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
188	0.03339	0.5559	b3232	zapE	-6.91	0.336884	267 -- 282	15 -- 35	divisome ATPase	_____________266____________________283\n_____________\|______________________\|\n5'-AGG...CCGAC___G__________________CCGUC...AAA-3'\n______________GAC_UUCA______AAAAGAGG\n______________\|\|\|_\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CUG_AAGU______UUUUCUCC\n3'-CGC...CGUCA________UCCCAA________ACGGC...AAG-5'\n_____________\|______________________\|\n_____________36_____________________14\n	276 -- 282	15 -- 21	-13.3674 kcal/mol	3.12995 kcal/mol	3.33058 kcal/mol	266 283@LB@ \| \|@LB@5'-AGG...CCGAC G CCGUC...AAA-3'@LB@ GAC UUCA AAAAGAGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUG AAGU UUUUCUCC@LB@3'-CGC...CGUCA UCCCAA ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -13.3674 kcal/mol@LB@Unfolding Energy - mRNA 3.12995 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 267 -- 282@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 15 -- 21@LB@
199	0.03481	0.5559	b0407	yajC	-8.41	0.195839	88 -- 104	15 -- 30	SecYEG protein translocase auxillary subunit	_____________87________________105\n_____________\|_________________\|\n5'-UCU...UUACG_____CUAUU_______GUAAA...UUU-3'\n______________CAAGG_____GAAGAGG\n______________\|\|\|\|\|_____:\|\|\|\|\|\|\n______________GUUCC_____UUUCUCC\n3'-CGC...CUGAA_____CAAU________ACGGC...AAG-5'\n_____________\|_________________\|\n_____________31________________14\n	98 -- 104	15 -- 21	-15.1331 kcal/mol	3.4367 kcal/mol	3.28624 kcal/mol	87 105@LB@ \| \|@LB@5'-UCU...UUACG CUAUU GUAAA...UUU-3'@LB@ CAAGG GAAGAGG@LB@ \|\|\|\|\| :\|\|\|\|\|\|@LB@ GUUCC UUUCUCC@LB@3'-CGC...CUGAA CAAU ACGGC...AAG-5'@LB@ \| \|@LB@ 31 14@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -15.1331 kcal/mol@LB@Unfolding Energy - mRNA 3.4367 kcal/mol@LB@Unfolding Energy - sRNA 3.28624 kcal/mol@LB@@LB@Position - mRNA 88 -- 104@LB@Position - sRNA 15 -- 30@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 15 -- 21@LB@
114	0.01931	0.5385	b1951	rcsA	-10.71	0.079523	269 -- 285	16 -- 29	transcriptional regulator of colanic acid capsular biosynthesis	_____________268_______________286\n_____________\|_________________\|\n5'-GUU...AGUAG__________AAA____AAAUC...UUG-3'\n______________AGGGGUUAAA___AGAG\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCCAAUUU___UCUC\n3'-CGC...UGAAG_________________CACGG...AAG-5'\n_____________\|_________________\|\n_____________30________________15\n	272 -- 278	20 -- 26	-15.5636 kcal/mol	1.76121 kcal/mol	3.08831 kcal/mol	268 286@LB@ \| \|@LB@5'-GUU...AGUAG AAA AAAUC...UUG-3'@LB@ AGGGGUUAAA AGAG@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCCAAUUU UCUC@LB@3'-CGC...UGAAG CACGG...AAG-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -15.5636 kcal/mol@LB@Unfolding Energy - mRNA 1.76121 kcal/mol@LB@Unfolding Energy - sRNA 3.08831 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 20 -- 26@LB@
