Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
187	0.01114	0.2089	b0801	ybiC	-12.72	0.041489	266 -- 279	27 -- 40	putative dehydrogenase	b0517	_____________265____________280\n_____________\|______________\|\n5'-GCU...CGUCA_______A______AACAA...UUG-3'\n______________GAUGGGU_GCGAGG\n______________\|\|\|\|:\|\|_:\|:\|\|\|\n______________CUACUCA_UGUUCC\n3'-UUU...UAAUA_______A______CGUGU...GUG-5'\n_____________\|______________\|\n_____________41_____________26\n	266 -- 272	34 -- 40	-18.8068 kcal/mol	3.48138 kcal/mol	2.60767 kcal/mol	265 280@LB@ \| \|@LB@5'-GCU...CGUCA A AACAA...UUG-3'@LB@ GAUGGGU GCGAGG@LB@ \|\|\|\|:\|\| :\|:\|\|\|@LB@ CUACUCA UGUUCC@LB@3'-UUU...UAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 41 26@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -18.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.48138 kcal/mol@LB@Unfolding Energy - sRNA 2.60767 kcal/mol@LB@@LB@Position - mRNA 266 -- 279@LB@Position - sRNA 27 -- 40@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 34 -- 40@LB@
83	0.004611	0.1855	b1593	ynfK	-13.15	0.034145	276 -- 295	66 -- 83	putative dethiobiotin synthetase		_____________275__________________296\n_____________\|____________________\|\n5'-CAC...UACAA________CUC_________AACGG-3'\n______________GCGUUAGC___CCAGGGAAA\n______________\|\|\|::\|:\|___\|\|\|\|\|\|\|\|\|\n______________CGCGGUUG___GGUCCCUUU\n3'-UUU...UAUGA________U___________AGAAC...GUG-5'\n_____________\|____________________\|\n_____________84___________________65\n	289 -- 295	66 -- 72	-26.3491 kcal/mol	5.84339 kcal/mol	7.35847 kcal/mol	275 296@LB@ \| \|@LB@5'-CAC...UACAA CUC AACGG-3'@LB@ GCGUUAGC CCAGGGAAA@LB@ \|\|\|::\|:\| \|\|\|\|\|\|\|\|\|@LB@ CGCGGUUG GGUCCCUUU@LB@3'-UUU...UAUGA U AGAAC...GUG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -26.3491 kcal/mol@LB@Unfolding Energy - mRNA 5.84339 kcal/mol@LB@Unfolding Energy - sRNA 7.35847 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 66 -- 72@LB@
50	0.002535	0.1727	b1879	flhA	-12.13	0.054078	218 -- 247	64 -- 89	putative flagellar export pore protein		_____________217______________________________248\n_____________\|________________________________\|\n5'-GCC...GCCGC___________U__CCGCAA___U________GACAC...CGA-3'\n______________GAUGCUGCGCC_GC______ACC___GAAAUC\n______________:\|\|:\|\|\|\|\|\|\|_:\|______\|\|\|___\|\|\|\|\|\|\n______________UUAUGACGCGG_UG______UGG___CUUUAG\n3'-UUU...CGCGC___________U___________UCC______AACCG...GUG-5'\n_____________\|________________________________\|\n_____________90_______________________________63\n	222 -- 228	79 -- 85	-26.8051 kcal/mol	6.79061 kcal/mol	7.88317 kcal/mol	217 248@LB@ \| \|@LB@5'-GCC...GCCGC U CCGCAA U GACAC...CGA-3'@LB@ GAUGCUGCGCC GC ACC GAAAUC@LB@ :\|\|:\|\|\|\|\|\|\| :\| \|\|\| \|\|\|\|\|\|@LB@ UUAUGACGCGG UG UGG CUUUAG@LB@3'-UUU...CGCGC U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -26.8051 kcal/mol@LB@Unfolding Energy - mRNA 6.79061 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 218 -- 247@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 79 -- 85@LB@
