Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
150	0.00729	0.1634	b3184	yhbE	-11.29	0.093352	190 -- 235	1 -- 50	EamA family inner membrane putative transporter	_____________189_________________________________________________236\n_____________\|___________________________________________________\|\n5'-AAG...UUGCA____AUAC___A____AA_____A____GGCAU___CAUUC__________GCUCA...UGG-3'\n______________GGGA____GGU___UG__GCAGC_GGCA_____UGG________UUUUGGC\n______________:\|\|\|____\|\|\|___\|\|__:\|\|\|\|_:\|\|\|_____\|\|\|________\|\|\|::\|\|\n______________UCCU____CCA___AC__UGUCG_UCGU_____ACC________AAAGUCG\n3'-UUU...CCGAU____CCA____AGG__CA_____A____AAAAU___CAAUACAA_______-5'\n_____________\|__________________________________________________\|\n_____________51_________________________________________________1\n	229 -- 235	1 -- 7	-25.8939 kcal/mol	9.93833 kcal/mol	4.6634 kcal/mol	189 236@LB@ \| \|@LB@5'-AAG...UUGCA AUAC A AA A GGCAU CAUUC GCUCA...UGG-3'@LB@ GGGA GGU UG GCAGC GGCA UGG UUUUGGC@LB@ :\|\|\| \|\|\| \|\| :\|\|\|\| :\|\|\| \|\|\| \|\|\|::\|\|@LB@ UCCU CCA AC UGUCG UCGU ACC AAAGUCG@LB@3'-UUU...CCGAU CCA AGG CA A AAAAU CAAUACAA -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -11.29 kcal/mol@LB@Hybridization Energy -25.8939 kcal/mol@LB@Unfolding Energy - mRNA 9.93833 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 190 -- 235@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
174	0.009477	0.1831	b3186	rplU	-11.27	0.094314	2 -- 27	9 -- 34	50S ribosomal subunit protein L21	_____________1____________________________28\n_____________\|____________________________\|\n__________5'-U_________G_A_____A____GAU___ACUGA...UUG-3'\n______________UAUGGUUAG_A___UAU_GGGU___UGU\n______________\|\|::\|:\|\|\|_\|___\|\|\|_\|\|\|\|___\|\|\|\n______________AUGUCGAUC_U___AUA_CCCA___ACA\n3'-UUU...GGACC_________G_AAA________AU____AAAAGUCG-5'\n_____________\|____________________________\|\n_____________35___________________________8\n	4 -- 10	26 -- 32	-16.432 kcal/mol	3.67439 kcal/mol	1.48697 kcal/mol	1 28@LB@ \| \|@LB@ 5'-U G A A GAU ACUGA...UUG-3'@LB@ UAUGGUUAG A UAU GGGU UGU@LB@ \|\|::\|:\|\|\| \| \|\|\| \|\|\|\| \|\|\|@LB@ AUGUCGAUC U AUA CCCA ACA@LB@3'-UUU...GGACC G AAA AU AAAAGUCG-5'@LB@ \| \|@LB@ 35 8@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -16.432 kcal/mol@LB@Unfolding Energy - mRNA 3.67439 kcal/mol@LB@Unfolding Energy - sRNA 1.48697 kcal/mol@LB@@LB@Position - mRNA 2 -- 27@LB@Position - sRNA 9 -- 34@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 26 -- 32@LB@
38	0.0007298	0.06455	b3196	yrbG	-13.22	0.033821	90 -- 115	1 -- 31	putative calcium/sodium:proton antiporter	_____________89______________________________116\n_____________\|_______________________________\|\n5'-UUC...GCGAA___________________UUAC________CGCAU...UUG-3'\n______________AGCUGGCAUUU_____GUU____UUUUUAGC\n______________\|\|\|\|:\|\|\|\|\|\|_____\|\|\|____\|\|\|\|:\|\|\|\n______________UCGAUCGUAAA_____CAA____AAAAGUCG\n3'-UUU...CCAUG___________AUACC___UACA________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	109 -- 115	1 -- 7	-21.7779 kcal/mol	7.06678 kcal/mol	1.48722 kcal/mol	89 116@LB@ \| \|@LB@5'-UUC...GCGAA UUAC CGCAU...UUG-3'@LB@ AGCUGGCAUUU GUU UUUUUAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ UCGAUCGUAAA CAA AAAAGUCG@LB@3'-UUU...CCAUG AUACC UACA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -21.7779 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 90 -- 115@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.004738	0.1404	b3197	kdsD	-14.34	0.017174	210 -- 240	1 -- 35	D-arabinose 5-phosphate isomerase	_____________209_________________________________241\n_____________\|___________________________________\|\n5'-AGG...CGCAC___G________ACC________U__AC_______AAGCA...ACA-3'\n______________GUA_AGUUA_CA______GGGUU_UG__UUUCAGC\n______________\|\|\|_\|\|:\|\|_\|\|______\|\|\|\|\|_\|\|__\|\|\|\|\|\|\|\n______________CAU_UCGAU_GU______CCCAA_AC__AAAGUCG\n3'-UUU...AGGAC___G_____C__AAAAUA_____U__AA_______-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	