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
175	0.009651	0.1848	b2016	yeeZ	-14.25	0.018278	222 -- 265	1 -- 50	putative epimerase	_____________221_______________________________________________________266\n_____________\|_________________________________________________________\|\n5'-ACC...UUGUC___UUA________A____CA___C______________________CAC_______GCGAG...CAC-3'\n______________GGG___GGGUGGUU___GG__UGC_GCUGGCG___________AUGU___UUUCAGC\n______________:\|\|___:\|\|\|\|\|\|\|___\|\|__\|:\|_\|\|\|:\|\|:___________\|\|\|\|___\|\|\|\|\|\|\|\n______________UCC___UCCACCAA___CC__AUG_CGAUCGU___________UACA___AAAGUCG\n3'-UUU...CCGAU______________GGA_______U_______AAAAUACCCAA____A_________-5'\n_____________\|________________________________________________________\|\n_____________51_______________________________________________________1\n	259 -- 265	1 -- 7	-34.6896 kcal/mol	15.7797 kcal/mol	4.6634 kcal/mol	221 266@LB@ \| \|@LB@5'-ACC...UUGUC UUA A CA C CAC GCGAG...CAC-3'@LB@ GGG GGGUGGUU GG UGC GCUGGCG AUGU UUUCAGC@LB@ :\|\| :\|\|\|\|\|\|\| \|\| \|:\| \|\|\|:\|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ UCC UCCACCAA CC AUG CGAUCGU UACA AAAGUCG@LB@3'-UUU...CCGAU GGA U AAAAUACCCAA A -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -14.25 kcal/mol@LB@Hybridization Energy -34.6896 kcal/mol@LB@Unfolding Energy - mRNA 15.7797 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 222 -- 265@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 1 -- 7@LB@
3	2.088e-07	0.000234	b2077	iceT	-18.53	0.000593	226 -- 254	1 -- 30	putative citrate/iron-citrate/zinc-citrate efflux transporter	_____________225____________________________255\n_____________\|______________________________\|\n5'-CGG...CACCC_______A_______A_____GC_______UUCUU...UUC-3'\n______________GUUGGCA__UUGUGG_UUGUG__UUUCGGC\n______________\|:\|:\|\|\|__\|\|:\|\|\|_\|\|:\|\|__\|\|\|\|:\|\|\n______________CGAUCGU__AAUACC_AAUAC__AAAGUCG\n3'-UUU...CAUGU_______AA______C_____AA_______-5'\n_____________\|_____________________________\|\n_____________31____________________________1\n	248 -- 254	1 -- 7	-30.4381 kcal/mol	10.4245 kcal/mol	1.48556 kcal/mol	225 255@LB@ \| \|@LB@5'-CGG...CACCC A A GC UUCUU...UUC-3'@LB@ GUUGGCA UUGUGG UUGUG UUUCGGC@LB@ \|:\|:\|\|\| \|\|:\|\|\| \|\|:\|\| \|\|\|\|:\|\|@LB@ CGAUCGU AAUACC AAUAC AAAGUCG@LB@3'-UUU...CAUGU AA C AA -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -18.53 kcal/mol@LB@Hybridization Energy -30.4381 kcal/mol@LB@Unfolding Energy - mRNA 10.4245 kcal/mol@LB@Unfolding Energy - sRNA 1.48556 kcal/mol@LB@@LB@Position - mRNA 226 -- 254@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 1 -- 7@LB@
