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
125	0.01241	0.3104	b0002	thrA	-8.21	0.235915	191 -- 205	9 -- 21	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________190_____________206\n_____________\|_______________\|\n5'-CCA...AACGA________CC_____AGUGU...UGG-3'\n______________GGUAACAA__AUGCG\n______________\|:\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAUUGUU__UACGC\n3'-UUU...UACUA_______________GCAGAAAG-5'\n_____________\|_______________\|\n_____________22______________8\n	192 -- 198	14 -- 20	-12.9357 kcal/mol	3.48482 kcal/mol	1.23627 kcal/mol	190 206@LB@ \| \|@LB@5'-CCA...AACGA CC AGUGU...UGG-3'@LB@ GGUAACAA AUGCG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUU UACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 22 8@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.9357 kcal/mol@LB@Unfolding Energy - mRNA 3.48482 kcal/mol@LB@Unfolding Energy - sRNA 1.23627 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 9 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 14 -- 20@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@
79	0.007292	0.3087	b0063	araB	-12.45	0.045578	14 -- 28	6 -- 20	L-ribulokinase	_____________13______________29\n_____________\|_______________\|\n5'-CGG...AAGCC________AA_____AACAA...GGU-3'\n______________AUGACAAA__CGCGU\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________UAUUGUUU__GCGCA\n3'-UUU...ACUAC________AC_____GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	15 -- 21	13 -- 19	-14.5023 kcal/mol	0.813134 kcal/mol	1.24244 kcal/mol	13 29@LB@ \| \|@LB@5'-CGG...AAGCC AA AACAA...GGU-3'@LB@ AUGACAAA CGCGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGUUU GCGCA@LB@3'-UUU...ACUAC AC GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -14.5023 kcal/mol@LB@Unfolding Energy - mRNA 0.813134 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 14 -- 28@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 13 -- 19@LB@
65	0.005951	0.3087	b0064	araC	-16.15	0.009664	167 -- 213	8 -- 48	ara regulon transcriptional activator; autorepressor	_____________166_____________________________________________214\n_____________\|_______________________________________________\|\n5'-GGA...CAAUU______U_________GGU____GU____AAAGUA____U__A____AAAAU...AUU-3'\n______________GGUUUC_UCUCUGAAU___GGGA__AUGA______UGGC_GA_GCGC\n______________::\|\|\|\|_\|\|\|\|\|\|\|\|\|___\|\|\|\|__\|\|\|\|______\|::\|_:\|_\|\|\|\|\n______________UUAAAG_AGAGACUUA___CCCU__UACU______AUUG_UU_CGCG\n3'-UUU...CGGUU______U_________AGU____AC______________U__A____CAGAAAG-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________7\n	174 -- 180	35 -- 41	-36.5778 kcal/mol	10.9694 kcal/mol	9.45905 kcal/mol	166 214@LB@ \| \|@LB@5'-GGA...CAAUU U GGU GU AAAGUA U A AAAAU...AUU-3'@LB@ GGUUUC UCUCUGAAU GGGA AUGA UGGC GA GCGC@LB@ ::\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|::\| :\| \|\|\|\|@LB@ UUAAAG AGAGACUUA CCCU UACU AUUG UU CGCG@LB@3'-UUU...CGGUU U AGU AC U A CAGAAAG-5'@LB@ \| \|@LB@ 49 7@LB@@LB@@LB@Energy -16.15 kcal/mol@LB@Hybridization Energy -36.5778 kcal/mol@LB@Unfolding Energy - mRNA 10.9694 kcal/mol@LB@Unfolding Energy - sRNA 9.45905 kcal/mol@LB@@LB@Position - mRNA 167 -- 213@LB@Position - sRNA 8 -- 48@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 35 -- 41@LB@
49	0.004401	0.299	b0093	ftsQ	-10.19	0.112476	259 -- 274	4 -- 20	divisome assembly protein membrane anchored protein involved in growth of wall at septum	_____________258_______________275\n_____________\|_________________\|\n5'-GCU...CCGCA________A________GGCGG...CCG-3'\n______________AUAAUGGA__CGCGUCU\n______________\|\|\|\|:::\|__\|\|\|\|\|\|\|\n______________UAUUGUUU__GCGCAGA\n3'-UUU...ACUAC________AC_______AAG-5'\n_____________\|_________________\|\n_____________21________________3\n	268 -- 274	4 -- 10	-13.8485 kcal/mol	2.40331 kcal/mol	1.25368 kcal/mol	258 275@LB@ \| \|@LB@5'-GCU...CCGCA A GGCGG...CCG-3'@LB@ AUAAUGGA CGCGUCU@LB@ \|\|\|\|:::\| \|\|\|\|\|\|\|@LB@ UAUUGUUU GCGCAGA@LB@3'-UUU...ACUAC AC AAG-5'@LB@ \| \|@LB@ 21 3@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -13.8485 kcal/mol@LB@Unfolding Energy - mRNA 2.40331 kcal/mol@LB@Unfolding Energy - sRNA 1.25368 kcal/mol@LB@@LB@Position - mRNA 259 -- 274@LB@Position - sRNA 4 -- 20@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 4 -- 10@LB@
