Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
130	0.01234	0.3033	b2958	yggN	-5.61	0.236844	227 -- 233	35 -- 41	DUF2884 family putative periplasmic protein	_____________226_____234\n_____________\|_______\|\n5'-ACG...GCGGC_______UCAGU...UUG-3'\n______________AGCACUU\n______________\|\|\|\|\|\|\|\n______________UCGUGAA\n3'-UUU...GUUCU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________42______34\n	227 -- 233	35 -- 41	-8.1936 kcal/mol	0.976472 kcal/mol	1.6033 kcal/mol	226 234@LB@ \| \|@LB@5'-ACG...GCGGC UCAGU...UUG-3'@LB@ AGCACUU@LB@ \|\|\|\|\|\|\|@LB@ UCGUGAA@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 34@LB@@LB@@LB@Energy -5.61 kcal/mol@LB@Hybridization Energy -8.1936 kcal/mol@LB@Unfolding Energy - mRNA 0.976472 kcal/mol@LB@Unfolding Energy - sRNA 1.6033 kcal/mol@LB@@LB@Position - mRNA 227 -- 233@LB@Position - sRNA 35 -- 41@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 35 -- 41@LB@
155	0.01672	0.3455	b1686	menI	-4.77	0.356790	227 -- 235	36 -- 44	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________226_______236\n_____________\|_________\|\n5'-GGC...ACCCU_________GAAUG...AUG-3'\n______________GGAAGCACU\n______________:\|\|\|\|\|\|\|\|\n______________UCUUCGUGA\n3'-UUU...UUCGU_________AUUUU...CAA-5'\n_____________\|_________\|\n_____________45________35\n	229 -- 235	36 -- 42	-13.4239 kcal/mol	4.1512 kcal/mol	4.5009 kcal/mol	226 236@LB@ \| \|@LB@5'-GGC...ACCCU GAAUG...AUG-3'@LB@ GGAAGCACU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUUCGUGA@LB@3'-UUU...UUCGU AUUUU...CAA-5'@LB@ \| \|@LB@ 45 35@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -13.4239 kcal/mol@LB@Unfolding Energy - mRNA 4.1512 kcal/mol@LB@Unfolding Energy - sRNA 4.5009 kcal/mol@LB@@LB@Position - mRNA 227 -- 235@LB@Position - sRNA 36 -- 44@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
189	0.02233	0.3796	b3417	malP	-8.63	0.040366	227 -- 245	35 -- 53	maltodextrin phosphorylase	_____________226_________________246\n_____________\|___________________\|\n5'-ACA...GAUAA__AAUUU____________UCACG...GCC-3'\n______________GC_____CAGGAAGCGCUU\n______________\|\|_____\|\|:\|\|\|\|\|:\|\|\|\n______________CG_____GUUCUUCGUGAA\n3'-UUU...UUGAA__AAUUC____________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	239 -- 245	35 -- 41	-18.4249 kcal/mol	3.68713 kcal/mol	6.10399 kcal/mol	226 246@LB@ \| \|@LB@5'-ACA...GAUAA AAUUU UCACG...GCC-3'@LB@ GC CAGGAAGCGCUU@LB@ \|\| \|\|:\|\|\|\|\|:\|\|\|@LB@ CG GUUCUUCGUGAA@LB@3'-UUU...UUGAA AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -18.4249 kcal/mol@LB@Unfolding Energy - mRNA 3.68713 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 227 -- 245@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 35 -- 41@LB@
81	0.005437	0.2146	b1073	flgB	-5.23	0.286610	229 -- 247	36 -- 53	flagellar component of cell-proximal portion of basal-body rod	_____________228_________________248\n_____________\|___________________\|\n5'-UGA...CUUAC____UCAA___________CAAUC...CCG-3'\n______________GUUU____CAAGAGGCGCU\n______________\|:\|\|____\|\|\|\|\|:\|\|:\|\|\n______________CGAA____GUUCUUCGUGA\n3'-UUU...UUGAA____UUC____________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________35\n	241 -- 247	36 -- 42	-18.0666 kcal/mol	6.73003 kcal/mol	6.10238 kcal/mol	228 248@LB@ \| \|@LB@5'-UGA...CUUAC UCAA CAAUC...CCG-3'@LB@ GUUU CAAGAGGCGCU@LB@ \|:\|\| \|\|\|\|\|:\|\|:\|\|@LB@ CGAA GUUCUUCGUGA@LB@3'-UUU...UUGAA UUC AUUUU...CAA-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -18.0666 kcal/mol@LB@Unfolding Energy - mRNA 6.73003 kcal/mol@LB@Unfolding Energy - sRNA 6.10238 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 36 -- 42@LB@
63	0.003338	0.1645	b2671	ygaC	-8.88	0.034356	231 -- 246	25 -- 40	uncharacterized protein	_____________230______________247\n_____________\|________________\|\n5'-UAU...CGCGC____________G___GUUUU...AAA-3'\n______________GUACUUGAAAAA_UCG\n______________\|:\|\|\|\|:\|\|\|\|\|_\|\|\|\n______________CGUGAAUUUUUU_AGC\n3'-UUU...UUCUU____________A___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	231 -- 237	34 -- 40	-15.9773 kcal/mol	5.44668 kcal/mol	1.64821 kcal/mol	230 247@LB@ \| \|@LB@5'-UAU...CGCGC G GUUUU...AAA-3'@LB@ GUACUUGAAAAA UCG@LB@ \|:\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ CGUGAAUUUUUU AGC@LB@3'-UUU...UUCUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -15.9773 kcal/mol@LB@Unfolding Energy - mRNA 5.44668 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 231 -- 246@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 34 -- 40@LB@
