Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
191	0.01094	0.1919	b3554	yiaF	-11.44	0.087025	256 -- 281	6 -- 37	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein	_____________255______________________________282\n_____________\|________________________________\|\n5'-AAU...AUUAA_____________CUGA_______________GAUAA...AGC-3'\n______________UGGU__AGUUAGC_____GUGGGU___GUUUU\n______________\|\|\|\|__\|\|:\|\|\|\|_____:\|\|\|\|\|___\|\|\|\|\|\n______________ACCA__UCGAUCG_____UACCCA___CAAAA\n3'-UUU...CAAGG____UG_______UAAAA______AUA_____AGUCG-5'\n_____________\|________________________________\|\n_____________38_______________________________5\n	260 -- 266	25 -- 31	-21.639 kcal/mol	7.5014 kcal/mol	2.70019 kcal/mol	255 282@LB@ \| \|@LB@5'-AAU...AUUAA CUGA GAUAA...AGC-3'@LB@ UGGU AGUUAGC GUGGGU GUUUU@LB@ \|\|\|\| \|\|:\|\|\|\| :\|\|\|\|\| \|\|\|\|\|@LB@ ACCA UCGAUCG UACCCA CAAAA@LB@3'-UUU...CAAGG UG UAAAA AUA AGUCG-5'@LB@ \| \|@LB@ 38 5@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.639 kcal/mol@LB@Unfolding Energy - mRNA 7.5014 kcal/mol@LB@Unfolding Energy - sRNA 2.70019 kcal/mol@LB@@LB@Position - mRNA 256 -- 281@LB@Position - sRNA 6 -- 37@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 25 -- 31@LB@
192	0.01101	0.1919	b2478	dapA	-6.78	0.505920	248 -- 269	25 -- 47	dihydrodipicolinate synthase	_____________247_____________________270\n_____________\|_______________________\|\n5'-GGC...GAAAA____AAUG____UCG________UUGAA...CCA-3'\n______________AGGU____UCUG____GGCUAGC\n______________\|\|\|\|____:\|\|\|____:\|\|\|\|\|\|\n______________UCCA____GGAC____UCGAUCG\n3'-UUU...AUUCC____CCAA____CAUG_______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	263 -- 269	25 -- 31	-19.6963 kcal/mol	8.35751 kcal/mol	4.55753 kcal/mol	247 270@LB@ \| \|@LB@5'-GGC...GAAAA AAUG UCG UUGAA...CCA-3'@LB@ AGGU UCUG GGCUAGC@LB@ \|\|\|\| :\|\|\| :\|\|\|\|\|\|@LB@ UCCA GGAC UCGAUCG@LB@3'-UUU...AUUCC CCAA CAUG UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -19.6963 kcal/mol@LB@Unfolding Energy - mRNA 8.35751 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 25 -- 31@LB@
193	0.01107	0.1919	b3532	bcsB	-10.24	0.150531	226 -- 241	15 -- 35	regulator of cellulose synthase cyclic di-GMP binding	_____________225___________________242\n_____________\|_____________________\|\n5'-AAG...GAUUU_______G_____________GAUGA...UCA-3'\n______________GUGCAGU__GC____UAUGGG\n______________\|\|:\|\|\|:__\|\|____\|\|\|\|\|\|\n______________CAUGUCG__CG____AUACCC\n3'-UUU...AGGAC_______AU__UAAA______AAUAC...UCG-5'\n_____________\|_____________________\|\n_____________36____________________14\n	226 -- 232	29 -- 35	-18.7324 kcal/mol	7.03896 kcal/mol	1.4496 kcal/mol	225 242@LB@ \| \|@LB@5'-AAG...GAUUU G GAUGA...UCA-3'@LB@ GUGCAGU GC UAUGGG@LB@ \|\|:\|\|\|: \|\| \|\|\|\|\|\|@LB@ CAUGUCG CG AUACCC@LB@3'-UUU...AGGAC AU UAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -18.7324 kcal/mol@LB@Unfolding Energy - mRNA 7.03896 kcal/mol@LB@Unfolding Energy - sRNA 1.4496 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 29 -- 35@LB@
