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
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@
46	0.003408	0.2484	b2518	ndk	-12.77	0.039848	1 -- 16	7 -- 21	multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'-phosphodiesterase		______________1_______________17\n______________\|_______________\|\n___________5'-___________A____GGGCA...AAA-3'\n______________GGUGAUGGAUG_CGUG\n______________\|:\|:\|:::\|\|\|_\|\|:\|\n______________CUAUUGUUUAC_GCGC\n3'-UUU...UACUA________________AGAAAG-5'\n_____________\|________________\|\n_____________22_______________6\n	5 -- 11	11 -- 17	-16.3595 kcal/mol	2.34366 kcal/mol	1.24179 kcal/mol	1 17@LB@ \| \|@LB@ 5'- A GGGCA...AAA-3'@LB@ GGUGAUGGAUG CGUG@LB@ \|:\|:\|:::\|\|\| \|\|:\|@LB@ CUAUUGUUUAC GCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -16.3595 kcal/mol@LB@Unfolding Energy - mRNA 2.34366 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 5 -- 11@LB@Position Seed - sRNA 11 -- 17@LB@
105	0.01074	0.3104	b3791	wecE	-13.91	0.024834	1 -- 12	7 -- 18	TDP-4-oxo-6-deoxy-D-glucose transaminase		______________1___________13\n______________\|___________\|\n___________5'-____________AAUUG...CCC-3'\n______________GACAGAUGCGCG\n______________:\|\|\|:\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	6 -- 12	7 -- 13	-19.4696 kcal/mol	4.34626 kcal/mol	1.20891 kcal/mol	1 13@LB@ \| \|@LB@ 5'- AAUUG...CCC-3'@LB@ GACAGAUGCGCG@LB@ :\|\|\|:\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -19.4696 kcal/mol@LB@Unfolding Energy - mRNA 4.34626 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 7 -- 13@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@
82	0.007621	0.3104	b3388	damX	-7.48	0.304490	3 -- 13	8 -- 18	cell division protein that binds to the septal ring		_____________2___________14\n_____________\|___________\|\n_________5'-GG__G________UUAAU...AAC-3'\n______________GA_AGAUGCGC\n______________:\|_\|:\|\|\|\|\|\|\n______________UU_UUUACGCG\n3'-UUU...UACUA__G________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	7 -- 13	8 -- 14	-13.7317 kcal/mol	5.04786 kcal/mol	1.20363 kcal/mol	2 14@LB@ \| \|@LB@ 5'-GG G UUAAU...AAC-3'@LB@ GA AGAUGCGC@LB@ :\| \|:\|\|\|\|\|\|@LB@ UU UUUACGCG@LB@3'-UUU...UACUA G CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -13.7317 kcal/mol@LB@Unfolding Energy - mRNA 5.04786 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 3 -- 13@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 8 -- 14@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@
172	0.01719	0.3104	b0678	nagB	-13.42	0.030481	5 -- 26	1 -- 17	glucosamine-6-phosphate deaminase		_____________4______________________27\n_____________\|______________________\|\n_______5'-UAUC______UAAAC___________GUGAG...GUC-3'\n______________GCAAAU_____GCGUGUCUUUU\n______________:\|\|\|\|\|_____\|\|\|:\|\|\|\|\|\|:\n______________UGUUUA_____CGCGCAGAAAG\n3'-UUU...ACUAU______________________-5'\n_____________\|_____________________\|\n_____________18____________________1\n	20 -- 26	1 -- 7	-18.2092 kcal/mol	3.54695 kcal/mol	1.23994 kcal/mol	4 27@LB@ \| \|@LB@ 5'-UAUC UAAAC GUGAG...GUC-3'@LB@ GCAAAU GCGUGUCUUUU@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|\|:@LB@ UGUUUA CGCGCAGAAAG@LB@3'-UUU...ACUAU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -18.2092 kcal/mol@LB@Unfolding Energy - mRNA 3.54695 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 5 -- 26@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
