Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
171	0.03054	0.5559	b0045	yaaU	-10.82	0.076059	142 -- 153	73 -- 84	putative MFS sugar transporter; membrane protein	_____________141__________154\n_____________\|____________\|\n5'-AAG...ACGGC_G__________GAUAC...UAC-3'\n______________U_AUGUUGGUUU\n______________\|_\|:\|\|\|\|\|:\|\|\n______________A_UGCAACCGAA\n3'-CGC...UUUCA_G__________AUCAA...AAG-5'\n_____________\|____________\|\n_____________85___________72\n	147 -- 153	73 -- 79	-12.9415 kcal/mol	1.60777 kcal/mol	0.508835 kcal/mol	141 154@LB@ \| \|@LB@5'-AAG...ACGGC G GAUAC...UAC-3'@LB@ U AUGUUGGUUU@LB@ \| \|:\|\|\|\|\|:\|\|@LB@ A UGCAACCGAA@LB@3'-CGC...UUUCA G AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -12.9415 kcal/mol@LB@Unfolding Energy - mRNA 1.60777 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 73 -- 79@LB@
172	0.03064	0.5559	b1542	ydfI	-13.08	0.030437	273 -- 290	69 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________272________________291\n_____________\|__________________\|\n5'-CUC...GAAUU______UUA_________GCAUU...ACC-3'\n______________GUUCAU___GGCUUUGGU\n______________\|\|\|\|\|:___\|\|\|\|\|\|:\|\|\n______________CAAGUG___CCGAAAUCA\n3'-CGC...GUUUU______CAA_________AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	284 -- 290	69 -- 75	-19.6529 kcal/mol	6.00837 kcal/mol	0.568509 kcal/mol	272 291@LB@ \| \|@LB@5'-CUC...GAAUU UUA GCAUU...ACC-3'@LB@ GUUCAU GGCUUUGGU@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\|\|@LB@ CAAGUG CCGAAAUCA@LB@3'-CGC...GUUUU CAA AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.6529 kcal/mol@LB@Unfolding Energy - mRNA 6.00837 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 273 -- 290@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
173	0.03066	0.5559	b2928	yggC	-11.87	0.049837	290 -- 298	75 -- 83	putative PanK family P-loop kinase	_____________289_______299\n_____________\|_________\|\n5'-GAA...CUGCA_________GG-3'\n______________CAUGUUGGC\n______________\|\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	292 -- 298	75 -- 81	-14.124 kcal/mol	1.76242 kcal/mol	0.492259 kcal/mol	289 299@LB@ \| \|@LB@5'-GAA...CUGCA GG-3'@LB@ CAUGUUGGC@LB@ \|\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -14.124 kcal/mol@LB@Unfolding Energy - mRNA 1.76242 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 290 -- 298@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 75 -- 81@LB@
174	0.03067	0.5559	b4005	purD	-11.17	0.066076	4 -- 22	73 -- 90	phosphoribosylglycinamide synthetase phosphoribosylamine-glycine ligase	_____________3___________________23\n_____________\|___________________\|\n________5'-GUG________CU__A______CUGAC...GUA-3'\n______________AAAGGUUC__CG_UGGCUU\n______________\|\|\|:\|\|\|\|__\|\|_\|\|\|\|\|\|\n______________UUUUCAAG__GC_ACCGAA\n3'-CGC...AGGCG________U___A______AUCAA...AAG-5'\n_____________\|___________________\|\n_____________91__________________72\n	5 -- 11	83 -- 89	-16.9563 kcal/mol	5.26463 kcal/mol	0.517799 kcal/mol	3 23@LB@ \| \|@LB@ 5'-GUG CU A CUGAC...GUA-3'@LB@ AAAGGUUC CG UGGCUU@LB@ \|\|\|:\|\|\|\| \|\| \|\|\|\|\|\|@LB@ UUUUCAAG GC ACCGAA@LB@3'-CGC...AGGCG U A AUCAA...AAG-5'@LB@ \| \|@LB@ 91 72@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -16.9563 kcal/mol@LB@Unfolding Energy - mRNA 5.26463 kcal/mol@LB@Unfolding Energy - sRNA 0.517799 kcal/mol@LB@@LB@Position - mRNA 4 -- 22@LB@Position - sRNA 73 -- 90@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 83 -- 89@LB@
