Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
25	0.001541	0.1727	b1948	fliP	-12.25	0.051366	190 -- 216	44 -- 71	flagellar biosynthesis protein		_____________189__________________________217\n_____________\|____________________________\|\n5'-AUU...GUAGC________C__A_________UU_____CUGUC...GCG-3'\n______________GGGAGAUC_UG__UGCGUCGU__AUUGU\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|:\|\|\|__\|\|\|:\|\n______________CCCUUUAG_AC__ACGCGGCA__UAAUA\n3'-UUU...GUGGU________A__CG________UU_____AUACU...GUG-5'\n_____________\|____________________________\|\n_____________72___________________________43\n	203 -- 209	51 -- 57	-29.2591 kcal/mol	10.1171 kcal/mol	6.89657 kcal/mol	189 217@LB@ \| \|@LB@5'-AUU...GUAGC C A UU CUGUC...GCG-3'@LB@ GGGAGAUC UG UGCGUCGU AUUGU@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\|:\|\|\| \|\|\|:\|@LB@ CCCUUUAG AC ACGCGGCA UAAUA@LB@3'-UUU...GUGGU A CG UU AUACU...GUG-5'@LB@ \| \|@LB@ 72 43@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -29.2591 kcal/mol@LB@Unfolding Energy - mRNA 10.1171 kcal/mol@LB@Unfolding Energy - sRNA 6.89657 kcal/mol@LB@@LB@Position - mRNA 190 -- 216@LB@Position - sRNA 44 -- 71@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 51 -- 57@LB@
80	0.004451	0.1855	b3578	yiaN	-12.19	0.052777	198 -- 212	52 -- 66	2 3-diketo-L-gulonate TRAP transporter large permease protein		_____________197_____________213\n_____________\|_______________\|\n5'-GGC...GCUUA___A___________AUUUU...UCU-3'\n______________AUC_UGGCUGUGCUG\n______________\|\|\|_\|\|\|\|\|\|:\|\|:\|\n______________UAG_ACCGACGCGGC\n3'-UUU...CCCUU___A___________AUUUA...GUG-5'\n_____________\|_______________\|\n_____________67______________51\n	206 -- 212	52 -- 58	-22.6247 kcal/mol	3.67694 kcal/mol	6.76246 kcal/mol	197 213@LB@ \| \|@LB@5'-GGC...GCUUA A AUUUU...UCU-3'@LB@ AUC UGGCUGUGCUG@LB@ \|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ UAG ACCGACGCGGC@LB@3'-UUU...CCCUU A AUUUA...GUG-5'@LB@ \| \|@LB@ 67 51@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -22.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.67694 kcal/mol@LB@Unfolding Energy - sRNA 6.76246 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 52 -- 66@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 52 -- 58@LB@
95	0.005084	0.1855	b3182	dacB	-12.18	0.052827	253 -- 263	2 -- 12	D-alanyl-D-alanine carboxypeptidase		_____________252_________264\n_____________\|___________\|\n5'-CCG...CAGUG___________AAUGU...GUG-3'\n______________UUCAGGCCGCA\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AAGUCCGGCGU\n3'-UUU...ACAAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	257 -- 263	2 -- 8	-21.5619 kcal/mol	3.68722 kcal/mol	5.66926 kcal/mol	252 264@LB@ \| \|@LB@5'-CCG...CAGUG AAUGU...GUG-3'@LB@ UUCAGGCCGCA@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AAGUCCGGCGU@LB@3'-UUU...ACAAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -21.5619 kcal/mol@LB@Unfolding Energy - mRNA 3.68722 kcal/mol@LB@Unfolding Energy - sRNA 5.66926 kcal/mol@LB@@LB@Position - mRNA 253 -- 263@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 2 -- 8@LB@
