Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
81	0.004938	0.2139	b0115	aceF	-13.95	0.048783	266 -- 289	7 -- 31	pyruvate dehydrogenase dihydrolipoyltransacetylase component E2	_____________265_________________________290\n_____________\|___________________________\|\n5'-GAU...CUGGU_________C__________UU_____CGAAC...CGC-3'\n______________CAAAGUGGG_GACA___AAG__GAAGC\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|___\|\|\|__:\|\|\|\|\n______________GUUUUACCC_CUGU___UUC__UUUCG\n3'-UUU...GAGGU______________AGU___U______UCACCG-5'\n_____________\|___________________________\|\n_____________32__________________________6\n	268 -- 274	23 -- 29	-21.1287 kcal/mol	4.65658 kcal/mol	2.52208 kcal/mol	265 290@LB@ \| \|@LB@5'-GAU...CUGGU C UU CGAAC...CGC-3'@LB@ CAAAGUGGG GACA AAG GAAGC@LB@ \|\|\|\|:\|\|\|\| \|\|\|\| \|\|\| :\|\|\|\|@LB@ GUUUUACCC CUGU UUC UUUCG@LB@3'-UUU...GAGGU AGU U UCACCG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -21.1287 kcal/mol@LB@Unfolding Energy - mRNA 4.65658 kcal/mol@LB@Unfolding Energy - sRNA 2.52208 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 23 -- 29@LB@
82	0.005087	0.2147	b2741	rpoS	-15.46	0.021295	2 -- 28	1 -- 25	RNA polymerase sigma S (sigma 38) factor	_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C___A___ACAA____UU___________AAAAA...AGG-3'\n______________GGG_ACA____GAAG__AAGGCGG_GGC\n______________\|\|\|_\|\|\|____:\|\|\|__\|\|:\|\|:\|_\|\|\|\n______________CCC_UGU____UUUC__UUUCGUC_CCG\n3'-UUU...UUUUA___C___AG______U________A___-5'\n_____________\|___________________________\|\n_____________26__________________________1\n	19 -- 25	5 -- 11	-23.9329 kcal/mol	5.95047 kcal/mol	2.51748 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C A ACAA UU AAAAA...AGG-3'@LB@ GGG ACA GAAG AAGGCGG GGC@LB@ \|\|\| \|\|\| :\|\|\| \|\|:\|\|:\| \|\|\|@LB@ CCC UGU UUUC UUUCGUC CCG@LB@3'-UUU...UUUUA C AG U A -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -23.9329 kcal/mol@LB@Unfolding Energy - mRNA 5.95047 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
83	0.005101	0.2147	b2610	ffh	-14.32	0.040245	57 -- 74	4 -- 21	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________56_________________75\n_____________\|__________________\|\n5'-AGG...GAGCA___AG_____________AUAGC...AAG-3'\n______________AUA__AAAGAGAAGCAGU\n______________\|:\|__\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__UUUCUUUUCGUCA\n3'-UUU...ACCCC___AG_____________CCG-5'\n_____________\|__________________\|\n_____________22_________________3\n	68 -- 74	4 -- 10	-18.2522 kcal/mol	2.42435 kcal/mol	1.51 kcal/mol	56 75@LB@ \| \|@LB@5'-AGG...GAGCA AG AUAGC...AAG-3'@LB@ AUA AAAGAGAAGCAGU@LB@ \|:\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU UUUCUUUUCGUCA@LB@3'-UUU...ACCCC AG CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -18.2522 kcal/mol@LB@Unfolding Energy - mRNA 2.42435 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 57 -- 74@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 4 -- 10@LB@
