Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
73	0.01516	0.6177	b0619	citA	-15.44	0.003129	164 -- 175	46 -- 57	sensory histidine kinase in two-component regulatory system with CitB	_____________163__________176\n_____________\|____________\|\n5'-CAU...UACAU____________CUCGG...UCA-3'\n______________CCGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	169 -- 175	46 -- 52	-20.3901 kcal/mol	2.21322 kcal/mol	2.7365 kcal/mol	163 176@LB@ \| \|@LB@5'-CAU...UACAU CUCGG...UCA-3'@LB@ CCGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -20.3901 kcal/mol@LB@Unfolding Energy - mRNA 2.21322 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 164 -- 175@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 46 -- 52@LB@
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator	_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
169	0.03425	0.6177	b0336	codB	-12.15	0.014930	188 -- 202	38 -- 52	cytosine transporter	_____________187_____________203\n_____________\|_______________\|\n5'-CCA...GCAAA_______________GUCGC...UUU-3'\n______________AAGGGGGAAUUUCGU\n______________\|\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUCUCCUUAAAGUA\n3'-UUU...GGCAG_______________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	196 -- 202	38 -- 44	-18.3448 kcal/mol	5.13025 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-CCA...GCAAA GUCGC...UUU-3'@LB@ AAGGGGGAAUUUCGU@LB@ \|\|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUCUCCUUAAAGUA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.3448 kcal/mol@LB@Unfolding Energy - mRNA 5.13025 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
94	0.01884	0.6177	b2048	cpsG	-10.80	0.028164	47 -- 56	45 -- 54	phosphomannomutase	_____________46_________57\n_____________\|__________\|\n5'-GGG...UUAUC__________UGAUG...GCG-3'\n______________UCGAAGAGGA\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	50 -- 56	45 -- 51	-14.144 kcal/mol	2.41054 kcal/mol	0.929144 kcal/mol	46 57@LB@ \| \|@LB@5'-GGG...UUAUC UGAUG...GCG-3'@LB@ UCGAAGAGGA@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -14.144 kcal/mol@LB@Unfolding Energy - mRNA 2.41054 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 47 -- 56@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 45 -- 51@LB@
4	0.0002658	0.2138	b1040	csgD	-11.06	0.024985	185 -- 199	38 -- 52	csgBAC operon transcriptional regulator	_____________184_____________200\n_____________\|_______________\|\n5'-UUA...UAAAA____C__________CAUGU...CGC-3'\n______________AAAG_GGGGUUUCAU\n______________\|\|\|\|_\|\|::\|\|\|\|\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	193 -- 199	38 -- 44	-14.3947 kcal/mol	2.26766 kcal/mol	1.0693 kcal/mol	184 200@LB@ \| \|@LB@5'-UUA...UAAAA C CAUGU...CGC-3'@LB@ AAAG GGGGUUUCAU@LB@ \|\|\|\| \|\|::\|\|\|\|\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -14.3947 kcal/mol@LB@Unfolding Energy - mRNA 2.26766 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 185 -- 199@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 38 -- 44@LB@
164	0.03346	0.6177	b1449	curA	-5.87	0.264423	114 -- 122	45 -- 53	curcumin/dihydrocurcumin reductase NADPH-dependent	_____________113_______123\n_____________\|_________\|\n5'-CGG...UGUUG_________UGUGA...UCG-3'\n______________CAGAGGGGA\n______________\|\|:\|\|:\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	116 -- 122	45 -- 51	-11.6619 kcal/mol	4.87234 kcal/mol	0.917553 kcal/mol	113 123@LB@ \| \|@LB@5'-CGG...UGUUG UGUGA...UCG-3'@LB@ CAGAGGGGA@LB@ \|\|:\|\|:\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -11.6619 kcal/mol@LB@Unfolding Energy - mRNA 4.87234 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 114 -- 122@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 45 -- 51@LB@
