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
121	0.006643	0.1913	b1813	nudL	-11.92	0.059353	114 -- 132	70 -- 86	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________113_________________133\n_____________\|___________________\|\n5'-CCU...GUGGA____U________G_____AAGAA...CUG-3'\n______________AUUG_CGCCGAUA_CCAGG\n______________\|:\|\|_\|\|\|\|:\|:\|_\|\|\|\|\|\n______________UGAC_GCGGUUGU_GGUCC\n3'-UUU...GCUUA___________________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	120 -- 126	75 -- 81	-24.7024 kcal/mol	5.50013 kcal/mol	7.27772 kcal/mol	113 133@LB@ \| \|@LB@5'-CCU...GUGGA U G AAGAA...CUG-3'@LB@ AUUG CGCCGAUA CCAGG@LB@ \|:\|\| \|\|\|\|:\|:\| \|\|\|\|\|@LB@ UGAC GCGGUUGU GGUCC@LB@3'-UUU...GCUUA CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -24.7024 kcal/mol@LB@Unfolding Energy - mRNA 5.50013 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 114 -- 132@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 75 -- 81@LB@
112	0.005982	0.1855	b1820	yobD	-7.30	0.411799	229 -- 243	1 -- 14	UPF0266 family inner membrane protein	_____________228_____________244\n_____________\|_______________\|\n5'-ACC...GAUUC______UC_______UCCUG...CCC-3'\n______________UUUUCA__GCCGCAC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________AAAAGU__CGGCGUG\n3'-UUU...UGACA______C________-5'\n_____________\|______________\|\n_____________15_____________1\n	237 -- 243	1 -- 7	-17.9899 kcal/mol	4.95197 kcal/mol	5.72803 kcal/mol	228 244@LB@ \| \|@LB@5'-ACC...GAUUC UC UCCUG...CCC-3'@LB@ UUUUCA GCCGCAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAAAGU CGGCGUG@LB@3'-UUU...UGACA C -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -17.9899 kcal/mol@LB@Unfolding Energy - mRNA 4.95197 kcal/mol@LB@Unfolding Energy - sRNA 5.72803 kcal/mol@LB@@LB@Position - mRNA 229 -- 243@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@LB@
175	0.01031	0.2074	b1834	yebT	-10.32	0.121003	270 -- 282	51 -- 62	MCE domain protein	_____________269___________283\n_____________\|_____________\|\n5'-UCU...CUUUC_______U_____UCAUC...UUG-3'\n______________UGGCUGC_GCCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\n______________ACCGACG_CGGCA\n3'-UUU...UUAGA_____________UUUAA...GUG-5'\n_____________\|_____________\|\n_____________63____________50\n	270 -- 276	56 -- 62	-21.4836 kcal/mol	6.28034 kcal/mol	4.8826 kcal/mol	269 283@LB@ \| \|@LB@5'-UCU...CUUUC U UCAUC...UUG-3'@LB@ UGGCUGC GCCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|@LB@ ACCGACG CGGCA@LB@3'-UUU...UUAGA UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -21.4836 kcal/mol@LB@Unfolding Energy - mRNA 6.28034 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 56 -- 62@LB@
35	0.001921	0.1727	b1849	purT	-12.35	0.048961	166 -- 192	67 -- 88	phosphoribosylglycinamide formyltransferase 2	_____________165_________________________193\n_____________\|___________________________\|\n5'-UUU...CGUUU_________G__GAAUUA_________UAUUC...GUC-3'\n______________AUACUGCGC_CG______AUCAGGGGA\n______________\|\|\|\|\|\|\|\|\|_\|:______\|:\|\|\|\|\|:\|\n______________UAUGACGCG_GU______UGGUCCCUU\n3'-UUU...GCGCU____________UG_____________UAGAA...GUG-5'\n_____________\|___________________________\|\n_____________89__________________________66\n	