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
43	0.003009	0.2325	b3429	glgA	-8.59	0.206361	152 -- 163	7 -- 22	glycogen synthase	_____________151______________164\n_____________\|________________\|\n5'-GUA...CGUGC________________AAAUG...ACG-3'\n______________UGGUAAC____GCGCG\n______________\|\|:\|\|\|\|____\|\|\|\|\|\n______________ACUAUUG____CGCGC\n3'-UUU...CUACU_______UUUA_____AGAAAG-5'\n_____________\|________________\|\n_____________23_______________6\n	152 -- 158	16 -- 22	-13.429 kcal/mol	3.59934 kcal/mol	1.24379 kcal/mol	151 164@LB@ \| \|@LB@5'-GUA...CGUGC AAAUG...ACG-3'@LB@ UGGUAAC GCGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ ACUAUUG CGCGC@LB@3'-UUU...CUACU UUUA AGAAAG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -13.429 kcal/mol@LB@Unfolding Energy - mRNA 3.59934 kcal/mol@LB@Unfolding Energy - sRNA 1.24379 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 16 -- 22@LB@
200	0.0195	0.3104	b3183	obgE	-7.01	0.355777	76 -- 83	4 -- 11	GTPase involved in cell partioning and DNA repair	_____________75_______84\n_____________\|________\|\n5'-UUU...UCUCG________GUCGU...GCC-3'\n______________GUGCGUUU\n______________\|:\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	77 -- 83	4 -- 10	-11.428 kcal/mol	3.26207 kcal/mol	1.15639 kcal/mol	75 84@LB@ \| \|@LB@5'-UUU...UCUCG GUCGU...GCC-3'@LB@ GUGCGUUU@LB@ \|:\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.428 kcal/mol@LB@Unfolding Energy - mRNA 3.26207 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 4 -- 10@LB@
155	0.0146	0.3104	b2614	grpE	-10.46	0.101070	105 -- 125	1 -- 22	heat shock protein	_____________104____________________126\n_____________\|______________________\|\n5'-GAG...AAGAU______________A__GC___CCUUG...CUG-3'\n______________UGAUGACAA_UGUG_GU__UUC\n______________\|\|\|\|:\|\|\|\|_\|\|:\|_\|\|__\|\|\|\n______________ACUAUUGUU_ACGC_CA__AAG\n3'-UUU...CUACU_________U____G__GA___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	107 -- 113	14 -- 20	-17.1017 kcal/mol	5.37697 kcal/mol	1.25963 kcal/mol	104 126@LB@ \| \|@LB@5'-GAG...AAGAU A GC CCUUG...CUG-3'@LB@ UGAUGACAA UGUG GU UUC@LB@ \|\|\|\|:\|\|\|\| \|\|:\| \|\| \|\|\|@LB@ ACUAUUGUU ACGC CA AAG@LB@3'-UUU...CUACU U G GA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.1017 kcal/mol@LB@Unfolding Energy - mRNA 5.37697 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 105 -- 125@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 14 -- 20@LB@
6	9.655e-05	0.04801	b4175	hflC	-9.47	0.148653	186 -- 211	5 -- 32	HflB protease modulator specific for phage lambda cII repressor	_____________185____________________________212\n_____________\|______________________________\|\n5'-UUA...CAGCG_________________________AA___AGUUA...GUU-3'\n______________UCAGGGG_GA__AUAAC_GAUGCGU__GUC\n______________\|\|\|\|\|\|:_\|\|__\|\|\|\|\|_:\|\|\|\|\|:__\|\|\|\n______________AGUCCCU_CU__UAUUG_UUACGCG__CAG\n3'-UUU...ACUUA_______A__AC_____U____________AAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________4\n	200 -- 206	8 -- 14	-26.2754 kcal/mol	8.97237 kcal/mol	7.8362 kcal/mol	185 212@LB@ \| \|@LB@5'-UUA...CAGCG AA AGUUA...GUU-3'@LB@ UCAGGGG GA AUAAC GAUGCGU GUC@LB@ \|\|\|\|\|\|: \|\| \|\|\|\|\| :\|\|\|\|\|: \|\|\|@LB@ AGUCCCU CU UAUUG UUACGCG CAG@LB@3'-UUU...ACUUA A AC U AAAG-5'@LB@ \| \|@LB@ 33 4@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -26.2754 kcal/mol@LB@Unfolding Energy - mRNA 8.97237 kcal/mol@LB@Unfolding Energy - sRNA 7.8362 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 5 -- 32@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
