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
50	0.009706	0.6129	b0109	nadC	-3.48	0.624399	8 -- 15	22 -- 29	quinolinate phosphoribosyltransferase		_____________7________16\n_____________\|________\|\n____5'-AGGCUAA________ACCAC...AAG-3'\n______________UAUUGUGC\n______________\|\|\|\|:\|\|\|\n______________AUAAUACG\n3'-UUU...AAAUA________GCAGU...ACA-5'\n_____________\|________\|\n_____________30_______21\n	9 -- 15	22 -- 28	-7.42611 kcal/mol	1.02369 kcal/mol	2.92038 kcal/mol	7 16@LB@ \| \|@LB@ 5'-AGGCUAA ACCAC...AAG-3'@LB@ UAUUGUGC@LB@ \|\|\|\|:\|\|\|@LB@ AUAAUACG@LB@3'-UUU...AAAUA GCAGU...ACA-5'@LB@ \| \|@LB@ 30 21@LB@@LB@@LB@Energy -3.48 kcal/mol@LB@Hybridization Energy -7.42611 kcal/mol@LB@Unfolding Energy - mRNA 1.02369 kcal/mol@LB@Unfolding Energy - sRNA 2.92038 kcal/mol@LB@@LB@Position - mRNA 8 -- 15@LB@Position - sRNA 22 -- 29@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 22 -- 28@LB@
54	0.01118	0.6177	b0127	yadG	-7.27	0.144346	282 -- 299	40 -- 55	putative ABC transporter ATPase		_____________281________________300\n_____________\|__________________\|\n5'-UGU...UGCAG_______C___U______U-3'\n______________GUCGAAG_GGG_GAUUUU\n______________\|\|\|:\|\|\|_:\|\|_:\|\|\|\|:\n______________CAGUUUC_UCC_UUAAAG\n3'-UUU...CCGGG__________________UAAAA...ACA-5'\n_____________\|__________________\|\n_____________56_________________39\n	282 -- 288	49 -- 55	-13.6497 kcal/mol	5.35692 kcal/mol	1.01784 kcal/mol	281 300@LB@ \| \|@LB@5'-UGU...UGCAG C U U-3'@LB@ GUCGAAG GGG GAUUUU@LB@ \|\|\|:\|\|\| :\|\| :\|\|\|\|:@LB@ CAGUUUC UCC UUAAAG@LB@3'-UUU...CCGGG UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -13.6497 kcal/mol@LB@Unfolding Energy - mRNA 5.35692 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 49 -- 55@LB@
129	0.02539	0.6177	b0129	yadI	-10.21	0.037333	124 -- 136	40 -- 52	putative PTS Enzyme IIA		_____________123___________137\n_____________\|_____________\|\n5'-CUG...UUGGG_____________GACGG...UGA-3'\n______________GGAGAGGAGUUUU\n______________::\|\|\|\|\|\|:\|\|\|:\n______________UUUCUCCUUAAAG\n3'-UUU...GGCAG_____________UAAAA...ACA-5'\n_____________\|_____________\|\n_____________53____________39\n	130 -- 136	40 -- 46	-14.8894 kcal/mol	3.74683 kcal/mol	0.936082 kcal/mol	123 137@LB@ \| \|@LB@5'-CUG...UUGGG GACGG...UGA-3'@LB@ GGAGAGGAGUUUU@LB@ ::\|\|\|\|\|\|:\|\|\|:@LB@ UUUCUCCUUAAAG@LB@3'-UUU...GGCAG UAAAA...ACA-5'@LB@ \| \|@LB@ 53 39@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -14.8894 kcal/mol@LB@Unfolding Energy - mRNA 3.74683 kcal/mol@LB@Unfolding Energy - sRNA 0.936082 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 40 -- 52@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 40 -- 46@LB@
110	0.02234	0.6177	b0141	yadN	-8.72	0.074917	179 -- 189	37 -- 47	putative fimbrial-like adhesin protein		_____________178_________190\n_____________\|___________\|\n5'-UUA...CUAAU___________AAAGG...GUG-3'\n______________GGAAUUUUAUU\n______________\|\|\|\|\|\|\|:\|\|\|\n______________CCUUAAAGUAA\n3'-UUU...UUUCU___________AAAAA...ACA-5'\n_____________\|___________\|\n_____________48__________36\n	183 -- 189	37 -- 43	-11.1734 kcal/mol	1.41261 kcal/mol	1.04525 kcal/mol	178 190@LB@ \| \|@LB@5'-UUA...CUAAU AAAGG...GUG-3'@LB@ GGAAUUUUAUU@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ CCUUAAAGUAA@LB@3'-UUU...UUUCU AAAAA...ACA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1734 kcal/mol@LB@Unfolding Energy - mRNA 1.41261 kcal/mol@LB@Unfolding Energy - sRNA 1.04525 kcal/mol@LB@@LB@Position - mRNA 179 -- 189@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 37 -- 43@LB@
