Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
149	0.005854	0.1368	b2166	psuK	-12.08	0.032688	265 -- 298	54 -- 89	pseudouridine kinase		_____________264___________________________________299\n_____________\|_____________________________________\|\n5'-UUU...UUCAC________UUAAA__________________UCC___UA-3'\n______________AUGAAUCA______UUAUGCGG__AUUCAAA___AGG\n______________\|:\|\|\|\|\|\|______:\|\|\|\|\|:\|__\|\|\|\|\|\|\|___\|\|\|\n______________UGCUUAGU______GAUACGUC__UAAGUUU___UCC\n3'-UUU...CAGCA________UAACAC________AU_______UU____UUCAU...ACG-5'\n_____________\|_____________________________________\|\n_____________90____________________________________53\n	279 -- 285	68 -- 74	-22.7366 kcal/mol	5.9989 kcal/mol	4.66068 kcal/mol	264 299@LB@ \| \|@LB@5'-UUU...UUCAC UUAAA UCC UA-3'@LB@ AUGAAUCA UUAUGCGG AUUCAAA AGG@LB@ \|:\|\|\|\|\|\| :\|\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UGCUUAGU GAUACGUC UAAGUUU UCC@LB@3'-UUU...CAGCA UAACAC AU UU UUCAU...ACG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -22.7366 kcal/mol@LB@Unfolding Energy - mRNA 5.9989 kcal/mol@LB@Unfolding Energy - sRNA 4.66068 kcal/mol@LB@@LB@Position - mRNA 265 -- 298@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 68 -- 74@LB@
162	0.006351	0.1377	b1869	yecN	-10.06	0.106335	266 -- 273	1 -- 8	MAPEG family inner membrane protein		_____________265______274\n_____________\|________\|\n5'-UCA...GUCGU________GAAUG...GCG-3'\n______________UCGCCUGC\n______________\|\|:\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	267 -- 273	1 -- 7	-14.5941 kcal/mol	2.17055 kcal/mol	2.36381 kcal/mol	265 274@LB@ \| \|@LB@5'-UCA...GUCGU GAAUG...GCG-3'@LB@ UCGCCUGC@LB@ \|\|:\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.06 kcal/mol@LB@Hybridization Energy -14.5941 kcal/mol@LB@Unfolding Energy - mRNA 2.17055 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 266 -- 273@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
181	0.007702	0.1499	b3145	yraK	-8.82	0.202558	266 -- 280	35 -- 49	putative fimbrial-like adhesin protein	b0533 b0941	_____________265_____________281\n_____________\|_______________\|\n5'-CGA...UCCUC____G__________CGACA...CGA-3'\n______________AGGA_GGUGUGGAGC\n______________\|:\|\|_::\|:\|\|\|\|\|\|\n______________UUCU_UUAUACCUCG\n3'-UUU...CUUCA____G__________CGUUG...ACG-5'\n_____________\|_______________\|\n_____________50______________34\n	274 -- 280	35 -- 41	-19.5909 kcal/mol	7.00879 kcal/mol	3.74396 kcal/mol	265 281@LB@ \| \|@LB@5'-CGA...UCCUC G CGACA...CGA-3'@LB@ AGGA GGUGUGGAGC@LB@ \|:\|\| ::\|:\|\|\|\|\|\|@LB@ UUCU UUAUACCUCG@LB@3'-UUU...CUUCA G CGUUG...ACG-5'@LB@ \| \|@LB@ 50 34@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -19.5909 kcal/mol@LB@Unfolding Energy - mRNA 7.00879 kcal/mol@LB@Unfolding Energy - sRNA 3.74396 kcal/mol@LB@@LB@Position - mRNA 266 -- 280@LB@Position - sRNA 35 -- 49@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 35 -- 41@LB@
