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
64	0.01278	0.5385	b1718	infC	-10.82	0.076139	1 -- 9	71 -- 79	translation initiation factor IF-3	______________1________10\n______________\|________\|\n___________5'-_________AAAUC...AGC-3'\n______________UUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	3 -- 9	71 -- 77	-11.2516 kcal/mol	0.206511 kcal/mol	0.222833 kcal/mol	1 10@LB@ \| \|@LB@ 5'- AAAUC...AGC-3'@LB@ UUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -11.2516 kcal/mol@LB@Unfolding Energy - mRNA 0.206511 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 1 -- 9@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 71 -- 77@LB@
69	0.01301	0.5385	b0174	ispU	-11.35	0.061456	97 -- 106	71 -- 80	undecaprenyl pyrophosphate synthase	_____________96_________107\n_____________\|__________\|\n5'-CGU...AAGUA__________UAAGG...AAA-3'\n______________GUUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CAACCGAAAU\n3'-CGC...AAGUG__________CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	100 -- 106	71 -- 77	-14.3232 kcal/mol	2.73321 kcal/mol	0.236872 kcal/mol	96 107@LB@ \| \|@LB@5'-CGU...AAGUA UAAGG...AAA-3'@LB@ GUUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CAACCGAAAU@LB@3'-CGC...AAGUG CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -14.3232 kcal/mol@LB@Unfolding Energy - mRNA 2.73321 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 97 -- 106@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 71 -- 77@LB@
76	0.01392	0.5385	b0066	thiQ	-9.74	0.117374	220 -- 232	71 -- 84	thiamine/thiamine pyrophosphate ABC transporter ATPase	_____________219____________233\n_____________\|______________\|\n5'-GCU...UGAUA____C_________CCACC...CAA-3'\n______________UCAC__UGGCUUUA\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________AGUG__ACCGAAAU\n3'-CGC...UUUCA____CA________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	226 -- 232	71 -- 77	-13.9563 kcal/mol	3.66363 kcal/mol	0.5567 kcal/mol	219 233@LB@ \| \|@LB@5'-GCU...UGAUA C CCACC...CAA-3'@LB@ UCAC UGGCUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGUG ACCGAAAU@LB@3'-CGC...UUUCA CA CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.9563 kcal/mol@LB@Unfolding Energy - mRNA 3.66363 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 220 -- 232@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 71 -- 77@LB@
84	0.01516	0.5385	b1871	cmoB	-9.91	0.109770	166 -- 183	71 -- 87	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent	_____________165________________184\n_____________\|__________________\|\n5'-CAC...ACUUU_______U_G____A___AAAGC...AGC-3'\n______________GGUUCAC_G_UGGC_UUA\n______________:\|\|\|\|\|\|_\|_\|\|\|\|_\|\|\|\n______________UCAAGUG_C_ACCG_AAU\n3'-CGC...CGUUU_________A____A___CAAUA...AAG-5'\n_____________\|__________________\|\n_____________88_________________70\n	166 -- 172	81 -- 87	-14.4863 kcal/mol	4.01825 kcal/mol	0.562376 kcal/mol	165 184@LB@ \| \|@LB@5'-CAC...ACUUU U G A AAAGC...AGC-3'@LB@ GGUUCAC G UGGC UUA@LB@ :\|\|\|\|\|\| \| \|\|\|\| \|\|\|@LB@ UCAAGUG C ACCG AAU@LB@3'-CGC...CGUUU A A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.4863 kcal/mol@LB@Unfolding Energy - mRNA 4.01825 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 166 -- 183@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 81 -- 87@LB@
95	0.01635	0.5385	b2287	nuoB	-8.27	0.206762	33 -- 42	71 -- 80	NADH:ubiquinone oxidoreductase chain B	_____________32_________43\n_____________\|__________\|\n5'-CAU...GCUGG__A_______UGGAA...UUA-3'\n______________GU_GGCUUUG\n______________\|\|_\|\|\|\|\|\|:\n______________CA_CCGAAAU\n3'-CGC...AAGUG__A_______CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	36 -- 42	71 -- 77	-10.0496 kcal/mol	1.54713 kcal/mol	0.236872 kcal/mol	32 43@LB@ \| \|@LB@5'-CAU...GCUGG A UGGAA...UUA-3'@LB@ GU GGCUUUG@LB@ \|\| \|\|\|\|\|\|:@LB@ CA CCGAAAU@LB@3'-CGC...AAGUG A CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -10.0496 kcal/mol@LB@Unfolding Energy - mRNA 1.54713 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 33 -- 42@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 71 -- 77@LB@
