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
192	0.01895	0.3104	b3333	gspL	-4.89	0.645256	110 -- 132	1 -- 21	general secretory pathway component cryptic	_____________109______________________133\n_____________\|________________________\|\n5'-GAU...CCAGG____________CAUAUU______AACCG...CGC-3'\n______________GAUGGCAAA_GC______UUUUUC\n______________\|\|\|::\|\|\|\|_\|\|______\|:\|\|\|\|\n______________CUAUUGUUU_CG______AGAAAG\n3'-UUU...UACUA_________A__CGC_________-5'\n_____________\|_______________________\|\n_____________22______________________1\n	110 -- 116	15 -- 21	-12.6455 kcal/mol	6.50221 kcal/mol	1.25763 kcal/mol	109 133@LB@ \| \|@LB@5'-GAU...CCAGG CAUAUU AACCG...CGC-3'@LB@ GAUGGCAAA GC UUUUUC@LB@ \|\|\|::\|\|\|\| \|\| \|:\|\|\|\|@LB@ CUAUUGUUU CG AGAAAG@LB@3'-UUU...UACUA A CGC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -4.89 kcal/mol@LB@Hybridization Energy -12.6455 kcal/mol@LB@Unfolding Energy - mRNA 6.50221 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 110 -- 132@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 15 -- 21@LB@
69	0.006491	0.3087	b3347	fkpA	-11.66	0.062814	96 -- 113	4 -- 22	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)	_____________95__________________114\n_____________\|___________________\|\n5'-UGG...AUAGA___________________GUAUG...CAG-3'\n______________UGAUAAUAGG_GCGUGUCU\n______________\|\|\|\|\|\|:\|::_\|\|\|:\|\|\|\|\n______________ACUAUUGUUU_CGCGCAGA\n3'-UUU...CUACU__________A________AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	107 -- 113	4 -- 10	-21.7718 kcal/mol	8.85627 kcal/mol	1.2572 kcal/mol	95 114@LB@ \| \|@LB@5'-UGG...AUAGA GUAUG...CAG-3'@LB@ UGAUAAUAGG GCGUGUCU@LB@ \|\|\|\|\|\|:\|:: \|\|\|:\|\|\|\|@LB@ ACUAUUGUUU CGCGCAGA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -21.7718 kcal/mol@LB@Unfolding Energy - mRNA 8.85627 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 96 -- 113@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 4 -- 10@LB@
188	0.0185	0.3104	b3364	tsgA	-7.52	0.300608	282 -- 299	12 -- 29	putative transporter	_____________281________________300\n_____________\|__________________\|\n5'-CCA...UCACC_____________G____A-3'\n______________GGGAUGGUGAUGG_AAAU\n______________\|\|\|\|\|\|:\|\|\|\|::_\|\|\|\|\n______________CCCUACUACUAUU_UUUA\n3'-UUU...UAAGU_____________G____CGCGC...AAG-5'\n_____________\|__________________\|\n_____________30_________________11\n	282 -- 288	23 -- 29	-23.3156 kcal/mol	8.39977 kcal/mol	7.39774 kcal/mol	281 300@LB@ \| \|@LB@5'-CCA...UCACC G A-3'@LB@ GGGAUGGUGAUGG AAAU@LB@ \|\|\|\|\|\|:\|\|\|\|:: \|\|\|\|@LB@ CCCUACUACUAUU UUUA@LB@3'-UUU...UAAGU G CGCGC...AAG-5'@LB@ \| \|@LB@ 30 11@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -23.3156 kcal/mol@LB@Unfolding Energy - mRNA 8.39977 kcal/mol@LB@Unfolding Energy - sRNA 7.39774 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 12 -- 29@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 23 -- 29@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@
82	0.007621	0.3104	b3388	damX	-7.48	0.304490	3 -- 13	8 -- 18	cell division protein that binds to the septal ring	_____________2___________14\n_____________\|___________\|\n_________5'-GG__G________UUAAU...AAC-3'\n______________GA_AGAUGCGC\n______________:\|_\|:\|\|\|\|\|\|\n______________UU_UUUACGCG\n3'-UUU...UACUA__G________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	7 -- 13	8 -- 14	-13.7317 kcal/mol	5.04786 kcal/mol	1.20363 kcal/mol	2 14@LB@ \| \|@LB@ 5'-GG G UUAAU...AAC-3'@LB@ GA AGAUGCGC@LB@ :\| \|:\|\|\|\|\|\|@LB@ UU UUUACGCG@LB@3'-UUU...UACUA G CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -13.7317 kcal/mol@LB@Unfolding Energy - mRNA 5.04786 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 3 -- 13@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 8 -- 14@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@