59	0.002989	0.1727	b2713	hydN	-12.16	0.053402	276 -- 298	54 -- 76	formate dehydrogenase-H [4Fe-4S] ferredoxin subunit	b3573	_____________275______________________299\n_____________\|________________________\|\n5'-CUU...UUUCU_______A_____A___A______AU-3'\n______________CAUCAGG_AAAUC__GG_CUGUGC\n______________\|\|:\|\|\|\|_\|\|\|\|\|__\|\|_\|\|\|:\|\|\n______________GUGGUCC_UUUAG__CC_GACGCG\n3'-UUU...CGGUU_______C_____AA_________GCAUU...GUG-5'\n_____________\|________________________\|\n_____________77_______________________53\n	276 -- 282	70 -- 76	-25.5609 kcal/mol	4.47784 kcal/mol	8.92391 kcal/mol	275 299@LB@ \| \|@LB@5'-CUU...UUUCU A A A AU-3'@LB@ CAUCAGG AAAUC GG CUGUGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|\|@LB@ GUGGUCC UUUAG CC GACGCG@LB@3'-UUU...CGGUU C AA GCAUU...GUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -25.5609 kcal/mol@LB@Unfolding Energy - mRNA 4.47784 kcal/mol@LB@Unfolding Energy - sRNA 8.92391 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 70 -- 76@LB@
50	0.002535	0.1727	b1879	flhA	-12.13	0.054078	218 -- 247	64 -- 89	putative flagellar export pore protein		_____________217______________________________248\n_____________\|________________________________\|\n5'-GCC...GCCGC___________U__CCGCAA___U________GACAC...CGA-3'\n______________GAUGCUGCGCC_GC______ACC___GAAAUC\n______________:\|\|:\|\|\|\|\|\|\|_:\|______\|\|\|___\|\|\|\|\|\|\n______________UUAUGACGCGG_UG______UGG___CUUUAG\n3'-UUU...CGCGC___________U___________UCC______AACCG...GUG-5'\n_____________\|________________________________\|\n_____________90_______________________________63\n	222 -- 228	79 -- 85	-26.8051 kcal/mol	6.79061 kcal/mol	7.88317 kcal/mol	217 248@LB@ \| \|@LB@5'-GCC...GCCGC U CCGCAA U GACAC...CGA-3'@LB@ GAUGCUGCGCC GC ACC GAAAUC@LB@ :\|\|:\|\|\|\|\|\|\| :\| \|\|\| \|\|\|\|\|\|@LB@ UUAUGACGCGG UG UGG CUUUAG@LB@3'-UUU...CGCGC U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -26.8051 kcal/mol@LB@Unfolding Energy - mRNA 6.79061 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 218 -- 247@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 79 -- 85@LB@
200	0.01246	0.2193	b0425	panE	-12.07	0.055655	285 -- 293	54 -- 62	2-dehydropantoate reductase NADPH-specific		_____________284_______294\n_____________\|_________\|\n5'-AUC...AGGGC_________GUACCGC-3'\n______________UGGCUGCGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACCGACGCG\n3'-UUU...UUAGA_________GCAUU...GUG-5'\n_____________\|_________\|\n_____________63________53\n	287 -- 293	54 -- 60	-19.0333 kcal/mol	2.09185 kcal/mol	4.8739 kcal/mol	284 294@LB@ \| \|@LB@5'-AUC...AGGGC GUACCGC-3'@LB@ UGGCUGCGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACCGACGCG@LB@3'-UUU...UUAGA GCAUU...GUG-5'@LB@ \| \|@LB@ 63 53@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -19.0333 kcal/mol@LB@Unfolding Energy - mRNA 2.09185 kcal/mol@LB@Unfolding Energy - sRNA 4.8739 kcal/mol@LB@@LB@Position - mRNA 285 -- 293@LB@Position - sRNA 54 -- 62@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 54 -- 60@LB@
117	0.006292	0.1893	b1769	ydjE	-12.05	0.056060	116 -- 139	36 -- 59	putative MFS sugar transporter membrane protein	b1775	_____________115______________________140\n_____________\|________________________\|\n5'-AUU...UGUUC_______U____A__AA_______UAAAG...UAA-3'\n______________CUGCGCC_UGAA_UA__AUGAUGA\n______________\|\|\|\|\|\|\|_\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________GACGCGG_AUUU_AU__UACUACU\n3'-UUU...GAACC_______C____A__AA_______CAAUG...GUG-5'\n_____________\|________________________\|\n_____________60_______________________35\n	