108	0.005783	0.1855	b3951	pflD	-15.90	0.009733	233 -- 258	63 -- 86	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________232________________________259\n_____________\|__________________________\|\n5'-GAU...ACUGC_____UU_________C_U_______CGCUG...AAA-3'\n______________ACUGU__GCCAAUACC_G_GAAAUCU\n______________\|\|\|\|:__\|\|\|\|\|:\|\|\|_\|_\|\|\|\|\|\|\|\n______________UGACG__CGGUUGUGG_C_CUUUAGA\n3'-UUU...GCUUA________________U_C_______ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	252 -- 258	63 -- 69	-27.9307 kcal/mol	4.64309 kcal/mol	7.38602 kcal/mol	232 259@LB@ \| \|@LB@5'-GAU...ACUGC UU C U CGCUG...AAA-3'@LB@ ACUGU GCCAAUACC G GAAAUCU@LB@ \|\|\|\|: \|\|\|\|\|:\|\|\| \| \|\|\|\|\|\|\|@LB@ UGACG CGGUUGUGG C CUUUAGA@LB@3'-UUU...GCUUA U C ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -27.9307 kcal/mol@LB@Unfolding Energy - mRNA 4.64309 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 63 -- 69@LB@
57	0.002848	0.1727	b2059	wcaA	-10.75	0.100075	282 -- 295	72 -- 85	putative glycosyl transferase		_____________281____________296\n_____________\|______________\|\n5'-AAC...CGGUU_________G____CAGCA-3'\n______________UUGCGCCAG_ACUA\n______________:\|\|\|\|\|\|\|:_\|\|:\|\n______________GACGCGGUU_UGGU\n3'-UUU...CUUAU_________G____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	284 -- 290	77 -- 83	-19.8604 kcal/mol	1.87274 kcal/mol	7.23443 kcal/mol	281 296@LB@ \| \|@LB@5'-AAC...CGGUU G CAGCA-3'@LB@ UUGCGCCAG ACUA@LB@ :\|\|\|\|\|\|\|: \|\|:\|@LB@ GACGCGGUU UGGU@LB@3'-UUU...CUUAU G CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -19.8604 kcal/mol@LB@Unfolding Energy - mRNA 1.87274 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 77 -- 83@LB@
3	3.071e-06	0.003055	b2100	yegV	-9.35	0.183884	5 -- 14	51 -- 60	putative kinase		_____________4__________15\n_____________\|__________\|\n_______5'-AAUC__________CCUGU...CUU-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	8 -- 14	51 -- 57	-21.1769 kcal/mol	6.95722 kcal/mol	4.87294 kcal/mol	4 15@LB@ \| \|@LB@ 5'-AAUC CCUGU...CUU-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -21.1769 kcal/mol@LB@Unfolding Energy - mRNA 6.95722 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 51 -- 57@LB@
156	0.009123	0.2059	b2683	ygaH	-13.79	0.025463	164 -- 213	27 -- 86	putative L-valine exporter norvaline resistance protein		_____________163______________________________________________________________214\n_____________\|________________________________________________________________\|\n5'-AUU...GCCUC_________________CAU________AAGGA_____C_________________C_______UUCUG...CAA-3'\n______________ACUGCGUUAAU_CCAGG____UC_UGGC_____GCGCC____________GAUGAG_UAUGAGG\n______________\|\|\|\|\|\|::\|\|:_\|\|\|\|\|____\|\|_\|\|\|\|_____\|\|\|\|\|____________\|\|\|\|\|\|_\|\|::\|\|\|\n______________UGACGCGGUUG_GGUCC____AG_ACCG_____CGCGG____________CUACUC_AUGUUCC\n3'-UUU...GCUUA___________U_____CUUU__A____A_________CAUUUAAUAAUA______A_______CGUGU...GUG-5'\n_____________\|________________________________________________________________\|\n_____________87_______________________________________________________________26\n	207 -- 213	27 -- 33	-50.2075 kcal/mol	19.3484 kcal/mol	17.0667 kcal/mol	163 214@LB@ \| \|@LB@5'-AUU...GCCUC CAU AAGGA C C UUCUG...CAA-3'@LB@ ACUGCGUUAAU CCAGG UC UGGC GCGCC GAUGAG UAUGAGG@LB@ \|\|\|\|\|\|::\|\|: \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\| \|\|::\|\|\|@LB@ UGACGCGGUUG GGUCC AG ACCG CGCGG CUACUC AUGUUCC@LB@3'-UUU...GCUUA U CUUU A A CAUUUAAUAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 87 26@LB@@LB@@LB@Energy -13.79 kcal/mol@LB@Hybridization Energy -50.2075 kcal/mol@LB@Unfolding Energy - mRNA 19.3484 kcal/mol@LB@Unfolding Energy - sRNA 17.0667 kcal/mol@LB@@LB@Position - mRNA 164 -- 213@LB@Position - sRNA 27 -- 86@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 27 -- 33@LB@
