Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
74	0.004124	0.1795	b2599	pheA	-8.54	0.042758	34 -- 48	29 -- 42	chorismate mutase and prephenate dehydratase P-protein	_____________33______________49\n_____________\|_______________\|\n5'-UGA...UACUA___U___________ACAAA...UCG-3'\n______________AAG_CACUUAAGGAA\n______________\|\|\|_\|\|\|\|\|\|\|::\|\|\n______________UUC_GUGAAUUUUUU\n3'-UUU...CGUUC_______________AAGCA...CAA-5'\n_____________\|_______________\|\n_____________43______________28\n	42 -- 48	29 -- 35	-11.0993 kcal/mol	0.931405 kcal/mol	1.62369 kcal/mol	33 49@LB@ \| \|@LB@5'-UGA...UACUA U ACAAA...UCG-3'@LB@ AAG CACUUAAGGAA@LB@ \|\|\| \|\|\|\|\|\|\|::\|\|@LB@ UUC GUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -11.0993 kcal/mol@LB@Unfolding Energy - mRNA 0.931405 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 34 -- 48@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 29 -- 35@LB@
123	0.0108	0.2828	b2606	rplS	-6.81	0.122900	220 -- 252	37 -- 58	50S ribosomal subunit protein L19	_____________219_______________________________253\n_____________\|_________________________________\|\n5'-AUA...UAAGC______AACAAGAGCAGAUG________C____CUUCC...UUG-3'\n______________AACUUG______________AAGCAGGA_GUAC\n______________\|\|\|\|\|\|______________\|\|\|\|\|:\|\|_\|:\|\|\n______________UUGAAC______________UUCGUUCU_CGUG\n3'-UUU...CUACU______GAA___________________U____AAUUU...CAA-5'\n_____________\|_________________________________\|\n_____________59________________________________36\n	241 -- 247	42 -- 48	-17.5998 kcal/mol	4.54246 kcal/mol	6.24354 kcal/mol	219 253@LB@ \| \|@LB@5'-AUA...UAAGC AACAAGAGCAGAUG C CUUCC...UUG-3'@LB@ AACUUG AAGCAGGA GUAC@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\| \|:\|\|@LB@ UUGAAC UUCGUUCU CGUG@LB@3'-UUU...CUACU GAA U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -17.5998 kcal/mol@LB@Unfolding Energy - mRNA 4.54246 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 220 -- 252@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 42 -- 48@LB@
114	0.009652	0.2693	b2614	grpE	-8.47	0.044767	262 -- 275	27 -- 41	heat shock protein	_____________261_____________276\n_____________\|_______________\|\n5'-GAG...GGAUC_____G_________GAGGC...CUG-3'\n______________AGCAC__AAGAGAUU\n______________\|\|\|\|\|__\|\|:\|:\|\|\|\n______________UCGUG__UUUUUUAA\n3'-UUU...GUUCU_____AA________GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	269 -- 275	27 -- 33	-11.1078 kcal/mol	0.992631 kcal/mol	1.6427 kcal/mol	261 276@LB@ \| \|@LB@5'-GAG...GGAUC G GAGGC...CUG-3'@LB@ AGCAC AAGAGAUU@LB@ \|\|\|\|\| \|\|:\|:\|\|\|@LB@ UCGUG UUUUUUAA@LB@3'-UUU...GUUCU AA GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -11.1078 kcal/mol@LB@Unfolding Energy - mRNA 0.992631 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 262 -- 275@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@LB@
