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
147	0.01411	0.3104	b0441	ppiD	-10.51	0.099467	81 -- 98	3 -- 21	periplasmic folding chaperone has an inactive PPIase domain		_____________80__________________99\n_____________\|___________________\|\n5'-GUA...UAUUC______UUUC_________GUGGG...ACC-3'\n______________GGUGAC_____UGCGUCUU\n______________\|:\|:\|\|_____:\|\|\|\|\|\|\|\n______________CUAUUG_____GCGCAGAA\n3'-UUU...UACUA______UUUAC________AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	92 -- 98	3 -- 9	-17.0331 kcal/mol	5.27038 kcal/mol	1.257 kcal/mol	80 99@LB@ \| \|@LB@5'-GUA...UAUUC UUUC GUGGG...ACC-3'@LB@ GGUGAC UGCGUCUU@LB@ \|:\|:\|\| :\|\|\|\|\|\|\|@LB@ CUAUUG GCGCAGAA@LB@3'-UUU...UACUA UUUAC AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -17.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.27038 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 81 -- 98@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 3 -- 9@LB@
41	0.00276	0.2279	b0889	lrp	-10.49	0.100208	207 -- 221	8 -- 21	leucine-responsive global transcriptional regulator		_____________206_____________222\n_____________\|_______________\|\n5'-GUG...UGGUA_________AA____CCUGG...AGC-3'\n______________GAUAGCAAG__GCGC\n______________\|\|\|\|:\|\|\|:__\|\|\|\|\n______________CUAUUGUUU__CGCG\n3'-UUU...UACUA_________A_____CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	209 -- 215	13 -- 19	-15.2704 kcal/mol	3.5472 kcal/mol	1.23638 kcal/mol	206 222@LB@ \| \|@LB@5'-GUG...UGGUA AA CCUGG...AGC-3'@LB@ GAUAGCAAG GCGC@LB@ \|\|\|\|:\|\|\|: \|\|\|\|@LB@ CUAUUGUUU CGCG@LB@3'-UUU...UACUA A CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -15.2704 kcal/mol@LB@Unfolding Energy - mRNA 3.5472 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 207 -- 221@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 13 -- 19@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@
99	0.009943	0.3104	b3405	ompR	-10.46	0.101388	231 -- 245	8 -- 21	response regulator in two-component regulatory system with EnvZ		_____________230_____________246\n_____________\|_______________\|\n5'-AAU...UGGUC________C______CUGCG...GCG-3'\n______________GAUGACGA_AUGCGC\n______________\|\|\|:\|\|:\|_\|\|\|\|\|\|\n______________CUAUUGUU_UACGCG\n3'-UUU...UACUA_______________CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	232 -- 238	14 -- 20	-17.2341 kcal/mol	5.5408 kcal/mol	1.23638 kcal/mol	230 246@LB@ \| \|@LB@5'-AAU...UGGUC C CUGCG...GCG-3'@LB@ GAUGACGA AUGCGC@LB@ \|\|\|:\|\|:\| \|\|\|\|\|\|@LB@ CUAUUGUU UACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.2341 kcal/mol@LB@Unfolding Energy - mRNA 5.5408 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 231 -- 245@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 14 -- 20@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@
195	0.01912	0.3104	b3910	yiiM	-10.43	0.102344	196 -- 205	9 -- 18	6-N-hydroxylaminopurine resistance protein		_____________195________206\n_____________\|__________\|\n5'-UAA...GAGGG__________AUAUC...UGC-3'\n______________AACAGAUGCG\n______________\|\|\|\|:\|\|\|\|\|\n______________UUGUUUACGC\n3'-UUU...UACUA__________GCAGAAAG-5'\n_____________\|__________\|\n_____________19_________8\n	199 -- 205	9 -- 15	-13.3675 kcal/mol	1.73119 kcal/mol	1.20319 kcal/mol	195 206@LB@ \| \|@LB@5'-UAA...GAGGG AUAUC...UGC-3'@LB@ AACAGAUGCG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ UUGUUUACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -13.3675 kcal/mol@LB@Unfolding Energy - mRNA 1.73119 kcal/mol@LB@Unfolding Energy - sRNA 1.20319 kcal/mol@LB@@LB@Position - mRNA 196 -- 205@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 9 -- 15@LB@
