Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
136	0.01532	0.3774	b3054	ygiF	-8.05	0.285135	192 -- 208	38 -- 53	inorganic triphosphatase	_____________191_______________209\n_____________\|_________________\|\n5'-GGC...GAUAA____AG__C________GGAAA...CCG-3'\n______________GUAA__GC_AUGGCUCA\n______________\|:\|\|__\|\|_\|\|\|\|\|:\|\|\n______________CGUU__CG_UACCGGGU\n3'-UUU...GUCAC____A___U________UGUCU...UUG-5'\n_____________\|_________________\|\n_____________54________________37\n	202 -- 208	38 -- 44	-16.8567 kcal/mol	4.04422 kcal/mol	4.7597 kcal/mol	191 209@LB@ \| \|@LB@5'-GGC...GAUAA AG C GGAAA...CCG-3'@LB@ GUAA GC AUGGCUCA@LB@ \|:\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU CG UACCGGGU@LB@3'-UUU...GUCAC A U UGUCU...UUG-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -16.8567 kcal/mol@LB@Unfolding Energy - mRNA 4.04422 kcal/mol@LB@Unfolding Energy - sRNA 4.7597 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 38 -- 44@LB@
149	0.01777	0.3828	b3024	ygiW	-12.90	0.027028	214 -- 237	39 -- 58	hydrogen peroxide and cadmium resistance periplasmic protein; stress-induced OB-fold protein	_____________213______________________238\n_____________\|________________________\|\n5'-UGA...AUUCG___CA_____CGCA__________UGUGC...AAA-3'\n______________CAG__GUAAU____GUAAUGGCCC\n______________\|\|\|__\|:\|\|\|____\|:\|\|\|\|\|\|\|\|\n______________GUC__CGUUA____CGUUACCGGG\n3'-UUU...UUUUA___AC___________________UUGUC...UUG-5'\n_____________\|________________________\|\n_____________59_______________________38\n	231 -- 237	39 -- 45	-23.1488 kcal/mol	3.67833 kcal/mol	6.56779 kcal/mol	213 238@LB@ \| \|@LB@5'-UGA...AUUCG CA CGCA UGUGC...AAA-3'@LB@ CAG GUAAU GUAAUGGCCC@LB@ \|\|\| \|:\|\|\| \|:\|\|\|\|\|\|\|\|@LB@ GUC CGUUA CGUUACCGGG@LB@3'-UUU...UUUUA AC UUGUC...UUG-5'@LB@ \| \|@LB@ 59 38@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -23.1488 kcal/mol@LB@Unfolding Energy - mRNA 3.67833 kcal/mol@LB@Unfolding Energy - sRNA 6.56779 kcal/mol@LB@@LB@Position - mRNA 214 -- 237@LB@Position - sRNA 39 -- 58@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 39 -- 45@LB@
68	0.005347	0.2645	b3184	yhbE	-8.71	0.217326	12 -- 35	8 -- 33	EamA family inner membrane putative transporter	_____________11_________________________36\n_____________\|__________________________\|\n5'-AAG...ACGGU___________C____AGU_______CCGAA...UGG-3'\n______________AAAGUGAAAUU___GA___UAAAGGC\n______________\|\|\|:\|:\|\|\|\|:___\|\|___\|\|\|\|\|\|\|\n______________UUUUAUUUUAG___CU___AUUUCCG\n3'-UUU...UUGUC___________ACA__GUU_______UAUAUUG-5'\n_____________\|__________________________\|\n_____________34_________________________7\n	29 -- 35	8 -- 14	-15.936 kcal/mol	2.19409 kcal/mol	5.02883 kcal/mol	11 36@LB@ \| \|@LB@5'-AAG...ACGGU C AGU CCGAA...UGG-3'@LB@ AAAGUGAAAUU GA UAAAGGC@LB@ \|\|\|:\|:\|\|\|\|: \|\| \|\|\|\|\|\|\|@LB@ UUUUAUUUUAG CU AUUUCCG@LB@3'-UUU...UUGUC ACA GUU UAUAUUG-5'@LB@ \| \|@LB@ 34 7@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -15.936 kcal/mol@LB@Unfolding Energy - mRNA 2.19409 kcal/mol@LB@Unfolding Energy - sRNA 5.02883 kcal/mol@LB@@LB@Position - mRNA 12 -- 35@LB@Position - sRNA 8 -- 33@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 8 -- 14@LB@
97	0.009098	0.3118	b3221	yhcH	-21.73	0.000051	38 -- 71	30 -- 66	DUF386 family protein cupin superfamily	_____________37____________________________________72\n_____________\|_____________________________________\|\n5'-AUC...GUGCG___U_________________U_______________GUAUC...AAG-3'\n______________UGG__GGUCGGUGGCA__GCG_UGGUCUGGCAGAAGG\n______________\|\|\|__::\|\|:\|\|\|\|\|\|__\|\|:_\|\|\|:\|:::\|\|\|\|\|::\n______________ACC__UUAGUCACCGU__CGU_ACCGGGUUGUCUUUU\n3'-UUU...AUACA___UU___________UA___U_______________AUUUU...UUG-5'\n_____________\|_____________________________________\|\n_____________67____________________________________29\n	