178	0.01053	0.208	b3582	sgbU	-5.91	0.640260	169 -- 196	65 -- 84	putative L-xylulose 5-phosphate 3-epimerase		_____________168__________________________197\n_____________\|____________________________\|\n5'-UCU...UUCCA_____AAAU_______AUCU________GCGCG...UUG-3'\n______________UGCGC____CGACGCU____GGGGAGGU\n______________\|\|\|\|\|____\|:\|\|:\|:____:\|\|\|\|::\|\n______________ACGCG____GUUGUGG____UCCCUUUA\n3'-UUU...UUAUG____________________________GAACC...GUG-5'\n_____________\|____________________________\|\n_____________85___________________________64\n	190 -- 196	65 -- 71	-23.9168 kcal/mol	10.6467 kcal/mol	7.36194 kcal/mol	168 197@LB@ \| \|@LB@5'-UCU...UUCCA AAAU AUCU GCGCG...UUG-3'@LB@ UGCGC CGACGCU GGGGAGGU@LB@ \|\|\|\|\| \|:\|\|:\|: :\|\|\|\|::\|@LB@ ACGCG GUUGUGG UCCCUUUA@LB@3'-UUU...UUAUG GAACC...GUG-5'@LB@ \| \|@LB@ 85 64@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -23.9168 kcal/mol@LB@Unfolding Energy - mRNA 10.6467 kcal/mol@LB@Unfolding Energy - sRNA 7.36194 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 65 -- 84@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 65 -- 71@LB@
164	0.009677	0.2068	b1956	yedQ	-11.74	0.064514	187 -- 209	18 -- 41	putative membrane-anchored diguanylate cyclase		_____________186______________________210\n_____________\|________________________\|\n5'-GAG...CAGGU________CGUC____________GAGAC...UAU-3'\n______________UGG_GAGU____AGGGUGCAGCAC\n______________\|\|:_\|\|\|\|____\|\|\|\|::\|\|\|\|\|\|\n______________ACU_CUCA____UCCCGUGUCGUG\n3'-UUU...AUAAU___A____AUGU____________ACAAA...GUG-5'\n_____________\|________________________\|\n_____________42_______________________17\n	203 -- 209	18 -- 24	-27.1151 kcal/mol	6.50018 kcal/mol	8.87585 kcal/mol	186 210@LB@ \| \|@LB@5'-GAG...CAGGU CGUC GAGAC...UAU-3'@LB@ UGG GAGU AGGGUGCAGCAC@LB@ \|\|: \|\|\|\| \|\|\|\|::\|\|\|\|\|\|@LB@ ACU CUCA UCCCGUGUCGUG@LB@3'-UUU...AUAAU A AUGU ACAAA...GUG-5'@LB@ \| \|@LB@ 42 17@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -27.1151 kcal/mol@LB@Unfolding Energy - mRNA 6.50018 kcal/mol@LB@Unfolding Energy - sRNA 8.87585 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 18 -- 41@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 18 -- 24@LB@
149	0.008735	0.2059	b3088	alx	-8.37	0.274530	278 -- 288	25 -- 35	putative membrane-bound redox modulator		_____________277_________289\n_____________\|___________\|\n5'-GGG...CUGUU___________GUCGU...CAC-3'\n______________GUUGCAGGGGC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CAAUGUUCCCG\n3'-UUU...CUACU___________UGUCG...GUG-5'\n_____________\|___________\|\n_____________36__________24\n	282 -- 288	25 -- 31	-18.295 kcal/mol	6.20791 kcal/mol	3.71635 kcal/mol	277 289@LB@ \| \|@LB@5'-GGG...CUGUU GUCGU...CAC-3'@LB@ GUUGCAGGGGC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CAAUGUUCCCG@LB@3'-UUU...CUACU UGUCG...GUG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -18.295 kcal/mol@LB@Unfolding Energy - mRNA 6.20791 kcal/mol@LB@Unfolding Energy - sRNA 3.71635 kcal/mol@LB@@LB@Position - mRNA 278 -- 288@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 282 -- 288@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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