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
136	0.01311	0.3104	b0694	kdpE	-14.36	0.020608	275 -- 287	2 -- 14	response regulator in two-component regulatory system with KdpD	_____________274___________288\n_____________\|_____________\|\n5'-ACG...GACGG_____________GAGGC...CGC-3'\n______________GAUGCGCGUCUUU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUACGCGCAGAAA\n3'-UUU...AUUGU_____________G-5'\n_____________\|_____________\|\n_____________15____________1\n	281 -- 287	2 -- 8	-20.3279 kcal/mol	4.79291 kcal/mol	1.17514 kcal/mol	274 288@LB@ \| \|@LB@5'-ACG...GACGG GAGGC...CGC-3'@LB@ GAUGCGCGUCUUU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUACGCGCAGAAA@LB@3'-UUU...AUUGU G-5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -20.3279 kcal/mol@LB@Unfolding Energy - mRNA 4.79291 kcal/mol@LB@Unfolding Energy - sRNA 1.17514 kcal/mol@LB@@LB@Position - mRNA 275 -- 287@LB@Position - sRNA 2 -- 14@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 2 -- 8@LB@
175	0.01743	0.3104	b0921	smtA	-12.81	0.039244	146 -- 164	2 -- 20	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________145_________________165\n_____________\|___________________\|\n5'-AUC...UGGCU________AUA________AUCAG...AUC-3'\n______________GUGACAAA___GCGUCUUU\n______________:\|:\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________UAUUGUUU___CGCAGAAA\n3'-UUU...ACUAC________ACG________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	158 -- 164	2 -- 8	-18.7664 kcal/mol	4.69909 kcal/mol	1.25604 kcal/mol	145 165@LB@ \| \|@LB@5'-AUC...UGGCU AUA AUCAG...AUC-3'@LB@ GUGACAAA GCGUCUUU@LB@ :\|:\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAUUGUUU CGCAGAAA@LB@3'-UUU...ACUAC ACG G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -18.7664 kcal/mol@LB@Unfolding Energy - mRNA 4.69909 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 146 -- 164@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 2 -- 8@LB@
190	0.01867	0.3104	b0196	rcsF	-10.27	0.109081	201 -- 211	2 -- 13	putative outer membrane protein	_____________200__________212\n_____________\|____________\|\n5'-AAU...AUACU____________ACCGA...AGC-3'\n______________AUGCGUG_CUUU\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________UACGCGC_GAAA\n3'-UUU...UUGUU_______A____G-5'\n_____________\|____________\|\n_____________14___________1\n	201 -- 207	7 -- 13	-12.8527 kcal/mol	1.40833 kcal/mol	1.17421 kcal/mol	200 212@LB@ \| \|@LB@5'-AAU...AUACU ACCGA...AGC-3'@LB@ AUGCGUG CUUU@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ UACGCGC GAAA@LB@3'-UUU...UUGUU A G-5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -12.8527 kcal/mol@LB@Unfolding Energy - mRNA 1.40833 kcal/mol@LB@Unfolding Energy - sRNA 1.17421 kcal/mol@LB@@LB@Position - mRNA 201 -- 211@LB@Position - sRNA 2 -- 13@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 7 -- 13@LB@
5	7.362e-05	0.04801	b0741	pal	-13.90	0.024968	103 -- 115	3 -- 16	peptidoglycan-associated outer membrane lipoprotein	_____________102____________116\n_____________\|______________\|\n5'-GGA...CGUUU______________CCGGC...GCG-3'\n______________CAAA_GCGCGUCUU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________GUUU_CGCGCAGAA\n3'-UUU...CUAUU____A_________AG-5'\n_____________\|______________\|\n_____________17_____________2\n	109 -- 115	3 -- 9	-18.0761 kcal/mol	2.94526 kcal/mol	1.22934 kcal/mol	102 116@LB@ \| \|@LB@5'-GGA...CGUUU CCGGC...GCG-3'@LB@ CAAA GCGCGUCUU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUUU CGCGCAGAA@LB@3'-UUU...CUAUU A AG-5'@LB@ \| \|@LB@ 17 2@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -18.0761 kcal/mol@LB@Unfolding Energy - mRNA 2.94526 kcal/mol@LB@Unfolding Energy - sRNA 1.22934 kcal/mol@LB@@LB@Position - mRNA 103 -- 115@LB@Position - sRNA 3 -- 16@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 3 -- 9@LB@