63	0.003338	0.1645	b2671	ygaC	-8.88	0.034356	231 -- 246	25 -- 40	uncharacterized protein	_____________230______________247\n_____________\|________________\|\n5'-UAU...CGCGC____________G___GUUUU...AAA-3'\n______________GUACUUGAAAAA_UCG\n______________\|:\|\|\|\|:\|\|\|\|\|_\|\|\|\n______________CGUGAAUUUUUU_AGC\n3'-UUU...UUCUU____________A___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	231 -- 237	34 -- 40	-15.9773 kcal/mol	5.44668 kcal/mol	1.64821 kcal/mol	230 247@LB@ \| \|@LB@5'-UAU...CGCGC G GUUUU...AAA-3'@LB@ GUACUUGAAAAA UCG@LB@ \|:\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ CGUGAAUUUUUU AGC@LB@3'-UUU...UUCUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -15.9773 kcal/mol@LB@Unfolding Energy - mRNA 5.44668 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 231 -- 246@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 34 -- 40@LB@
116	0.009699	0.2693	b2708	srlQ	-8.08	0.057211	196 -- 214	36 -- 49	D-arabinose 5-phosphate isomerase	_____________195_________________215\n_____________\|___________________\|\n5'-UAC...GGAGA______UGAGU________ACUGA...GCG-3'\n______________GAGCAA_____GAAGCACU\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UUCGUU_____CUUCGUGA\n3'-UUU...ACGAA___________________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________50__________________35\n	208 -- 214	36 -- 42	-17.2491 kcal/mol	3.12814 kcal/mol	6.03645 kcal/mol	195 215@LB@ \| \|@LB@5'-UAC...GGAGA UGAGU ACUGA...GCG-3'@LB@ GAGCAA GAAGCACU@LB@ :\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUCGUU CUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -17.2491 kcal/mol@LB@Unfolding Energy - mRNA 3.12814 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 36 -- 42@LB@
27	0.0008083	0.09021	b2711	norW	-10.17	0.014477	99 -- 112	13 -- 26	NADH:flavorubredoxin oxidoreductase	_____________98_____________113\n_____________\|______________\|\n5'-GAA...CAGGA______________CGCCG...UUG-3'\n______________CGUUGCGCCAGGAA\n______________\|\|\|\|:\|:\|\|\|\|\|\|\|\n______________GCAAUGUGGUCCUU\n3'-UUU...UUUAA______________UAGAC...CAA-5'\n_____________\|______________\|\n_____________27_____________12\n	106 -- 112	13 -- 19	-23.5838 kcal/mol	5.14562 kcal/mol	8.27144 kcal/mol	98 113@LB@ \| \|@LB@5'-GAA...CAGGA CGCCG...UUG-3'@LB@ CGUUGCGCCAGGAA@LB@ \|\|\|\|:\|:\|\|\|\|\|\|\|@LB@ GCAAUGUGGUCCUU@LB@3'-UUU...UUUAA UAGAC...CAA-5'@LB@ \| \|@LB@ 27 12@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -23.5838 kcal/mol@LB@Unfolding Energy - mRNA 5.14562 kcal/mol@LB@Unfolding Energy - sRNA 8.27144 kcal/mol@LB@@LB@Position - mRNA 99 -- 112@LB@Position - sRNA 13 -- 26@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 13 -- 19@LB@
42	0.001686	0.1293	b2733	mutS	-6.21	0.172669	203 -- 222	25 -- 42	methyl-directed mismatch repair protein	_____________202__________________223\n_____________\|____________________\|\n5'-GAU...CCCAU______AA_________U__ACGCC...UGG-3'\n______________GAGUGC__UAGAAAAUU_CG\n______________:\|\|::\|__\|\|:\|\|\|\|\|\|_\|\|\n______________UUCGUG__AUUUUUUAA_GC\n3'-UUU...CGUUC______A_____________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________43___________________24\n	213 -- 219	27 -- 33	-10.4027 kcal/mol	2.54535 kcal/mol	1.64855 kcal/mol	202 223@LB@ \| \|@LB@5'-GAU...CCCAU AA U ACGCC...UGG-3'@LB@ GAGUGC UAGAAAAUU CG@LB@ :\|\|::\| \|\|:\|\|\|\|\|\| \|\|@LB@ UUCGUG AUUUUUUAA GC@LB@3'-UUU...CGUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.21 kcal/mol@LB@Hybridization Energy -10.4027 kcal/mol@LB@Unfolding Energy - mRNA 2.54535 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 27 -- 33@LB@
