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
131	0.007315	0.1966	b3824	rhtB	-9.48	0.174149	77 -- 100	63 -- 87	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________76________________________101\n_____________\|_________________________\|\n5'-ACG...CUUUU______UGA_________U______GCCUC...ACC-3'\n______________UGCUGC___AACAUCGGG__AAUCU\n______________\|:\|\|\|\|___\|\|\|\|:\|:\|\|__\|\|\|\|\|\n______________AUGACG___UUGUGGUCC__UUAGA\n3'-UUU...CGCUU______CGG_________CU_____ACCGA...GUG-5'\n_____________\|_________________________\|\n_____________88________________________62\n	88 -- 94	70 -- 76	-24.9255 kcal/mol	8.06413 kcal/mol	7.38606 kcal/mol	76 101@LB@ \| \|@LB@5'-ACG...CUUUU UGA U GCCUC...ACC-3'@LB@ UGCUGC AACAUCGGG AAUCU@LB@ \|:\|\|\|\| \|\|\|\|:\|:\|\| \|\|\|\|\|@LB@ AUGACG UUGUGGUCC UUAGA@LB@3'-UUU...CGCUU CGG CU ACCGA...GUG-5'@LB@ \| \|@LB@ 88 62@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.9255 kcal/mol@LB@Unfolding Energy - mRNA 8.06413 kcal/mol@LB@Unfolding Energy - sRNA 7.38606 kcal/mol@LB@@LB@Position - mRNA 77 -- 100@LB@Position - sRNA 63 -- 87@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 70 -- 76@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@
133	0.007533	0.1993	b2194	ccmH	-11.64	0.067570	191 -- 199	1 -- 9	heme lyase CcmH subunit	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAAGG_________AAUGA...AGU-3'\n______________AGGCCGCAC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	193 -- 199	1 -- 7	-19.8862 kcal/mol	2.96679 kcal/mol	5.10726 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAAGG AAUGA...AGU-3'@LB@ AGGCCGCAC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -19.8862 kcal/mol@LB@Unfolding Energy - mRNA 2.96679 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 1 -- 7@LB@
134	0.007678	0.1993	b3139	agaC	-7.83	0.338422	255 -- 275	57 -- 74	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________254___________________276\n_____________\|_____________________\|\n5'-AAC...UUGUU_______UUGAU_________GAAGC...CGA-3'\n______________CUGGGGA_____UUUUGGCUG\n______________\|::\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________GGUCCCU_____AGAACCGAC\n3'-UUU...GUUGU_______UU____________GCGGC...GUG-5'\n_____________\|_____________________\|\n_____________75____________________56\n	269 -- 275	57 -- 63	-21.9136 kcal/mol	6.09668 kcal/mol	7.9843 kcal/mol	254 276@LB@ \| \|@LB@5'-AAC...UUGUU UUGAU GAAGC...CGA-3'@LB@ CUGGGGA UUUUGGCUG@LB@ \|::\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GGUCCCU AGAACCGAC@LB@3'-UUU...GUUGU UU GCGGC...GUG-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -21.9136 kcal/mol@LB@Unfolding Energy - mRNA 6.09668 kcal/mol@LB@Unfolding Energy - sRNA 7.9843 kcal/mol@LB@@LB@Position - mRNA 255 -- 275@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 57 -- 63@LB@
135	0.007679	0.1993	b0096	lpxC	-11.14	0.084212	289 -- 298	76 -- 85	UDP-3-O-acyl N-acetylglucosamine deacetylase	_____________288________299\n_____________\|__________\|\n5'-GAA...ACGCC__________CA-3'\n______________CUGCGCCGGC\n______________\|\|\|\|\|\|\|::\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	292 -- 298	76 -- 82	-18.1767 kcal/mol	1.93848 kcal/mol	5.09564 kcal/mol	288 299@LB@ \| \|@LB@5'-GAA...ACGCC CA-3'@LB@ CUGCGCCGGC@LB@ \|\|\|\|\|\|\|::\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -18.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.93848 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 76 -- 82@LB@
136	0.007706	0.1993	b2188	yejM	-8.60	0.250530	107 -- 119	70 -- 83	essential inner membrane DUF3413 domain-containing protein; lipid A production and membrane permeability factor	_____________106____________120\n_____________\|______________\|\n5'-CGC...CCCCG______________CAAUU...UUG-3'\n______________GC_CCAACGCCAGG\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\n______________CG_GGUUGUGGUCC\n3'-UUU...UAUGA__C___________CUUUA...GUG-5'\n_____________\|______________\|\n_____________84_____________69\n	113 -- 119	70 -- 76	-22.9581 kcal/mol	7.21499 kcal/mol	7.14463 kcal/mol	106 120@LB@ \| \|@LB@5'-CGC...CCCCG CAAUU...UUG-3'@LB@ GC CCAACGCCAGG@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|@LB@ CG GGUUGUGGUCC@LB@3'-UUU...UAUGA C CUUUA...GUG-5'@LB@ \| \|@LB@ 84 69@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.9581 kcal/mol@LB@Unfolding Energy - mRNA 7.21499 kcal/mol@LB@Unfolding Energy - sRNA 7.14463 kcal/mol@LB@@LB@Position - mRNA 107 -- 119@LB@Position - sRNA 70 -- 83@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 70 -- 76@LB@
