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
55	0.005043	0.3024	b1625	cnu	-10.91	0.084723	38 -- 57	1 -- 21	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________37____________________58\n_____________\|_____________________\|\n5'-UUU...UCAGG_________________AC__UUUUC...AUC-3'\n______________GAUAGUAAA_GCGCGUU__UC\n______________\|\|\|\|::\|\|\|_\|\|\|\|\|\|:__\|\|\n______________CUAUUGUUU_CGCGCAG__AG\n3'-UUU...UACUA_________A_______AA__-5'\n_____________\|____________________\|\n_____________22___________________1\n	47 -- 53	5 -- 11	-17.9355 kcal/mol	5.76636 kcal/mol	1.25763 kcal/mol	37 58@LB@ \| \|@LB@5'-UUU...UCAGG AC UUUUC...AUC-3'@LB@ GAUAGUAAA GCGCGUU UC@LB@ \|\|\|\|::\|\|\| \|\|\|\|\|\|: \|\|@LB@ CUAUUGUUU CGCGCAG AG@LB@3'-UUU...UACUA A AA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -17.9355 kcal/mol@LB@Unfolding Energy - mRNA 5.76636 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 38 -- 57@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 5 -- 11@LB@
59	0.005538	0.3084	b2812	tcdA	-16.71	0.007603	29 -- 48	1 -- 19	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________28___________________49\n_____________\|____________________\|\n5'-GUG...AUUAU____U___________G___AUGCC...UUU-3'\n______________UGAC_AAGUGCGCGUU_UUC\n______________\|:\|\|_\|\|:\|\|\|\|\|\|\|:_\|\|\|\n______________AUUG_UUUACGCGCAG_AAG\n3'-UUU...CUACU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	38 -- 44	5 -- 11	-22.1898 kcal/mol	4.2278 kcal/mol	1.25156 kcal/mol	28 49@LB@ \| \|@LB@5'-GUG...AUUAU U G AUGCC...UUU-3'@LB@ UGAC AAGUGCGCGUU UUC@LB@ \|:\|\| \|\|:\|\|\|\|\|\|\|: \|\|\|@LB@ AUUG UUUACGCGCAG AAG@LB@3'-UUU...CUACU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -22.1898 kcal/mol@LB@Unfolding Energy - mRNA 4.2278 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 29 -- 48@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 5 -- 11@LB@
61	0.005608	0.3084	b2174	lpxT	-9.09	0.171357	170 -- 179	1 -- 10	lipid A 1-diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase	_____________169________180\n_____________\|__________\|\n5'-GAA...UUGCC__________AGUAA...CGA-3'\n______________UGCGUUUUUC\n______________:\|\|\|\|:\|\|\|\|\n______________GCGCAGAAAG\n3'-UUU...UUUAC__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-13.1644 kcal/mol	2.90849 kcal/mol	1.16635 kcal/mol	169 180@LB@ \| \|@LB@5'-GAA...UUGCC AGUAA...CGA-3'@LB@ UGCGUUUUUC@LB@ :\|\|\|\|:\|\|\|\|@LB@ GCGCAGAAAG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -13.1644 kcal/mol@LB@Unfolding Energy - mRNA 2.90849 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
62	0.005646	0.3084	b1242	ychE	-13.92	0.024785	141 -- 151	1 -- 11	UPF0056 family inner membrane protein	_____________140_________152\n_____________\|___________\|\n5'-CAU...UGUCA___________CAACC...GCA-3'\n______________GCGCGUCUUUU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________CGCGCAGAAAG\n3'-UUU...GUUUA___________-5'\n_____________\|__________\|\n_____________12_________1\n	145 -- 151	1 -- 7	-17.9236 kcal/mol	2.83374 kcal/mol	1.17076 kcal/mol	140 152@LB@ \| \|@LB@5'-CAU...UGUCA CAACC...GCA-3'@LB@ GCGCGUCUUUU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ CGCGCAGAAAG@LB@3'-UUU...GUUUA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.9236 kcal/mol@LB@Unfolding Energy - mRNA 2.83374 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 141 -- 151@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
64	0.005939	0.3087	b3237	argR	-9.39	0.153279	85 -- 104	1 -- 19	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________84____________________105\n_____________\|_____________________\|\n5'-ACA...AAAUU_______AUCC__________AUAAC...UGC-3'\n______________UGAUAAA____CGC_UCUUUC\n______________\|:\|:\|\|\|____\|\|\|_\|\|\|\|\|\|\n______________AUUGUUU____GCG_AGAAAG\n3'-UUU...CUACU_______AC_____C______-5'\n_____________\|____________________\|\n_____________20___________________1\n	85 -- 91	13 -- 19	-12.1021 kcal/mol	1.46458 kcal/mol	1.25156 kcal/mol	84 105@LB@ \| \|@LB@5'-ACA...AAAUU AUCC AUAAC...UGC-3'@LB@ UGAUAAA CGC UCUUUC@LB@ \|:\|:\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AUUGUUU GCG AGAAAG@LB@3'-UUU...CUACU AC C -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.46458 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 85 -- 104@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 13 -- 19@LB@