123	0.01235	0.3104	b0097	secM	-7.65	0.286972	189 -- 203	7 -- 21	regulator of secA translation	_____________188_____________204\n_____________\|_______________\|\n5'-UGG...AUCGG________UAA____AGUGG...CGC-3'\n______________GAUGGCAA___CGUG\n______________\|\|\|::\|\|\|___\|\|:\|\n______________CUAUUGUU___GCGC\n3'-UUU...UACUA________UAC____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	190 -- 196	14 -- 20	-12.5088 kcal/mol	3.61266 kcal/mol	1.24179 kcal/mol	188 204@LB@ \| \|@LB@5'-UGG...AUCGG UAA AGUGG...CGC-3'@LB@ GAUGGCAA CGUG@LB@ \|\|\|::\|\|\| \|\|:\|@LB@ CUAUUGUU GCGC@LB@3'-UUU...UACUA UAC AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -12.5088 kcal/mol@LB@Unfolding Energy - mRNA 3.61266 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 14 -- 20@LB@
111	0.01125	0.3104	b0102	zapD	-10.07	0.117779	99 -- 113	8 -- 22	FtsZ stabilizer	_____________98______________114\n_____________\|_______________\|\n5'-ACC...GUCAU_________CG____ACCGG...CCA-3'\n______________UGAUAAUAA__GCGC\n______________\|\|\|\|\|\|:\|\|__\|\|\|\|\n______________ACUAUUGUU__CGCG\n3'-UUU...CUACU_________UA____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	101 -- 107	14 -- 20	-15.8633 kcal/mol	4.55182 kcal/mol	1.23838 kcal/mol	98 114@LB@ \| \|@LB@5'-ACC...GUCAU CG ACCGG...CCA-3'@LB@ UGAUAAUAA GCGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACUAUUGUU CGCG@LB@3'-UUU...CUACU UA CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -15.8633 kcal/mol@LB@Unfolding Energy - mRNA 4.55182 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 99 -- 113@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 14 -- 20@LB@
173	0.0173	0.3104	b0145	dksA	-10.49	0.099910	175 -- 187	5 -- 21	transcriptional regulator of rRNA transcription; DnaK suppressor protein	_____________174_______________188\n_____________\|_________________\|\n5'-AAU...GGAUC_________________AAGGA...AUG-3'\n______________GAUA____GUGCGUGUU\n______________\|\|\|\|____:\|\|\|\|:\|\|:\n______________CUAU____UACGCGCAG\n3'-UUU...UACUA____UGUU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	181 -- 187	5 -- 11	-14.603 kcal/mol	2.85898 kcal/mol	1.24955 kcal/mol	174 188@LB@ \| \|@LB@5'-AAU...GGAUC AAGGA...AUG-3'@LB@ GAUA GUGCGUGUU@LB@ \|\|\|\| :\|\|\|\|:\|\|:@LB@ CUAU UACGCGCAG@LB@3'-UUU...UACUA UGUU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -14.603 kcal/mol@LB@Unfolding Energy - mRNA 2.85898 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 175 -- 187@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 5 -- 11@LB@
24	0.001508	0.1943	b0150	fhuA	-11.07	0.079438	192 -- 210	5 -- 21	ferrichrome outer membrane transporter	_____________191_________________211\n_____________\|___________________\|\n5'-GGA...UCAGA____UAC___UG_______CCAAA...CAG-3'\n______________GAUA___CAA__GCGCGUU\n______________\|\|\|\|___\|\|\|__\|\|\|\|\|\|:\n______________CUAU___GUU__CGCGCAG\n3'-UUU...UACUA____U_____UA_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	204 -- 210	5 -- 11	-17.2518 kcal/mol	4.92886 kcal/mol	1.24955 kcal/mol	191 211@LB@ \| \|@LB@5'-GGA...UCAGA UAC UG CCAAA...CAG-3'@LB@ GAUA CAA GCGCGUU@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:@LB@ CUAU GUU CGCGCAG@LB@3'-UUU...UACUA U UA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -17.2518 kcal/mol@LB@Unfolding Energy - mRNA 4.92886 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 192 -- 210@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
3	3.559e-05	0.03436	b0168	map	-14.62	0.018437	228 -- 248	5 -- 21	methionine aminopeptidase	_____________227___________________249\n_____________\|_____________________\|\n5'-CUU...CAGAA____UCGAAA___________GCUGG...AAC-3'\n______________GAUA______AAAUGCGCGUC\n______________\|\|\|\|______\|\|\|\|\|\|\|\|\|\|\|\n______________CUAU______UUUACGCGCAG\n3'-UUU...UACUA____UG_______________AAAG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	242 -- 248	5 -- 11	-19.3611 kcal/mol	3.48659 kcal/mol	1.24955 kcal/mol	227 249@LB@ \| \|@LB@5'-CUU...CAGAA UCGAAA GCUGG...AAC-3'@LB@ GAUA AAAUGCGCGUC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CUAU UUUACGCGCAG@LB@3'-UUU...UACUA UG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -19.3611 kcal/mol@LB@Unfolding Energy - mRNA 3.48659 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 228 -- 248@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 5 -- 11@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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