57 -- 63	38 -- 44	-43.4799 kcal/mol	10.7586 kcal/mol	10.9916 kcal/mol	37 72@LB@ \| \|@LB@5'-AUC...GUGCG U U GUAUC...AAG-3'@LB@ UGG GGUCGGUGGCA GCG UGGUCUGGCAGAAGG@LB@ \|\|\| ::\|\|:\|\|\|\|\|\| \|\|: \|\|\|:\|:::\|\|\|\|\|::@LB@ ACC UUAGUCACCGU CGU ACCGGGUUGUCUUUU@LB@3'-UUU...AUACA UU UA U AUUUU...UUG-5'@LB@ \| \|@LB@ 67 29@LB@@LB@@LB@Energy -21.73 kcal/mol@LB@Hybridization Energy -43.4799 kcal/mol@LB@Unfolding Energy - mRNA 10.7586 kcal/mol@LB@Unfolding Energy - sRNA 10.9916 kcal/mol@LB@@LB@Position - mRNA 38 -- 71@LB@Position - sRNA 30 -- 66@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 38 -- 44@LB@
12	0.0004505	0.1262	b3248	yhdE	-11.12	0.070056	184 -- 205	1 -- 21	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________183_____________________206\n_____________\|_______________________\|\n5'-UUA...UUGCA______________UUC______UUCUC...AGC-3'\n______________GUG_CAAUAAAGGU___UAUGAC\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:___\|\|\|:\|\|\n______________CAC_GUUAUUUCCG___AUAUUG\n3'-UUU...UUAGA___U__________U________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-19.9684 kcal/mol	4.43203 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-UUA...UUGCA UUC UUCUC...AGC-3'@LB@ GUG CAAUAAAGGU UAUGAC@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: \|\|\|:\|\|@LB@ CAC GUUAUUUCCG AUAUUG@LB@3'-UUU...UUAGA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -19.9684 kcal/mol@LB@Unfolding Energy - mRNA 4.43203 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
183	0.02285	0.4143	b3262	yhdJ	-12.72	0.029953	3 -- 23	44 -- 69	DNA adenine methyltransferase SAM-dependent	_____________2__________________________24\n_____________\|__________________________\|\n_________5'-CC__________________________ACACC...GUG-3'\n______________UGUUGGA____CA_UGGUGAUGCAAU\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|::\|\|\|\|\|\|\|\n______________ACAACCU____GU_ACCGUUACGUUA\n3'-UUU...AAUAU_______UUUA__C____________CCGGG...UUG-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	17 -- 23	44 -- 50	-23.8856 kcal/mol	6.69358 kcal/mol	4.47358 kcal/mol	2 24@LB@ \| \|@LB@ 5'-CC ACACC...GUG-3'@LB@ UGUUGGA CA UGGUGAUGCAAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|::\|\|\|\|\|\|\|@LB@ ACAACCU GU ACCGUUACGUUA@LB@3'-UUU...AAUAU UUUA C CCGGG...UUG-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -23.8856 kcal/mol@LB@Unfolding Energy - mRNA 6.69358 kcal/mol@LB@Unfolding Energy - sRNA 4.47358 kcal/mol@LB@@LB@Position - mRNA 3 -- 23@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 44 -- 50@LB@
147	0.01713	0.3828	b3354	yheU	-14.93	0.008191	201 -- 276	7 -- 70	UPF0270 family protein	_____________200_____________________________________________________________________________277\n_____________\|_______________________________________________________________________________\|\n5'-CUG...AAAUC______AU_____C_______GACCUCUCC_____AACGC________UU____GAAAGCUU____UUAC_________CCGAU...GUA-3'\n______________AUGUUG_____UC_GUGGCAA_________CCCGA_____UGGAAAAU__AAUU________UGUG____GUGAAGGCA\n______________\|\|\|\|\|\|_____\|\|_\|\|\|\|\|\|\|_________\|\|\|:\|_____::\|\|\|\|\|\|__\|\|\|:________\|\|\|\|____:\|:\|\|\|\|\|\|\n______________UACAAC_____AG_CACCGUU_________GGGUU_____GUCUUUUA__UUAG________ACAC____UAUUUCCGU\n3'-UUU...AAAUA______CUUUU__U_______ACGUUACC___________________UU________________UGU__________AUAUUG-5'\n_____________\|_______________________________________________________________________________\|\n_____________71______________________________________________________________________________6\n	270 -- 276	7 -- 13	-40.9535 kcal/mol	13.8654 kcal/mol	12.1606 kcal/mol	200 277@LB@ \| \|@LB@5'-CUG...AAAUC AU C GACCUCUCC AACGC UU GAAAGCUU UUAC CCGAU...GUA-3'@LB@ AUGUUG UC GUGGCAA CCCGA UGGAAAAU AAUU UGUG GUGAAGGCA@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|\|\| \|\|\|:\| ::\|\|\|\|\|\| \|\|\|: \|\|\|\| :\|:\|\|\|\|\|\|@LB@ UACAAC AG CACCGUU GGGUU GUCUUUUA UUAG ACAC UAUUUCCGU@LB@3'-UUU...AAAUA CUUUU U ACGUUACC UU UGU AUAUUG-5'@LB@ \| \|@LB@ 71 6@LB@@LB@@LB@Energy -14.93 kcal/mol@LB@Hybridization Energy -40.9535 kcal/mol@LB@Unfolding Energy - mRNA 13.8654 kcal/mol@LB@Unfolding Energy - sRNA 12.1606 kcal/mol@LB@@LB@Position - mRNA 201 -- 276@LB@Position - sRNA 7 -- 70@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 7 -- 13@LB@
95	0.008588	0.304	b4551	yheV	-11.20	0.067476	257 -- 273	47 -- 65	DUF2387 family putative metal-binding protein	_____________256_________________274\n_____________\|___________________\|\n5'-AUC...GCGCA___U_____A_________GGCGC...UUG-3'\n______________GGA___UCA_UGGCGAUGU\n______________\|\|\|___\|\|\|_\|\|\|\|:\|\|\|:\n______________CCU___AGU_ACCGUUACG\n3'-UUU...UACAA___UUU___C_________UUACC...UUG-5'\n_____________\|___________________\|\n_____________66__________________46\n	267 -- 273	47 -- 53	-19.3348 kcal/mol	4.06987 kcal/mol	4.06844 kcal/mol	256 274@LB@ \| \|@LB@5'-AUC...GCGCA U A GGCGC...UUG-3'@LB@ GGA UCA UGGCGAUGU@LB@ \|\|\| \|\|\| \|\|\|\|:\|\|\|:@LB@ CCU AGU ACCGUUACG@LB@3'-UUU...UACAA UUU C UUACC...UUG-5'@LB@ \| \|@LB@ 66 46@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.3348 kcal/mol@LB@Unfolding Energy - mRNA 4.06987 kcal/mol@LB@Unfolding Energy - sRNA 4.06844 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 47 -- 65@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 47 -- 53@LB@
91	0.007817	0.2889	b3380	yhfW	-10.82	0.081759	179 -- 205	41 -- 67	phosphopentomutase-related metalloenzyme superfamily protein	_____________178_________________________206\n_____________\|___________________________\|\n5'-CUC...CAGUC_______C__UC___G__C________GCGAU...GUG-3'\n______________UUGGAAA_UC__UGG_GG_GUAAUGGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_::_\|:\|\|\|\|\|\|\n______________AACCUUU_AG__ACC_UU_CGUUACCG\n3'-UUU...UAUAC_______U__UC___G__A________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________68__________________________40\n	199 -- 205	41 -- 47	-26.7792 kcal/mol	10.1319 kcal/mol	5.83043 kcal/mol	178 206@LB@ \| \|@LB@5'-CUC...CAGUC C UC G C GCGAU...GUG-3'@LB@ UUGGAAA UC UGG GG GUAAUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| :: \|:\|\|\|\|\|\|@LB@ AACCUUU AG ACC UU CGUUACCG@LB@3'-UUU...UAUAC U UC G A GGUUG...UUG-5'@LB@ \| \|@LB@ 68 40@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -26.7792 kcal/mol@LB@Unfolding Energy - mRNA 10.1319 kcal/mol@LB@Unfolding Energy - sRNA 5.83043 kcal/mol@LB@@LB@Position - mRNA 179 -- 205@LB@Position - sRNA 41 -- 67@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
70	0.005852	0.2791	b3524	yhjG	-5.99	0.576071	198 -- 212	7 -- 18	putative inner membrane-anchored periplasmic AsmA family protein	_____________197_____________213\n_____________\|_______________\|\n5'-UUG...AGCGA_______GCA_____GGCAA...GAC-3'\n______________ACGAUGA___AGGCA\n______________\|\|:\|\|:\|___\|\|\|\|\|\n______________UGUUAUU___UCCGU\n3'-UUU...GACAC_______________AUAUUG-5'\n_____________\|_______________\|\n_____________19______________6\n	198 -- 204	12 -- 18	-10.9915 kcal/mol	1.73561 kcal/mol	3.26755 kcal/mol	197 213@LB@ \| \|@LB@5'-UUG...AGCGA GCA GGCAA...GAC-3'@LB@ ACGAUGA AGGCA@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGUUAUU UCCGU@LB@3'-UUU...GACAC AUAUUG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -10.9915 kcal/mol@LB@Unfolding Energy - mRNA 1.73561 kcal/mol@LB@Unfolding Energy - sRNA 3.26755 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@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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