186 -- 192	67 -- 73	-25.9621 kcal/mol	6.22738 kcal/mol	7.38319 kcal/mol	165 193@LB@ \| \|@LB@5'-UUU...CGUUU G GAAUUA UAUUC...GUC-3'@LB@ AUACUGCGC CG AUCAGGGGA@LB@ \|\|\|\|\|\|\|\|\| \|: \|:\|\|\|\|\|:\|@LB@ UAUGACGCG GU UGGUCCCUU@LB@3'-UUU...GCGCU UG UAGAA...GUG-5'@LB@ \| \|@LB@ 89 66@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -25.9621 kcal/mol@LB@Unfolding Energy - mRNA 6.22738 kcal/mol@LB@Unfolding Energy - sRNA 7.38319 kcal/mol@LB@@LB@Position - mRNA 166 -- 192@LB@Position - sRNA 67 -- 88@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 67 -- 73@LB@
44	0.002208	0.1727	b1859	znuB	-7.63	0.365449	19 -- 38	72 -- 88	zinc ABC transporter permease	_____________18___________________39\n_____________\|____________________\|\n5'-AUG...AUGAA__________UGAAU_____CAUUU...AUU-3'\n______________GUGCUGUGCC_____CACCA\n______________:\|:\|\|\|:\|\|\|_____\|\|\|\|\|\n______________UAUGACGCGG_____GUGGU\n3'-UUU...GCGCU__________UU________CCCUU...GUG-5'\n_____________\|____________________\|\n_____________89___________________71\n	22 -- 28	79 -- 85	-22.3137 kcal/mol	7.44481 kcal/mol	7.24148 kcal/mol	18 39@LB@ \| \|@LB@5'-AUG...AUGAA UGAAU CAUUU...AUU-3'@LB@ GUGCUGUGCC CACCA@LB@ :\|:\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAUGACGCGG GUGGU@LB@3'-UUU...GCGCU UU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -22.3137 kcal/mol@LB@Unfolding Energy - mRNA 7.44481 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 19 -- 38@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 79 -- 85@LB@
7	0.0001601	0.08054	b1864	yebC	-15.40	0.012230	213 -- 249	54 -- 89	UPF0082 family protein	_____________212_____________________________________250\n_____________\|_______________________________________\|\n5'-CGU...GUCAU____AA__G___________AC_____GUAAA_______AGGAU...UAA-3'\n______________AGUA__UG_GCCAACACCAG____AUC_____GCUGCGC\n______________\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|\|\|____\|\|\|_____\|\|\|\|\|\|\|\n______________UUAU__AC_CGGUUGUGGUC____UAG_____CGACGCG\n3'-UUU...CGCGC____G___G___________CCUU___AAC_________GCAUU...GUG-5'\n_____________\|_______________________________________\|\n_____________90______________________________________53\n	243 -- 249	54 -- 60	-38.8431 kcal/mol	7.10336 kcal/mol	16.3388 kcal/mol	212 250@LB@ \| \|@LB@5'-CGU...GUCAU AA G AC GUAAA AGGAU...UAA-3'@LB@ AGUA UG GCCAACACCAG AUC GCUGCGC@LB@ \|:\|\| \|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UUAU AC CGGUUGUGGUC UAG CGACGCG@LB@3'-UUU...CGCGC G G CCUU AAC GCAUU...GUG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -38.8431 kcal/mol@LB@Unfolding Energy - mRNA 7.10336 kcal/mol@LB@Unfolding Energy - sRNA 16.3388 kcal/mol@LB@@LB@Position - mRNA 213 -- 249@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@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@
