Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
144	0.02798	0.6177	b0682	chiQ	-9.70	0.047426	184 -- 197	41 -- 56	chitosugar-induced verified lipoprotein	_____________183______________198\n_____________\|________________\|\n5'-CGG...CCGCA____U___________GCUAU...ACA-3'\n______________CGUU___GAGGAAUUU\n______________\|\|\|:___\|\|\|\|\|\|\|\|\|\n______________GCAG___CUCCUUAAA\n3'-UUU...ACCGG____UUU_________GUAAA...ACA-5'\n_____________\|________________\|\n_____________57_______________40\n	191 -- 197	41 -- 47	-13.1137 kcal/mol	2.46147 kcal/mol	0.955312 kcal/mol	183 198@LB@ \| \|@LB@5'-CGG...CCGCA U GCUAU...ACA-3'@LB@ CGUU GAGGAAUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GCAG CUCCUUAAA@LB@3'-UUU...ACCGG UUU GUAAA...ACA-5'@LB@ \| \|@LB@ 57 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.1137 kcal/mol@LB@Unfolding Energy - mRNA 2.46147 kcal/mol@LB@Unfolding Energy - sRNA 0.955312 kcal/mol@LB@@LB@Position - mRNA 184 -- 197@LB@Position - sRNA 41 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
4	0.0002658	0.2138	b1040	csgD	-11.06	0.024985	185 -- 199	38 -- 52	csgBAC operon transcriptional regulator	_____________184_____________200\n_____________\|_______________\|\n5'-UUA...UAAAA____C__________CAUGU...CGC-3'\n______________AAAG_GGGGUUUCAU\n______________\|\|\|\|_\|\|::\|\|\|\|\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	193 -- 199	38 -- 44	-14.3947 kcal/mol	2.26766 kcal/mol	1.0693 kcal/mol	184 200@LB@ \| \|@LB@5'-UUA...UAAAA C CAUGU...CGC-3'@LB@ AAAG GGGGUUUCAU@LB@ \|\|\|\| \|\|::\|\|\|\|\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -14.3947 kcal/mol@LB@Unfolding Energy - mRNA 2.26766 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 185 -- 199@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 38 -- 44@LB@
15	0.003313	0.593	b3133	agaV	-12.53	0.012445	185 -- 194	44 -- 53	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________184________195\n_____________\|__________\|\n5'-UCA...CAAAA__________CACGC...UAG-3'\n______________CAAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-14.1596 kcal/mol	0.702602 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UCA...CAAAA CACGC...UAG-3'@LB@ CAAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.1596 kcal/mol@LB@Unfolding Energy - mRNA 0.702602 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
83	0.0176	0.6177	b2457	eutM	-9.48	0.052376	185 -- 194	44 -- 53	ethanolamine utilization protein putative carboxysome structural protein	_____________184________195\n_____________\|__________\|\n5'-UAU...CCUGA__________AGCAC...UUA-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-11.8586 kcal/mol	1.44575 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UAU...CCUGA AGCAC...UUA-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.8586 kcal/mol@LB@Unfolding Energy - mRNA 1.44575 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
141	0.02753	0.6177	b3215	yhcA	-6.30	0.221284	185 -- 194	39 -- 48	putative periplasmic chaperone protein	_____________184________195\n_____________\|__________\|\n5'-ACG...AUUAC__________AUUUA...AAA-3'\n______________AGGAGUUUUA\n______________\|\|\|\|:\|\|\|:\|\n______________UCCUUAAAGU\n3'-UUU...GUUUC__________AAAAA...ACA-5'\n_____________\|__________\|\n_____________49_________38\n	187 -- 193	40 -- 46	-10.0044 kcal/mol	2.68942 kcal/mol	1.01866 kcal/mol	184 195@LB@ \| \|@LB@5'-ACG...AUUAC AUUUA...AAA-3'@LB@ AGGAGUUUUA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UCCUUAAAGU@LB@3'-UUU...GUUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 49 38@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.0044 kcal/mol@LB@Unfolding Energy - mRNA 2.68942 kcal/mol@LB@Unfolding Energy - sRNA 1.01866 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 39 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
