\|@LB@ UCC CC GACC UGUCGAUCGU@LB@3'-UUU...AUUCC A AAG A AAAAU...UCG-5'@LB@ \| \|@LB@ 48 23@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -27.3128 kcal/mol@LB@Unfolding Energy - mRNA 10.1529 kcal/mol@LB@Unfolding Energy - sRNA 4.55893 kcal/mol@LB@@LB@Position - mRNA 3 -- 22@LB@Position - sRNA 24 -- 47@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 24 -- 30@LB@
166	0.008687	0.1759	b3210	arcB	-6.83	0.499810	260 -- 284	24 -- 46	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________259_______________________285\n_____________\|_________________________\|\n5'-UGC...GGUCU____C_C____CAAUGUU_______CUGGC...UUC-3'\n______________GGUG_G_UUCU_______GCUGGCG\n______________\|\|\|\|_\|_\|\|\|:_______\|\|\|:\|\|:\n______________CCAC_C_AAGG_______CGAUCGU\n3'-UUU...UUCCU___________ACCAUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	278 -- 284	24 -- 30	-17.917 kcal/mol	6.53164 kcal/mol	4.55813 kcal/mol	259 285@LB@ \| \|@LB@5'-UGC...GGUCU C C CAAUGUU CUGGC...UUC-3'@LB@ GGUG G UUCU GCUGGCG@LB@ \|\|\|\| \| \|\|\|: \|\|\|:\|\|:@LB@ CCAC C AAGG CGAUCGU@LB@3'-UUU...UUCCU ACCAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -17.917 kcal/mol@LB@Unfolding Energy - mRNA 6.53164 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 260 -- 284@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 24 -- 30@LB@
198	0.01161	0.1971	b2712	hypF	-10.23	0.151482	281 -- 290	24 -- 33	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein	_____________280________291\n_____________\|__________\|\n5'-GAA...GUCUG__________CAGCA...UAA-3'\n______________GCAGCUGGCA\n______________:\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	284 -- 290	24 -- 30	-16.4359 kcal/mol	4.77953 kcal/mol	1.42716 kcal/mol	280 291@LB@ \| \|@LB@5'-GAA...GUCUG CAGCA...UAA-3'@LB@ GCAGCUGGCA@LB@ :\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -16.4359 kcal/mol@LB@Unfolding Energy - mRNA 4.77953 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 281 -- 290@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
21	0.0001799	0.02879	b0107	hofB	-20.93	0.000028	267 -- 289	25 -- 48	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________266______________________290\n_____________\|________________________\|\n5'-CCA...GCGAA__________A__U__________CGAUG...CUU-3'\n______________GAGGUGGUUC_UG_UGCGG_UAGU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|_\|:\|:\|_\|\|\|:\n______________CUCCACCAAG_AC_AUGUC_AUCG\n3'-UUU...GAUUC__________G__C_____G____UAAAA...UCG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	270 -- 276	39 -- 45	-28.7026 kcal/mol	3.21789 kcal/mol	4.55759 kcal/mol	266 290@LB@ \| \|@LB@5'-CCA...GCGAA A U CGAUG...CUU-3'@LB@ GAGGUGGUUC UG UGCGG UAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|:\|:\| \|\|\|:@LB@ CUCCACCAAG AC AUGUC AUCG@LB@3'-UUU...GAUUC G C G UAAAA...UCG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -20.93 kcal/mol@LB@Hybridization Energy -28.7026 kcal/mol@LB@Unfolding Energy - mRNA 3.21789 kcal/mol@LB@Unfolding Energy - sRNA 4.55759 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 39 -- 45@LB@
34	0.0006341	0.06268	b3312	rpmC	-15.21	0.009642	105 -- 128	25 -- 49	50S ribosomal subunit protein L29	_____________104________________________129\n_____________\|__________________________\|\n5'-AAA...GAAAU___C____________A_G_______CCGUG...CAA-3'\n______________GGA_GGU_GUUCC_GG_A_AGCUGGC\n______________\|\|\|_\|\|\|_\|\|\|\|\|_\|\|_\|_\|\|\|\|:\|\|\n______________CCU_CCA_CAAGG_CC_U_UCGAUCG\n3'-UUU...CGAUU_______C_____A__A_G_______UAAAA...UCG-5'\n_____________\|__________________________\|\n_____________50_________________________24\n	122 -- 128	25 -- 31	-29.6215 kcal/mol	9.85059 kcal/mol	4.5577 kcal/mol	104 129@LB@ \| \|@LB@5'-AAA...GAAAU C A G CCGUG...CAA-3'@LB@ GGA GGU GUUCC GG A AGCUGGC@LB@ \|\|\| \|\|\| \|\|\|\|\| \|\| \| \|\|\|\|:\|\|@LB@ CCU CCA CAAGG CC U UCGAUCG@LB@3'-UUU...CGAUU C A A G UAAAA...UCG-5'@LB@ \| \|@LB@ 50 24@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -29.6215 kcal/mol@LB@Unfolding Energy - mRNA 9.85059 kcal/mol@LB@Unfolding Energy - sRNA 4.5577 kcal/mol@LB@@LB@Position - mRNA 105 -- 128@LB@Position - sRNA 25 -- 49@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 25 -- 31@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease	_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@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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