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	Additional homologs
197	0.02537	0.4256	b3317	rplB	-11.01	0.074049	182 -- 205	41 -- 62	50S ribosomal subunit protein L2		_____________181______________________206\n_____________\|________________________\|\n5'-GCA...UGAGU_______AG_A_____A_______AGUUG...UGC-3'\n______________AAGUCGG__G_GUAAU_CAAUGGC\n______________\|\|:\|\|:\|__\|_\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUUAGUC__C_CGUUA_GUUACCG\n3'-UUU...AACCU_______A________C_______GGUUG...UUG-5'\n_____________\|________________________\|\n_____________63_______________________40\n	199 -- 205	41 -- 47	-19.8959 kcal/mol	4.6063 kcal/mol	4.27585 kcal/mol	181 206@LB@ \| \|@LB@5'-GCA...UGAGU AG A A AGUUG...UGC-3'@LB@ AAGUCGG G GUAAU CAAUGGC@LB@ \|\|:\|\|:\| \| \|:\|\|\| \|\|\|\|\|\|\|@LB@ UUUAGUC C CGUUA GUUACCG@LB@3'-UUU...AACCU A C GGUUG...UUG-5'@LB@ \| \|@LB@ 63 40@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -19.8959 kcal/mol@LB@Unfolding Energy - mRNA 4.6063 kcal/mol@LB@Unfolding Energy - sRNA 4.27585 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 41 -- 62@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
45	0.002879	0.2151	b3319	rplD	-8.41	0.246804	191 -- 204	42 -- 54	50S ribosomal subunit protein L4		_____________190____________205\n_____________\|______________\|\n5'-UCA...CGUAA__A___A_______AAUUA...UUG-3'\n______________GG_GAU_GCAAUGG\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CC_UUA_CGUUACC\n3'-UUU...AGUCA__G___________GGGUU...UUG-5'\n_____________\|______________\|\n_____________55_____________41\n	198 -- 204	42 -- 48	-13.9027 kcal/mol	1.99374 kcal/mol	3.49932 kcal/mol	190 205@LB@ \| \|@LB@5'-UCA...CGUAA A A AAUUA...UUG-3'@LB@ GG GAU GCAAUGG@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CC UUA CGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.9027 kcal/mol@LB@Unfolding Energy - mRNA 1.99374 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
8	0.0003008	0.1262	b3191	mlaB	-9.66	0.142648	16 -- 23	51 -- 58	ABC transporter maintaining OM lipid asymmetry cytoplasmic STAS component		_____________15_______24\n_____________\|________\|\n5'-GUG...ACUUC________UAAAA...AGG-3'\n______________CAGUGGCG\n______________\|\|\|\|\|\|\|:\n______________GUCACCGU\n3'-UUU...UUUUA________UACGU...UUG-5'\n_____________\|________\|\n_____________59_______50\n	17 -- 23	51 -- 57	-13.9143 kcal/mol	1.55672 kcal/mol	2.69685 kcal/mol	15 24@LB@ \| \|@LB@5'-GUG...ACUUC UAAAA...AGG-3'@LB@ CAGUGGCG@LB@ \|\|\|\|\|\|\|:@LB@ GUCACCGU@LB@3'-UUU...UUUUA UACGU...UUG-5'@LB@ \| \|@LB@ 59 50@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.9143 kcal/mol@LB@Unfolding Energy - mRNA 1.55672 kcal/mol@LB@Unfolding Energy - sRNA 2.69685 kcal/mol@LB@@LB@Position - mRNA 16 -- 23@LB@Position - sRNA 51 -- 58@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 51 -- 57@LB@