46	0.009202	0.6129	b0183	rnhB	-8.44	0.085048	25 -- 32	48 -- 55	ribonuclease HII degrades RNA of DNA-RNA hybrids		_____________24_______33\n_____________\|________\|\n5'-AAU...AGUUA________AUUAU...UCC-3'\n______________GUCAAAGA\n______________\|\|\|\|\|\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	26 -- 32	48 -- 54	-9.30452 kcal/mol	0.544993 kcal/mol	0.318869 kcal/mol	24 33@LB@ \| \|@LB@5'-AAU...AGUUA AUUAU...UCC-3'@LB@ GUCAAAGA@LB@ \|\|\|\|\|\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -9.30452 kcal/mol@LB@Unfolding Energy - mRNA 0.544993 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 25 -- 32@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 48 -- 54@LB@
108	0.0217	0.6177	b0243	proA	-8.76	0.073409	183 -- 193	47 -- 57	gamma-glutamylphosphate reductase		_____________182_________194\n_____________\|___________\|\n5'-AAU...AUUAC___________CAGGC...AUG-3'\n______________CCGUUAAGGAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	187 -- 193	47 -- 53	-14.7866 kcal/mol	3.29159 kcal/mol	2.73556 kcal/mol	182 194@LB@ \| \|@LB@5'-AAU...AUUAC CAGGC...AUG-3'@LB@ CCGUUAAGGAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -14.7866 kcal/mol@LB@Unfolding Energy - mRNA 3.29159 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 187 -- 193@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@
168	0.03398	0.6177	b0321	yahG	-8.56	0.080369	183 -- 192	44 -- 53	DUF1116 family protein	b4572	_____________182________193\n_____________\|__________\|\n5'-AUC...AUCUG__________GAAGC...AAC-3'\n______________CAAAGGGGAG\n______________\|\|\|\|\|:\|\|\|:\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	186 -- 192	44 -- 50	-12.9704 kcal/mol	3.47901 kcal/mol	0.927997 kcal/mol	182 193@LB@ \| \|@LB@5'-AUC...AUCUG GAAGC...AAC-3'@LB@ CAAAGGGGAG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.9704 kcal/mol@LB@Unfolding Energy - mRNA 3.47901 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 183 -- 192@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 44 -- 50@LB@
179	0.03684	0.6177	b0335	prpE	-7.81	0.113441	203 -- 221	38 -- 55	propionate--CoA ligase		_____________202_________________222\n_____________\|___________________\|\n5'-GCC...AUUAU___UUUU__C_________CAGCG...AAA-3'\n______________GUC____AG_GAAUUUUAU\n______________\|\|\|____\|\|_\|\|\|\|\|\|:\|\|\n______________CAG____UC_CUUAAAGUA\n3'-UUU...CCGGG___UUUC____________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	215 -- 221	38 -- 44	-10.8576 kcal/mol	1.87676 kcal/mol	1.17036 kcal/mol	202 222@LB@ \| \|@LB@5'-GCC...AUUAU UUUU C CAGCG...AAA-3'@LB@ GUC AG GAAUUUUAU@LB@ \|\|\| \|\| \|\|\|\|\|\|:\|\|@LB@ CAG UC CUUAAAGUA@LB@3'-UUU...CCGGG UUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -10.8576 kcal/mol@LB@Unfolding Energy - mRNA 1.87676 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@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@

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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