99	0.009943	0.3104	b3405	ompR	-10.46	0.101388	231 -- 245	8 -- 21	response regulator in two-component regulatory system with EnvZ	_____________230_____________246\n_____________\|_______________\|\n5'-AAU...UGGUC________C______CUGCG...GCG-3'\n______________GAUGACGA_AUGCGC\n______________\|\|\|:\|\|:\|_\|\|\|\|\|\|\n______________CUAUUGUU_UACGCG\n3'-UUU...UACUA_______________CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	232 -- 238	14 -- 20	-17.2341 kcal/mol	5.5408 kcal/mol	1.23638 kcal/mol	230 246@LB@ \| \|@LB@5'-AAU...UGGUC C CUGCG...GCG-3'@LB@ GAUGACGA AUGCGC@LB@ \|\|\|:\|\|:\| \|\|\|\|\|\|@LB@ CUAUUGUU UACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.2341 kcal/mol@LB@Unfolding Energy - mRNA 5.5408 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 231 -- 245@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 14 -- 20@LB@
135	0.01297	0.3104	b3409	feoB	-9.25	0.161231	74 -- 82	5 -- 13	ferrous iron transporter protein B and GTP-binding protein; membrane protein	_____________73________83\n_____________\|_________\|\n5'-CCG...AUGUG_________GCUCC...GGG-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	76 -- 82	5 -- 11	-15.2985 kcal/mol	4.89519 kcal/mol	1.15134 kcal/mol	73 83@LB@ \| \|@LB@5'-CCG...AUGUG GCUCC...GGG-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.2985 kcal/mol@LB@Unfolding Energy - mRNA 4.89519 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 74 -- 82@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 5 -- 11@LB@
131	0.01264	0.3104	b3412	bioH	-11.05	0.080071	12 -- 32	7 -- 31	pimeloyl-ACP methyl ester carboxylesterase	_____________11________________________33\n_____________\|_________________________\|\n5'-GGC...GACCG______A__________________GCGGG...ACG-3'\n______________CAGGGA_GAUGG____GAGUGUGUG\n______________\|\|\|\|\|\|_\|\|\|\|:____:\|:\|\|:\|:\|\n______________GUCCCU_CUACU____UUUACGCGC\n3'-UUU...CUUAA______A_____AUUG_________AGAAAG-5'\n_____________\|_________________________\|\n_____________32________________________6\n	26 -- 32	7 -- 13	-25.3011 kcal/mol	6.49654 kcal/mol	7.75103 kcal/mol	11 33@LB@ \| \|@LB@5'-GGC...GACCG A GCGGG...ACG-3'@LB@ CAGGGA GAUGG GAGUGUGUG@LB@ \|\|\|\|\|\| \|\|\|\|: :\|:\|\|:\|:\|@LB@ GUCCCU CUACU UUUACGCGC@LB@3'-UUU...CUUAA A AUUG AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -25.3011 kcal/mol@LB@Unfolding Energy - mRNA 6.49654 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 12 -- 32@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 7 -- 13@LB@
43	0.003009	0.2325	b3429	glgA	-8.59	0.206361	152 -- 163	7 -- 22	glycogen synthase	_____________151______________164\n_____________\|________________\|\n5'-GUA...CGUGC________________AAAUG...ACG-3'\n______________UGGUAAC____GCGCG\n______________\|\|:\|\|\|\|____\|\|\|\|\|\n______________ACUAUUG____CGCGC\n3'-UUU...CUACU_______UUUA_____AGAAAG-5'\n_____________\|________________\|\n_____________23_______________6\n	152 -- 158	16 -- 22	-13.429 kcal/mol	3.59934 kcal/mol	1.24379 kcal/mol	151 164@LB@ \| \|@LB@5'-GUA...CGUGC AAAUG...ACG-3'@LB@ UGGUAAC GCGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ ACUAUUG CGCGC@LB@3'-UUU...CUACU UUUA AGAAAG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -13.429 kcal/mol@LB@Unfolding Energy - mRNA 3.59934 kcal/mol@LB@Unfolding Energy - sRNA 1.24379 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 16 -- 22@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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service.

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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