31	0.001682	0.1727	b1887	cheW	-12.93	0.037697	13 -- 28	70 -- 86	purine-binding chemotaxis protein	_____________12________________29\n_____________\|_________________\|\n5'-GUG...AAUUA_________________UUGUG...UCC-3'\n______________AUUG_GUCAACACCAGG\n______________\|:\|\|_\|:\|\|\|\|\|\|\|\|\|\|\n______________UGAC_CGGUUGUGGUCC\n3'-UUU...GCUUA____G____________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	22 -- 28	70 -- 76	-24.746 kcal/mol	4.53921 kcal/mol	7.27772 kcal/mol	12 29@LB@ \| \|@LB@5'-GUG...AAUUA UUGUG...UCC-3'@LB@ AUUG GUCAACACCAGG@LB@ \|:\|\| \|:\|\|\|\|\|\|\|\|\|\|@LB@ UGAC CGGUUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -24.746 kcal/mol@LB@Unfolding Energy - mRNA 4.53921 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 13 -- 28@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 70 -- 76@LB@
70	0.003478	0.1727	b1919	dcyD	-7.16	0.432573	249 -- 279	53 -- 83	D-cysteine desulfhydrase PLP-dependent	_____________248_______________________________280\n_____________\|_________________________________\|\n5'-CUG...UCGGC____________CUC___U________C_____UUUCU...GGG-3'\n______________GCGCCAACGCCG___GAA_AUCU__GC_GCGCU\n______________\|\|\|\|\|\|\|\|:\|\|:___\|\|\|_\|\|\|\|__\|\|_\|\|\|\|:\n______________CGCGGUUGUGGU___CUU_UAGA__CG_CGCGG\n3'-UUU...UAUGA____________CC_________AC__A_____CAUUU...GUG-5'\n_____________\|_________________________________\|\n_____________84________________________________52\n	252 -- 258	74 -- 80	-36.5845 kcal/mol	12.956 kcal/mol	16.4685 kcal/mol	248 280@LB@ \| \|@LB@5'-CUG...UCGGC CUC U C UUUCU...GGG-3'@LB@ GCGCCAACGCCG GAA AUCU GC GCGCU@LB@ \|\|\|\|\|\|\|\|:\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|:@LB@ CGCGGUUGUGGU CUU UAGA CG CGCGG@LB@3'-UUU...UAUGA CC AC A CAUUU...GUG-5'@LB@ \| \|@LB@ 84 52@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -36.5845 kcal/mol@LB@Unfolding Energy - mRNA 12.956 kcal/mol@LB@Unfolding Energy - sRNA 16.4685 kcal/mol@LB@@LB@Position - mRNA 249 -- 279@LB@Position - sRNA 53 -- 83@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 74 -- 80@LB@
132	0.007501	0.1993	b1947	fliO	-6.89	0.474041	212 -- 250	53 -- 93	flagellar biosynthesis protein	_____________211_____________________________________________251\n_____________\|_______________________________________________\|\n5'-AUG...AACCA______________AAUCUUCC_______UU________________ACUGC...UCG-3'\n______________CGC___UACUGUGC________GCGCCGG_____UCU__GCUGCGCC\n______________\|\|\|___\|\|\|\|\|:\|\|________:\|:\|\|:\|_____\|\|\|__\|\|\|\|\|\|\|\|\n______________GCG___AUGACGCG________UGUGGUC_____AGA__CGACGCGG\n3'-UUU...CCCAC___CUU________GU_____________CCUUU___AC________CAUUU...GUG-5'\n_____________\|_______________________________________________\|\n_____________94______________________________________________52\n	244 -- 250	53 -- 59	-40.0502 kcal/mol	16.0889 kcal/mol	17.0683 kcal/mol	211 251@LB@ \| \|@LB@5'-AUG...AACCA AAUCUUCC UU ACUGC...UCG-3'@LB@ CGC UACUGUGC GCGCCGG UCU GCUGCGCC@LB@ \|\|\| \|\|\|\|\|:\|\| :\|:\|\|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GCG AUGACGCG UGUGGUC AGA CGACGCGG@LB@3'-UUU...CCCAC CUU GU CCUUU AC CAUUU...GUG-5'@LB@ \| \|@LB@ 94 52@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -40.0502 kcal/mol@LB@Unfolding Energy - mRNA 16.0889 kcal/mol@LB@Unfolding Energy - sRNA 17.0683 kcal/mol@LB@@LB@Position - mRNA 212 -- 250@LB@Position - sRNA 53 -- 93@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 53 -- 59@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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