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	Additional homologs
91	0.009339	0.3104	b2562	yfhL	-11.62	0.063873	146 -- 160	6 -- 20	putative 4Fe-4S cluster-containing protein		_____________145_____________161\n_____________\|_______________\|\n5'-AGC...UCUGA____A__________AUAAU...UUA-3'\n______________GUAA_GAAUGCGCGU\n______________:\|\|\|_:\|\|\|\|\|\|\|\|\|\n______________UAUU_UUUACGCGCA\n3'-UUU...ACUAC____G__________GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	154 -- 160	6 -- 12	-16.8242 kcal/mol	3.96482 kcal/mol	1.24244 kcal/mol	145 161@LB@ \| \|@LB@5'-AGC...UCUGA A AUAAU...UUA-3'@LB@ GUAA GAAUGCGCGU@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UAUU UUUACGCGCA@LB@3'-UUU...ACUAC G GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -16.8242 kcal/mol@LB@Unfolding Energy - mRNA 3.96482 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 146 -- 160@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 154 -- 160@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@
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@
171	0.01687	0.3104	b1512	lsrR	-11.43	0.068975	231 -- 262	7 -- 31	lsr operon transcriptional repressor	b4295	_____________230______________________________263\n_____________\|________________________________\|\n5'-GCU...CAGAA______AUGUG___A__AG_______C_____GAUCG...AGA-3'\n______________CAGGGA_____UGA_GA__AACAGGU_GCGCG\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|::\|_\|\|\|\|\|\n______________GUCCCU_____ACU_CU__UUGUUUA_CGCGC\n3'-UUU...CUUAA______________A__A______________AGAAAG-5'\n_____________\|________________________________\|\n_____________32_______________________________6\n	250 -- 256	12 -- 18	-27.0439 kcal/mol	7.86672 kcal/mol	7.75103 kcal/mol	230 263@LB@ \| \|@LB@5'-GCU...CAGAA AUGUG A AG C GAUCG...AGA-3'@LB@ CAGGGA UGA GA AACAGGU GCGCG@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|::\| \|\|\|\|\|@LB@ GUCCCU ACU CU UUGUUUA CGCGC@LB@3'-UUU...CUUAA A A AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -27.0439 kcal/mol@LB@Unfolding Energy - mRNA 7.86672 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 231 -- 262@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 12 -- 18@LB@
21	0.0009524	0.1536	b0241	phoE	-11.39	0.070016	174 -- 180	5 -- 11	outer membrane phosphoporin protein E	b0929 b2215 b1377	_____________173_____181\n_____________\|_______\|\n5'-AGC...UAUUC_______AAUUA...AUG-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	174 -- 180	5 -- 11	-12.879 kcal/mol	0.378776 kcal/mol	1.11145 kcal/mol	173 181@LB@ \| \|@LB@5'-AGC...UAUUC AAUUA...AUG-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -12.879 kcal/mol@LB@Unfolding Energy - mRNA 0.378776 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 174 -- 180@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 5 -- 11@LB@
33	0.002096	0.2094	b0937	ssuE	-11.36	0.070700	201 -- 209	5 -- 13	NAD(P)H-dependent FMN reductase		_____________200_______210\n_____________\|_________\|\n5'-CUG...AGAGU_________AUCAC...AGG-3'\n______________AUGCGUGUC\n______________\|\|\|\|\|:\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.6108 kcal/mol	2.09491 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-CUG...AGAGU AUCAC...AGG-3'@LB@ AUGCGUGUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.6108 kcal/mol@LB@Unfolding Energy - mRNA 2.09491 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