194	0.01107	0.1919	b3288	fmt	-14.89	0.012048	76 -- 114	11 -- 48	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase	_____________75_______________________________________115\n_____________\|________________________________________\|\n5'-AUU...AGCAU___A___AUCA___________AAACUG_______A____CUGUC...UGU-3'\n______________GAG_UGG____CCUGGU_CGGC______UUUAUGG_UUAU\n______________\|\|\|_\|\|\|____\|\|\|\|\|\|_\|:\|\|______\|\|\|\|\|\|\|_\|\|\|\|\n______________CUC_ACC____GGACCA_GUCG______AAAUACC_AAUA\n3'-UUU...GAUUC___C___AA________U____AUCGUA_______C____CAAAA...UCG-5'\n_____________\|________________________________________\|\n_____________49_______________________________________10\n	103 -- 109	16 -- 22	-29.2084 kcal/mol	9.72928 kcal/mol	4.59227 kcal/mol	75 115@LB@ \| \|@LB@5'-AUU...AGCAU A AUCA AAACUG A CUGUC...UGU-3'@LB@ GAG UGG CCUGGU CGGC UUUAUGG UUAU@LB@ \|\|\| \|\|\| \|\|\|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ CUC ACC GGACCA GUCG AAAUACC AAUA@LB@3'-UUU...GAUUC C AA U AUCGUA C CAAAA...UCG-5'@LB@ \| \|@LB@ 49 10@LB@@LB@@LB@Energy -14.89 kcal/mol@LB@Hybridization Energy -29.2084 kcal/mol@LB@Unfolding Energy - mRNA 9.72928 kcal/mol@LB@Unfolding Energy - sRNA 4.59227 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 11 -- 48@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 16 -- 22@LB@
195	0.01134	0.1946	b0633	rlpA	-8.12	0.339483	43 -- 55	25 -- 37	septal ring protein suppressor of prc minor lipoprotein	_____________42____________56\n_____________\|_____________\|\n5'-CGG...AAUAU_________A___GGUAU...CUG-3'\n______________UGGUAUGGU_AGC\n______________\|\|\|\|\|::\|:_\|\|\|\n______________ACCAUGUCG_UCG\n3'-UUU...CAAGG_________A___UAAAA...UCG-5'\n_____________\|_____________\|\n_____________38____________24\n	45 -- 51	29 -- 35	-15.087 kcal/mol	4.33932 kcal/mol	2.62824 kcal/mol	42 56@LB@ \| \|@LB@5'-CGG...AAUAU A GGUAU...CUG-3'@LB@ UGGUAUGGU AGC@LB@ \|\|\|\|\|::\|: \|\|\|@LB@ ACCAUGUCG UCG@LB@3'-UUU...CAAGG A UAAAA...UCG-5'@LB@ \| \|@LB@ 38 24@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -15.087 kcal/mol@LB@Unfolding Energy - mRNA 4.33932 kcal/mol@LB@Unfolding Energy - sRNA 2.62824 kcal/mol@LB@@LB@Position - mRNA 43 -- 55@LB@Position - sRNA 25 -- 37@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 29 -- 35@LB@
196	0.01135	0.1946	b1515	lsrD	-9.63	0.194390	56 -- 86	16 -- 44	autoinducer 2 import system permease protein	_____________55______________________________87\n_____________\|_______________________________\|\n5'-AGC...GGGUC_______GC___CGGU__________G____ACGCC...AUA-3'\n______________UGGUUCU__UGG____GCUGGUGUUU_AUGG\n______________\|\|\|\|\|\|:__\|\|\|____\|\|\|:\|::\|\|\|_\|\|\|\|\n______________ACCAAGG__ACC____CGAUCGUAAA_UACC\n3'-UUU...CCUCC____________AUGU__________A____CAAUA...UCG-5'\n_____________\|_______________________________\|\n_____________45______________________________15\n	56 -- 62	38 -- 44	-28.9595 kcal/mol	14.7558 kcal/mol	4.57147 kcal/mol	55 87@LB@ \| \|@LB@5'-AGC...GGGUC GC CGGU G ACGCC...AUA-3'@LB@ UGGUUCU UGG GCUGGUGUUU AUGG@LB@ \|\|\|\|\|\|: \|\|\| \|\|\|:\|::\|\|\| \|\|\|\|@LB@ ACCAAGG ACC CGAUCGUAAA UACC@LB@3'-UUU...CCUCC AUGU A CAAUA...UCG-5'@LB@ \| \|@LB@ 45 15@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -28.9595 kcal/mol@LB@Unfolding Energy - mRNA 14.7558 kcal/mol@LB@Unfolding Energy - sRNA 4.57147 kcal/mol@LB@@LB@Position - mRNA 56 -- 86@LB@Position - sRNA 16 -- 44@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 38 -- 44@LB@
