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
159	0.01499	0.3104	b2476	purC	-11.66	0.062723	28 -- 49	4 -- 22	phosphoribosylaminoimidazole-succinocarboxamide synthetase		_____________27_____________________50\n_____________\|______________________\|\n5'-GGA...UGAUA_____C____AC__________GCAGG...CAG-3'\n______________UGAUA_GCAA__GUGUGCGUCU\n______________\|\|\|\|\|_:\|\|\|__:\|\|:\|\|\|\|\|\|\n______________ACUAU_UGUU__UACGCGCAGA\n3'-UUU...CUACU______________________AAG-5'\n_____________\|______________________\|\n_____________23_____________________3\n	43 -- 49	4 -- 10	-20.6907 kcal/mol	7.77162 kcal/mol	1.2572 kcal/mol	27 50@LB@ \| \|@LB@5'-GGA...UGAUA C AC GCAGG...CAG-3'@LB@ UGAUA GCAA GUGUGCGUCU@LB@ \|\|\|\|\| :\|\|\| :\|\|:\|\|\|\|\|\|@LB@ ACUAU UGUU UACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -20.6907 kcal/mol@LB@Unfolding Energy - mRNA 7.77162 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 28 -- 49@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 4 -- 10@LB@
131	0.01264	0.3104	b3412	bioH	-11.05	0.080071	12 -- 32	7 -- 31	pimeloyl-ACP methyl ester carboxylesterase		_____________11________________________33\n_____________\|_________________________\|\n5'-GGC...GACCG______A__________________GCGGG...ACG-3'\n______________CAGGGA_GAUGG____GAGUGUGUG\n______________\|\|\|\|\|\|_\|\|\|\|:____:\|:\|\|:\|:\|\n______________GUCCCU_CUACU____UUUACGCGC\n3'-UUU...CUUAA______A_____AUUG_________AGAAAG-5'\n_____________\|_________________________\|\n_____________32________________________6\n	26 -- 32	7 -- 13	-25.3011 kcal/mol	6.49654 kcal/mol	7.75103 kcal/mol	11 33@LB@ \| \|@LB@5'-GGC...GACCG A GCGGG...ACG-3'@LB@ CAGGGA GAUGG GAGUGUGUG@LB@ \|\|\|\|\|\| \|\|\|\|: :\|:\|\|:\|:\|@LB@ GUCCCU CUACU UUUACGCGC@LB@3'-UUU...CUUAA A AUUG AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -25.3011 kcal/mol@LB@Unfolding Energy - mRNA 6.49654 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 12 -- 32@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 7 -- 13@LB@
185	0.01831	0.3104	b3164	pnp	-7.42	0.310961	131 -- 137	8 -- 14	polynucleotide phosphorylase/polyadenylase		_____________130_____138\n_____________\|_______\|\n5'-AGC...GCGAG_______AGAAG...UUA-3'\n______________GAUGCGC\n______________:\|\|\|\|\|\|\n______________UUACGCG\n3'-UUU...AUUGU_______CAGAAAG-5'\n_____________\|_______\|\n_____________15______7\n	131 -- 137	8 -- 14	-10.1419 kcal/mol	2.24272 kcal/mol	0.481462 kcal/mol	130 138@LB@ \| \|@LB@5'-AGC...GCGAG AGAAG...UUA-3'@LB@ GAUGCGC@LB@ :\|\|\|\|\|\|@LB@ UUACGCG@LB@3'-UUU...AUUGU CAGAAAG-5'@LB@ \| \|@LB@ 15 7@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -10.1419 kcal/mol@LB@Unfolding Energy - mRNA 2.24272 kcal/mol@LB@Unfolding Energy - sRNA 0.481462 kcal/mol@LB@@LB@Position - mRNA 131 -- 137@LB@Position - sRNA 8 -- 14@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 8 -- 14@LB@
44	0.003062	0.2325	b3847	pepQ	-9.98	0.122201	144 -- 157	8 -- 21	proline dipeptidase		_____________143____________158\n_____________\|______________\|\n5'-UUG...CUCUG_____AC_______UAAGA...UUC-3'\n______________GAUGA__GAUGUGC\n______________\|\|\|:\|__:\|\|\|:\|\|\n______________CUAUU__UUACGCG\n3'-UUU...UACUA_____GU_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	151 -- 157	8 -- 14	-13.3112 kcal/mol	2.09686 kcal/mol	1.23638 kcal/mol	143 158@LB@ \| \|@LB@5'-UUG...CUCUG AC UAAGA...UUC-3'@LB@ GAUGA GAUGUGC@LB@ \|\|\|:\| :\|\|\|:\|\|@LB@ CUAUU UUACGCG@LB@3'-UUU...UACUA GU CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -13.3112 kcal/mol@LB@Unfolding Energy - mRNA 2.09686 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 144 -- 157@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 8 -- 14@LB@
97	0.009805	0.3104	b1306	pspC	-10.74	0.090670	128 -- 139	7 -- 18	psp operon transcription co-activator		_____________127__________140\n_____________\|____________\|\n5'-CCG...AGCAA____________AACGU...CGG-3'\n______________AACGGAUGCGCG\n______________\|\|\|::\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	133 -- 139	7 -- 13	-18.5075 kcal/mol	6.55818 kcal/mol	1.20891 kcal/mol	127 140@LB@ \| \|@LB@5'-CCG...AGCAA AACGU...CGG-3'@LB@ AACGGAUGCGCG@LB@ \|\|\|::\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.5075 kcal/mol@LB@Unfolding Energy - mRNA 6.55818 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 128 -- 139@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 7 -- 13@LB@
