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
2	9.051e-06	0.01532	b2745	truD	-15.77	0.011349	54 -- 69	2 -- 17	tRNA(Glu) pseudouridine(13) synthase	_____________53_______________70\n_____________\|________________\|\n5'-AAC...AUUCC____________G___AUUGC...UGG-3'\n______________ACAAAUGCGCGU_UUU\n______________\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGUUUACGCGCA_AAA\n3'-UUU...ACUAU____________G___G-5'\n_____________\|________________\|\n_____________18_______________1\n	59 -- 65	6 -- 12	-22.0257 kcal/mol	5.01487 kcal/mol	1.23894 kcal/mol	53 70@LB@ \| \|@LB@5'-AAC...AUUCC G AUUGC...UGG-3'@LB@ ACAAAUGCGCGU UUU@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGUUUACGCGCA AAA@LB@3'-UUU...ACUAU G G-5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -22.0257 kcal/mol@LB@Unfolding Energy - mRNA 5.01487 kcal/mol@LB@Unfolding Energy - sRNA 1.23894 kcal/mol@LB@@LB@Position - mRNA 54 -- 69@LB@Position - sRNA 2 -- 17@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 6 -- 12@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@
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@
174	0.01734	0.3104	b3470	tusA	-9.03	0.174990	268 -- 281	8 -- 22	mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase	_____________267_____________282\n_____________\|_______________\|\n5'-CAU...ACCGG_______________AAAAC...UGC-3'\n______________UGAUGAU_GGUGCGC\n______________\|\|\|\|:\|:_::\|\|\|\|\|\n______________ACUAUUG_UUACGCG\n3'-UUU...CUACU_______U_______CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	275 -- 281	8 -- 14	-15.1295 kcal/mol	4.85785 kcal/mol	1.23838 kcal/mol	267 282@LB@ \| \|@LB@5'-CAU...ACCGG AAAAC...UGC-3'@LB@ UGAUGAU GGUGCGC@LB@ \|\|\|\|:\|: ::\|\|\|\|\|@LB@ ACUAUUG UUACGCG@LB@3'-UUU...CUACU U CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -15.1295 kcal/mol@LB@Unfolding Energy - mRNA 4.85785 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 268 -- 281@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 8 -- 14@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein	_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
146	0.01406	0.3104	b3831	udp	-7.35	0.318150	153 -- 161	1 -- 9	uridine phosphorylase	_____________152_______162\n_____________\|_________\|\n5'-AUC...GUAAA_________UGCUU...AGA-3'\n______________GUGUCUUUU\n______________\|:\|\|\|\|\|\|:\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	155 -- 161	1 -- 7	-10.4616 kcal/mol	1.99462 kcal/mol	1.11751 kcal/mol	152 162@LB@ \| \|@LB@5'-AUC...GUAAA UGCUU...AGA-3'@LB@ GUGUCUUUU@LB@ \|:\|\|\|\|\|\|:@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -10.4616 kcal/mol@LB@Unfolding Energy - mRNA 1.99462 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 153 -- 161@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 1 -- 7@LB@
94	0.009498	0.3104	b4198	ulaF	-10.74	0.090813	136 -- 150	6 -- 20	L-ribulose 5-phosphate 4-epimerase	_____________135_____________151\n_____________\|_______________\|\n5'-GUC...CAGAA________A______GAUUG...GCG-3'\n______________GUGGCGAA_GCGCGU\n______________:\|::\|:\|\|_\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCA\n3'-UUU...ACUAC________A______GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	137 -- 143	13 -- 19	-18.1084 kcal/mol	6.12954 kcal/mol	1.24244 kcal/mol	135 151@LB@ \| \|@LB@5'-GUC...CAGAA A GAUUG...GCG-3'@LB@ GUGGCGAA GCGCGU@LB@ :\|::\|:\|\| \|\|\|\|\|\|@LB@ UAUUGUUU CGCGCA@LB@3'-UUU...ACUAC A GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.1084 kcal/mol@LB@Unfolding Energy - mRNA 6.12954 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 136 -- 150@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 13 -- 19@LB@
191	0.01886	0.3104	b3494	uspB	-6.32	0.440313	280 -- 286	5 -- 11	universal stress (ethanol tolerance) protein B	_____________279_____287\n_____________\|_______\|\n5'-AAU...ACUAC_______GUUAG...UGC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	280 -- 286	5 -- 11	-11.0709 kcal/mol	3.63469 kcal/mol	1.11145 kcal/mol	279 287@LB@ \| \|@LB@5'-AAU...ACUAC GUUAG...UGC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -11.0709 kcal/mol@LB@Unfolding Energy - mRNA 3.63469 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 280 -- 286@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 5 -- 11@LB@
17	0.0005644	0.1124	b0949	uup	-13.14	0.034258	282 -- 297	4 -- 21	replication regulatory ABC-F family DNA-binding ATPase	_____________281________________298\n_____________\|__________________\|\n5'-GAU...UCGAA__________________GUC-3'\n______________GAUAACGAA__CGUGUUU\n______________\|\|\|\|\|\|:\|\|__\|\|:\|\|:\|\n______________CUAUUGUUU__GCGCAGA\n3'-UUU...UACUA_________AC_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	291 -- 297	4 -- 10	-16.3224 kcal/mol	1.92683 kcal/mol	1.2552 kcal/mol	281 298@LB@ \| \|@LB@5'-GAU...UCGAA GUC-3'@LB@ GAUAACGAA CGUGUUU@LB@ \|\|\|\|\|\|:\|\| \|\|:\|\|:\|@LB@ CUAUUGUUU GCGCAGA@LB@3'-UUU...UACUA AC AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 1.92683 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 4 -- 10@LB@
56	0.005155	0.3024	b3091	uxaA	-13.05	0.035558	147 -- 159	6 -- 19	altronate hydrolase	_____________146____________160\n_____________\|______________\|\n5'-CUG...UGCUU______________GACUA...CGC-3'\n______________UAAC_AAUGCGCGU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AUUG_UUACGCGCA\n3'-UUU...CUACU____U_________GAAAG-5'\n_____________\|______________\|\n_____________20_____________5\n	153 -- 159	6 -- 12	-17.3524 kcal/mol	3.0727 kcal/mol	1.22941 kcal/mol	146 160@LB@ \| \|@LB@5'-CUG...UGCUU GACUA...CGC-3'@LB@ UAAC AAUGCGCGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ AUUG UUACGCGCA@LB@3'-UUU...CUACU U GAAAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -17.3524 kcal/mol@LB@Unfolding Energy - mRNA 3.0727 kcal/mol@LB@Unfolding Energy - sRNA 1.22941 kcal/mol@LB@@LB@Position - mRNA 147 -- 159@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 153 -- 159@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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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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