Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
106	0.0109	0.3104	b2510	yfgJ	-10.53	0.098521	243 -- 261	5 -- 21	DUF1407 family protein	_____________242_________________262\n_____________\|___________________\|\n5'-UAA...AUCAG________CC_________GCCGA...UUU-3'\n______________GAUAACGG__AUGCGCGUU\n______________\|\|\|\|\|\|::__\|\|\|\|\|\|\|\|:\n______________CUAUUGUU__UACGCGCAG\n3'-UUU...UACUA___________________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	255 -- 261	5 -- 11	-20.9599 kcal/mol	9.18032 kcal/mol	1.24955 kcal/mol	242 262@LB@ \| \|@LB@5'-UAA...AUCAG CC GCCGA...UUU-3'@LB@ GAUAACGG AUGCGCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|\|\|\|:@LB@ CUAUUGUU UACGCGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -20.9599 kcal/mol@LB@Unfolding Energy - mRNA 9.18032 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
107	0.01107	0.3104	b0723	sdhA	-7.08	0.348281	169 -- 200	7 -- 42	succinate dehydrogenase flavoprotein subunit	_____________168__________________________________201\n_____________\|____________________________________\|\n5'-GGU...ACGUG____A________UU_______UG____________AUGAA...GUG-3'\n______________AUUU_UGGAUUCG___GUGGUG_____GGGUGUGUG\n______________\|\|:\|_\|\|:\|\|\|\|:___:\|\|:\|\|_____:::\|\|:\|:\|\n______________UAGA_ACUUAAGU___UACUAC_____UUUACGCGC\n3'-UUU...UAAAG____G________CCC______UAUUG_________AGAAAG-5'\n_____________\|____________________________________\|\n_____________43___________________________________6\n	194 -- 200	7 -- 13	-22.2639 kcal/mol	5.75915 kcal/mol	9.42962 kcal/mol	168 201@LB@ \| \|@LB@5'-GGU...ACGUG A UU UG AUGAA...GUG-3'@LB@ AUUU UGGAUUCG GUGGUG GGGUGUGUG@LB@ \|\|:\| \|\|:\|\|\|\|: :\|\|:\|\| :::\|\|:\|:\|@LB@ UAGA ACUUAAGU UACUAC UUUACGCGC@LB@3'-UUU...UAAAG G CCC UAUUG AGAAAG-5'@LB@ \| \|@LB@ 43 6@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -22.2639 kcal/mol@LB@Unfolding Energy - mRNA 5.75915 kcal/mol@LB@Unfolding Energy - sRNA 9.42962 kcal/mol@LB@@LB@Position - mRNA 169 -- 200@LB@Position - sRNA 7 -- 42@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 7 -- 13@LB@
108	0.01118	0.3104	b2565	recO	-9.71	0.135448	294 -- 300	5 -- 11	gap repair protein	_____________293____300\n_____________\|______\|\n5'-GAA...GGCGC_______-3'\n______________GUGCGUC\n______________\|:\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	294 -- 300	5 -- 11	-11.8762 kcal/mol	1.05403 kcal/mol	1.11145 kcal/mol	293 300@LB@ \| \|@LB@5'-GAA...GGCGC -3'@LB@ GUGCGUC@LB@ \|:\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -11.8762 kcal/mol@LB@Unfolding Energy - mRNA 1.05403 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 5 -- 11@LB@
109	0.01118	0.3104	b3195	mlaF	-11.81	0.058997	89 -- 105	1 -- 18	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________88_________________106\n_____________\|__________________\|\n5'-UUU...AGUAA___________AG_____GCUAA...GAG-3'\n______________AACAAAUGC_C__CUUUC\n______________\|\|\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUGUUUACG_G__GAAAG\n3'-UUU...UACUA_________C_CA_____-5'\n_____________\|_________________\|\n_____________19________________1\n	91 -- 97	10 -- 16	-16.9522 kcal/mol	3.89814 kcal/mol	1.24077 kcal/mol	88 106@LB@ \| \|@LB@5'-UUU...AGUAA AG GCUAA...GAG-3'@LB@ AACAAAUGC C CUUUC@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUGUUUACG G GAAAG@LB@3'-UUU...UACUA C CA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -16.9522 kcal/mol@LB@Unfolding Energy - mRNA 3.89814 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 89 -- 105@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 10 -- 16@LB@
110	0.01118	0.3104	b1726	yniB	-10.98	0.082506	169 -- 185	3 -- 23	putative inner membrane protein	_____________168___________________186\n_____________\|_____________________\|\n5'-AAG...ACUAA_____________________AAUCA...UGA-3'\n______________GUGA_AACGA___CGCGUCUU\n______________:\|\|\|_\|\|\|:\|___\|\|\|\|\|\|\|\|\n______________UACU_UUGUU___GCGCAGAA\n3'-UUU...CCUAC____A_____UAC________AG-5'\n_____________\|_____________________\|\n_____________24____________________2\n	179 -- 185	3 -- 9	-16.6558 kcal/mol	3.14383 kcal/mol	2.53367 kcal/mol	168 186@LB@ \| \|@LB@5'-AAG...ACUAA AAUCA...UGA-3'@LB@ GUGA AACGA CGCGUCUU@LB@ :\|\|\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ UACU UUGUU GCGCAGAA@LB@3'-UUU...CCUAC A UAC AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -16.6558 kcal/mol@LB@Unfolding Energy - mRNA 3.14383 kcal/mol@LB@Unfolding Energy - sRNA 2.53367 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 3 -- 9@LB@
