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
89	0.004811	0.1855	b4336	yjiN	-13.14	0.034257	120 -- 134	70 -- 84	zinc-type alcohol dehydrogenase-like protein		_____________119_____________135\n_____________\|_______________\|\n5'-GGU...UCGCG_______________CAGCC...CCA-3'\n______________UGCGCCAGCAUCAGG\n______________\|\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________ACGCGGUUGUGGUCC\n3'-UUU...UUAUG_______________CUUUA...GUG-5'\n_____________\|_______________\|\n_____________85______________69\n	128 -- 134	70 -- 76	-28.7852 kcal/mol	8.39668 kcal/mol	7.24859 kcal/mol	119 135@LB@ \| \|@LB@5'-GGU...UCGCG CAGCC...CCA-3'@LB@ UGCGCCAGCAUCAGG@LB@ \|\|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ ACGCGGUUGUGGUCC@LB@3'-UUU...UUAUG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -28.7852 kcal/mol@LB@Unfolding Energy - mRNA 8.39668 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 120 -- 134@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 70 -- 76@LB@
96	0.005105	0.1855	b0870	ltaE	-12.99	0.036706	93 -- 116	68 -- 88	L-allo-threonine aldolase PLP-dependent		_____________92_______________________117\n_____________\|________________________\|\n5'-GUC...UGUAU_________G___U______C___CGCGG...ACC-3'\n______________AUGCUGCGC_CAA_CAUCAG_GGA\n______________\|\|:\|\|\|\|\|\|_\|\|\|_\|\|:\|\|\|_\|\|\|\n______________UAUGACGCG_GUU_GUGGUC_CCU\n3'-UUU...GCGCU________________________UUAGA...GUG-5'\n_____________\|________________________\|\n_____________89_______________________67\n	95 -- 101	80 -- 86	-29.0922 kcal/mol	8.72289 kcal/mol	7.38144 kcal/mol	92 117@LB@ \| \|@LB@5'-GUC...UGUAU G U C CGCGG...ACC-3'@LB@ AUGCUGCGC CAA CAUCAG GGA@LB@ \|\|:\|\|\|\|\|\| \|\|\| \|\|:\|\|\| \|\|\|@LB@ UAUGACGCG GUU GUGGUC CCU@LB@3'-UUU...GCGCU UUAGA...GUG-5'@LB@ \| \|@LB@ 89 67@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -29.0922 kcal/mol@LB@Unfolding Energy - mRNA 8.72289 kcal/mol@LB@Unfolding Energy - sRNA 7.38144 kcal/mol@LB@@LB@Position - mRNA 93 -- 116@LB@Position - sRNA 68 -- 88@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 80 -- 86@LB@
33	0.001709	0.1727	b0023	rpsT	-12.95	0.037339	65 -- 78	72 -- 85	30S ribosomal subunit protein S20		_____________64_____________79\n_____________\|______________\|\n5'-UGA...GAAUC________U_____CGUAA...AGA-3'\n______________CUGCGCCA_CACUA\n______________\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________GACGCGGU_GUGGU\n3'-UUU...CUUAU________U_____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	66 -- 72	78 -- 84	-22.3173 kcal/mol	2.13275 kcal/mol	7.23443 kcal/mol	64 79@LB@ \| \|@LB@5'-UGA...GAAUC U CGUAA...AGA-3'@LB@ CUGCGCCA CACUA@LB@ \|\|\|\|\|\|\|\| \|\|\|:\|@LB@ GACGCGGU GUGGU@LB@3'-UUU...CUUAU U CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -22.3173 kcal/mol@LB@Unfolding Energy - mRNA 2.13275 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 65 -- 78@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 78 -- 84@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@
166	0.009748	0.2068	b1261	trpB	-12.89	0.038353	88 -- 97	52 -- 61	tryptophan synthase beta subunit		_____________87_________98\n_____________\|__________\|\n5'-UGG...AAACC__________GACUU...UCA-3'\n______________GGCUGCGCCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCGACGCGGC\n3'-UUU...UAGAA__________AUUUA...GUG-5'\n_____________\|__________\|\n_____________62_________51\n	91 -- 97	52 -- 58	-23.3299 kcal/mol	5.56351 kcal/mol	4.87533 kcal/mol	87 98@LB@ \| \|@LB@5'-UGG...AAACC GACUU...UCA-3'@LB@ GGCUGCGCCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCGACGCGGC@LB@3'-UUU...UAGAA AUUUA...GUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -23.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.56351 kcal/mol@LB@Unfolding Energy - sRNA 4.87533 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