66	0.006019	0.3087	b0223	yafJ	-7.05	0.351504	68 -- 78	1 -- 10	type 2 glutamine amidotransferase family protein	_____________67__________79\n_____________\|___________\|\n5'-GCG...GCUGA________A__AUGCC...AAG-3'\n______________CGCGUCUU_UC\n______________\|\|\|\|\|\|\|\|_\|\|\n______________GCGCAGAA_AG\n3'-UUU...UUUAC___________-5'\n_____________\|__________\|\n_____________11_________1\n	69 -- 75	3 -- 9	-12.9748 kcal/mol	4.76165 kcal/mol	1.16635 kcal/mol	67 79@LB@ \| \|@LB@5'-GCG...GCUGA A AUGCC...AAG-3'@LB@ CGCGUCUU UC@LB@ \|\|\|\|\|\|\|\| \|\|@LB@ GCGCAGAA AG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.05 kcal/mol@LB@Hybridization Energy -12.9748 kcal/mol@LB@Unfolding Energy - mRNA 4.76165 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 68 -- 78@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 3 -- 9@LB@
73	0.006809	0.3087	b4146	epmB	-12.79	0.039583	278 -- 298	1 -- 22	EF-P-Lys34 lysylation protein; weak lysine 2 3-aminomutase	_____________277____________________299\n_____________\|______________________\|\n5'-UUC...GAUCC______ACUUC___________GA-3'\n______________UGAUGA______UGCGUCUUUU\n______________\|\|\|\|:\|______:\|\|\|\|\|\|\|\|:\n______________ACUAUU______GCGCAGAAAG\n3'-UUU...CUACU______GUUUAC__________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	292 -- 298	1 -- 7	-16.8007 kcal/mol	2.75078 kcal/mol	1.25963 kcal/mol	277 299@LB@ \| \|@LB@5'-UUC...GAUCC ACUUC GA-3'@LB@ UGAUGA UGCGUCUUUU@LB@ \|\|\|\|:\| :\|\|\|\|\|\|\|\|:@LB@ ACUAUU GCGCAGAAAG@LB@3'-UUU...CUACU GUUUAC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -16.8007 kcal/mol@LB@Unfolding Energy - mRNA 2.75078 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 278 -- 298@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.008151	0.3104	b0914	msbA	-12.09	0.052799	181 -- 198	1 -- 18	lipid ABC transporter permease/ATPase	_____________180________________199\n_____________\|__________________\|\n5'-AGC...AUUUC_________UG_______GAAUG...CGU-3'\n______________AACAAAUGC__GUUUUUU\n______________\|\|\|\|\|\|\|\|\|__\|\|:\|\|\|:\n______________UUGUUUACG__CAGAAAG\n3'-UUU...UACUA_________CG_______-5'\n_____________\|_________________\|\n_____________19________________1\n	192 -- 198	1 -- 7	-16.7201 kcal/mol	3.39277 kcal/mol	1.24077 kcal/mol	180 199@LB@ \| \|@LB@5'-AGC...AUUUC UG GAAUG...CGU-3'@LB@ AACAAAUGC GUUUUUU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ UUGUUUACG CAGAAAG@LB@3'-UUU...UACUA CG -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -16.7201 kcal/mol@LB@Unfolding Energy - mRNA 3.39277 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 1 -- 7@LB@
87	0.008927	0.3104	b0195	tsaA	-8.24	0.234029	220 -- 237	1 -- 18	tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase SAM-dependent	_____________219________________238\n_____________\|__________________\|\n5'-GAA...GUUCG_______AG_____A___GCUCG...ACG-3'\n______________AGCAAAU__GCGUU_UUC\n______________\|:\|\|\|\|\|__\|\|\|\|:_\|\|\|\n______________UUGUUUA__CGCAG_AAG\n3'-UUU...UACUA_______CG_____A___-5'\n_____________\|_________________\|\n_____________19________________1\n	220 -- 226	12 -- 18	-15.6275 kcal/mol	6.14962 kcal/mol	1.24077 kcal/mol	219 238@LB@ \| \|@LB@5'-GAA...GUUCG AG A GCUCG...ACG-3'@LB@ AGCAAAU GCGUU UUC@LB@ \|:\|\|\|\|\| \|\|\|\|: \|\|\|@LB@ UUGUUUA CGCAG AAG@LB@3'-UUU...UACUA CG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -8.24 kcal/mol@LB@Hybridization Energy -15.6275 kcal/mol@LB@Unfolding Energy - mRNA 6.14962 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 12 -- 18@LB@
95	0.009629	0.3104	b0781	moaA	-11.57	0.065137	257 -- 279	1 -- 21	molybdopterin biosynthesis protein A	_____________256_____________________280\n_____________\|_______________________\|\n5'-ACG...CUGUC___U__C_________AA_____GUUGC...CGG-3'\n______________GAU_AC_GAUGUGUGU__CUUUC\n______________\|\|\|_\|\|_:\|\|\|:\|:\|\|__\|\|\|\|\|\n______________CUA_UG_UUACGCGCA__GAAAG\n3'-UUU...UACUA___U__U________________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	266 -- 272	6 -- 12	-18.6522 kcal/mol	5.82624 kcal/mol	1.25763 kcal/mol	256 280@LB@ \| \|@LB@5'-ACG...CUGUC U C AA GUUGC...CGG-3'@LB@ GAU AC GAUGUGUGU CUUUC@LB@ \|\|\| \|\| :\|\|\|:\|:\|\| \|\|\|\|\|@LB@ CUA UG UUACGCGCA GAAAG@LB@3'-UUU...UACUA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -18.6522 kcal/mol@LB@Unfolding Energy - mRNA 5.82624 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 6 -- 12@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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