234 -- 240	1 -- 7	-24.924 kcal/mol	9.08416 kcal/mol	1.49508 kcal/mol	209 241@LB@ \| \|@LB@5'-AGG...CGCAC G ACC U AC AAGCA...ACA-3'@LB@ GUA AGUUA CA GGGUU UG UUUCAGC@LB@ \|\|\| \|\|:\|\| \|\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CAU UCGAU GU CCCAA AC AAAGUCG@LB@3'-UUU...AGGAC G C AAAAUA U AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.924 kcal/mol@LB@Unfolding Energy - mRNA 9.08416 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 210 -- 240@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
170	0.009245	0.1803	b3205	yhbJ	-9.78	0.183109	251 -- 276	13 -- 39	adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase	_____________250__________________________277\n_____________\|____________________________\|\n5'-CGG...GUCGC____C__________AAGA_________UUUAC...CCG-3'\n______________CCUG_GUGC_GCUGG_____UAUGGGUU\n______________\|\|\|\|_\|\|:\|_\|\|\|:\|_____\|\|\|\|\|\|\|\|\n______________GGAC_CAUG_CGAUC_____AUACCCAA\n3'-UUU...ACCAA_________U_____GUAAA________UACAA...UCG-5'\n_____________\|____________________________\|\n_____________40___________________________12\n	270 -- 276	13 -- 19	-27.4258 kcal/mol	13.0784 kcal/mol	4.56849 kcal/mol	250 277@LB@ \| \|@LB@5'-CGG...GUCGC C AAGA UUUAC...CCG-3'@LB@ CCUG GUGC GCUGG UAUGGGUU@LB@ \|\|\|\| \|\|:\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ GGAC CAUG CGAUC AUACCCAA@LB@3'-UUU...ACCAA U GUAAA UACAA...UCG-5'@LB@ \| \|@LB@ 40 12@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -27.4258 kcal/mol@LB@Unfolding Energy - mRNA 13.0784 kcal/mol@LB@Unfolding Energy - sRNA 4.56849 kcal/mol@LB@@LB@Position - mRNA 251 -- 276@LB@Position - sRNA 13 -- 39@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 13 -- 19@LB@
166	0.008687	0.1759	b3210	arcB	-6.83	0.499810	260 -- 284	24 -- 46	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________259_______________________285\n_____________\|_________________________\|\n5'-UGC...GGUCU____C_C____CAAUGUU_______CUGGC...UUC-3'\n______________GGUG_G_UUCU_______GCUGGCG\n______________\|\|\|\|_\|_\|\|\|:_______\|\|\|:\|\|:\n______________CCAC_C_AAGG_______CGAUCGU\n3'-UUU...UUCCU___________ACCAUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	278 -- 284	24 -- 30	-17.917 kcal/mol	6.53164 kcal/mol	4.55813 kcal/mol	259 285@LB@ \| \|@LB@5'-UGC...GGUCU C C CAAUGUU CUGGC...UUC-3'@LB@ GGUG G UUCU GCUGGCG@LB@ \|\|\|\| \| \|\|\|: \|\|\|:\|\|:@LB@ CCAC C AAGG CGAUCGU@LB@3'-UUU...UUCCU ACCAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -17.917 kcal/mol@LB@Unfolding Energy - mRNA 6.53164 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 260 -- 284@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 24 -- 30@LB@
25	0.0003503	0.04652	b3233	yhcB	-13.45	0.029595	190 -- 239	1 -- 50	DUF1043 family inner membrane-anchored protein	_____________189_______________________________________________________240\n_____________\|_________________________________________________________\|\n5'-UUU...ACAAC_____AU____CAUGA_____GA___U______UAAU_________GUCG_______AUCAU...CGU-3'\n______________GGGAG___GUU_____CCUGG__AUA_GC__GC______UGGGUUA______UCGGC\n______________:\|\|\|\|___\|\|\|_____\|\|\|\|\|__\|:\|_\|\|__\|\|______\|\|\|\|\|\|\|______\|\|:\|\|\n______________UCCUC___CAA_____GGACC__UGU_CG__CG______ACCCAAU______AGUCG\n3'-UUU...CCGAU_____CAC_____________A_______AU__UAAAAU_______ACAAAA_____-5'\n_____________\|________________________________________________________\|\n_____________51_______________________________________________________1\n	224 -- 230	12 -- 18	-32.3864 kcal/mol	14.269 kcal/mol	4.6634 kcal/mol	189 240@LB@ \| \|@LB@5'-UUU...ACAAC AU CAUGA GA U UAAU GUCG AUCAU...CGU-3'@LB@ GGGAG GUU CCUGG AUA GC GC UGGGUUA UCGGC@LB@ :\|\|\|\| \|\|\| \|\|\|\|\| \|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|:\|\|@LB@ UCCUC CAA GGACC UGU CG CG ACCCAAU AGUCG@LB@3'-UUU...CCGAU CAC A AU UAAAAU ACAAAA -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -13.45 kcal/mol@LB@Hybridization Energy -32.3864 kcal/mol@LB@Unfolding Energy - mRNA 14.269 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 190 -- 239@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 12 -- 18@LB@