132	0.01257	0.3067	b2516	rodZ	-8.98	0.032240	231 -- 240	34 -- 43	MreB assembly cytoskeletal protein	_____________230________241\n_____________\|__________\|\n5'-UAA...AAAAU__________CUACC...UUG-3'\n______________GAAGCACUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CUUCGUGAAU\n3'-UUU...UCGUU__________UUUUU...CAA-5'\n_____________\|__________\|\n_____________44_________33\n	234 -- 240	34 -- 40	-13.7965 kcal/mol	1.10051 kcal/mol	3.71643 kcal/mol	230 241@LB@ \| \|@LB@5'-UAA...AAAAU CUACC...UUG-3'@LB@ GAAGCACUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CUUCGUGAAU@LB@3'-UUU...UCGUU UUUUU...CAA-5'@LB@ \| \|@LB@ 44 33@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.7965 kcal/mol@LB@Unfolding Energy - mRNA 1.10051 kcal/mol@LB@Unfolding Energy - sRNA 3.71643 kcal/mol@LB@@LB@Position - mRNA 231 -- 240@LB@Position - sRNA 34 -- 43@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 34 -- 40@LB@
131	0.01234	0.3033	b4139	aspA	-5.03	0.315570	237 -- 252	26 -- 41	aspartate ammonia-lyase	_____________236______________253\n_____________\|________________\|\n5'-GAU...UGUUG_____CA_________CAGCU...ACU-3'\n______________GGUAC__GGGAAGUUC\n______________:\|:\|\|__:::\|\|:\|\|\|\n______________UCGUG__UUUUUUAAG\n3'-UUU...GUUCU_____AA_________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	246 -- 252	26 -- 32	-10.8102 kcal/mol	4.127 kcal/mol	1.64829 kcal/mol	236 253@LB@ \| \|@LB@5'-GAU...UGUUG CA CAGCU...ACU-3'@LB@ GGUAC GGGAAGUUC@LB@ :\|:\|\| :::\|\|:\|\|\|@LB@ UCGUG UUUUUUAAG@LB@3'-UUU...GUUCU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -10.8102 kcal/mol@LB@Unfolding Energy - mRNA 4.127 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 237 -- 252@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 26 -- 32@LB@
140	0.01344	0.3093	b0426	yajQ	-3.92	0.510019	240 -- 246	37 -- 43	phage Phi6 host factor ATP/GTP binding protein	_____________239_____247\n_____________\|_______\|\n5'-UAA...UUCAG_______GUAAC...GUA-3'\n______________GAAGCAC\n______________\|\|\|\|\|\|\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	240 -- 246	37 -- 43	-10.1802 kcal/mol	2.59742 kcal/mol	3.6595 kcal/mol	239 247@LB@ \| \|@LB@5'-UAA...UUCAG GUAAC...GUA-3'@LB@ GAAGCAC@LB@ \|\|\|\|\|\|\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -3.92 kcal/mol@LB@Hybridization Energy -10.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.59742 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 37 -- 43@LB@
17	0.0004446	0.08107	b1976	mtfA	-9.25	0.026966	241 -- 268	36 -- 59	anti-repressor for DgsA(Mlc)	_____________240___________________________269\n_____________\|_____________________________\|\n5'-AUA...ACAUC________CCUUCCCU_____________AUCGA...AAC-3'\n______________AAAC_UGC________GGCAGGAAGCACU\n______________\|\|\|\|_\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|\n______________UUUG_ACG________UCGUUCUUCGUGA\n3'-UUU...CCUAC____A___AAU__________________AUUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________35\n	262 -- 268	36 -- 42	-23.9855 kcal/mol	8.48573 kcal/mol	6.24948 kcal/mol	240 269@LB@ \| \|@LB@5'-AUA...ACAUC CCUUCCCU AUCGA...AAC-3'@LB@ AAAC UGC GGCAGGAAGCACU@LB@ \|\|\|\| \|\|\| :\|\|\|:\|\|\|\|\|\|\|\|@LB@ UUUG ACG UCGUUCUUCGUGA@LB@3'-UUU...CCUAC A AAU AUUUU...CAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.9855 kcal/mol@LB@Unfolding Energy - mRNA 8.48573 kcal/mol@LB@Unfolding Energy - sRNA 6.24948 kcal/mol@LB@@LB@Position - mRNA 241 -- 268@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 36 -- 42@LB@
59	0.003153	0.1645	b1220	ychO	-8.71	0.038404	242 -- 262	37 -- 56	putative invasin	_____________241___________________263\n_____________\|_____________________\|\n5'-UCA...UUACU________U______C_____AGCUA...CAA-3'\n______________CUUGCUUG_AGCAGG_GGUAC\n______________\|\|\|\|\|\|\|:_\|\|\|\|:\|_:\|:\|\|\n______________GAACGAAU_UCGUUC_UCGUG\n3'-UUU...ACUUU_______________U_____AAUUU...CAA-5'\n_____________\|_____________________\|\n_____________57____________________36\n	242 -- 248	50 -- 56	-24.8668 kcal/mol	9.95535 kcal/mol	6.20049 kcal/mol	241 263@LB@ \| \|@LB@5'-UCA...UUACU U C AGCUA...CAA-3'@LB@ CUUGCUUG AGCAGG GGUAC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| :\|:\|\|@LB@ GAACGAAU UCGUUC UCGUG@LB@3'-UUU...ACUUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -24.8668 kcal/mol@LB@Unfolding Energy - mRNA 9.95535 kcal/mol@LB@Unfolding Energy - sRNA 6.20049 kcal/mol@LB@@LB@Position - mRNA 242 -- 262@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 50 -- 56@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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