84	0.005241	0.2147	b2513	yfgM	-12.13	0.116945	176 -- 204	2 -- 26	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________175___________________________205\n_____________\|_____________________________\|\n5'-GGC...GUUAC____UUAAGG_________G_CAGC____AAAUU...UUG-3'\n______________UGGG______AAGGAGAAG_A____GUGG\n______________\|\|\|\|______\|\|:\|\|:\|\|\|_\|____\|\|\|\|\n______________ACCC______UUUCUUUUC_U____CACC\n3'-UUU...GUUUU____CUGUAG_________G_________G-5'\n_____________\|_____________________________\|\n_____________27____________________________1\n	188 -- 194	8 -- 14	-19.1762 kcal/mol	4.53021 kcal/mol	2.5184 kcal/mol	175 205@LB@ \| \|@LB@5'-GGC...GUUAC UUAAGG G CAGC AAAUU...UUG-3'@LB@ UGGG AAGGAGAAG A GUGG@LB@ \|\|\|\| \|\|:\|\|:\|\|\| \| \|\|\|\|@LB@ ACCC UUUCUUUUC U CACC@LB@3'-UUU...GUUUU CUGUAG G G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -19.1762 kcal/mol@LB@Unfolding Energy - mRNA 4.53021 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 176 -- 204@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 8 -- 14@LB@
85	0.0054	0.2147	b4461	yfjD	-16.56	0.010978	60 -- 89	2 -- 27	UPF0053 family inner membrane protein	_____________59______________________________90\n_____________\|_______________________________\|\n5'-GAA...CUGCU___________AUCAU______U________ACGCC...UCA-3'\n______________GUGGGGACAUU_____GAAGGA_GGC_GUGG\n______________:\|\|\|\|\|\|\|\|\|:_____:\|\|\|:\|_:\|\|_\|\|\|\|\n______________UACCCCUGUAG_____UUUCUU_UCG_CACC\n3'-UUU...UGUUU______________________U___U____G-5'\n_____________\|_______________________________\|\n_____________28______________________________1\n	64 -- 70	17 -- 23	-31.7913 kcal/mol	12.7137 kcal/mol	2.51866 kcal/mol	59 90@LB@ \| \|@LB@5'-GAA...CUGCU AUCAU U ACGCC...UCA-3'@LB@ GUGGGGACAUU GAAGGA GGC GUGG@LB@ :\|\|\|\|\|\|\|\|\|: :\|\|\|:\| :\|\| \|\|\|\|@LB@ UACCCCUGUAG UUUCUU UCG CACC@LB@3'-UUU...UGUUU U U G-5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -31.7913 kcal/mol@LB@Unfolding Energy - mRNA 12.7137 kcal/mol@LB@Unfolding Energy - sRNA 2.51866 kcal/mol@LB@@LB@Position - mRNA 60 -- 89@LB@Position - sRNA 2 -- 27@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 17 -- 23@LB@
86	0.005461	0.2147	b0002	thrA	-11.41	0.159352	219 -- 235	1 -- 25	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________218_________________________236\n_____________\|___________________________\|\n5'-CCA...AGUUC__C__U_____________________AAAUG...UGG-3'\n______________GG_GG_ACAU__________CAGUGGC\n______________\|\|_\|\|_\|\|\|\|__________\|\|\|\|\|\|\|\n______________CC_CC_UGUA__________GUCACCG\n3'-UUU...UUUUA__________GUUUCUUUUC_______-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	229 -- 235	1 -- 7	-18.4664 kcal/mol	4.54068 kcal/mol	2.51748 kcal/mol	218 236@LB@ \| \|@LB@5'-CCA...AGUUC C U AAAUG...UGG-3'@LB@ GG GG ACAU CAGUGGC@LB@ \|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CC CC UGUA GUCACCG@LB@3'-UUU...UUUUA GUUUCUUUUC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -18.4664 kcal/mol@LB@Unfolding Energy - mRNA 4.54068 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
87	0.005508	0.2147	b0083	ftsL	-13.20	0.070894	129 -- 146	1 -- 23	membrane bound cell division leucine zipper septum protein	_____________128_____________________147\n_____________\|_______________________\|\n5'-CGU...AUGCC_______________________UGAGA...UGC-3'\n______________GGGC___GAAGAAGAG__GUGGC\n______________\|\|:\|___:\|\|\|\|\|:\|\|__\|\|\|\|\|\n______________CCUG___UUUCUUUUC__CACCG\n3'-UUU...UUACC____UAG_________GU_____-5'\n_____________\|______________________\|\n_____________24_____________________1\n	135 -- 141	8 -- 14	-20.4792 kcal/mol	5.69631 kcal/mol	1.57928 kcal/mol	128 147@LB@ \| \|@LB@5'-CGU...AUGCC UGAGA...UGC-3'@LB@ GGGC GAAGAAGAG GUGGC@LB@ \|\|:\| :\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUG UUUCUUUUC CACCG@LB@3'-UUU...UUACC UAG GU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -20.4792 kcal/mol@LB@Unfolding Energy - mRNA 5.69631 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 129 -- 146@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 8 -- 14@LB@