111	0.01125	0.3104	b0102	zapD	-10.07	0.117779	99 -- 113	8 -- 22	FtsZ stabilizer	_____________98______________114\n_____________\|_______________\|\n5'-ACC...GUCAU_________CG____ACCGG...CCA-3'\n______________UGAUAAUAA__GCGC\n______________\|\|\|\|\|\|:\|\|__\|\|\|\|\n______________ACUAUUGUU__CGCG\n3'-UUU...CUACU_________UA____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	101 -- 107	14 -- 20	-15.8633 kcal/mol	4.55182 kcal/mol	1.23838 kcal/mol	98 114@LB@ \| \|@LB@5'-ACC...GUCAU CG ACCGG...CCA-3'@LB@ UGAUAAUAA GCGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACUAUUGUU CGCG@LB@3'-UUU...CUACU UA CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -15.8633 kcal/mol@LB@Unfolding Energy - mRNA 4.55182 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 99 -- 113@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 14 -- 20@LB@
112	0.01125	0.3104	b2515	ispG	-10.24	0.110168	132 -- 140	4 -- 12	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase	_____________131_______141\n_____________\|_________\|\n5'-CGU...CAGGU_________GACCC...UGA-3'\n______________UGCGCGUCU\n______________\|\|\|\|\|\|\|\|\|\n______________ACGCGCAGA\n3'-UUU...UGUUU_________AAG-5'\n_____________\|_________\|\n_____________13________3\n	134 -- 140	4 -- 10	-16.4542 kcal/mol	5.04928 kcal/mol	1.16019 kcal/mol	131 141@LB@ \| \|@LB@5'-CGU...CAGGU GACCC...UGA-3'@LB@ UGCGCGUCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGCGCAGA@LB@3'-UUU...UGUUU AAG-5'@LB@ \| \|@LB@ 13 3@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -16.4542 kcal/mol@LB@Unfolding Energy - mRNA 5.04928 kcal/mol@LB@Unfolding Energy - sRNA 1.16019 kcal/mol@LB@@LB@Position - mRNA 132 -- 140@LB@Position - sRNA 4 -- 12@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 4 -- 10@LB@
113	0.01159	0.3104	b1279	yciS	-9.20	0.164515	90 -- 101	6 -- 18	DUF1049 family inner membrane protein function unknown	_____________89____________102\n_____________\|_____________\|\n5'-ACC...UCAUC_____________GGAUG...UGU-3'\n______________AAC_AAUGCGUGU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________UUG_UUACGCGCA\n3'-UUU...UACUA___U_________GAAAG-5'\n_____________\|_____________\|\n_____________19____________5\n	95 -- 101	6 -- 12	-13.4585 kcal/mol	3.04139 kcal/mol	1.21878 kcal/mol	89 102@LB@ \| \|@LB@5'-ACC...UCAUC GGAUG...UGU-3'@LB@ AAC AAUGCGUGU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ UUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 19 5@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -13.4585 kcal/mol@LB@Unfolding Energy - mRNA 3.04139 kcal/mol@LB@Unfolding Energy - sRNA 1.21878 kcal/mol@LB@@LB@Position - mRNA 90 -- 101@LB@Position - sRNA 6 -- 18@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 6 -- 12@LB@
114	0.01161	0.3104	b3392	hofP	-8.60	0.204995	138 -- 147	1 -- 11	DNA catabolic protein	_____________137_________148\n_____________\|___________\|\n5'-ACU...CGUGA___________GUUAA...GCG-3'\n______________GC_CGUUUUUC\n______________\|\|_\|\|\|:\|\|\|\|\n______________CG_GCAGAAAG\n3'-UUU...GUUUA__C________-5'\n_____________\|__________\|\n_____________12_________1\n	141 -- 147	1 -- 7	-12.6405 kcal/mol	2.86562 kcal/mol	1.17076 kcal/mol	137 148@LB@ \| \|@LB@5'-ACU...CGUGA GUUAA...GCG-3'@LB@ GC CGUUUUUC@LB@ \|\| \|\|\|:\|\|\|\|@LB@ CG GCAGAAAG@LB@3'-UUU...GUUUA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6405 kcal/mol@LB@Unfolding Energy - mRNA 2.86562 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 138 -- 147@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 1 -- 7@LB@
115	0.01182	0.3104	b3367	nirC	-10.39	0.104055	218 -- 233	4 -- 19	nitrite transporter	_____________217______________234\n_____________\|________________\|\n5'-AUG...ACUAU_____________G__AACGC...UGG-3'\n______________UAAUAAGUGUGCG_CU\n______________\|\|\|:\|\|:\|\|:\|\|\|_\|\|\n______________AUUGUUUACGCGC_GA\n3'-UUU...CUACU_____________A__AAG-5'\n_____________\|________________\|\n_____________20_______________3\n	224 -- 230	7 -- 13	-17.3607 kcal/mol	5.72929 kcal/mol	1.2406 kcal/mol	217 234@LB@ \| \|@LB@5'-AUG...ACUAU G AACGC...UGG-3'@LB@ UAAUAAGUGUGCG CU@LB@ \|\|\|:\|\|:\|\|:\|\|\| \|\|@LB@ AUUGUUUACGCGC GA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -17.3607 kcal/mol@LB@Unfolding Energy - mRNA 5.72929 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 7 -- 13@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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