8	0.000265	0.1166	b1244	oppB	-12.83	0.039495	280 -- 295	70 -- 84	oligopeptide ABC transporter permease		_____________279______________296\n_____________\|________________\|\n5'-UCC...UAUGA______UC________AAGCC-3'\n______________UGCGCC__GCGCCGGG\n______________\|\|\|\|\|\|__:\|:\|\|:\|\|\n______________ACGCGG__UGUGGUCC\n3'-UUU...UUAUG______U_________CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	289 -- 295	70 -- 76	-25.4509 kcal/mol	5.37602 kcal/mol	7.24859 kcal/mol	279 296@LB@ \| \|@LB@5'-UCC...UAUGA UC AAGCC-3'@LB@ UGCGCC GCGCCGGG@LB@ \|\|\|\|\|\| :\|:\|\|:\|\|@LB@ ACGCGG UGUGGUCC@LB@3'-UUU...UUAUG U CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -25.4509 kcal/mol@LB@Unfolding Energy - mRNA 5.37602 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@LB@
13	0.0004745	0.1198	b1688	ydiK	-12.82	0.039628	213 -- 226	68 -- 82	UPF0118 family inner membrane protein		_____________212_____________227\n_____________\|_______________\|\n5'-AUG...AUGUU_______________UGUCG...CCU-3'\n______________CGUCAGC_CCAGGGA\n______________\|\|:\|\|:\|_\|\|\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	220 -- 226	68 -- 74	-23.7232 kcal/mol	3.92329 kcal/mol	6.98098 kcal/mol	212 227@LB@ \| \|@LB@5'-AUG...AUGUU UGUCG...CCU-3'@LB@ CGUCAGC CCAGGGA@LB@ \|\|:\|\|:\| \|\|\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.7232 kcal/mol@LB@Unfolding Energy - mRNA 3.92329 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 213 -- 226@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 68 -- 74@LB@
52	0.002619	0.1727	b2720	hycF	-12.75	0.040951	8 -- 55	44 -- 94	formate hydrogenlyase complex iron-sulfur protein		_____________7______________________________________________________56\n_____________\|______________________________________________________\|\n____5'-CGACCCU____UAC_________GG_________________CCGA_______CU______CGGUA...CAG-3'\n______________GCGC___AUGCUGCGC__CAACACC______GUUU____UGCGCCG__GAUUAU\n______________\|\|\|\|___\|\|:\|\|\|\|\|\|__\|\|\|\|\|\|\|______:\|:\|____\|\|\|\|\|\|\|__:\|\|\|\|\|\n______________CGCG___UAUGACGCG__GUUGUGG______UAGA____ACGCGGC__UUAAUA\n3'-UUU...CCCCA____CU___________________UCCCUU____ACCG_______AU______AUACU...GUG-5'\n_____________\|______________________________________________________\|\n_____________95_____________________________________________________43\n	41 -- 47	52 -- 58	-46.3174 kcal/mol	16.2176 kcal/mol	17.3533 kcal/mol	7 56@LB@ \| \|@LB@ 5'-CGACCCU UAC GG CCGA CU CGGUA...CAG-3'@LB@ GCGC AUGCUGCGC CAACACC GUUU UGCGCCG GAUUAU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\| \|\|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CGCG UAUGACGCG GUUGUGG UAGA ACGCGGC UUAAUA@LB@3'-UUU...CCCCA CU UCCCUU ACCG AU AUACU...GUG-5'@LB@ \| \|@LB@ 95 43@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -46.3174 kcal/mol@LB@Unfolding Energy - mRNA 16.2176 kcal/mol@LB@Unfolding Energy - sRNA 17.3533 kcal/mol@LB@@LB@Position - mRNA 8 -- 55@LB@Position - sRNA 44 -- 94@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 52 -- 58@LB@
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@
6	0.0001378	0.08054	b3860	dsbA	-12.69	0.042007	89 -- 111	55 -- 75	periplasmic protein disulfide isomerase I		_____________88______________________112\n_____________\|_______________________\|\n5'-UUU...GGUUA_______A_____AC________ACAGA...AAC-3'\n______________ACCGGGG_AGAUU__UGGCUGCG\n______________\|\|\|:\|\|\|_\|:\|\|:__\|\|\|\|\|\|\|\|\n______________UGGUCCC_UUUAG__ACCGACGC\n3'-UUU...GGUUG_____________A_________GGCAU...GUG-5'\n_____________\|_______________________\|\n_____________76______________________54\n	105 -- 111	55 -- 61	-30.5184 kcal/mol	9.58616 kcal/mol	8.24199 kcal/mol	88 112@LB@ \| \|@LB@5'-UUU...GGUUA A AC ACAGA...AAC-3'@LB@ ACCGGGG AGAUU UGGCUGCG@LB@ \|\|\|:\|\|\| \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UGGUCCC UUUAG ACCGACGC@LB@3'-UUU...GGUUG A GGCAU...GUG-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -30.5184 kcal/mol@LB@Unfolding Energy - mRNA 9.58616 kcal/mol@LB@Unfolding Energy - sRNA 8.24199 kcal/mol@LB@@LB@Position - mRNA 89 -- 111@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 55 -- 61@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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