175	0.03099	0.5559	b2149	mglA	-9.34	0.136967	92 -- 105	70 -- 84	methyl-galactoside ABC transporter ATPase	_____________91______________106\n_____________\|_______________\|\n5'-CGA...GUACC__________G____AUAAA...AUU-3'\n______________UUAUGUUGGC__UAG\n______________\|:\|:\|\|\|\|\|\|__\|\|\|\n______________AGUGCAACCG__AUC\n3'-CGC...UUUCA__________AA___AAUAA...AAG-5'\n_____________\|_______________\|\n_____________85______________69\n	95 -- 101	75 -- 81	-15.5186 kcal/mol	5.61316 kcal/mol	0.563314 kcal/mol	91 106@LB@ \| \|@LB@5'-CGA...GUACC G AUAAA...AUU-3'@LB@ UUAUGUUGGC UAG@LB@ \|:\|:\|\|\|\|\|\| \|\|\|@LB@ AGUGCAACCG AUC@LB@3'-CGC...UUUCA AA AAUAA...AAG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -15.5186 kcal/mol@LB@Unfolding Energy - mRNA 5.61316 kcal/mol@LB@Unfolding Energy - sRNA 0.563314 kcal/mol@LB@@LB@Position - mRNA 92 -- 105@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 75 -- 81@LB@
176	0.03112	0.5559	b2536	hcaT	-7.63	0.261550	240 -- 259	67 -- 85	putative 3-phenylpropionic transporter	_____________239__________________260\n_____________\|____________________\|\n5'-UCG...GCUAU_____AUACUU_________CGGCA...GGA-3'\n______________UUCAC______UUUUAGUUA\n______________\|\|\|\|\|______:\|\|\|\|\|\|\|\|\n______________AAGUG______GAAAUCAAU\n3'-CGC...UUUUC_____CAACC__________AAGCU...AAG-5'\n_____________\|____________________\|\n_____________86___________________66\n	253 -- 259	67 -- 73	-10.0019 kcal/mol	1.80629 kcal/mol	0.569003 kcal/mol	239 260@LB@ \| \|@LB@5'-UCG...GCUAU AUACUU CGGCA...GGA-3'@LB@ UUCAC UUUUAGUUA@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AAGUG GAAAUCAAU@LB@3'-CGC...UUUUC CAACC AAGCU...AAG-5'@LB@ \| \|@LB@ 86 66@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -10.0019 kcal/mol@LB@Unfolding Energy - mRNA 1.80629 kcal/mol@LB@Unfolding Energy - sRNA 0.569003 kcal/mol@LB@@LB@Position - mRNA 240 -- 259@LB@Position - sRNA 67 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 67 -- 73@LB@
177	0.03112	0.5559	b0080	cra	-12.94	0.032158	57 -- 78	62 -- 84	transcriptional repressor-activator for carbon metabolism	_____________56_______________________79\n_____________\|________________________\|\n5'-GGC...ACAUG_________G____UU________AAUCA...AAA-3'\n______________UCACGUUGG_CUUU__UUG__CGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|__\|\|:__\|\|\|\n______________AGUGCAACC_GAAA__AAU__GCU\n3'-CGC...UUUCA______________UC___AA___CAACU...AAG-5'\n_____________\|________________________\|\n_____________85_______________________61\n	59 -- 65	76 -- 82	-19.2849 kcal/mol	4.65103 kcal/mol	1.6921 kcal/mol	56 79@LB@ \| \|@LB@5'-GGC...ACAUG G UU AAUCA...AAA-3'@LB@ UCACGUUGG CUUU UUG CGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|: \|\|\|@LB@ AGUGCAACC GAAA AAU GCU@LB@3'-CGC...UUUCA UC AA CAACU...AAG-5'@LB@ \| \|@LB@ 85 61@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -19.2849 kcal/mol@LB@Unfolding Energy - mRNA 4.65103 kcal/mol@LB@Unfolding Energy - sRNA 1.6921 kcal/mol@LB@@LB@Position - mRNA 57 -- 78@LB@Position - sRNA 62 -- 84@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 76 -- 82@LB@