170	0.01687	0.3104	b0033	carB	-11.35	0.071227	1 -- 15	5 -- 17	carbamoyl-phosphate synthase large subunit		______________1______________16\n______________\|______________\|\n___________5'-_____CC________ACGCA...CGU-3'\n______________GCAAA__UGCGUGUC\n______________:\|\|\|\|__\|\|\|\|:\|\|\|\n______________UGUUU__ACGCGCAG\n3'-UUU...ACUAU_______________AAAG-5'\n_____________\|_______________\|\n_____________18______________4\n	9 -- 15	5 -- 11	-15.984 kcal/mol	3.41554 kcal/mol	1.22241 kcal/mol	1 16@LB@ \| \|@LB@ 5'- CC ACGCA...CGU-3'@LB@ GCAAA UGCGUGUC@LB@ :\|\|\|\| \|\|\|\|:\|\|\|@LB@ UGUUU ACGCGCAG@LB@3'-UUU...ACUAU AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -15.984 kcal/mol@LB@Unfolding Energy - mRNA 3.41554 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 5 -- 11@LB@
139	0.01337	0.3104	b1255	yciC	-11.25	0.074167	287 -- 299	1 -- 13	UPF0259 family inner membrane protein		_____________286___________300\n_____________\|_____________\|\n5'-AAU...UUGCU__________A__A-3'\n______________AUGUGCGUUU_UC\n______________\|\|\|:\|\|\|\|:\|_\|\|\n______________UACGCGCAGA_AG\n3'-UUU...UUGUU__________A__-5'\n_____________\|____________\|\n_____________14___________1\n	290 -- 296	4 -- 10	-15.0519 kcal/mol	2.63141 kcal/mol	1.17519 kcal/mol	286 300@LB@ \| \|@LB@5'-AAU...UUGCU A A-3'@LB@ AUGUGCGUUU UC@LB@ \|\|\|:\|\|\|\|:\| \|\|@LB@ UACGCGCAGA AG@LB@3'-UUU...UUGUU A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -15.0519 kcal/mol@LB@Unfolding Energy - mRNA 2.63141 kcal/mol@LB@Unfolding Energy - sRNA 1.17519 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 4 -- 10@LB@
18	0.00061	0.1147	b2126	yehU	-11.17	0.076396	235 -- 252	1 -- 18	inner membrane putative sensory kinase in two-component system with YehT		_____________234________________253\n_____________\|__________________\|\n5'-GUC...GCUUC__________________UAGUC...UAA-3'\n______________AGCAGAUGUGCGUUUUUU\n______________\|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:\n______________UUGUUUACGCGCAGAAAG\n3'-UUU...UACUA__________________-5'\n_____________\|_________________\|\n_____________19________________1\n	246 -- 252	1 -- 7	-22.3117 kcal/mol	9.89973 kcal/mol	1.24077 kcal/mol	234 253@LB@ \| \|@LB@5'-GUC...GCUUC UAGUC...UAA-3'@LB@ AGCAGAUGUGCGUUUUUU@LB@ \|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:@LB@ UUGUUUACGCGCAGAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -22.3117 kcal/mol@LB@Unfolding Energy - mRNA 9.89973 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 235 -- 252@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 1 -- 7@LB@
19	0.0006629	0.1181	b2909	ygfB	-11.13	0.077732	186 -- 206	4 -- 22	UPF0149 family protein		_____________185___________________207\n_____________\|_____________________\|\n5'-AAA...CCCUU___C_________UUA_____AUACA...UCA-3'\n______________UGA_GACGAAUGC___UGUCU\n______________\|\|\|_:\|\|:\|\|\|\|\|___:\|\|\|\|\n______________ACU_UUGUUUACG___GCAGA\n3'-UUU...CUACU___A_________C_______AAG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	192 -- 198	10 -- 16	-17.2827 kcal/mol	4.89762 kcal/mol	1.2572 kcal/mol	185 207@LB@ \| \|@LB@5'-AAA...CCCUU C UUA AUACA...UCA-3'@LB@ UGA GACGAAUGC UGUCU@LB@ \|\|\| :\|\|:\|\|\|\|\| :\|\|\|\|@LB@ ACU UUGUUUACG GCAGA@LB@3'-UUU...CUACU A C AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -17.2827 kcal/mol@LB@Unfolding Energy - mRNA 4.89762 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@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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