145	0.006858	0.158	b2079	baeR	-14.59	0.014658	61 -- 107	1 -- 46	response regulator in two-component regulatory system with BaeS	_____________60________________________________________________108\n_____________\|_________________________________________________\|\n5'-CAG...CCAGC__C______G__C__G________A____CC__AACAU____GA_____ACAUA...CGA-3'\n______________GG_GGUUCC_GG_UG_GGCUGGCG_UUUG__UG_____UGUU____AGC\n______________\|\|_\|\|\|\|\|\|_\|\|_\|:_:\|\|\|:\|\|:_\|\|\|:__\|\|_____\|\|\|\|____\|\|\|\n______________CC_CCAAGG_CC_AU_UCGAUCGU_AAAU__AC_____ACAA____UCG\n3'-UUU...UUCCU__A______A_____G________A________CCAAU____AAAG___-5'\n_____________\|________________________________________________\|\n_____________47_______________________________________________1\n	78 -- 84	24 -- 30	-36.7072 kcal/mol	17.5074 kcal/mol	4.60935 kcal/mol	60 108@LB@ \| \|@LB@5'-CAG...CCAGC C G C G A CC AACAU GA ACAUA...CGA-3'@LB@ GG GGUUCC GG UG GGCUGGCG UUUG UG UGUU AGC@LB@ \|\| \|\|\|\|\|\| \|\| \|: :\|\|\|:\|\|: \|\|\|: \|\| \|\|\|\| \|\|\|@LB@ CC CCAAGG CC AU UCGAUCGU AAAU AC ACAA UCG@LB@3'-UUU...UUCCU A A G A CCAAU AAAG -5'@LB@ \| \|@LB@ 47 1@LB@@LB@@LB@Energy -14.59 kcal/mol@LB@Hybridization Energy -36.7072 kcal/mol@LB@Unfolding Energy - mRNA 17.5074 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 61 -- 107@LB@Position - sRNA 1 -- 46@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 24 -- 30@LB@
155	0.007835	0.1694	b2239	glpQ	-10.90	0.112133	59 -- 106	1 -- 45	periplasmic glycerophosphodiester phosphodiesterase	_____________58________________________________________________107\n_____________\|_________________________________________________\|\n5'-CGG...ACACC____AC_____C__CUG__A_____GC_______UA____A__GG____AGCAU...UCA-3'\n______________GUGG__UUCUU_GG___GG_UGGCG__UUUAUGG___AUG_UU__CGGC\n______________\|\|\|\|__\|\|\|:\|_\|\|___:\|_\|:\|\|:__\|\|\|\|\|\|\|___\|\|\|_\|\|__\|:\|\|\n______________CACC__AAGGA_CC___UC_AUCGU__AAAUACC___UAC_AA__GUCG\n3'-UUU...UCCUC______________AUG__G_____A________CAA___A__AA____-5'\n_____________\|________________________________________________\|\n_____________46_______________________________________________1\n	86 -- 92	16 -- 22	-29.5358 kcal/mol	14.0238 kcal/mol	4.60935 kcal/mol	58 107@LB@ \| \|@LB@5'-CGG...ACACC AC C CUG A GC UA A GG AGCAU...UCA-3'@LB@ GUGG UUCUU GG GG UGGCG UUUAUGG AUG UU CGGC@LB@ \|\|\|\| \|\|\|:\| \|\| :\| \|:\|\|: \|\|\|\|\|\|\| \|\|\| \|\| \|:\|\|@LB@ CACC AAGGA CC UC AUCGU AAAUACC UAC AA GUCG@LB@3'-UUU...UCCUC AUG G A CAA A AA -5'@LB@ \| \|@LB@ 46 1@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -29.5358 kcal/mol@LB@Unfolding Energy - mRNA 14.0238 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 59 -- 106@LB@Position - sRNA 1 -- 45@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 16 -- 22@LB@
22	0.0002072	0.03165	b2341	fadJ	-8.08	0.343546	182 -- 217	1 -- 44	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase	_____________181__________________________________________218\n_____________\|____________________________________________\|\n5'-CAU...GGCAA__________A________AAUA______AA____ACA______GUUUA...CGG-3'\n______________UGGUUCU_GG___GGC_GG______AUGG___AUG____UCAGC\n______________\|\|\|\|\|\|:_\|\|___:\|\|_:\|______\|\|\|\|___\|\|\|____\|\|\|\|\|\n______________ACCAAGG_CC___UCG_UC______UACC___UAC____AGUCG\n3'-UUU...CCUCC_______A__AUG___A__GUAAAA____CAA___AAAA_____-5'\n_____________\|___________________________________________\|\n_____________45__________________________________________1\n	