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
106	0.003955	0.1254	b1767	ansA	-7.74	0.383564	250 -- 272	11 -- 34	cytoplasmic L-asparaginase 1	_____________249______________________273\n_____________\|________________________\|\n5'-UGC...CGGGA______GUUCCGAGCA________AUACC...GCC-3'\n______________UGCAGC___________GGGUUAU\n______________\|:\|\|\|\|___________\|\|\|\|\|\|\|\n______________AUGUCG___________CCCAAUA\n3'-UUU...GGACC______AUCGUAAAAUA_______CAAAA...UCG-5'\n_____________\|________________________\|\n_____________35_______________________10\n	266 -- 272	11 -- 17	-16.5796 kcal/mol	7.36686 kcal/mol	1.47152 kcal/mol	249 273@LB@ \| \|@LB@5'-UGC...CGGGA GUUCCGAGCA AUACC...GCC-3'@LB@ UGCAGC GGGUUAU@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|@LB@ AUGUCG CCCAAUA@LB@3'-UUU...GGACC AUCGUAAAAUA CAAAA...UCG-5'@LB@ \| \|@LB@ 35 10@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -16.5796 kcal/mol@LB@Unfolding Energy - mRNA 7.36686 kcal/mol@LB@Unfolding Energy - sRNA 1.47152 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 11 -- 34@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 11 -- 17@LB@
180	0.01039	0.1919	b1778	msrB	-9.69	0.189810	88 -- 95	29 -- 36	methionine sulfoxide reductase B	_____________87_______96\n_____________\|________\|\n5'-CUU...AUUUA________CAUUU...GUC-3'\n______________GGUGCAGC\n______________\|\|\|:\|\|\|\|\n______________CCAUGUCG\n3'-UUU...AAGGA________AUCGU...UCG-5'\n_____________\|________\|\n_____________37_______28\n	89 -- 95	29 -- 35	-13.558 kcal/mol	2.69806 kcal/mol	1.16901 kcal/mol	87 96@LB@ \| \|@LB@5'-CUU...AUUUA CAUUU...GUC-3'@LB@ GGUGCAGC@LB@ \|\|\|:\|\|\|\|@LB@ CCAUGUCG@LB@3'-UUU...AAGGA AUCGU...UCG-5'@LB@ \| \|@LB@ 37 28@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -13.558 kcal/mol@LB@Unfolding Energy - mRNA 2.69806 kcal/mol@LB@Unfolding Energy - sRNA 1.16901 kcal/mol@LB@@LB@Position - mRNA 88 -- 95@LB@Position - sRNA 29 -- 36@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 29 -- 35@LB@
159	0.008045	0.1694	b1780	yeaD	-12.23	0.058242	44 -- 57	32 -- 44	D-hexose-6-phosphate epimerase-like protein	_____________43_____________58\n_____________\|______________\|\n5'-GAU...GAAAC____A_________GACAA...AUC-3'\n______________UGGU_UCCUGGUAC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________ACCA_AGGACCAUG\n3'-UUU...CCUCC______________UCGAU...UCG-5'\n_____________\|______________\|\n_____________45_____________31\n	51 -- 57	32 -- 38	-20.6656 kcal/mol	5.17692 kcal/mol	3.25604 kcal/mol	43 58@LB@ \| \|@LB@5'-GAU...GAAAC A GACAA...AUC-3'@LB@ UGGU UCCUGGUAC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ ACCA AGGACCAUG@LB@3'-UUU...CCUCC UCGAU...UCG-5'@LB@ \| \|@LB@ 45 31@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -20.6656 kcal/mol@LB@Unfolding Energy - mRNA 5.17692 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 32 -- 44@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 32 -- 38@LB@
33	0.0006117	0.0623	b1795	yeaQ	-12.41	0.053010	276 -- 283	42 -- 49	UPF0410 family protein	_____________275______284\n_____________\|________\|\n5'-AUA...AAGAU________AUUCU...UCC-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	277 -- 283	42 -- 48	-16.41 kcal/mol	1.22894 kcal/mol	2.77009 kcal/mol	275 284@LB@ \| \|@LB@5'-AUA...AAGAU AUUCU...UCC-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -16.41 kcal/mol@LB@Unfolding Energy - mRNA 1.22894 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 276 -- 283@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