171	0.02062	0.4033	b3192	mlaC	-11.25	0.065504	113 -- 124	47 -- 58	ABC transporter maintaining OM lipid asymmetry periplasmic binding protein		_____________112__________125\n_____________\|____________\|\n5'-GGA...AAGAA____________GCCAG...AGG-3'\n______________UAGUGGCGAUGC\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GUCACCGUUACG\n3'-UUU...UUUUA____________UUACC...UUG-5'\n_____________\|____________\|\n_____________59___________46\n	118 -- 124	47 -- 53	-20.0531 kcal/mol	5.42731 kcal/mol	3.37136 kcal/mol	112 125@LB@ \| \|@LB@5'-GGA...AAGAA GCCAG...AGG-3'@LB@ UAGUGGCGAUGC@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GUCACCGUUACG@LB@3'-UUU...UUUUA UUACC...UUG-5'@LB@ \| \|@LB@ 59 46@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -20.0531 kcal/mol@LB@Unfolding Energy - mRNA 5.42731 kcal/mol@LB@Unfolding Energy - sRNA 3.37136 kcal/mol@LB@@LB@Position - mRNA 113 -- 124@LB@Position - sRNA 47 -- 58@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 47 -- 53@LB@
196	0.02524	0.4256	b1805	fadD	-8.19	0.269381	280 -- 298	55 -- 72	acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase)		_____________279_________________299\n_____________\|___________________\|\n5'-UUG...GGUAG_______U___C_______CG-3'\n______________AUAUGUU_GAG_AGUCGGU\n______________\|\|\|\|\|\|\|_\|\|:_\|:\|\|:\|\|\n______________UAUACAA_CUU_UUAGUCA\n3'-UUU...AAAAA_______C___________CCGUU...UUG-5'\n_____________\|___________________\|\n_____________73__________________54\n	292 -- 298	55 -- 61	-14.048 kcal/mol	3.20699 kcal/mol	2.64594 kcal/mol	279 299@LB@ \| \|@LB@5'-UUG...GGUAG U C CG-3'@LB@ AUAUGUU GAG AGUCGGU@LB@ \|\|\|\|\|\|\| \|\|: \|:\|\|:\|\|@LB@ UAUACAA CUU UUAGUCA@LB@3'-UUU...AAAAA C CCGUU...UUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -14.048 kcal/mol@LB@Unfolding Energy - mRNA 3.20699 kcal/mol@LB@Unfolding Energy - sRNA 2.64594 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 55 -- 61@LB@
131	0.01428	0.3654	b2099	yegU	-10.27	0.106798	246 -- 258	42 -- 54	ADP-ribosylglycohydrolase family protein		_____________245___________259\n_____________\|_____________\|\n5'-GUG...CGUUA__G__________GGAUG...CAC-3'\n______________GG_GAUGCGAUGG\n______________\|\|_:\|\|\|\|:\|\|\|\|\n______________CC_UUACGUUACC\n3'-UUU...AGUCA__G__________GGGUU...UUG-5'\n_____________\|_____________\|\n_____________55____________41\n	252 -- 258	42 -- 48	-19.8763 kcal/mol	6.10373 kcal/mol	3.49932 kcal/mol	245 259@LB@ \| \|@LB@5'-GUG...CGUUA G GGAUG...CAC-3'@LB@ GG GAUGCGAUGG@LB@ \|\| :\|\|\|\|:\|\|\|\|@LB@ CC UUACGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -19.8763 kcal/mol@LB@Unfolding Energy - mRNA 6.10373 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 42 -- 48@LB@
55	0.003921	0.237	b1781	yeaE	-12.93	0.026626	223 -- 235	47 -- 59	aldo-keto reductase methylglyoxal to acetol NADPH-dependent		_____________222___________236\n_____________\|_____________\|\n5'-GUU...UCAAU_____________CUCAC...CAG-3'\n______________UUAGUGGCGAUGU\n______________\|:\|\|\|\|\|\|:\|\|\|:\n______________AGUCACCGUUACG\n3'-UUU...CUUUU_____________UUACC...UUG-5'\n_____________\|_____________\|\n_____________60____________46\n	229 -- 235	47 -- 53	-19.9127 kcal/mol	3.5603 kcal/mol	3.42309 kcal/mol	222 236@LB@ \| \|@LB@5'-GUU...UCAAU CUCAC...CAG-3'@LB@ UUAGUGGCGAUGU@LB@ \|:\|\|\|\|\|\|:\|\|\|:@LB@ AGUCACCGUUACG@LB@3'-UUU...CUUUU UUACC...UUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -19.9127 kcal/mol@LB@Unfolding Energy - mRNA 3.5603 kcal/mol@LB@Unfolding Energy - sRNA 3.42309 kcal/mol@LB@@LB@Position - mRNA 223 -- 235@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 47 -- 53@LB@