182 -- 188	38 -- 44	-22.4043 kcal/mol	9.71146 kcal/mol	4.60934 kcal/mol	181 218@LB@ \| \|@LB@5'-CAU...GGCAA A AAUA AA ACA GUUUA...CGG-3'@LB@ UGGUUCU GG GGC GG AUGG AUG UCAGC@LB@ \|\|\|\|\|\|: \|\| :\|\| :\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ ACCAAGG CC UCG UC UACC UAC AGUCG@LB@3'-UUU...CCUCC A AUG A GUAAAA CAA AAAA -5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -22.4043 kcal/mol@LB@Unfolding Energy - mRNA 9.71146 kcal/mol@LB@Unfolding Energy - sRNA 4.60934 kcal/mol@LB@@LB@Position - mRNA 182 -- 217@LB@Position - sRNA 1 -- 44@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 38 -- 44@LB@
114	0.004808	0.1404	b2372	yfdV	-9.14	0.236047	240 -- 266	1 -- 35	putative transporter	_____________239____________________________________267\n_____________\|______________________________________\|\n5'-UUC...UUAUC___AU__U______________________________GGCAG...CUC-3'\n______________GUA__CA_GCU_GU______UGGGUUAU____UUUAGC\n______________\|\|\|__\|\|_\|\|\|_\|:______\|\|\|\|\|\|\|\|____\|\|:\|\|\|\n______________CAU__GU_CGA_CG______ACCCAAUA____AAGUCG\n3'-UUU...AGGAC___________U__UAAAAU________CAAA______-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	254 -- 260	11 -- 17	-17.7969 kcal/mol	7.16419 kcal/mol	1.49508 kcal/mol	239 267@LB@ \| \|@LB@5'-UUC...UUAUC AU U GGCAG...CUC-3'@LB@ GUA CA GCU GU UGGGUUAU UUUAGC@LB@ \|\|\| \|\| \|\|\| \|: \|\|\|\|\|\|\|\| \|\|:\|\|\|@LB@ CAU GU CGA CG ACCCAAUA AAGUCG@LB@3'-UUU...AGGAC U UAAAAU CAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -17.7969 kcal/mol@LB@Unfolding Energy - mRNA 7.16419 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 240 -- 266@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
15	0.0001004	0.02121	b2416	ptsI	-14.97	0.011388	179 -- 212	1 -- 32	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________178_________________________________213\n_____________\|___________________________________\|\n5'-GUG...AAAAU____CACA____AGG___________A___CA___AUUUU...CCG-3'\n______________CAGU____AGUA___UA_GGGUUAUG_UUU__GGC\n______________\|\|\|:____\|\|:\|___\|\|_\|\|\|\|\|\|\|\|_\|\|\|__:\|\|\n______________GUCG____UCGU___AU_CCCAAUAC_AAA__UCG\n3'-UUU...ACCAU____A_______AAA__A________A___AG___-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	197 -- 203	10 -- 16	-21.5882 kcal/mol	5.12711 kcal/mol	1.49075 kcal/mol	178 213@LB@ \| \|@LB@5'-GUG...AAAAU CACA AGG A CA AUUUU...CCG-3'@LB@ CAGU AGUA UA GGGUUAUG UUU GGC@LB@ \|\|\|: \|\|:\| \|\| \|\|\|\|\|\|\|\| \|\|\| :\|\|@LB@ GUCG UCGU AU CCCAAUAC AAA UCG@LB@3'-UUU...ACCAU A AAA A A AG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.97 kcal/mol@LB@Hybridization Energy -21.5882 kcal/mol@LB@Unfolding Energy - mRNA 5.12711 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 10 -- 16@LB@