172	0.03476	0.6177	b3441	yhhY	-9.34	0.055938	185 -- 193	45 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________184_______194\n_____________\|_________\|\n5'-CCC...UACCC_________CAAAG...UGC-3'\n______________CAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	187 -- 193	45 -- 51	-12.8083 kcal/mol	2.54681 kcal/mol	0.917553 kcal/mol	184 194@LB@ \| \|@LB@5'-CCC...UACCC CAAAG...UGC-3'@LB@ CAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -12.8083 kcal/mol@LB@Unfolding Energy - mRNA 2.54681 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 185 -- 193@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
198	0.04148	0.6177	b1067	yceH	-6.24	0.226874	185 -- 202	38 -- 56	UPF0502 family protein	_____________184_________________203\n_____________\|___________________\|\n5'-GCA...CCGGC__C___________C____GAAAU...GUG-3'\n______________CG_UAAGGAG_AAU_UCAU\n______________\|\|_:\|\|:\|\|\|_\|\|\|_\|\|\|\|\n______________GC_GUUUCUC_UUA_AGUA\n3'-UUU...ACCGG__A_______C___A____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	188 -- 194	47 -- 53	-10.8881 kcal/mol	3.47135 kcal/mol	1.17918 kcal/mol	184 203@LB@ \| \|@LB@5'-GCA...CCGGC C C GAAAU...GUG-3'@LB@ CG UAAGGAG AAU UCAU@LB@ \|\| :\|\|:\|\|\| \|\|\| \|\|\|\|@LB@ GC GUUUCUC UUA AGUA@LB@3'-UUU...ACCGG A C A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -10.8881 kcal/mol@LB@Unfolding Energy - mRNA 3.47135 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 185 -- 202@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
26	0.004859	0.5992	b1753	ynjA	-8.90	0.068656	186 -- 195	43 -- 52	carboxymuconolactone decarboxylase family protein	_____________185________196\n_____________\|__________\|\n5'-ACU...CGCCA__________GCCUG...GGU-3'\n______________GAAGAGGAAU\n______________:\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	189 -- 195	43 -- 49	-11.6028 kcal/mol	1.83308 kcal/mol	0.865937 kcal/mol	185 196@LB@ \| \|@LB@5'-ACU...CGCCA GCCUG...GGU-3'@LB@ GAAGAGGAAU@LB@ :\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -11.6028 kcal/mol@LB@Unfolding Energy - mRNA 1.83308 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 43 -- 49@LB@
38	0.007716	0.6129	b0480	ushA	-6.97	0.165152	186 -- 197	45 -- 55	bifunctional UDP-sugar hydrolase/5'-nucleotidase	_____________185__________198\n_____________\|____________\|\n5'-AGG...AUCAG_________A__AGUAU...AAA-3'\n______________GUCAGGGAG_GA\n______________\|\|\|\|::\|\|\|_\|\|\n______________CAGUUUCUC_CU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	188 -- 194	47 -- 53	-13.3467 kcal/mol	5.44454 kcal/mol	0.930875 kcal/mol	185 198@LB@ \| \|@LB@5'-AGG...AUCAG A AGUAU...AAA-3'@LB@ GUCAGGGAG GA@LB@ \|\|\|\|::\|\|\| \|\|@LB@ CAGUUUCUC CU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -13.3467 kcal/mol@LB@Unfolding Energy - mRNA 5.44454 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
51	0.009714	0.6129	b1736	chbA	-9.09	0.063099	186 -- 194	44 -- 52	N N'-diacetylchitobiose-specific enzyme IIA component of PTS	_____________185_______195\n_____________\|_________\|\n5'-GGU...AGAAA_________CGAUG...GCC-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	188 -- 194	44 -- 50	-11.469 kcal/mol	1.52278 kcal/mol	0.860683 kcal/mol	185 195@LB@ \| \|@LB@5'-GGU...AGAAA CGAUG...GCC-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -11.469 kcal/mol@LB@Unfolding Energy - mRNA 1.52278 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@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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