88	0.005527	0.2147	b3525	yhjH	-13.65	0.056862	190 -- 212	5 -- 23	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________189_____________________213\n_____________\|_______________________\|\n5'-UUA...ACACA_______UUU__UGAU_______GUUAU...CCU-3'\n______________GGACAUC___GA____AAGGCAG\n______________\|\|\|\|\|\|\|___\|\|____\|\|:\|\|\|\|\n______________CCUGUAG___CU____UUUCGUC\n3'-UUU...UUACC_______UUU_____________ACCG-5'\n_____________\|_______________________\|\n_____________24______________________4\n	206 -- 212	5 -- 11	-19.0549 kcal/mol	3.83037 kcal/mol	1.57523 kcal/mol	189 213@LB@ \| \|@LB@5'-UUA...ACACA UUU UGAU GUUAU...CCU-3'@LB@ GGACAUC GA AAGGCAG@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ CCUGUAG CU UUUCGUC@LB@3'-UUU...UUACC UUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -19.0549 kcal/mol@LB@Unfolding Energy - mRNA 3.83037 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 5 -- 11@LB@
89	0.005593	0.2147	b3398	yrfF	-14.72	0.032340	186 -- 206	1 -- 31	putative RcsCDB-response attenuator inner membrane protein	_____________185______________________________207\n_____________\|________________________________\|\n5'-UUA...CUAAG_____________________________A__ACCAU...GGA-3'\n______________UAAGAUGGGGA__________AAGCA_UG_GC\n______________:\|\|:\|\|\|\|\|\|\|__________\|\|\|\|\|_\|\|_\|\|\n______________GUUUUACCCCU__________UUCGU_AC_CG\n3'-UUU...GAGGU___________GUAGUUUCUU_____C_____-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	190 -- 196	21 -- 27	-21.8606 kcal/mol	4.59782 kcal/mol	2.53929 kcal/mol	185 207@LB@ \| \|@LB@5'-UUA...CUAAG A ACCAU...GGA-3'@LB@ UAAGAUGGGGA AAGCA UG GC@LB@ :\|\|:\|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|@LB@ GUUUUACCCCU UUCGU AC CG@LB@3'-UUU...GAGGU GUAGUUUCUU C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -21.8606 kcal/mol@LB@Unfolding Energy - mRNA 4.59782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 21 -- 27@LB@
90	0.005632	0.2147	b1234	rssA	-9.83	0.291555	191 -- 222	1 -- 26	putative patatin-like family phospholipase	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GAU...AAUCU__C____AUAAU_______AUAAAAA_______UGGCG...AAA-3'\n______________UG_GGGA_____GAGAAAG_______UAG_GGC\n______________\|\|_\|\|\|\|_____:\|\|\|\|\|:_______:\|\|_\|\|\|\n______________AC_CCCU_____UUCUUUU_______GUC_CCG\n3'-UUU...GUUUU_______GUAGU_______C_________A___-5'\n_____________\|________________________________\|\n_____________27_______________________________1\n	203 -- 209	9 -- 15	-16.1024 kcal/mol	3.75149 kcal/mol	2.51842 kcal/mol	190 223@LB@ \| \|@LB@5'-GAU...AAUCU C AUAAU AUAAAAA UGGCG...AAA-3'@LB@ UG GGGA GAGAAAG UAG GGC@LB@ \|\| \|\|\|\| :\|\|\|\|\|: :\|\| \|\|\|@LB@ AC CCCU UUCUUUU GUC CCG@LB@3'-UUU...GUUUU GUAGU C A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -16.1024 kcal/mol@LB@Unfolding Energy - mRNA 3.75149 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@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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