183	0.007971	0.1528	b1874	cutC	-9.62	0.134922	271 -- 300	54 -- 87	copper homeostasis protein		_____________270________________________________300\n_____________\|__________________________________\|\n5'-CCG...AGACA_____G____A__________CCC___________-3'\n______________GAGUU_AAUU_UGC___GCAG_____CAAAAGAGG\n______________\|\|:\|:_\|\|\|\|_\|\|\|___\|\|\|\|_____\|\|\|\|\|:\|\|\|\n______________CUUAG_UUAA_ACG___CGUC_____GUUUUUUCC\n3'-UUU...GCAUG__________C___AUA____AUUAA_________UUCAU...ACG-5'\n_____________\|___________________________________\|\n_____________88__________________________________53\n	294 -- 300	54 -- 60	-18.7273 kcal/mol	5.34866 kcal/mol	3.76003 kcal/mol	270 300@LB@ \| \|@LB@5'-CCG...AGACA G A CCC -3'@LB@ GAGUU AAUU UGC GCAG CAAAAGAGG@LB@ \|\|:\|: \|\|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CUUAG UUAA ACG CGUC GUUUUUUCC@LB@3'-UUU...GCAUG C AUA AUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 88 53@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -18.7273 kcal/mol@LB@Unfolding Energy - mRNA 5.34866 kcal/mol@LB@Unfolding Energy - sRNA 3.76003 kcal/mol@LB@@LB@Position - mRNA 271 -- 300@LB@Position - sRNA 54 -- 87@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 54 -- 60@LB@
16	3.593e-05	0.007912	b2294	yfbU	-10.97	0.063921	276 -- 297	1 -- 22	UPF0304 family protein		_____________275____________________298\n_____________\|______________________\|\n5'-GCA...CAAAU___GA_____ACCG________AAA-3'\n______________GCU__ACGUU____UCGCCUGC\n______________\|\|\|__\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________CGA__UGCAA____AGUGGACG\n3'-UUU...GGUAG___AC_____CGUA________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	291 -- 297	1 -- 7	-25.1893 kcal/mol	6.12655 kcal/mol	8.09964 kcal/mol	275 298@LB@ \| \|@LB@5'-GCA...CAAAU GA ACCG AAA-3'@LB@ GCU ACGUU UCGCCUGC@LB@ \|\|\| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CGA UGCAA AGUGGACG@LB@3'-UUU...GGUAG AC CGUA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -25.1893 kcal/mol@LB@Unfolding Energy - mRNA 6.12655 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 276 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
99	0.003254	0.1114	b2839	lysR	-9.43	0.148712	276 -- 282	1 -- 7	transcriptional activator of lysA; autorepressor		_____________275_____283\n_____________\|_______\|\n5'-GGC...CGGCA_______UACAC...CAA-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	276 -- 282	1 -- 7	-13.2779 kcal/mol	1.51062 kcal/mol	2.34039 kcal/mol	275 283@LB@ \| \|@LB@5'-GGC...CGGCA UACAC...CAA-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2779 kcal/mol@LB@Unfolding Energy - mRNA 1.51062 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
179	0.007631	0.1495	b3229	sspA	-8.36	0.252415	276 -- 298	54 -- 83	stringent starvation protein A phage P1 late gene activator RNAP-associated acid-resistance protein inactive glutathione S-transferase homolog		_____________275_____________________________299\n_____________\|_______________________________\|\n5'-CCA...AGGUC__C____________________________UG-3'\n______________CG_AUUGUGCUG_GC_______UGAGAAAGG\n______________\|:_\|\|\|\|\|\|\|\|:_\|\|_______::\|:\|\|\|\|\|\n______________GU_UAACACGAU_CG_______GUUUUUUCC\n3'-UUU...GCUUA____________A__UCAUUAA_________UUCAU...ACG-5'\n_____________\|_______________________________\|\n_____________84______________________________53\n	292 -- 298	54 -- 60	-18.0489 kcal/mol	5.94535 kcal/mol	3.74667 kcal/mol	275 299@LB@ \| \|@LB@5'-CCA...AGGUC C UG-3'@LB@ CG AUUGUGCUG GC UGAGAAAGG@LB@ \|: \|\|\|\|\|\|\|\|: \|\| ::\|:\|\|\|\|\|@LB@ GU UAACACGAU CG GUUUUUUCC@LB@3'-UUU...GCUUA A UCAUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 84 53@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -18.0489 kcal/mol@LB@Unfolding Energy - mRNA 5.94535 kcal/mol@LB@Unfolding Energy - sRNA 3.74667 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 54 -- 60@LB@