105	0.008762	0.2688	b2735	ygbI	-7.10	0.103888	185 -- 196	38 -- 49	DeoR family putative transcriptional regulator	_____________184__________197\n_____________\|____________\|\n5'-UUC...GGACA___G________AAAGU...AUA-3'\n______________AAG_AAGGAGCA\n______________\|\|\|_\|\|\|:\|\|\|\|\n______________UUC_UUCUUCGU\n3'-UUU...ACGAA___G________GAAUU...CAA-5'\n_____________\|____________\|\n_____________50___________37\n	190 -- 196	38 -- 44	-14.2659 kcal/mol	1.1364 kcal/mol	6.02696 kcal/mol	184 197@LB@ \| \|@LB@5'-UUC...GGACA G AAAGU...AUA-3'@LB@ AAG AAGGAGCA@LB@ \|\|\| \|\|\|:\|\|\|\|@LB@ UUC UUCUUCGU@LB@3'-UUU...ACGAA G GAAUU...CAA-5'@LB@ \| \|@LB@ 50 37@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -14.2659 kcal/mol@LB@Unfolding Energy - mRNA 1.1364 kcal/mol@LB@Unfolding Energy - sRNA 6.02696 kcal/mol@LB@@LB@Position - mRNA 185 -- 196@LB@Position - sRNA 38 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 38 -- 44@LB@
1	4.307e-10	1.387e-06	b2741	rpoS	-17.23	0.000044	75 -- 104	10 -- 40	RNA polymerase sigma S (sigma 38) factor	_____________74______________________________105\n_____________\|_______________________________\|\n5'-CGG...CGCUU______U______________AG________CGUAA...AGG-3'\n______________GCAUUU__GAAAUUCGUUACA__GGGAAAUC\n______________\|\|\|:\|\|__:\|\|\|\|\|\|\|\|\|\|\|\|__:\|\|\|\|\|\|\|\n______________CGUGAA__UUUUAAGCAAUGU__UCCUUUAG\n3'-UUU...UUCUU______UU_____________GG________ACUAC...CAA-5'\n_____________\|_______________________________\|\n_____________41______________________________9\n	98 -- 104	10 -- 16	-32.4258 kcal/mol	5.97429 kcal/mol	9.22048 kcal/mol	74 105@LB@ \| \|@LB@5'-CGG...CGCUU U AG CGUAA...AGG-3'@LB@ GCAUUU GAAAUUCGUUACA GGGAAAUC@LB@ \|\|\|:\|\| :\|\|\|\|\|\|\|\|\|\|\|\| :\|\|\|\|\|\|\|@LB@ CGUGAA UUUUAAGCAAUGU UCCUUUAG@LB@3'-UUU...UUCUU UU GG ACUAC...CAA-5'@LB@ \| \|@LB@ 41 9@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -32.4258 kcal/mol@LB@Unfolding Energy - mRNA 5.97429 kcal/mol@LB@Unfolding Energy - sRNA 9.22048 kcal/mol@LB@@LB@Position - mRNA 75 -- 104@LB@Position - sRNA 10 -- 40@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 10 -- 16@LB@
180	0.02111	0.3768	b2753	iap	-4.77	0.357003	164 -- 179	25 -- 40	aminopeptidase in alkaline phosphatase isozyme conversion	_____________163______________180\n_____________\|________________\|\n5'-UAG...CUAUG___G_A__________CAUGG...CUA-3'\n______________GCG_U_AAAAAAUUUG\n______________\|\|:_\|_\|\|\|\|\|\|\|\|:\|\n______________CGU_A_UUUUUUAAGC\n3'-UUU...UUCUU___G_A__________AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	170 -- 176	28 -- 34	-8.71545 kcal/mol	2.29678 kcal/mol	1.64821 kcal/mol	163 180@LB@ \| \|@LB@5'-UAG...CUAUG G A CAUGG...CUA-3'@LB@ GCG U AAAAAAUUUG@LB@ \|\|: \| \|\|\|\|\|\|\|\|:\|@LB@ CGU A UUUUUUAAGC@LB@3'-UUU...UUCUU G A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -8.71545 kcal/mol@LB@Unfolding Energy - mRNA 2.29678 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 28 -- 34@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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