Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
43	0.002722	0.2088	b0192	nlpE	-8.83	0.206883	4 -- 33	38 -- 65	lipoprotein involved with copper homeostasis and adhesion	_____________3_______________________________34\n_____________\|_______________________________\|\n________5'-UCA____CUGAACC_____A____CUC_______GCUGG...CGC-3'\n______________GGAA________GCGA_GCAG___UGGCCCG\n______________\|\|\|\|________\|\|:\|_\|\|\|:___\|\|\|\|\|\|:\n______________CCUU________CGUU_CGUU___ACCGGGU\n3'-UUU...UACAA____UUAGUCAC____A______________UGUCU...UUG-5'\n_____________\|_______________________________\|\n_____________66______________________________37\n	27 -- 33	38 -- 44	-23.0011 kcal/mol	7.49976 kcal/mol	6.67322 kcal/mol	3 34@LB@ \| \|@LB@ 5'-UCA CUGAACC A CUC GCUGG...CGC-3'@LB@ GGAA GCGA GCAG UGGCCCG@LB@ \|\|\|\| \|\|:\| \|\|\|: \|\|\|\|\|\|:@LB@ CCUU CGUU CGUU ACCGGGU@LB@3'-UUU...UACAA UUAGUCAC A UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -23.0011 kcal/mol@LB@Unfolding Energy - mRNA 7.49976 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 4 -- 33@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 38 -- 44@LB@
103	0.009615	0.3118	b4045	yjbJ	-8.83	0.207064	48 -- 67	39 -- 60	stress-induced protein UPF0337 family	_____________47______________________68\n_____________\|_______________________\|\n5'-CGU...GCGGC____C_______________A__UGGUU...AAG-3'\n______________GUCA_UGGC___GCAAUGGU_CC\n______________:\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|:_\|\|\n______________UAGU_ACCG___CGUUACCG_GG\n3'-UUU...CCUUU____C____UUA___________UUGUC...UUG-5'\n_____________\|_______________________\|\n_____________61______________________38\n	58 -- 64	41 -- 47	-22.6105 kcal/mol	7.1744 kcal/mol	6.61009 kcal/mol	47 68@LB@ \| \|@LB@5'-CGU...GCGGC C A UGGUU...AAG-3'@LB@ GUCA UGGC GCAAUGGU CC@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|\|\|: \|\|@LB@ UAGU ACCG CGUUACCG GG@LB@3'-UUU...CCUUU C UUA UUGUC...UUG-5'@LB@ \| \|@LB@ 61 38@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -22.6105 kcal/mol@LB@Unfolding Energy - mRNA 7.1744 kcal/mol@LB@Unfolding Energy - sRNA 6.61009 kcal/mol@LB@@LB@Position - mRNA 48 -- 67@LB@Position - sRNA 39 -- 60@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 41 -- 47@LB@
96	0.009004	0.3118	b3981	secE	-8.82	0.207803	253 -- 270	42 -- 57	preprotein translocase membrane subunit	_____________252________________271\n_____________\|__________________\|\n5'-UAA...GAUGA_____GUCGU________CAUUG...ACU-3'\n______________AGUGG_____UGUGGUGG\n______________\|\|\|\|\|_____\|\|:::\|\|\|\n______________UCACC_____ACGUUACC\n3'-UUU...UUUAG_____GUU__________GGGUU...UUG-5'\n_____________\|__________________\|\n_____________58_________________41\n	264 -- 270	42 -- 48	-15.0916 kcal/mol	2.64473 kcal/mol	3.62906 kcal/mol	252 271@LB@ \| \|@LB@5'-UAA...GAUGA GUCGU CAUUG...ACU-3'@LB@ AGUGG UGUGGUGG@LB@ \|\|\|\|\| \|\|:::\|\|\|@LB@ UCACC ACGUUACC@LB@3'-UUU...UUUAG GUU GGGUU...UUG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -15.0916 kcal/mol@LB@Unfolding Energy - mRNA 2.64473 kcal/mol@LB@Unfolding Energy - sRNA 3.62906 kcal/mol@LB@@LB@Position - mRNA 253 -- 270@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 42 -- 48@LB@