188	0.008258	0.1545	b3803	hemX	-8.31	0.258101	280 -- 297	46 -- 62	putative uroporphyrinogen III methyltransferase		_____________279________________298\n_____________\|__________________\|\n5'-AAA...CGCAA_______AAA________ACA-3'\n______________CAGAAAA___GAGUAAGA\n______________\|\|:\|\|\|\|___:\|\|\|\|\|\|\|\n______________GUUUUUU___UUCAUUCU\n3'-UUU...AUUAA_______CC_________GUUAU...ACG-5'\n_____________\|__________________\|\n_____________63_________________45\n	291 -- 297	46 -- 52	-11.8819 kcal/mol	0.215347 kcal/mol	3.36135 kcal/mol	279 298@LB@ \| \|@LB@5'-AAA...CGCAA AAA ACA-3'@LB@ CAGAAAA GAGUAAGA@LB@ \|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ GUUUUUU UUCAUUCU@LB@3'-UUU...AUUAA CC GUUAU...ACG-5'@LB@ \| \|@LB@ 63 45@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -11.8819 kcal/mol@LB@Unfolding Energy - mRNA 0.215347 kcal/mol@LB@Unfolding Energy - sRNA 3.36135 kcal/mol@LB@@LB@Position - mRNA 280 -- 297@LB@Position - sRNA 46 -- 62@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 46 -- 52@LB@
127	0.004567	0.1258	b2320	pdxB	-8.62	0.223386	291 -- 299	20 -- 28	erythronate-4-phosphate dehydrogenase		_____________290_______300\n_____________\|_________\|\n5'-ACG...CAAUC_________C-3'\n______________CCCGUCGCU\n______________\|\|\|:\|\|\|\|\|\n______________GGGUAGCGA\n3'-UUU...GUUGC_________ACUGC...ACG-5'\n_____________\|_________\|\n_____________29________19\n	293 -- 299	20 -- 26	-15.7186 kcal/mol	1.54056 kcal/mol	5.56153 kcal/mol	290 300@LB@ \| \|@LB@5'-ACG...CAAUC C-3'@LB@ CCCGUCGCU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGUAGCGA@LB@3'-UUU...GUUGC ACUGC...ACG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -15.7186 kcal/mol@LB@Unfolding Energy - mRNA 1.54056 kcal/mol@LB@Unfolding Energy - sRNA 5.56153 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 20 -- 26@LB@
120	0.004053	0.119	b2441	eutB	-6.09	0.606518	293 -- 299	73 -- 79	ethanolamine ammonia-lyase large subunit heavy chain		_____________292_____300\n_____________\|_______\|\n5'-CUG...GGGGA_______G-3'\n______________UGUGCUG\n______________\|\|\|\|\|\|:\n______________ACACGAU\n3'-UUU...AGUUA_______ACGUC...ACG-5'\n_____________\|_______\|\n_____________80______72\n	293 -- 299	73 -- 79	-8.7652 kcal/mol	1.34517 kcal/mol	1.33434 kcal/mol	292 300@LB@ \| \|@LB@5'-CUG...GGGGA G-3'@LB@ UGUGCUG@LB@ \|\|\|\|\|\|:@LB@ ACACGAU@LB@3'-UUU...AGUUA ACGUC...ACG-5'@LB@ \| \|@LB@ 80 72@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.7652 kcal/mol@LB@Unfolding Energy - mRNA 1.34517 kcal/mol@LB@Unfolding Energy - sRNA 1.33434 kcal/mol@LB@@LB@Position - mRNA 293 -- 299@LB@Position - sRNA 73 -- 79@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 73 -- 79@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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usability assessment

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service.

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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