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	Additional homologs
164	0.03346	0.6177	b1449	curA	-5.87	0.264423	114 -- 122	45 -- 53	curcumin/dihydrocurcumin reductase NADPH-dependent		_____________113_______123\n_____________\|_________\|\n5'-CGG...UGUUG_________UGUGA...UCG-3'\n______________CAGAGGGGA\n______________\|\|:\|\|:\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	116 -- 122	45 -- 51	-11.6619 kcal/mol	4.87234 kcal/mol	0.917553 kcal/mol	113 123@LB@ \| \|@LB@5'-CGG...UGUUG UGUGA...UCG-3'@LB@ CAGAGGGGA@LB@ \|\|:\|\|:\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -11.6619 kcal/mol@LB@Unfolding Energy - mRNA 4.87234 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 114 -- 122@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 45 -- 51@LB@
139	0.02683	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
177	0.03616	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
11	0.002274	0.593	b1476	fdnI	-10.73	0.029150	152 -- 175	44 -- 69	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________151________________________176\n_____________\|__________________________\|\n5'-CGU...ACUAC____G______________UA_____GUGGA...UUU-3'\n______________AUCG_UAUUGGCCCG__AA__AGGAA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\|__\|\|__\|\|\|\|\|\n______________UAGC_AUAACCGGGC__UU__UCCUU\n3'-UUU...GGUUA____G__________AG__UC_____AAAGU...ACA-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	160 -- 166	55 -- 61	-29.2423 kcal/mol	7.20098 kcal/mol	11.3099 kcal/mol	151 176@LB@ \| \|@LB@5'-CGU...ACUAC G UA GUGGA...UUU-3'@LB@ AUCG UAUUGGCCCG AA AGGAA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ UAGC AUAACCGGGC UU UCCUU@LB@3'-UUU...GGUUA G AG UC AAAGU...ACA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -10.73 kcal/mol@LB@Hybridization Energy -29.2423 kcal/mol@LB@Unfolding Energy - mRNA 7.20098 kcal/mol@LB@Unfolding Energy - sRNA 11.3099 kcal/mol@LB@@LB@Position - mRNA 152 -- 175@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 55 -- 61@LB@
160	0.0322	0.6177	b1550	gnsB	-8.75	0.073686	189 -- 197	44 -- 52	Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)	b4517	_____________188_______198\n_____________\|_________\|\n5'-UGG...GACUA_________AUGAU...UUA-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.5466 kcal/mol	1.93458 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-UGG...GACUA AUGAU...UUA-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.5466 kcal/mol@LB@Unfolding Energy - mRNA 1.93458 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
161	0.03295	0.6177	b1630	rsxD	-5.86	0.265655	34 -- 42	49 -- 57	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex		_____________33________43\n_____________\|_________\|\n5'-AGC...AGCUG_________CGGCU...CAG-3'\n______________CCGUCGAAG\n______________\|\|\|\|\|:\|\|\|\n______________GGCAGUUUC\n3'-UUU...AACCG_________UCCUU...ACA-5'\n_____________\|_________\|\n_____________58________48\n	36 -- 42	49 -- 55	-12.0908 kcal/mol	3.50131 kcal/mol	2.72876 kcal/mol	33 43@LB@ \| \|@LB@5'-AGC...AGCUG CGGCU...CAG-3'@LB@ CCGUCGAAG@LB@ \|\|\|\|\|:\|\|\|@LB@ GGCAGUUUC@LB@3'-UUU...AACCG UCCUU...ACA-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.0908 kcal/mol@LB@Unfolding Energy - mRNA 3.50131 kcal/mol@LB@Unfolding Energy - sRNA 2.72876 kcal/mol@LB@@LB@Position - mRNA 34 -- 42@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 49 -- 55@LB@
117	0.02321	0.6177	b1712	ihfA	-8.91	0.068436	115 -- 126	45 -- 56	integration host factor (IHF) DNA-binding protein alpha subunit		_____________114__________127\n_____________\|____________\|\n5'-CGU...ACACU__AA________GAUUG...AGA-3'\n______________CG__GAAGAGGA\n______________\|\|__:\|\|\|\|\|\|\|\n______________GC__UUUCUCCU\n3'-UUU...ACCGG__AG________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	120 -- 126	45 -- 51	-12.2887 kcal/mol	2.43966 kcal/mol	0.938337 kcal/mol	114 127@LB@ \| \|@LB@5'-CGU...ACACU AA GAUUG...AGA-3'@LB@ CG GAAGAGGA@LB@ \|\| :\|\|\|\|\|\|\|@LB@ GC UUUCUCCU@LB@3'-UUU...ACCGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -12.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.43966 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 115 -- 126@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 45 -- 51@LB@
116	0.02318	0.6177	b1726	yniB	-7.96	0.105879	188 -- 195	47 -- 54	putative inner membrane protein		_____________187______196\n_____________\|________\|\n5'-AAG...CUUAA________AACUC...UGA-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	189 -- 195	47 -- 53	-9.99546 kcal/mol	1.13532 kcal/mol	0.897871 kcal/mol	187 196@LB@ \| \|@LB@5'-AAG...CUUAA AACUC...UGA-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -9.99546 kcal/mol@LB@Unfolding Energy - mRNA 1.13532 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 188 -- 195@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 189 -- 195@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@
2	6.241e-06	0.01004	b1737	chbC	-18.35	0.000789	134 -- 152	38 -- 56	N N'-diacetylchitobiose-specific enzyme IIC component of PTS		_____________133_________________153\n_____________\|___________________\|\n5'-GUU...UUUCC__________UU_______AAAUC...UUC-3'\n______________CGUCAAAGAG__AUUUCAU\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________GCAGUUUCUC__UAAAGUA\n3'-UUU...ACCGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	146 -- 152	38 -- 44	-21.3647 kcal/mol	1.83077 kcal/mol	1.17918 kcal/mol	133 153@LB@ \| \|@LB@5'-GUU...UUUCC UU AAAUC...UUC-3'@LB@ CGUCAAAGAG AUUUCAU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCAGUUUCUC UAAAGUA@LB@3'-UUU...ACCGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -21.3647 kcal/mol@LB@Unfolding Energy - mRNA 1.83077 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 134 -- 152@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 38 -- 44@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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