26	0.001545	0.1943	b1678	ldtE	-10.42	0.102915	208 -- 217	2 -- 11	murein L D-transpeptidase		_____________207________218\n_____________\|__________\|\n5'-UCU...GAAAC__________GCUUA...GCC-3'\n______________GCGCGUCUUU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGCGCAGAAA\n3'-UUU...GUUUA__________G-5'\n_____________\|__________\|\n_____________12_________1\n	211 -- 217	2 -- 8	-16.5846 kcal/mol	4.99595 kcal/mol	1.16977 kcal/mol	207 218@LB@ \| \|@LB@5'-UCU...GAAAC GCUUA...GCC-3'@LB@ GCGCGUCUUU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCAGAAA@LB@3'-UUU...GUUUA G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -16.5846 kcal/mol@LB@Unfolding Energy - mRNA 4.99595 kcal/mol@LB@Unfolding Energy - sRNA 1.16977 kcal/mol@LB@@LB@Position - mRNA 208 -- 217@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@LB@
115	0.01182	0.3104	b3367	nirC	-10.39	0.104055	218 -- 233	4 -- 19	nitrite transporter		_____________217______________234\n_____________\|________________\|\n5'-AUG...ACUAU_____________G__AACGC...UGG-3'\n______________UAAUAAGUGUGCG_CU\n______________\|\|\|:\|\|:\|\|:\|\|\|_\|\|\n______________AUUGUUUACGCGC_GA\n3'-UUU...CUACU_____________A__AAG-5'\n_____________\|________________\|\n_____________20_______________3\n	224 -- 230	7 -- 13	-17.3607 kcal/mol	5.72929 kcal/mol	1.2406 kcal/mol	217 234@LB@ \| \|@LB@5'-AUG...ACUAU G AACGC...UGG-3'@LB@ UAAUAAGUGUGCG CU@LB@ \|\|\|:\|\|:\|\|:\|\|\| \|\|@LB@ AUUGUUUACGCGC GA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -17.3607 kcal/mol@LB@Unfolding Energy - mRNA 5.72929 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 7 -- 13@LB@
67	0.006163	0.3087	b0773	ybhB	-10.36	0.105479	214 -- 228	7 -- 20	kinase inhibitor homolog UPF0098 family	b0545	_____________213_____________229\n_____________\|_______________\|\n5'-UGU...CAUCA_______UC______AUGGC...AUC-3'\n______________GUAACGA__UGCGCG\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\n______________UAUUGUU__ACGCGC\n3'-UUU...ACUAC_______U_______AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	214 -- 220	14 -- 20	-16.0436 kcal/mol	4.44842 kcal/mol	1.23906 kcal/mol	213 229@LB@ \| \|@LB@5'-UGU...CAUCA UC AUGGC...AUC-3'@LB@ GUAACGA UGCGCG@LB@ :\|\|\|\|:\| \|\|\|\|\|\|@LB@ UAUUGUU ACGCGC@LB@3'-UUU...ACUAC U AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.0436 kcal/mol@LB@Unfolding Energy - mRNA 4.44842 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 214 -- 228@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@LB@
137	0.01327	0.3104	b3858	yihD	-10.36	0.105347	5 -- 11	5 -- 11	DUF1040 protein YihD		_____________4_______12\n_____________\|_______\|\n_______5'-AUAA_______AGCGA...CGA-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	5 -- 11	5 -- 11	-14.974 kcal/mol	3.50324 kcal/mol	1.11145 kcal/mol	4 12@LB@ \| \|@LB@ 5'-AUAA AGCGA...CGA-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -14.974 kcal/mol@LB@Unfolding Energy - mRNA 3.50324 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 5 -- 11@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 5 -- 11@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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