120	0.02045	0.5385	b0979	cbdB	-12.05	0.046235	177 -- 194	16 -- 34	cytochrome bd-II oxidase subunit II	_____________176_________________195\n_____________\|___________________\|\n5'-AUA...ACGCA__AA_______________AAAAU...GCU-3'\n______________GC__CAGGGG_UAAAGGAG\n______________:\|__\|\|:\|\|\|_\|\|\|\|:\|\|\|\n______________UG__GUUCCC_AUUUUCUC\n3'-CGC...GUCAC__AA______A________CACGG...AAG-5'\n_____________\|___________________\|\n_____________35__________________15\n	188 -- 194	16 -- 22	-18.7902 kcal/mol	3.40633 kcal/mol	3.33043 kcal/mol	176 195@LB@ \| \|@LB@5'-AUA...ACGCA AA AAAAU...GCU-3'@LB@ GC CAGGGG UAAAGGAG@LB@ :\| \|\|:\|\|\| \|\|\|\|:\|\|\|@LB@ UG GUUCCC AUUUUCUC@LB@3'-CGC...GUCAC AA A CACGG...AAG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -18.7902 kcal/mol@LB@Unfolding Energy - mRNA 3.40633 kcal/mol@LB@Unfolding Energy - sRNA 3.33043 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 16 -- 22@LB@
169	0.03038	0.5559	b2912	fau	-9.38	0.135051	85 -- 98	22 -- 35	5-formyltetrahydrofolate cyclo-ligase family protein	_____________84_____________99\n_____________\|______________\|\n5'-GAA...ACCAA__G___________CAGCC...UGG-3'\n______________GG_UUCAAGGGUUA\n______________\|:_\|\|\|\|\|\|\|\|\|\|\|\n______________CU_AAGUUCCCAAU\n3'-CGC...CGUCA__G___________UUUCU...AAG-5'\n_____________\|______________\|\n_____________36_____________21\n	92 -- 98	22 -- 28	-18.6025 kcal/mol	5.89438 kcal/mol	3.32987 kcal/mol	84 99@LB@ \| \|@LB@5'-GAA...ACCAA G CAGCC...UGG-3'@LB@ GG UUCAAGGGUUA@LB@ \|: \|\|\|\|\|\|\|\|\|\|\|@LB@ CU AAGUUCCCAAU@LB@3'-CGC...CGUCA G UUUCU...AAG-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -18.6025 kcal/mol@LB@Unfolding Energy - mRNA 5.89438 kcal/mol@LB@Unfolding Energy - sRNA 3.32987 kcal/mol@LB@@LB@Position - mRNA 85 -- 98@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 22 -- 28@LB@
133	0.02275	0.5385	b0177	bamA	-6.79	0.350358	265 -- 271	23 -- 29	BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor	_____________264_____272\n_____________\|_______\|\n5'-CUG...UGCUG_______CGUAG...GCC-3'\n______________AAGGGUU\n______________\|\|\|\|\|\|\|\n______________UUCCCAA\n3'-CGC...UGAAG_______UUUUC...AAG-5'\n_____________\|_______\|\n_____________30______22\n	265 -- 271	23 -- 29	-7.93739 kcal/mol	1.09969 kcal/mol	0.0462613 kcal/mol	264 272@LB@ \| \|@LB@5'-CUG...UGCUG CGUAG...GCC-3'@LB@ AAGGGUU@LB@ \|\|\|\|\|\|\|@LB@ UUCCCAA@LB@3'-CGC...UGAAG UUUUC...AAG-5'@LB@ \| \|@LB@ 30 22@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -7.93739 kcal/mol@LB@Unfolding Energy - mRNA 1.09969 kcal/mol@LB@Unfolding Energy - sRNA 0.0462613 kcal/mol@LB@@LB@Position - mRNA 265 -- 271@LB@Position - sRNA 23 -- 29@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
121	0.02058	0.5385	b0796	ybiH	-9.41	0.133616	217 -- 230	24 -- 36	DUF1956 domain-containing tetR family putative transcriptional regulator	_____________216____________231\n_____________\|______________\|\n5'-CGG...UGCCA____AA________GAACA...CCA-3'\n______________UGAC__UCAAGGGU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACUG__AGUUCCCA\n3'-CGC...CCGUC____A_________AUUUU...AAG-5'\n_____________\|______________\|\n_____________37_____________23\n	224 -- 230	24 -- 30	-15.9856 kcal/mol	3.24975 kcal/mol	3.33025 kcal/mol	216 231@LB@ \| \|@LB@5'-CGG...UGCCA AA GAACA...CCA-3'@LB@ UGAC UCAAGGGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACUG AGUUCCCA@LB@3'-CGC...CCGUC A AUUUU...AAG-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -15.9856 kcal/mol@LB@Unfolding Energy - mRNA 3.24975 kcal/mol@LB@Unfolding Energy - sRNA 3.33025 kcal/mol@LB@@LB@Position - mRNA 217 -- 230@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 24 -- 30@LB@