178	0.03115	0.5559	b2528	iscA	-9.66	0.120899	187 -- 207	62 -- 80	FeS cluster assembly protein	_____________186___________________208\n_____________\|_____________________\|\n5'-UUC...UAAGA____A_G_________G____UUACA...CCG-3'\n______________GUUG_G_UUUGGUUAU_UCGA\n______________\|\|\|\|_\|_\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CAAC_C_AAAUCAAUA_AGCU\n3'-CGC...AAGUG______G______________CAACU...AAG-5'\n_____________\|_____________________\|\n_____________81____________________61\n	196 -- 202	66 -- 72	-17.7068 kcal/mol	7.30815 kcal/mol	0.737855 kcal/mol	186 208@LB@ \| \|@LB@5'-UUC...UAAGA A G G UUACA...CCG-3'@LB@ GUUG G UUUGGUUAU UCGA@LB@ \|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CAAC C AAAUCAAUA AGCU@LB@3'-CGC...AAGUG G CAACU...AAG-5'@LB@ \| \|@LB@ 81 61@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -17.7068 kcal/mol@LB@Unfolding Energy - mRNA 7.30815 kcal/mol@LB@Unfolding Energy - sRNA 0.737855 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 62 -- 80@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 66 -- 72@LB@
179	0.03159	0.5559	b0790	ybhP	-12.03	0.046743	250 -- 264	71 -- 85	endo/exonuclease/phosphatase family protein	_____________249_____________265\n_____________\|_______________\|\n5'-AGU...CAAUA_____AAA_______CCGCG...UUC-3'\n______________UUCAC___GGCUUUA\n______________\|\|\|\|\|___\|\|\|\|\|\|\|\n______________AAGUG___CCGAAAU\n3'-CGC...UUUUC_____CAA_______CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	258 -- 264	71 -- 77	-13.6298 kcal/mol	1.04243 kcal/mol	0.560731 kcal/mol	249 265@LB@ \| \|@LB@5'-AGU...CAAUA AAA CCGCG...UUC-3'@LB@ UUCAC GGCUUUA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAGUG CCGAAAU@LB@3'-CGC...UUUUC CAA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.6298 kcal/mol@LB@Unfolding Energy - mRNA 1.04243 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 250 -- 264@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 71 -- 77@LB@
180	0.03162	0.5559	b1941	fliI	-9.97	0.106944	57 -- 70	74 -- 88	flagellum-specific ATP synthase	_____________56______________71\n_____________\|_______________\|\n5'-CUG...ACCUU________A______GGCGC...GCG-3'\n______________AAGUUUGC__UGGCU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\n______________UUCAAGUG__ACCGA\n3'-CGC...GCGUU________CA_____AAUCA...AAG-5'\n_____________\|_______________\|\n_____________89______________73\n	58 -- 64	81 -- 87	-13.0478 kcal/mol	2.55971 kcal/mol	0.516514 kcal/mol	56 71@LB@ \| \|@LB@5'-CUG...ACCUU A GGCGC...GCG-3'@LB@ AAGUUUGC UGGCU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ UUCAAGUG ACCGA@LB@3'-CGC...GCGUU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 89 73@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -13.0478 kcal/mol@LB@Unfolding Energy - mRNA 2.55971 kcal/mol@LB@Unfolding Energy - sRNA 0.516514 kcal/mol@LB@@LB@Position - mRNA 57 -- 70@LB@Position - sRNA 74 -- 88@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 81 -- 87@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)

Job resubmission

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service.

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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