46	0.00106	0.07744	b3234	degQ	-13.26	0.033170	226 -- 262	1 -- 35	serine endoprotease periplasmic	_____________225____________________________________263\n_____________\|______________________________________\|\n5'-CUG...GUUGA______________AAG___C______ACUCUC_____GUCAU...UUG-3'\n______________GUGCA_UUAGCGUU___UGU_GGGUUA______UCGGC\n______________\|\|:\|\|_:\|\|\|\|:\|\|___\|:\|_\|\|\|\|\|\|______\|\|:\|\|\n______________CAUGU_GAUCGUAA___AUA_CCCAAU______AGUCG\n3'-UUU...AGGAC_____C________A____________ACAAAA_____-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	232 -- 238	22 -- 28	-28.0432 kcal/mol	13.2904 kcal/mol	1.49508 kcal/mol	225 263@LB@ \| \|@LB@5'-CUG...GUUGA AAG C ACUCUC GUCAU...UUG-3'@LB@ GUGCA UUAGCGUU UGU GGGUUA UCGGC@LB@ \|\|:\|\| :\|\|\|\|:\|\| \|:\| \|\|\|\|\|\| \|\|:\|\|@LB@ CAUGU GAUCGUAA AUA CCCAAU AGUCG@LB@3'-UUU...AGGAC C A ACAAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -28.0432 kcal/mol@LB@Unfolding Energy - mRNA 13.2904 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 22 -- 28@LB@
177	0.009845	0.1869	b3241	aaeA	-6.34	0.565531	229 -- 235	29 -- 35	p-hydroxybenzoic acid efflux system component	_____________228_____236\n_____________\|_______\|\n5'-UCC...CUCCC_______CAUCA...CCG-3'\n______________GUACGGC\n______________\|\|\|\|:\|\|\n______________CAUGUCG\n3'-UUU...AGGAC_______AUCGU...UCG-5'\n_____________\|_______\|\n_____________36______28\n	229 -- 235	29 -- 35	-10.2139 kcal/mol	2.71034 kcal/mol	1.16584 kcal/mol	228 236@LB@ \| \|@LB@5'-UCC...CUCCC CAUCA...CCG-3'@LB@ GUACGGC@LB@ \|\|\|\|:\|\|@LB@ CAUGUCG@LB@3'-UUU...AGGAC AUCGU...UCG-5'@LB@ \| \|@LB@ 36 28@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.2139 kcal/mol@LB@Unfolding Energy - mRNA 2.71034 kcal/mol@LB@Unfolding Energy - sRNA 1.16584 kcal/mol@LB@@LB@Position - mRNA 229 -- 235@LB@Position - sRNA 29 -- 35@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 29 -- 35@LB@
194	0.01107	0.1919	b3288	fmt	-14.89	0.012048	76 -- 114	11 -- 48	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase	_____________75_______________________________________115\n_____________\|________________________________________\|\n5'-AUU...AGCAU___A___AUCA___________AAACUG_______A____CUGUC...UGU-3'\n______________GAG_UGG____CCUGGU_CGGC______UUUAUGG_UUAU\n______________\|\|\|_\|\|\|____\|\|\|\|\|\|_\|:\|\|______\|\|\|\|\|\|\|_\|\|\|\|\n______________CUC_ACC____GGACCA_GUCG______AAAUACC_AAUA\n3'-UUU...GAUUC___C___AA________U____AUCGUA_______C____CAAAA...UCG-5'\n_____________\|________________________________________\|\n_____________49_______________________________________10\n	103 -- 109	16 -- 22	-29.2084 kcal/mol	9.72928 kcal/mol	4.59227 kcal/mol	75 115@LB@ \| \|@LB@5'-AUU...AGCAU A AUCA AAACUG A CUGUC...UGU-3'@LB@ GAG UGG CCUGGU CGGC UUUAUGG UUAU@LB@ \|\|\| \|\|\| \|\|\|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ CUC ACC GGACCA GUCG AAAUACC AAUA@LB@3'-UUU...GAUUC C AA U AUCGUA C CAAAA...UCG-5'@LB@ \| \|@LB@ 49 10@LB@@LB@@LB@Energy -14.89 kcal/mol@LB@Hybridization Energy -29.2084 kcal/mol@LB@Unfolding Energy - mRNA 9.72928 kcal/mol@LB@Unfolding Energy - sRNA 4.59227 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 11 -- 48@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 16 -- 22@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)

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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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