137	0.02646	0.6177	b3807	cyaY	-4.99	0.375460	213 -- 221	38 -- 46	iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein	_____________212_______222\n_____________\|_________\|\n5'-UGA...ACAGU_________CGCCU...AAA-3'\n______________GAAUUUCAU\n______________\|\|\|\|\|\|\|\|\|\n______________CUUAAAGUA\n3'-UUU...UUCUC_________AAAAA...ACA-5'\n_____________\|_________\|\n_____________47________37\n	215 -- 221	38 -- 44	-7.89908 kcal/mol	1.90809 kcal/mol	1.00074 kcal/mol	212 222@LB@ \| \|@LB@5'-UGA...ACAGU CGCCU...AAA-3'@LB@ GAAUUUCAU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUAAAGUA@LB@3'-UUU...UUCUC AAAAA...ACA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.99 kcal/mol@LB@Hybridization Energy -7.89908 kcal/mol@LB@Unfolding Energy - mRNA 1.90809 kcal/mol@LB@Unfolding Energy - sRNA 1.00074 kcal/mol@LB@@LB@Position - mRNA 213 -- 221@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
14	0.003078	0.593	b0886	cydC	-10.90	0.026971	183 -- 199	39 -- 56	glutathione/cysteine ABC transporter export permease/ATPase	_____________182________________200\n_____________\|__________________\|\n5'-GCG...CCCAU_____________A____AAUGC...UCG-3'\n______________CGUC_AGGAGGAG_UUUA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|:\|\n______________GCAG_UUCUCCUU_AAGU\n3'-UUU...ACCGG____U________A____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	188 -- 194	44 -- 50	-16.2318 kcal/mol	4.17801 kcal/mol	1.15786 kcal/mol	182 200@LB@ \| \|@LB@5'-GCG...CCCAU A AAUGC...UCG-3'@LB@ CGUC AGGAGGAG UUUA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|:\|@LB@ GCAG UUCUCCUU AAGU@LB@3'-UUU...ACCGG U A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -16.2318 kcal/mol@LB@Unfolding Energy - mRNA 4.17801 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 183 -- 199@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
96	0.01897	0.6177	b2422	cysA	-7.76	0.115977	190 -- 202	38 -- 50	sulfate/thiosulfate transporter subunit	_____________189___________203\n_____________\|_____________\|\n5'-GGU...CAGCA_______CA____GAGCA...UGC-3'\n______________GGAGGAA__UCAU\n______________:\|\|\|\|\|\|__\|\|\|\|\n______________UCUCCUU__AGUA\n3'-UUU...CAGUU_______AA____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________51____________37\n	190 -- 196	44 -- 50	-11.8687 kcal/mol	3.04673 kcal/mol	1.0603 kcal/mol	189 203@LB@ \| \|@LB@5'-GGU...CAGCA CA GAGCA...UGC-3'@LB@ GGAGGAA UCAU@LB@ :\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCUU AGUA@LB@3'-UUU...CAGUU AA AAAAA...ACA-5'@LB@ \| \|@LB@ 51 37@LB@@LB@@LB@Energy -7.76 kcal/mol@LB@Hybridization Energy -11.8687 kcal/mol@LB@Unfolding Energy - mRNA 3.04673 kcal/mol@LB@Unfolding Energy - sRNA 1.0603 kcal/mol@LB@@LB@Position - mRNA 190 -- 202@LB@Position - sRNA 38 -- 50@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
17	0.003407	0.593	b3607	cysE	-9.56	0.050591	4 -- 44	27 -- 56	serine acetyltransferase	_____________3__________________________________________45\n_____________\|__________________________________________\|\n________5'-CGG_______AUGCCAAUAACC______A_____CAAG_______AUUGC...CGA-3'\n______________CGUUGAA____________GAGGAA_UUUAU_____UAUUAU\n______________\|\|\|::\|\|____________\|\|\|\|\|\|_\|\|:\|\|_____\|\|\|\|\|\|\n______________GCAGUUU____________CUCCUU_AAGUA_____AUAAUA\n3'-UUU...ACCGG_________________________A_____AAAAA______AUACG...ACA-5'\n_____________\|__________________________________________\|\n_____________57_________________________________________26\n	4 -- 10	50 -- 56	-14.2001 kcal/mol	3.44433 kcal/mol	1.19682 kcal/mol	3 45@LB@ \| \|@LB@ 5'-CGG AUGCCAAUAACC A CAAG AUUGC...CGA-3'@LB@ CGUUGAA GAGGAA UUUAU UAUUAU@LB@ \|\|\|::\|\| \|\|\|\|\|\| \|\|:\|\| \|\|\|\|\|\|@LB@ GCAGUUU CUCCUU AAGUA AUAAUA@LB@3'-UUU...ACCGG A AAAAA AUACG...ACA-5'@LB@ \| \|@LB@ 57 26@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -14.2001 kcal/mol@LB@Unfolding Energy - mRNA 3.44433 kcal/mol@LB@Unfolding Energy - sRNA 1.19682 kcal/mol@LB@@LB@Position - mRNA 4 -- 44@LB@Position - sRNA 27 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 50 -- 56@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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