23	0.0002818	0.04118	b1813	nudL	-13.86	0.023273	1 -- 17	22 -- 39	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	______________1_________________18\n______________\|_________________\|\n___________5'-__________________GGCUA...CUG-3'\n______________CCUGGUGCGGC_AGCAUU\n______________\|\|\|\|\|\|:\|:\|\|_\|\|\|\|\|\|\n______________GGACCAUGUCG_UCGUAA\n3'-UUU...ACCAA___________A______AAUAC...UCG-5'\n_____________\|__________________\|\n_____________40_________________21\n	5 -- 11	29 -- 35	-27.845 kcal/mol	9.43444 kcal/mol	4.55392 kcal/mol	1 18@LB@ \| \|@LB@ 5'- GGCUA...CUG-3'@LB@ CCUGGUGCGGC AGCAUU@LB@ \|\|\|\|\|\|:\|:\|\| \|\|\|\|\|\|@LB@ GGACCAUGUCG UCGUAA@LB@3'-UUU...ACCAA A AAUAC...UCG-5'@LB@ \| \|@LB@ 40 21@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -27.845 kcal/mol@LB@Unfolding Energy - mRNA 9.43444 kcal/mol@LB@Unfolding Energy - sRNA 4.55392 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 22 -- 39@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@LB@
70	0.00193	0.09081	b1823	cspC	-11.95	0.067388	30 -- 62	1 -- 36	stress protein member of the CspA-family	_____________29___________________________________63\n_____________\|____________________________________\|\n5'-UAU...AACGA____________UG______U__GGCA_________AAAGA...UCU-3'\n______________GGUACAGUU__C__UUUAUG_GU_____UUUUCAGU\n______________\|\|\|\|\|\|\|:\|__\|__\|\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|:\n______________CCAUGUCGA__G__AAAUAC_CA_____AAAAGUCG\n3'-UUU...AAGGA_________UC_UA______C__AUACA________-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	56 -- 62	1 -- 7	-24.9618 kcal/mol	11.5162 kcal/mol	1.49509 kcal/mol	29 63@LB@ \| \|@LB@5'-UAU...AACGA UG U GGCA AAAGA...UCU-3'@LB@ GGUACAGUU C UUUAUG GU UUUUCAGU@LB@ \|\|\|\|\|\|\|:\| \| \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ CCAUGUCGA G AAAUAC CA AAAAGUCG@LB@3'-UUU...AAGGA UC UA C AUACA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -11.95 kcal/mol@LB@Hybridization Energy -24.9618 kcal/mol@LB@Unfolding Energy - mRNA 11.5162 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 30 -- 62@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
18	0.0001426	0.02662	b1824	yobF	-14.57	0.014857	186 -- 218	1 -- 36	DUF2527 family heat-induced protein	_____________185__________________________________219\n_____________\|____________________________________\|\n5'-GCC...AACGA____________UG______U__GGCA_________AAAGA...UGU-3'\n______________GGUACAGUU__C__UUUAUG_GU_____UUUUCAGU\n______________\|\|\|\|\|\|\|:\|__\|__\|\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|:\n______________CCAUGUCGA__G__AAAUAC_CA_____AAAAGUCG\n3'-UUU...AAGGA_________UC_UA______C__AUACA________-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	212 -- 218	1 -- 7	-24.9268 kcal/mol	8.86182 kcal/mol	1.49509 kcal/mol	185 219@LB@ \| \|@LB@5'-GCC...AACGA UG U GGCA AAAGA...UGU-3'@LB@ GGUACAGUU C UUUAUG GU UUUUCAGU@LB@ \|\|\|\|\|\|\|:\| \| \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ CCAUGUCGA G AAAUAC CA AAAAGUCG@LB@3'-UUU...AAGGA UC UA C AUACA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -24.9268 kcal/mol@LB@Unfolding Energy - mRNA 8.86182 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 186 -- 218@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 1 -- 7@LB@
