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
102	0.02032	0.6177	b1267	yciO	-10.56	0.031637	188 -- 197	44 -- 53	putative RNA binding protein		_____________187________198\n_____________\|__________\|\n5'-GCG...CACCA__________AUUAU...CAA-3'\n______________CAGAGAGGGA\n______________\|\|:\|\|\|\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	46 -- 52	-13.8947 kcal/mol	2.40877 kcal/mol	0.927997 kcal/mol	187 198@LB@ \| \|@LB@5'-GCG...CACCA AUUAU...CAA-3'@LB@ CAGAGAGGGA@LB@ \|\|:\|\|\|\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.8947 kcal/mol@LB@Unfolding Energy - mRNA 2.40877 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 188 -- 197@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@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@
120	0.02398	0.6177	b0283	paoD	-10.02	0.040757	188 -- 198	44 -- 54	moco insertion factor for PaoABC aldehyde oxidoreductase		_____________187_________199\n_____________\|___________\|\n5'-AGG...GUGGU___________CAAUG...AGG-3'\n______________UUAAGGAGGAA\n______________\|:\|\|:\|\|\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	192 -- 198	44 -- 50	-12.5456 kcal/mol	1.58604 kcal/mol	0.939671 kcal/mol	187 199@LB@ \| \|@LB@5'-AGG...GUGGU CAAUG...AGG-3'@LB@ UUAAGGAGGAA@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.5456 kcal/mol@LB@Unfolding Energy - mRNA 1.58604 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 188 -- 198@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
126	0.02445	0.6177	b4364	yjjP	-5.95	0.256190	188 -- 200	42 -- 53	DUF1212 family inner membrane protein		_____________187___________201\n_____________\|_____________\|\n5'-UCA...UAUGA_______C_____AUGCA...UUU-3'\n______________CAAAGGG_GAGUU\n______________\|\|\|\|\|:\|_\|\|:\|\|\n______________GUUUCUC_CUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	188 -- 194	47 -- 53	-11.6429 kcal/mol	4.76073 kcal/mol	0.933904 kcal/mol	187 201@LB@ \| \|@LB@5'-UCA...UAUGA C AUGCA...UUU-3'@LB@ CAAAGGG GAGUU@LB@ \|\|\|\|\|:\| \|\|:\|\|@LB@ GUUUCUC CUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -11.6429 kcal/mol@LB@Unfolding Energy - mRNA 4.76073 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@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@
169	0.03425	0.6177	b0336	codB	-12.15	0.014930	188 -- 202	38 -- 52	cytosine transporter		_____________187_____________203\n_____________\|_______________\|\n5'-CCA...GCAAA_______________GUCGC...UUU-3'\n______________AAGGGGGAAUUUCGU\n______________\|\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUCUCCUUAAAGUA\n3'-UUU...GGCAG_______________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	196 -- 202	38 -- 44	-18.3448 kcal/mol	5.13025 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-CCA...GCAAA GUCGC...UUU-3'@LB@ AAGGGGGAAUUUCGU@LB@ \|\|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUCUCCUUAAAGUA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.3448 kcal/mol@LB@Unfolding Energy - mRNA 5.13025 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@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@
74	0.01569	0.6177	b3012	dkgA	-8.72	0.074604	189 -- 197	44 -- 52	2 5-diketo-D-gluconate reductase A		_____________188_______198\n_____________\|_________\|\n5'-CUG...AUAUA_________CGUAU...CCA-3'\n______________AAGGAGGAA\n______________\|\|:\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.1725 kcal/mol	1.58724 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-CUG...AUAUA CGUAU...CCA-3'@LB@ AAGGAGGAA@LB@ \|\|:\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1725 kcal/mol@LB@Unfolding Energy - mRNA 1.58724 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@
77	0.01626	0.6177	b1414	ydcF	-7.59	0.125301	189 -- 198	44 -- 53	DUF218 superfamily protein SAM-binding		_____________188________199\n_____________\|__________\|\n5'-GGU...AACGA__________CCAUG...UGC-3'\n______________UAAGGAGGAA\n______________:\|\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	192 -- 198	44 -- 50	-11.4771 kcal/mol	2.95852 kcal/mol	0.927997 kcal/mol	188 199@LB@ \| \|@LB@5'-GGU...AACGA CCAUG...UGC-3'@LB@ UAAGGAGGAA@LB@ :\|\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -11.4771 kcal/mol@LB@Unfolding Energy - mRNA 2.95852 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 189 -- 198@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@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@

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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