195	0.02483	0.4256	b2905	gcvT	-11.07	0.071827	75 -- 92	41 -- 59	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex		_____________74__________________93\n_____________\|___________________\|\n5'-CUG...CUGUU_____________UCA___AAAAG...AAA-3'\n______________UCGGUGGUAA_GU___GGC\n______________\|\|:\|\|\|\|:\|\|_\|:___\|\|\|\n______________AGUCACCGUU_CG___CCG\n3'-UUU...CUUUU__________A__UUA___GGUUG...UUG-5'\n_____________\|___________________\|\n_____________60__________________40\n	78 -- 84	50 -- 56	-19.3336 kcal/mol	3.99003 kcal/mol	4.26967 kcal/mol	74 93@LB@ \| \|@LB@5'-CUG...CUGUU UCA AAAAG...AAA-3'@LB@ UCGGUGGUAA GU GGC@LB@ \|\|:\|\|\|\|:\|\| \|: \|\|\|@LB@ AGUCACCGUU CG CCG@LB@3'-UUU...CUUUU A UUA GGUUG...UUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -19.3336 kcal/mol@LB@Unfolding Energy - mRNA 3.99003 kcal/mol@LB@Unfolding Energy - sRNA 4.26967 kcal/mol@LB@@LB@Position - mRNA 75 -- 92@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 50 -- 56@LB@
153	0.01791	0.3828	b2384	ypdE	-7.27	0.383330	233 -- 249	39 -- 54	aminopeptidase	b4305 b3898	_____________232_______________250\n_____________\|_________________\|\n5'-AUU...AGCGA____G_______C____CCUCG...UGC-3'\n______________GGCA_AUGCGAU_GCCU\n______________\|\|\|\|_\|\|\|\|:\|\|_\|\|\|:\n______________CCGU_UACGUUA_CGGG\n3'-UUU...AGUCA____________C____UUGUC...UUG-5'\n_____________\|_________________\|\n_____________55________________38\n	238 -- 244	44 -- 50	-20.1031 kcal/mol	8.07514 kcal/mol	4.76022 kcal/mol	232 250@LB@ \| \|@LB@5'-AUU...AGCGA G C CCUCG...UGC-3'@LB@ GGCA AUGCGAU GCCU@LB@ \|\|\|\| \|\|\|\|:\|\| \|\|\|:@LB@ CCGU UACGUUA CGGG@LB@3'-UUU...AGUCA C UUGUC...UUG-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -20.1031 kcal/mol@LB@Unfolding Energy - mRNA 8.07514 kcal/mol@LB@Unfolding Energy - sRNA 4.76022 kcal/mol@LB@@LB@Position - mRNA 233 -- 249@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 44 -- 50@LB@
65	0.005052	0.2614	b0451	amtB	-9.90	0.127883	170 -- 220	11 -- 61	ammonium transporter		_____________169____________________________________________________221\n_____________\|______________________________________________________\|\n5'-CCA...GCUGU____UC_____CACA____CA__AA_______________AUA_C_________AACUG...CGU-3'\n______________AAUC__UGGCA____GCAA__GG__CGA___AAAAUGAAG___G_GACGAUAAA\n______________\|\|\|\|__\|\|\|\|\|____\|\|\|\|__\|\|__\|:\|___\|\|\|\|\|:\|\|:___\|_\|\|\|:\|\|\|\|\|\n______________UUAG__ACCGU____CGUU__CC__GUU___UUUUAUUUU___C_CUGUUAUUU\n3'-UUU...ACCUU____UC_____UA______A___GG___GUC_________AGA_A_________CCGUA...UUG-5'\n_____________\|______________________________________________________\|\n_____________62_____________________________________________________10\n	214 -- 220	11 -- 17	-30.4323 kcal/mol	9.41224 kcal/mol	11.1248 kcal/mol	169 221@LB@ \| \|@LB@5'-CCA...GCUGU UC CACA CA AA AUA C AACUG...CGU-3'@LB@ AAUC UGGCA GCAA GG CGA AAAAUGAAG G GACGAUAAA@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\| \|\| \|:\| \|\|\|\|\|:\|\|: \| \|\|\|:\|\|\|\|\|@LB@ UUAG ACCGU CGUU CC GUU UUUUAUUUU C CUGUUAUUU@LB@3'-UUU...ACCUU UC UA A GG GUC AGA A CCGUA...UUG-5'@LB@ \| \|@LB@ 62 10@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -30.4323 kcal/mol@LB@Unfolding Energy - mRNA 9.41224 kcal/mol@LB@Unfolding Energy - sRNA 11.1248 kcal/mol@LB@@LB@Position - mRNA 170 -- 220@LB@Position - sRNA 11 -- 61@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@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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