160	0.02795	0.5559	b1475	fdnH	-7.98	0.230122	69 -- 80	24 -- 35	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible	_____________68___________81\n_____________\|____________\|\n5'-CGC...ACUGG____________GUCGC...UUA-3'\n______________GGCUUUGAGGGU\n______________\|:\|\|\|::\|\|\|\|\|\n______________CUGAAGUUCCCA\n3'-CGC...CGUCA____________AUUUU...AAG-5'\n_____________\|____________\|\n_____________36___________23\n	74 -- 80	24 -- 30	-17.8377 kcal/mol	6.53052 kcal/mol	3.32971 kcal/mol	68 81@LB@ \| \|@LB@5'-CGC...ACUGG GUCGC...UUA-3'@LB@ GGCUUUGAGGGU@LB@ \|:\|\|\|::\|\|\|\|\|@LB@ CUGAAGUUCCCA@LB@3'-CGC...CGUCA AUUUU...AAG-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -17.8377 kcal/mol@LB@Unfolding Energy - mRNA 6.53052 kcal/mol@LB@Unfolding Energy - sRNA 3.32971 kcal/mol@LB@@LB@Position - mRNA 69 -- 80@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 24 -- 30@LB@
7	0.001275	0.5385	b2175	mepS	-13.85	0.022182	178 -- 188	25 -- 35	murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase	_____________177_________189\n_____________\|___________\|\n5'-CAA...UUAAG___________AAAAC...CAA-3'\n______________GACUUCAAGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________CUGAAGUUCCC\n3'-CGC...CGUCA___________AAUUU...AAG-5'\n_____________\|___________\|\n_____________36__________24\n	182 -- 188	25 -- 31	-19.9152 kcal/mol	2.73903 kcal/mol	3.32958 kcal/mol	177 189@LB@ \| \|@LB@5'-CAA...UUAAG AAAAC...CAA-3'@LB@ GACUUCAAGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ CUGAAGUUCCC@LB@3'-CGC...CGUCA AAUUU...AAG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 2.73903 kcal/mol@LB@Unfolding Energy - sRNA 3.32958 kcal/mol@LB@@LB@Position - mRNA 178 -- 188@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 25 -- 31@LB@
159	0.02757	0.5559	b2701	mltB	-11.73	0.052671	73 -- 129	32 -- 90	membrane-bound lytic murein transglycosylase B	_____________72_________________________________________________________________130\n_____________\|__________________________________________________________________\|\n5'-AGA...UGAAU_____GAUA___AG__GAA_________________UUAUGU___G_____UAU____________ACCGC...GAA-3'\n______________AAAAG____GCG__GG___________UGAGUUGAG______AAA_UC_CG___CGGGCAGUGACU\n______________\|\|\|\|\|____:\|\|__\|\|___________:\|\|\|\|\|\|\|\|______\|\|\|_\|\|_\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUUC____UGC__CC___________GCUCAACUC______UUU_AG_GC___GCCCGUCACUGA\n3'-CGC...AGGCG_____AAG____AA__GAAAUCAAUAA__________________G__A__UUU____________AGUUC...AAG-5'\n_____________\|__________________________________________________________________\|\n_____________91_________________________________________________________________31\n	94 -- 100	56 -- 62	-46.1733 kcal/mol	15.4898 kcal/mol	18.9502 kcal/mol	72 130@LB@ \| \|@LB@5'-AGA...UGAAU GAUA AG GAA UUAUGU G UAU ACCGC...GAA-3'@LB@ AAAAG GCG GG UGAGUUGAG AAA UC CG CGGGCAGUGACU@LB@ \|\|\|\|\| :\|\| \|\| :\|\|\|\|\|\|\|\| \|\|\| \|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUUC UGC CC GCUCAACUC UUU AG GC GCCCGUCACUGA@LB@3'-CGC...AGGCG AAG AA GAAAUCAAUAA G A UUU AGUUC...AAG-5'@LB@ \| \|@LB@ 91 31@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -46.1733 kcal/mol@LB@Unfolding Energy - mRNA 15.4898 kcal/mol@LB@Unfolding Energy - sRNA 18.9502 kcal/mol@LB@@LB@Position - mRNA 73 -- 129@LB@Position - sRNA 32 -- 90@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 56 -- 62@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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