26	0.00144	0.1863	b4406	yaeP	-8.75	0.213688	187 -- 204	2 -- 20	UPF0253 family protein	_____________186_________________205\n_____________\|___________________\|\n5'-ACC...AGUGC_____G_____________AAAAA...UGC-3'\n______________UGACA__GAGGGCAUGUGG\n______________\|\|\|\|\|__:\|:\|\|\|\|\|:\|::\n______________ACUGU__UUUCCGUAUAUU\n3'-UUU...UAGAC_____UA____________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	197 -- 203	3 -- 9	-20.0716 kcal/mol	7.09254 kcal/mol	4.22649 kcal/mol	186 205@LB@ \| \|@LB@5'-ACC...AGUGC G AAAAA...UGC-3'@LB@ UGACA GAGGGCAUGUGG@LB@ \|\|\|\|\| :\|:\|\|\|\|\|:\|::@LB@ ACUGU UUUCCGUAUAUU@LB@3'-UUU...UAGAC UA G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -20.0716 kcal/mol@LB@Unfolding Energy - mRNA 7.09254 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 187 -- 204@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
77	0.006658	0.2822	b3347	fkpA	-8.74	0.214444	80 -- 111	4 -- 28	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)	_____________79________________________________112\n_____________\|_________________________________\|\n5'-UGG...CAAAA________AAAAUAGA_________________CUGUA...CAG-3'\n______________AGAGUCUG________UGAUAAU_AGGGCGUGU\n______________\|:\|:\|\|\|\|________\|\|\|:\|\|\|_\|:\|\|\|:\|:\|\n______________UUUUAGAC________ACUGUUA_UUCCGUAUA\n3'-UUU...UUUUA_______________________U_________UUG-5'\n_____________\|_________________________________\|\n_____________29________________________________3\n	104 -- 110	5 -- 11	-22.6947 kcal/mol	9.05802 kcal/mol	4.89231 kcal/mol	79 112@LB@ \| \|@LB@5'-UGG...CAAAA AAAAUAGA CUGUA...CAG-3'@LB@ AGAGUCUG UGAUAAU AGGGCGUGU@LB@ \|:\|:\|\|\|\| \|\|\|:\|\|\| \|:\|\|\|:\|:\|@LB@ UUUUAGAC ACUGUUA UUCCGUAUA@LB@3'-UUU...UUUUA U UUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -22.6947 kcal/mol@LB@Unfolding Energy - mRNA 9.05802 kcal/mol@LB@Unfolding Energy - sRNA 4.89231 kcal/mol@LB@@LB@Position - mRNA 80 -- 111@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 5 -- 11@LB@
68	0.005347	0.2645	b3184	yhbE	-8.71	0.217326	12 -- 35	8 -- 33	EamA family inner membrane putative transporter	_____________11_________________________36\n_____________\|__________________________\|\n5'-AAG...ACGGU___________C____AGU_______CCGAA...UGG-3'\n______________AAAGUGAAAUU___GA___UAAAGGC\n______________\|\|\|:\|:\|\|\|\|:___\|\|___\|\|\|\|\|\|\|\n______________UUUUAUUUUAG___CU___AUUUCCG\n3'-UUU...UUGUC___________ACA__GUU_______UAUAUUG-5'\n_____________\|__________________________\|\n_____________34_________________________7\n	29 -- 35	8 -- 14	-15.936 kcal/mol	2.19409 kcal/mol	5.02883 kcal/mol	11 36@LB@ \| \|@LB@5'-AAG...ACGGU C AGU CCGAA...UGG-3'@LB@ AAAGUGAAAUU GA UAAAGGC@LB@ \|\|\|:\|:\|\|\|\|: \|\| \|\|\|\|\|\|\|@LB@ UUUUAUUUUAG CU AUUUCCG@LB@3'-UUU...UUGUC ACA GUU UAUAUUG-5'@LB@ \| \|@LB@ 34 7@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -15.936 kcal/mol@LB@Unfolding Energy - mRNA 2.19409 kcal/mol@LB@Unfolding Energy - sRNA 5.02883 kcal/mol@LB@@LB@Position - mRNA 12 -- 35@LB@Position - sRNA 8 -- 33@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 8 -- 14@LB@
54	0.003913	0.237	b0387	yaiI	-8.67	0.221647	168 -- 177	9 -- 18	UPF0178 family protein	_____________167________178\n_____________\|__________\|\n5'-CAC...GCGAC__________AUUAC...CAA-3'\n______________ACAAUAGAGG\n______________\|\|\|\|\|\|:\|\|\|\n______________UGUUAUUUCC\n3'-UUU...GACAC__________GUAUAUUG-5'\n_____________\|__________\|\n_____________19_________8\n	171 -- 177	9 -- 15	-10.6786 kcal/mol	1.38452 kcal/mol	0.627418 kcal/mol	167 178@LB@ \| \|@LB@5'-CAC...GCGAC AUUAC...CAA-3'@LB@ ACAAUAGAGG@LB@ \|\|\|\|\|\|:\|\|\|@LB@ UGUUAUUUCC@LB@3'-UUU...GACAC GUAUAUUG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -8.67 kcal/mol@LB@Hybridization Energy -10.6786 kcal/mol@LB@Unfolding Energy - mRNA 1.38452 kcal/mol@LB@Unfolding Energy - sRNA 0.627418 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 9 -- 15@LB@