179	0.01766	0.3104	b0377	sbmA	-9.49	0.147268	6 -- 15	3 -- 12	peptide antibiotic transporter	b1496	_____________5__________16\n_____________\|__________\|\n______5'-GAUCC_______G__AAUCC...ACU-3'\n______________UGCGCGU_UU\n______________\|\|\|\|\|\|\|_\|\|\n______________ACGCGCA_AA\n3'-UUU...UGUUU_______G__AG-5'\n_____________\|__________\|\n_____________13_________2\n	6 -- 12	6 -- 12	-14.1156 kcal/mol	3.45883 kcal/mol	1.16529 kcal/mol	5 16@LB@ \| \|@LB@ 5'-GAUCC G AAUCC...ACU-3'@LB@ UGCGCGU UU@LB@ \|\|\|\|\|\|\| \|\|@LB@ ACGCGCA AA@LB@3'-UUU...UGUUU G AG-5'@LB@ \| \|@LB@ 13 2@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -14.1156 kcal/mol@LB@Unfolding Energy - mRNA 3.45883 kcal/mol@LB@Unfolding Energy - sRNA 1.16529 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 3 -- 12@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 6 -- 12@LB@
197	0.01929	0.3104	b2185	rplY	-8.58	0.206984	8 -- 20	7 -- 19	50S ribosomal subunit protein L25		_____________7_____________21\n_____________\|_____________\|\n____5'-CCAGUAC_____________AAAAA...GCA-3'\n______________UGGCAGGUGCGUG\n______________\|::\|\|::\|\|\|\|:\|\n______________AUUGUUUACGCGC\n3'-UUU...CUACU_____________AGAAAG-5'\n_____________\|_____________\|\n_____________20____________6\n	14 -- 20	7 -- 13	-17.3397 kcal/mol	7.54262 kcal/mol	1.21943 kcal/mol	7 21@LB@ \| \|@LB@ 5'-CCAGUAC AAAAA...GCA-3'@LB@ UGGCAGGUGCGUG@LB@ \|::\|\|::\|\|\|\|:\|@LB@ AUUGUUUACGCGC@LB@3'-UUU...CUACU AGAAAG-5'@LB@ \| \|@LB@ 20 6@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -17.3397 kcal/mol@LB@Unfolding Energy - mRNA 7.54262 kcal/mol@LB@Unfolding Energy - sRNA 1.21943 kcal/mol@LB@@LB@Position - mRNA 8 -- 20@LB@Position - sRNA 7 -- 19@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 7 -- 13@LB@
116	0.01184	0.3104	b1218	chaC	-12.45	0.045440	10 -- 29	8 -- 30	cation transport regulator		_____________9_______________________30\n_____________\|_______________________\|\n5'-AUA...GCCAA_______________________AUAAA...CGC-3'\n______________AGGG__GAUGAUGAUAAAUG_GC\n______________\|\|\|\|__\|\|\|\|\|\|:\|:\|\|\|\|\|_\|\|\n______________UCCC__CUACUAUUGUUUAC_CG\n3'-UUU...UUAAG____UA______________G__CAGAAAG-5'\n_____________\|_______________________\|\n_____________31______________________7\n	21 -- 27	11 -- 17	-25.0616 kcal/mol	5.19055 kcal/mol	7.41684 kcal/mol	9 30@LB@ \| \|@LB@5'-AUA...GCCAA AUAAA...CGC-3'@LB@ AGGG GAUGAUGAUAAAUG GC@LB@ \|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|\| \|\|@LB@ UCCC CUACUAUUGUUUAC CG@LB@3'-UUU...UUAAG UA G CAGAAAG-5'@LB@ \| \|@LB@ 31 7@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -25.0616 kcal/mol@LB@Unfolding Energy - mRNA 5.19055 kcal/mol@LB@Unfolding Energy - sRNA 7.41684 kcal/mol@LB@@LB@Position - mRNA 10 -- 29@LB@Position - sRNA 8 -- 30@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 11 -- 17@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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