133 -- 139	36 -- 42	-22.8542 kcal/mol	3.06151 kcal/mol	7.74108 kcal/mol	115 140@LB@ \| \|@LB@5'-AUU...UGUUC U A AA UAAAG...UAA-3'@LB@ CUGCGCC UGAA UA AUGAUGA@LB@ \|\|\|\|\|\|\| \|:\|\| \|\| \|\|\|\|\|\|\|@LB@ GACGCGG AUUU AU UACUACU@LB@3'-UUU...GAACC C A AA CAAUG...GUG-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -22.8542 kcal/mol@LB@Unfolding Energy - mRNA 3.06151 kcal/mol@LB@Unfolding Energy - sRNA 7.74108 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 36 -- 42@LB@
40	0.002113	0.1727	b2314	dedD	-12.04	0.056230	10 -- 25	1 -- 19	membrane-anchored periplasmic protein involved in septation		_____________9___________________26\n_____________\|___________________\|\n5'-UUG...GCGCC____GAA____________GGUGC...AUU-3'\n______________ACUG______GGGCCGCGC\n______________\|\|\|\|______:\|\|\|\|\|\|:\|\n______________UGAC______UCCGGCGUG\n3'-UUU...UGUCG____AAAAAG_________-5'\n_____________\|__________________\|\n_____________20_________________1\n	19 -- 25	1 -- 7	-21.4331 kcal/mol	3.12458 kcal/mol	6.26391 kcal/mol	9 26@LB@ \| \|@LB@5'-UUG...GCGCC GAA GGUGC...AUU-3'@LB@ ACUG GGGCCGCGC@LB@ \|\|\|\| :\|\|\|\|\|\|:\|@LB@ UGAC UCCGGCGUG@LB@3'-UUU...UGUCG AAAAAG -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.04 kcal/mol@LB@Hybridization Energy -21.4331 kcal/mol@LB@Unfolding Energy - mRNA 3.12458 kcal/mol@LB@Unfolding Energy - sRNA 6.26391 kcal/mol@LB@@LB@Position - mRNA 10 -- 25@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 1 -- 7@LB@
186	0.01109	0.2089	b3234	degQ	-11.96	0.058310	267 -- 277	3 -- 13	serine endoprotease periplasmic		_____________266_________278\n_____________\|___________\|\n5'-CUG...CGUCA___________CGCGU...UUG-3'\n______________UUUCAGGCCGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AAAGUCCGGCG\n3'-UUU...GACAA___________UG-5'\n_____________\|___________\|\n_____________14__________2\n	271 -- 277	3 -- 9	-19.4081 kcal/mol	1.79109 kcal/mol	5.63489 kcal/mol	266 278@LB@ \| \|@LB@5'-CUG...CGUCA CGCGU...UUG-3'@LB@ UUUCAGGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AAAGUCCGGCG@LB@3'-UUU...GACAA UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 5.63489 kcal/mol@LB@@LB@Position - mRNA 267 -- 277@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 3 -- 9@LB@
103	0.005609	0.1855	b2912	fau	-11.92	0.059425	103 -- 124	64 -- 85	5-formyltetrahydrofolate cyclo-ligase family protein		_____________102____________________125\n_____________\|______________________\|\n5'-GAA...ACAGC_____G_______UC_______CCCUU...UGG-3'\n______________CUGCG_CGGCAUC__GGAGAUU\n______________\|\|\|\|\|_\|::\|\|:\|__\|\|\|:\|\|:\n______________GACGC_GUUGUGG__CCUUUAG\n3'-UUU...CUUAU_____G_______UC_______AACCG...GUG-5'\n_____________\|______________________\|\n_____________86_____________________63\n	118 -- 124	64 -- 70	-27.7471 kcal/mol	8.44142 kcal/mol	7.38387 kcal/mol	102 125@LB@ \| \|@LB@5'-GAA...ACAGC G UC CCCUU...UGG-3'@LB@ CUGCG CGGCAUC GGAGAUU@LB@ \|\|\|\|\| \|::\|\|:\| \|\|\|:\|\|:@LB@ GACGC GUUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -27.7471 kcal/mol@LB@Unfolding Energy - mRNA 8.44142 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 103 -- 124@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 64 -- 70@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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