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@
68	0.006348	0.3087	b1202	ycgV	-6.40	0.429936	233 -- 244	4 -- 18	putative adhesin	b2647	_____________232_____________245\n_____________\|_______________\|\n5'-ACU...ACCAA_______________CGCUG...UUG-3'\n______________AGCAGAU___CGUCU\n______________\|:\|\|:\|\|___\|\|\|\|\|\n______________UUGUUUA___GCAGA\n3'-UUU...UACUA_______CGC_____AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	233 -- 239	12 -- 18	-9.8712 kcal/mol	2.23703 kcal/mol	1.22995 kcal/mol	232 245@LB@ \| \|@LB@5'-ACU...ACCAA CGCUG...UUG-3'@LB@ AGCAGAU CGUCU@LB@ \|:\|\|:\|\| \|\|\|\|\|@LB@ UUGUUUA GCAGA@LB@3'-UUU...UACUA CGC AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -9.8712 kcal/mol@LB@Unfolding Energy - mRNA 2.23703 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 233 -- 244@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 12 -- 18@LB@
163	0.0151	0.3104	b1517	lsrF	-8.60	0.205199	166 -- 179	8 -- 21	putative autoinducer-2 (AI-2) aldolase		_____________165____________180\n_____________\|______________\|\n5'-AAA...AAUAC___UU_U_______AUUAC...AUU-3'\n______________GAU__C_GAUGUGC\n______________\|\|\|__\|_:\|\|\|:\|\|\n______________CUA__G_UUACGCG\n3'-UUU...UACUA___UU_U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	173 -- 179	8 -- 14	-12.6785 kcal/mol	2.84069 kcal/mol	1.23638 kcal/mol	165 180@LB@ \| \|@LB@5'-AAA...AAUAC UU U AUUAC...AUU-3'@LB@ GAU C GAUGUGC@LB@ \|\|\| \| :\|\|\|:\|\|@LB@ CUA G UUACGCG@LB@3'-UUU...UACUA UU U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6785 kcal/mol@LB@Unfolding Energy - mRNA 2.84069 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 166 -- 179@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 8 -- 14@LB@
36	0.002407	0.2206	b2550	yphH	-13.17	0.033778	238 -- 251	7 -- 20	putative DNA-binding transcriptional regulator		_____________237____________252\n_____________\|______________\|\n5'-AGG...CCACC______________AUUCU...UGG-3'\n______________AUAACAAAUGCGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UAUUGUUUACGCGC\n3'-UUU...ACUAC______________AGAAAG-5'\n_____________\|______________\|\n_____________21_____________6\n	245 -- 251	7 -- 13	-19.0929 kcal/mol	4.67933 kcal/mol	1.23906 kcal/mol	237 252@LB@ \| \|@LB@5'-AGG...CCACC AUUCU...UGG-3'@LB@ AUAACAAAUGCGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UAUUGUUUACGCGC@LB@3'-UUU...ACUAC AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -19.0929 kcal/mol@LB@Unfolding Energy - mRNA 4.67933 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 238 -- 251@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 7 -- 13@LB@
96	0.009671	0.3104	b0941	elfG	-12.70	0.041082	222 -- 232	5 -- 15	putative fimbrial-like adhesin protein	b3145 b0533	_____________221_________233\n_____________\|___________\|\n5'-UUU...GAGAA___________AUUAC...GGC-3'\n______________AAAUGCGUGUC\n______________\|\|\|\|\|\|\|:\|\|\|\n______________UUUACGCGCAG\n3'-UUU...UAUUG___________AAAG-5'\n_____________\|___________\|\n_____________16__________4\n	226 -- 232	5 -- 11	-17.0283 kcal/mol	3.13128 kcal/mol	1.19708 kcal/mol	221 233@LB@ \| \|@LB@5'-UUU...GAGAA AUUAC...GGC-3'@LB@ AAAUGCGUGUC@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ UUUACGCGCAG@LB@3'-UUU...UAUUG AAAG-5'@LB@ \| \|@LB@ 16 4@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.0283 kcal/mol@LB@Unfolding Energy - mRNA 3.13128 kcal/mol@LB@Unfolding Energy - sRNA 1.19708 kcal/mol@LB@@LB@Position - mRNA 222 -- 232@LB@Position - sRNA 5 -- 15@LB@Position Seed - mRNA 226 -- 232@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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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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