197	0.01153	0.1967	b0610	rnk	-10.49	0.135367	130 -- 162	7 -- 39	regulator of nucleoside diphosphate kinase	_____________129__________________________________163\n_____________\|____________________________________\|\n5'-UCU...CGCCG___________G__G_____CUUU____________AUCUG...CGU-3'\n______________CCUG__ACGGU_AG_GUUUU____UGGG_UAUGUUU\n______________\|\|\|\|__\|\|:\|:_\|\|_:\|\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\n______________GGAC__UGUCG_UC_UAAAA____ACCC_AUACAAA\n3'-UUU...ACCAA____CA_____A__G_____U_______A_______AAGUCG-5'\n_____________\|____________________________________\|\n_____________40___________________________________6\n	156 -- 162	7 -- 13	-25.6411 kcal/mol	10.5512 kcal/mol	4.60345 kcal/mol	129 163@LB@ \| \|@LB@5'-UCU...CGCCG G G CUUU AUCUG...CGU-3'@LB@ CCUG ACGGU AG GUUUU UGGG UAUGUUU@LB@ \|\|\|\| \|\|:\|: \|\| :\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GGAC UGUCG UC UAAAA ACCC AUACAAA@LB@3'-UUU...ACCAA CA A G U A AAGUCG-5'@LB@ \| \|@LB@ 40 6@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.6411 kcal/mol@LB@Unfolding Energy - mRNA 10.5512 kcal/mol@LB@Unfolding Energy - sRNA 4.60345 kcal/mol@LB@@LB@Position - mRNA 130 -- 162@LB@Position - sRNA 7 -- 39@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 7 -- 13@LB@
198	0.01161	0.1971	b2712	hypF	-10.23	0.151482	281 -- 290	24 -- 33	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein	_____________280________291\n_____________\|__________\|\n5'-GAA...GUCUG__________CAGCA...UAA-3'\n______________GCAGCUGGCA\n______________:\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	284 -- 290	24 -- 30	-16.4359 kcal/mol	4.77953 kcal/mol	1.42716 kcal/mol	280 291@LB@ \| \|@LB@5'-GAA...GUCUG CAGCA...UAA-3'@LB@ GCAGCUGGCA@LB@ :\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -16.4359 kcal/mol@LB@Unfolding Energy - mRNA 4.77953 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 281 -- 290@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
199	0.0118	0.1975	b0077	ilvI	-11.98	0.066447	6 -- 27	1 -- 30	acetolactate synthase 3 large subunit	_____________5______________________________28\n_____________\|______________________________\|\n______5'-AAAUU_______AG_______A_____________CGAUU...UUU-3'\n______________GCU_GUA__UUGUGGG________UUCAGC\n______________\|\|\|_\|:\|__\|\|:\|\|\|\|________\|\|\|\|\|\|\n______________CGA_CGU__AAUACCC________AAGUCG\n3'-UUU...CAUGU___U___AA_______AAUACAAA______-5'\n_____________\|_____________________________\|\n_____________31____________________________1\n	14 -- 20	15 -- 21	-19.3299 kcal/mol	5.86615 kcal/mol	1.48556 kcal/mol	5 28@LB@ \| \|@LB@ 5'-AAAUU AG A CGAUU...UUU-3'@LB@ GCU GUA UUGUGGG UUCAGC@LB@ \|\|\| \|:\| \|\|:\|\|\|\| \|\|\|\|\|\|@LB@ CGA CGU AAUACCC AAGUCG@LB@3'-UUU...CAUGU U AA AAUACAAA -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.86615 kcal/mol@LB@Unfolding Energy - sRNA 1.48556 kcal/mol@LB@@LB@Position - mRNA 6 -- 27@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 15 -- 21@LB@
200	0.01185	0.1975	b0025	ribF	-6.09	0.598433	35 -- 41	28 -- 34	bifunctional riboflavin kinase/FAD synthetase	_____________34______42\n_____________\|_______\|\n5'-UGG...GUGAA_______UUUCC...GCG-3'\n______________UACAGCU\n______________\|\|\|\|\|\|\|\n______________AUGUCGA\n3'-UUU...GGACC_______UCGUA...UCG-5'\n_____________\|_______\|\n_____________35______27\n	35 -- 41	28 -- 34	-8.9914 kcal/mol	1.72675 kcal/mol	1.17027 kcal/mol	34 42@LB@ \| \|@LB@5'-UGG...GUGAA UUUCC...GCG-3'@LB@ UACAGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGUCGA@LB@3'-UUU...GGACC UCGUA...UCG-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.9914 kcal/mol@LB@Unfolding Energy - mRNA 1.72675 kcal/mol@LB@Unfolding Energy - sRNA 1.17027 kcal/mol@LB@@LB@Position - mRNA 35 -- 41@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 35 -- 41@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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