82	0.002694	0.1082	b2474	tmcA	-11.34	0.091143	115 -- 147	1 -- 34	elongator methionine tRNA (ac4C34) acetyltransferase	_____________114________________________________148\n_____________\|__________________________________\|\n5'-GAU...AACGC__________UUAAACGU____UCGACAG_____GAUCC...UUG-3'\n______________UACAGCUGGU________GGUU________CGGC\n______________\|\|\|\|\|\|\|:\|:________\|\|\|\|________\|:\|\|\n______________AUGUCGAUCG________CCAA________GUCG\n3'-UUU...GGACC__________UAAAAUAC____UACAAAAA____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	118 -- 124	25 -- 31	-23.7384 kcal/mol	10.9014 kcal/mol	1.49507 kcal/mol	114 148@LB@ \| \|@LB@5'-GAU...AACGC UUAAACGU UCGACAG GAUCC...UUG-3'@LB@ UACAGCUGGU GGUU CGGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|:\|\|@LB@ AUGUCGAUCG CCAA GUCG@LB@3'-UUU...GGACC UAAAAUAC UACAAAAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -23.7384 kcal/mol@LB@Unfolding Energy - mRNA 10.9014 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 115 -- 147@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 25 -- 31@LB@
127	0.005388	0.142	b2721	hycE	-10.66	0.125013	137 -- 158	1 -- 36	hydrogenase 3 large subunit	_____________136___________________________________159\n_____________\|_____________________________________\|\n5'-UUC...GGCUG___UU____UU__________________________GUUCG...UGA-3'\n______________GGU__GGCU__GCAU_______________UUUUAGC\n______________\|\|\|__:\|\|\|__\|\|\|\|_______________\|\|\|:\|\|\|\n______________CCA__UCGA__CGUA_______________AAAGUCG\n3'-UUU...AAGGA___UG____U_____AAAUACCCAAUACAA_______-5'\n_____________\|____________________________________\|\n_____________37___________________________________1\n	152 -- 158	1 -- 7	-16.3373 kcal/mol	4.17778 kcal/mol	1.49509 kcal/mol	136 159@LB@ \| \|@LB@5'-UUC...GGCUG UU UU GUUCG...UGA-3'@LB@ GGU GGCU GCAU UUUUAGC@LB@ \|\|\| :\|\|\| \|\|\|\| \|\|\|:\|\|\|@LB@ CCA UCGA CGUA AAAGUCG@LB@3'-UUU...AAGGA UG U AAAUACCCAAUACAA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -16.3373 kcal/mol@LB@Unfolding Energy - mRNA 4.17778 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 137 -- 158@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
151	0.007423	0.1652	b2895	fldB	-9.53	0.202764	191 -- 224	1 -- 31	flavodoxin 2	_____________190__________________________________225\n_____________\|____________________________________\|\n5'-CGG...CGAGA____UA____AUGAA_______CU_______A____UCCAG...AUA-3'\n______________AGCU__CGUU_____UAUGGGU____UUUUU_CGGU\n______________\|\|\|\|__\|:\|\|_____\|\|\|\|\|\|\|____\|\|\|\|\|_\|:\|:\n______________UCGA__GUAA_____AUACCCA____AAAAA_GUCG\n3'-UUU...CCAUG____UC____A___________AUAC__________-5'\n_____________\|___________________________________\|\n_____________32__________________________________1\n	206 -- 212	14 -- 20	-17.4845 kcal/mol	6.4701 kcal/mol	1.48722 kcal/mol	190 225@LB@ \| \|@LB@5'-CGG...CGAGA UA AUGAA CU A UCCAG...AUA-3'@LB@ AGCU CGUU UAUGGGU UUUUU CGGU@LB@ \|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|:\|:@LB@ UCGA GUAA AUACCCA AAAAA GUCG@LB@3'-UUU...CCAUG UC A AUAC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -17.4845 kcal/mol@LB@Unfolding Energy - mRNA 6.4701 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 191 -- 224@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 14 -- 20@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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