137	0.007754	0.1993	b4024	lysC	-8.53	0.257132	131 -- 141	73 -- 85	lysine-sensitive aspartokinase 3	_____________130___________142\n_____________\|_____________\|\n5'-UGA...UCGCU_____________CGUCU...UGC-3'\n______________CUGCGCC__CACC\n______________\|\|\|\|\|\|\|__\|\|\|\|\n______________GACGCGG__GUGG\n3'-UUU...CUUAU_______UU____UCCCU...GUG-5'\n_____________\|_____________\|\n_____________86____________72\n	131 -- 137	79 -- 85	-18.3373 kcal/mol	2.85158 kcal/mol	6.95176 kcal/mol	130 142@LB@ \| \|@LB@5'-UGA...UCGCU CGUCU...UGC-3'@LB@ CUGCGCC CACC@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ GACGCGG GUGG@LB@3'-UUU...CUUAU UU UCCCU...GUG-5'@LB@ \| \|@LB@ 86 72@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.3373 kcal/mol@LB@Unfolding Energy - mRNA 2.85158 kcal/mol@LB@Unfolding Energy - sRNA 6.95176 kcal/mol@LB@@LB@Position - mRNA 131 -- 141@LB@Position - sRNA 73 -- 85@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 79 -- 85@LB@
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit	_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
139	0.008022	0.2031	b0311	betA	-9.91	0.144745	36 -- 54	64 -- 80	choline dehydrogenase a flavoprotein	_____________35__________________55\n_____________\|___________________\|\n5'-CGU...CUGGA________U____C_____CCCGG...AAG-3'\n______________UCAACACC_GGGG_GAAUC\n______________:\|\|\|\|\|\|\|_:\|\|\|_:\|\|\|\|\n______________GGUUGUGG_UCCC_UUUAG\n3'-UUU...GACGC___________________AACCG...GUG-5'\n_____________\|___________________\|\n_____________81__________________63\n	37 -- 43	73 -- 79	-20.9821 kcal/mol	4.03056 kcal/mol	7.04361 kcal/mol	35 55@LB@ \| \|@LB@5'-CGU...CUGGA U C CCCGG...AAG-3'@LB@ UCAACACC GGGG GAAUC@LB@ :\|\|\|\|\|\|\| :\|\|\| :\|\|\|\|@LB@ GGUUGUGG UCCC UUUAG@LB@3'-UUU...GACGC AACCG...GUG-5'@LB@ \| \|@LB@ 81 63@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -20.9821 kcal/mol@LB@Unfolding Energy - mRNA 4.03056 kcal/mol@LB@Unfolding Energy - sRNA 7.04361 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 64 -- 80@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 73 -- 79@LB@
140	0.008117	0.2031	b3221	yhcH	-13.19	0.033484	158 -- 212	34 -- 73	DUF386 family protein cupin superfamily	_____________157_____________________________________________________213\n_____________\|_______________________________________________________\|\n5'-AUC...UGAUG____UUUAC__GG___________UGGCCCAGGGAGAA_______G_________GAAGU...AAG-3'\n______________CAGG_____UU__GGCUGCGCUGU______________AAAUUAU_AUGAUGGGU\n______________\|\|\|\|_____\|:__\|\|\|\|\|\|\|\|:\|\|______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:\|\|\n______________GUCC_____AG__CCGACGCGGCA______________UUUAAUA_UACUACUCA\n3'-UUU...UUGUG____CUUU___AA________________________________A_________AUGUU...GUG-5'\n_____________\|_______________________________________________________\|\n_____________74______________________________________________________33\n	206 -- 212	34 -- 40	-41.3429 kcal/mol	18.8865 kcal/mol	9.26614 kcal/mol	157 213@LB@ \| \|@LB@5'-AUC...UGAUG UUUAC GG UGGCCCAGGGAGAA G GAAGU...AAG-3'@LB@ CAGG UU GGCUGCGCUGU AAAUUAU AUGAUGGGU@LB@ \|\|\|\| \|: \|\|\|\|\|\|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ GUCC AG CCGACGCGGCA UUUAAUA UACUACUCA@LB@3'-UUU...UUGUG CUUU AA A AUGUU...GUG-5'@LB@ \| \|@LB@ 74 33@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -41.3429 kcal/mol@LB@Unfolding Energy - mRNA 18.8865 kcal/mol@LB@Unfolding Energy - sRNA 9.26614 kcal/mol@LB@@LB@Position - mRNA 158 -- 212@LB@Position - sRNA 34 -- 73@LB@Position Seed - mRNA 206 -- 212@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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