124	0.02124	0.5385	b0198	metI	-9.85	0.112177	270 -- 285	71 -- 87	DL-methionine transporter subunit	_____________269_______________286\n_____________\|_________________\|\n5'-UCA...UAUCC_____UU__________UGAUU...CGG-3'\n______________GGUUU___UUGGCUUUG\n______________:\|\|\|:___\|\|\|\|\|\|\|\|:\n______________UCAAG___AACCGAAAU\n3'-CGC...CGUUU_____UGC_________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	279 -- 285	71 -- 77	-13.0228 kcal/mol	2.60961 kcal/mol	0.562376 kcal/mol	269 286@LB@ \| \|@LB@5'-UCA...UAUCC UU UGAUU...CGG-3'@LB@ GGUUU UUGGCUUUG@LB@ :\|\|\|: \|\|\|\|\|\|\|\|:@LB@ UCAAG AACCGAAAU@LB@3'-CGC...CGUUU UGC CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.0228 kcal/mol@LB@Unfolding Energy - mRNA 2.60961 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 270 -- 285@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 71 -- 77@LB@
132	0.0226	0.5385	b2721	hycE	-8.05	0.224194	140 -- 148	71 -- 79	hydrogenase 3 large subunit	_____________139_______149\n_____________\|_________\|\n5'-UUC...UGGGU_________CAUUU...UGA-3'\n______________UUGGCUUUG\n______________\|\|\|\|\|\|\|\|:\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	142 -- 148	71 -- 77	-10.5671 kcal/mol	2.29615 kcal/mol	0.222833 kcal/mol	139 149@LB@ \| \|@LB@5'-UUC...UGGGU CAUUU...UGA-3'@LB@ UUGGCUUUG@LB@ \|\|\|\|\|\|\|\|:@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -10.5671 kcal/mol@LB@Unfolding Energy - mRNA 2.29615 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 140 -- 148@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@LB@
145	0.02443	0.5467	b2569	lepA	-12.53	0.038132	5 -- 17	71 -- 85	back-translocating elongation factor EF4 GTPase	_____________4_______________18\n_____________\|_______________\|\n_______5'-UGAU_______________UUGCA...ACC-3'\n______________UUCAC__UGGCUUUG\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\n______________AAGUG__ACCGAAAU\n3'-CGC...UUUUC_____CA________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	11 -- 17	71 -- 77	-14.3569 kcal/mol	1.27074 kcal/mol	0.560731 kcal/mol	4 18@LB@ \| \|@LB@ 5'-UGAU UUGCA...ACC-3'@LB@ UUCAC UGGCUUUG@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AAGUG ACCGAAAU@LB@3'-CGC...UUUUC CA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.3569 kcal/mol@LB@Unfolding Energy - mRNA 1.27074 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 5 -- 17@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 71 -- 77@LB@
164	0.02889	0.5559	b1512	lsrR	-7.59	0.264791	265 -- 277	71 -- 84	lsr operon transcriptional repressor	_____________264____________278\n_____________\|______________\|\n5'-GCU...GCGGA______________CUAUC...AGA-3'\n______________UCGCG_UGGUUUUA\n______________\|\|:\|\|_\|\|\|:\|\|\|\|\n______________AGUGC_ACCGAAAU\n3'-CGC...UUUCA_____A________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	271 -- 277	71 -- 77	-14.8882 kcal/mol	6.73904 kcal/mol	0.5567 kcal/mol	264 278@LB@ \| \|@LB@5'-GCU...GCGGA CUAUC...AGA-3'@LB@ UCGCG UGGUUUUA@LB@ \|\|:\|\| \|\|\|:\|\|\|\|@LB@ AGUGC ACCGAAAU@LB@3'-CGC...UUUCA A CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -14.8882 kcal/mol@LB@Unfolding Energy - mRNA 6.73904 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 265 -- 277@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
166	0.02918	0.5559	b3518	yhjA	-9.21	0.144312	113 -- 127	71 -- 85	putative cytochrome C peroxidase	_____________112_____________128\n_____________\|_______________\|\n5'-CCG...UGUUU______A________UCUCG...GCA-3'\n______________UUUAUG_UGGCUUUG\n______________\|\|:\|:\|_\|\|\|\|\|\|\|:\n______________AAGUGC_ACCGAAAU\n3'-CGC...UUUUC______A________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	121 -- 127	71 -- 77	-14.7899 kcal/mol	5.0213 kcal/mol	0.560731 kcal/mol	112 128@LB@ \| \|@LB@5'-CCG...UGUUU A UCUCG...GCA-3'@LB@ UUUAUG UGGCUUUG@LB@ \|\|:\|:\| \|\|\|\|\|\|\|:@LB@ AAGUGC ACCGAAAU@LB@3'-CGC...UUUUC A CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -9.21 kcal/mol@LB@Hybridization Energy -14.7899 kcal/mol@LB@Unfolding Energy - mRNA 5.0213 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 113 -- 127@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 71 -- 77@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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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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