186	0.02292	0.4143	b2717	hycI	-8.63	0.225035	220 -- 254	38 -- 70	protease involved in processing C-terminal end of HycE	_____________219___________________________________255\n_____________\|_____________________________________\|\n5'-AGC...ACUCU_______C__UAG__UGAUG______________G__GGUCC...ACU-3'\n______________GUGUUGG_AA___CA_____GGCGAUG__AUGGC_CA\n______________:\|\|\|\|\|\|_\|\|___\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|_\|\|\n______________UACAACC_UU___GU_____CCGUUAC__UACCG_GU\n3'-UUU...AAAUA__________UUA__CA__________GU_____G__UGUCU...UUG-5'\n_____________\|_____________________________________\|\n_____________71____________________________________37\n	240 -- 246	48 -- 54	-27.127 kcal/mol	11.1995 kcal/mol	7.29667 kcal/mol	219 255@LB@ \| \|@LB@5'-AGC...ACUCU C UAG UGAUG G GGUCC...ACU-3'@LB@ GUGUUGG AA CA GGCGAUG AUGGC CA@LB@ :\|\|\|\|\|\| \|\| \|\| \|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UACAACC UU GU CCGUUAC UACCG GU@LB@3'-UUU...AAAUA UUA CA GU G UGUCU...UUG-5'@LB@ \| \|@LB@ 71 37@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -27.127 kcal/mol@LB@Unfolding Energy - mRNA 11.1995 kcal/mol@LB@Unfolding Energy - sRNA 7.29667 kcal/mol@LB@@LB@Position - mRNA 220 -- 254@LB@Position - sRNA 38 -- 70@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 48 -- 54@LB@
115	0.0114	0.3326	b2531	iscR	-8.61	0.227442	42 -- 64	8 -- 31	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________41_______________________65\n_____________\|________________________\|\n5'-AUG...GCCAC_______AAA______C_______UAAAU...AAC-3'\n______________GAUAAAA____UGGCA_UGAAGGU\n______________:\|\|\|\|\|\|____\|\|:\|\|_\|:\|\|\|\|:\n______________UUAUUUU____ACUGU_AUUUCCG\n3'-UUU...GUCUU_______AGAC_____U_______UAUAUUG-5'\n_____________\|________________________\|\n_____________32_______________________7\n	58 -- 64	8 -- 14	-15.5579 kcal/mol	1.96266 kcal/mol	4.98963 kcal/mol	41 65@LB@ \| \|@LB@5'-AUG...GCCAC AAA C UAAAU...AAC-3'@LB@ GAUAAAA UGGCA UGAAGGU@LB@ :\|\|\|\|\|\| \|\|:\|\| \|:\|\|\|\|:@LB@ UUAUUUU ACUGU AUUUCCG@LB@3'-UUU...GUCUU AGAC U UAUAUUG-5'@LB@ \| \|@LB@ 32 7@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -15.5579 kcal/mol@LB@Unfolding Energy - mRNA 1.96266 kcal/mol@LB@Unfolding Energy - sRNA 4.98963 kcal/mol@LB@@LB@Position - mRNA 42 -- 64@LB@Position - sRNA 8 -- 31@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 8 -- 14@LB@
154	0.01792	0.3828	b2610	ffh	-8.53	0.234957	246 -- 258	48 -- 60	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________245___________259\n_____________\|_____________\|\n5'-AGG...GCAAU_________C___GACGC...AAG-3'\n______________AUCAGUGGC_GUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|\n______________UAGUCACCG_UAC\n3'-UUU...CCUUU_________U___GUUAC...UUG-5'\n_____________\|_____________\|\n_____________61____________47\n	248 -- 254	52 -- 58	-18.214 kcal/mol	6.29175 kcal/mol	3.39422 kcal/mol	245 259@LB@ \| \|@LB@5'-AGG...GCAAU C GACGC...AAG-3'@LB@ AUCAGUGGC GUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|@LB@ UAGUCACCG UAC@LB@3'-UUU...CCUUU U GUUAC...UUG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.214 kcal/mol@LB@Unfolding Energy - mRNA 6.29175 kcal/mol@LB@Unfolding Energy - sRNA 3.39422 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 52 -- 58@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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