2	1.307e-08	2.196e-05	b1825	yebO	-18.49	0.000616	254 -- 287	16 -- 49	putative inner membrane protein	_____________253__________________________________288\n_____________\|____________________________________\|\n5'-GUC...GUAUC__U__________CU___CG_________C______UUUUU...AUC-3'\n______________GG_GGUGGUUCUU__UAU__GGCU__CAU_UUGUGG\n______________\|\|_\|\|\|\|\|\|\|\|:\|__\|\|:__:\|\|\|__\|\|\|_\|\|:\|\|\|\n______________CC_CCACCAAGGA__AUG__UCGA__GUA_AAUACC\n3'-UUU...CGAUU__U__________CC_________UC___A______CAAUA...UCG-5'\n_____________\|____________________________________\|\n_____________50___________________________________15\n	260 -- 266	37 -- 43	-30.8156 kcal/mol	7.75183 kcal/mol	4.57266 kcal/mol	253 288@LB@ \| \|@LB@5'-GUC...GUAUC U CU CG C UUUUU...AUC-3'@LB@ GG GGUGGUUCUU UAU GGCU CAU UUGUGG@LB@ \|\| \|\|\|\|\|\|\|\|:\| \|\|: :\|\|\| \|\|\| \|\|:\|\|\|@LB@ CC CCACCAAGGA AUG UCGA GUA AAUACC@LB@3'-UUU...CGAUU U CC UC A CAAUA...UCG-5'@LB@ \| \|@LB@ 50 15@LB@@LB@@LB@Energy -18.49 kcal/mol@LB@Hybridization Energy -30.8156 kcal/mol@LB@Unfolding Energy - mRNA 7.75183 kcal/mol@LB@Unfolding Energy - sRNA 4.57266 kcal/mol@LB@@LB@Position - mRNA 254 -- 287@LB@Position - sRNA 16 -- 49@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 37 -- 43@LB@
69	0.001909	0.09081	b1830	prc	-10.38	0.141777	185 -- 217	2 -- 49	carboxy-terminal protease for penicillin-binding protein 3	_____________184______________________________________________218\n_____________\|________________________________________________\|\n5'-CGA...GAAAC_______________GC__________GAAC_________________GCUUA...CGG-3'\n______________GGAGG_____CC_GG__CAG___GCAU__________AUGUUUUUUAG\n______________\|\|\|\|\|_____\|\|_\|\|__\|\|\|___\|\|\|\|__________\|\|\|\|\|\|\|\|:\|\|\n______________CCUCC_____GG_CC__GUC___CGUA__________UACAAAAAGUC\n3'-UUU...CGAUU_____ACCAA__A__AU___GAU____AAAUACCCAA___________G-5'\n_____________\|________________________________________________\|\n_____________50_______________________________________________1\n	211 -- 217	2 -- 8	-24.9215 kcal/mol	9.93043 kcal/mol	4.60955 kcal/mol	184 218@LB@ \| \|@LB@5'-CGA...GAAAC GC GAAC GCUUA...CGG-3'@LB@ GGAGG CC GG CAG GCAU AUGUUUUUUAG@LB@ \|\|\|\|\| \|\| \|\| \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ CCUCC GG CC GUC CGUA UACAAAAAGUC@LB@3'-UUU...CGAUU ACCAA A AU GAU AAAUACCCAA G-5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -24.9215 kcal/mol@LB@Unfolding Energy - mRNA 9.93043 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 185 -- 217@LB@Position - sRNA 2 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@LB@
110	0.004262	0.1302	b1871	cmoB	-11.44	0.086999	165 -- 182	22 -- 44	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent	_____________164______________________183\n_____________\|________________________\|\n5'-CAC...AACUU______A_________________AAAAG...AGC-3'\n______________UGGUUC_CUGG______UGGCAUU\n______________\|\|\|\|\|\|_\|\|\|\|______\|:\|\|\|\|\|\n______________ACCAAG_GACC______AUCGUAA\n3'-UUU...CCUCC___________AUGUCG_______AAUAC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________21\n	176 -- 182	22 -- 28	-20.1895 kcal/mol	4.19283 kcal/mol	4.55859 kcal/mol	164 183@LB@ \| \|@LB@5'-CAC...AACUU A AAAAG...AGC-3'@LB@ UGGUUC CUGG UGGCAUU@LB@ \|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ ACCAAG GACC AUCGUAA@LB@3'-UUU...CCUCC AUGUCG AAUAC...UCG-5'@LB@ \| \|@LB@ 45 21@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.1895 kcal/mol@LB@Unfolding Energy - mRNA 4.19283 kcal/mol@LB@Unfolding Energy - sRNA 4.55859 kcal/mol@LB@@LB@Position - mRNA 165 -- 182@LB@Position - sRNA 22 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 22 -- 28@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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