15	0.000461	0.102	b2140	dusC	-12.07	0.053129	194 -- 211	3 -- 22	tRNA-dihydrouridine synthase C	_____________193__________________212\n_____________\|____________________\|\n5'-AAU...GCGGG_________________G__ACUGG...UUG-3'\n______________UGAUGAU__AUGCGUGU_UU\n______________\|\|\|\|:\|:__\|\|\|\|\|:\|\|_\|\|\n______________ACUAUUG__UACGCGCA_AA\n3'-UUU...CUACU_______UU________G__AG-5'\n_____________\|____________________\|\n_____________23___________________2\n	202 -- 208	6 -- 12	-18.0697 kcal/mol	4.73944 kcal/mol	1.259 kcal/mol	193 212@LB@ \| \|@LB@5'-AAU...GCGGG G ACUGG...UUG-3'@LB@ UGAUGAU AUGCGUGU UU@LB@ \|\|\|\|:\|: \|\|\|\|\|:\|\| \|\|@LB@ ACUAUUG UACGCGCA AA@LB@3'-UUU...CUACU UU G AG-5'@LB@ \| \|@LB@ 23 2@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -18.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.73944 kcal/mol@LB@Unfolding Energy - sRNA 1.259 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 3 -- 22@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
37	0.00241	0.2206	b2455	eutE	-11.61	0.064061	286 -- 298	3 -- 15	aldehyde oxidoreductase ethanolamine utilization protein	_____________285___________299\n_____________\|_____________\|\n5'-GGU...UCAUG_____G_______CG-3'\n______________AGAUG_GCGUUUU\n______________\|:\|\|\|_\|\|\|\|:\|\|\n______________UUUAC_CGCAGAA\n3'-UUU...UAUUG_____G_______AG-5'\n_____________\|_____________\|\n_____________16____________2\n	292 -- 298	3 -- 9	-14.5549 kcal/mol	1.73631 kcal/mol	1.20903 kcal/mol	285 299@LB@ \| \|@LB@5'-GGU...UCAUG G CG-3'@LB@ AGAUG GCGUUUU@LB@ \|:\|\|\| \|\|\|\|:\|\|@LB@ UUUAC CGCAGAA@LB@3'-UUU...UAUUG G AG-5'@LB@ \| \|@LB@ 16 2@LB@@LB@@LB@Energy -11.61 kcal/mol@LB@Hybridization Energy -14.5549 kcal/mol@LB@Unfolding Energy - mRNA 1.73631 kcal/mol@LB@Unfolding Energy - sRNA 1.20903 kcal/mol@LB@@LB@Position - mRNA 286 -- 298@LB@Position - sRNA 3 -- 15@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 3 -- 9@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@
142	0.01346	0.3104	b0729	sucD	-11.71	0.061414	39 -- 57	3 -- 21	succinyl-CoA synthetase NAD(P)-binding alpha subunit	_____________38__________________58\n_____________\|___________________\|\n5'-GUU...GGCGC_________A___G__G__AACGU...CUA-3'\n______________GGUAGCAGA_GUG_GU_UU\n______________\|:\|\|:\|\|:\|_\|:\|_\|\|_\|\|\n______________CUAUUGUUU_CGC_CA_AA\n3'-UUU...UACUA_________A___G__G__AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	41 -- 47	13 -- 19	-17.4316 kcal/mol	4.46052 kcal/mol	1.257 kcal/mol	38 58@LB@ \| \|@LB@5'-GUU...GGCGC A G G AACGU...CUA-3'@LB@ GGUAGCAGA GUG GU UU@LB@ \|:\|\|:\|\|:\| \|:\| \|\| \|\|@LB@ CUAUUGUUU CGC CA AA@LB@3'-UUU...UACUA A G G AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -17.4316 kcal/mol@LB@Unfolding Energy - mRNA 4.46052 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 39 -- 57@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 13 -- 19@LB@
147	0.01411	0.3104	b0441	ppiD	-10.51	0.099467	81 -- 98	3 -- 21	periplasmic folding chaperone has an inactive PPIase domain	_____________80__________________99\n_____________\|___________________\|\n5'-GUA...UAUUC______UUUC_________GUGGG...ACC-3'\n______________GGUGAC_____UGCGUCUU\n______________\|:\|:\|\|_____:\|\|\|\|\|\|\|\n______________CUAUUG_____GCGCAGAA\n3'-UUU...UACUA______UUUAC________AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	92 -- 98	3 -- 9	-17.0331 kcal/mol	5.27038 kcal/mol	1.257 kcal/mol	80 99@LB@ \| \|@LB@5'-GUA...UAUUC UUUC GUGGG...ACC-3'@LB@ GGUGAC UGCGUCUU@LB@ \|:\|:\|\| :\|\|\|\|\|\|\|@LB@ CUAUUG GCGCAGAA@LB@3'-UUU...UACUA UUUAC AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -17.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.27038 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 81 -- 98@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 3 -- 9@LB@
158	0.01496	0.3104	b4278	insG	-10.00	0.121023	32 -- 48	3 -- 20	IS4 transposase	_____________31_________________49\n_____________\|__________________\|\n5'-GUU...UCCAC________A_________GUUAC...CUC-3'\n______________AUAACAAA__CGCGUUUU\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAUUGUUU__GCGCAGAA\n3'-UUU...ACUAC________AC________AG-5'\n_____________\|__________________\|\n_____________21_________________2\n	42 -- 48	3 -- 9	-15.3953 kcal/mol	4.13684 kcal/mol	1.25547 kcal/mol	31 49@LB@ \| \|@LB@5'-GUU...UCCAC A GUUAC...CUC-3'@LB@ AUAACAAA CGCGUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAUUGUUU GCGCAGAA@LB@3'-UUU...ACUAC AC AG-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -15.3953 kcal/mol@LB@Unfolding Energy - mRNA 4.13684 kcal/mol@LB@Unfolding Energy - sRNA 1.25547 kcal/mol@LB@@LB@Position - mRNA 32 -- 48@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 3 -- 9@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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