28	0.001743	0.2094	b2308	hisQ	-15.00	0.015715	1 -- 16	7 -- 21	histidine ABC transporter permease	______________1_______________17\n______________\|_______________\|\n___________5'-_________C______AAGCA...UUG-3'\n______________GAUAACGAA_UGCGCG\n______________\|\|\|\|\|\|:\|\|_\|\|\|\|\|\|\n______________CUAUUGUUU_ACGCGC\n3'-UUU...UACUA________________AGAAAG-5'\n_____________\|________________\|\n_____________22_______________6\n	3 -- 9	13 -- 19	-21.0778 kcal/mol	4.83206 kcal/mol	1.24179 kcal/mol	1 17@LB@ \| \|@LB@ 5'- C AAGCA...UUG-3'@LB@ GAUAACGAA UGCGCG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|\|@LB@ CUAUUGUUU ACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.0778 kcal/mol@LB@Unfolding Energy - mRNA 4.83206 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 1 -- 16@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 13 -- 19@LB@
160	0.015	0.3104	b2022	hisB	-11.12	0.077869	165 -- 171	5 -- 11	histidinol-phosphatase and imidazoleglycerol-phosphate dehydratase	_____________164_____172\n_____________\|_______\|\n5'-CAG...AGCCA_______AUUGA...AAC-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	165 -- 171	5 -- 11	-14.7431 kcal/mol	2.50821 kcal/mol	1.11145 kcal/mol	164 172@LB@ \| \|@LB@5'-CAG...AGCCA AUUGA...AAC-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.7431 kcal/mol@LB@Unfolding Energy - mRNA 2.50821 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 165 -- 171@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 5 -- 11@LB@
27	0.001549	0.1943	b0440	hupB	-11.81	0.059023	134 -- 149	5 -- 20	HU DNA-binding transcriptional regulator beta subunit	_____________133______________150\n_____________\|________________\|\n5'-CGC...CUGAU_____UGC________CGUAC...CUG-3'\n______________AUAAC___UGCGCGUU\n______________\|\|\|\|\|___\|\|\|\|\|\|\|:\n______________UAUUG___ACGCGCAG\n3'-UUU...ACUAC_____UUU________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	143 -- 149	5 -- 11	-15.9939 kcal/mol	2.93365 kcal/mol	1.24804 kcal/mol	133 150@LB@ \| \|@LB@5'-CGC...CUGAU UGC CGUAC...CUG-3'@LB@ AUAAC UGCGCGUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ UAUUG ACGCGCAG@LB@3'-UUU...ACUAC UUU AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -15.9939 kcal/mol@LB@Unfolding Energy - mRNA 2.93365 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 134 -- 149@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 5 -- 11@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@
158	0.01496	0.3104	b4278	insG	-10.00	0.121023	32 -- 48	3 -- 20	IS4 transposase	_____________31_________________49\n_____________\|__________________\|\n5'-GUU...UCCAC________A_________GUUAC...CUC-3'\n______________AUAACAAA__CGCGUUUU\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAUUGUUU__GCGCAGAA\n3'-UUU...ACUAC________AC________AG-5'\n_____________\|__________________\|\n_____________21_________________2\n	42 -- 48	3 -- 9	-15.3953 kcal/mol	4.13684 kcal/mol	1.25547 kcal/mol	31 49@LB@ \| \|@LB@5'-GUU...UCCAC A GUUAC...CUC-3'@LB@ AUAACAAA CGCGUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAUUGUUU GCGCAGAA@LB@3'-UUU...ACUAC AC AG-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -15.3953 kcal/mol@LB@Unfolding Energy - mRNA 4.13684 kcal/mol@LB@Unfolding Energy - sRNA 1.25547 kcal/mol@LB@@LB@Position - mRNA 32 -- 48@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 3 -- 9@LB@
180	0.01774	0.3104	b0593	entC	-14.03	0.023631	112 -- 128	4 -- 19	isochorismate synthase 1	_____________111_______________129\n_____________\|_________________\|\n5'-GGC...AGAGU_____U___________GCUUU...CAG-3'\n______________UGACA_AGUGCGCGUUU\n______________\|:\|\|\|_\|:\|\|\|\|\|\|\|:\|\n______________AUUGU_UUACGCGCAGA\n3'-UUU...CUACU_________________AAG-5'\n_____________\|_________________\|\n_____________20________________3\n	122 -- 128	4 -- 10	-18.4725 kcal/mol	3.19872 kcal/mol	1.2406 kcal/mol	111 129@LB@ \| \|@LB@5'-GGC...AGAGU U GCUUU...CAG-3'@LB@ UGACA AGUGCGCGUUU@LB@ \|:\|\|\| \|:\|\|\|\|\|\|\|:\|@LB@ AUUGU UUACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -18.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.19872 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 112 -- 128@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 4 -- 10@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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