Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
10	2.605e-05	0.009165	b3599	mtlA	-16.58	0.000118	1 -- 31	4 -- 28	mannitol-specific PTS enzyme: IIA IIB and IIC components	______________1_______________________________32\n______________\|_______________________________\|\n___________5'-___________ACGUCAA________C_____CCUAU...UCA-3'\n______________GAU_GAACGUC_______UUACCUCU_UACCC\n______________\|\|\|_\|\|\|\|:\|\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUA_CUUGUAG_______AAUGGAGA_AUGGG\n3'-AUU...ACUUU___U______________________C_____AUG-5'\n_____________\|________________________________\|\n_____________29_______________________________3\n	19 -- 25	10 -- 16	-27.7982 kcal/mol	3.19385 kcal/mol	8.04825 kcal/mol	1 32@LB@ \| \|@LB@ 5'- ACGUCAA C CCUAU...UCA-3'@LB@ GAU GAACGUC UUACCUCU UACCC@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUA CUUGUAG AAUGGAGA AUGGG@LB@3'-AUU...ACUUU U C AUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -16.58 kcal/mol@LB@Hybridization Energy -27.7982 kcal/mol@LB@Unfolding Energy - mRNA 3.19385 kcal/mol@LB@Unfolding Energy - sRNA 8.04825 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 10 -- 16@LB@
40	0.0004513	0.03766	b3291	mscL	-6.99	0.263134	48 -- 58	55 -- 65	mechanosensitive channel protein high conductance	_____________47__________59\n_____________\|___________\|\n5'-UGU...UCUUC________C__UUUCU...UCU-3'\n______________CAGCCAAG_CC\n______________\|\|\|\|\|\|\|:_\|\|\n______________GUCGGUUU_GG\n3'-AUU...UAUAA________A__CUAAU...AUG-5'\n_____________\|___________\|\n_____________66__________54\n	49 -- 55	58 -- 64	-14.9389 kcal/mol	1.90813 kcal/mol	6.05961 kcal/mol	47 59@LB@ \| \|@LB@5'-UGU...UCUUC C UUUCU...UCU-3'@LB@ CAGCCAAG CC@LB@ \|\|\|\|\|\|\|: \|\|@LB@ GUCGGUUU GG@LB@3'-AUU...UAUAA A CUAAU...AUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -14.9389 kcal/mol@LB@Unfolding Energy - mRNA 1.90813 kcal/mol@LB@Unfolding Energy - sRNA 6.05961 kcal/mol@LB@@LB@Position - mRNA 48 -- 58@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 58 -- 64@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter	_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@LB@
58	0.000878	0.0531	b2150	mglB	-10.24	0.038484	153 -- 179	1 -- 24	methyl-galactoside transporter subunit	_____________152__________________________180\n_____________\|____________________________\|\n5'-GUA...CCGCC______________AAGCAC________AUAAG...AUA-3'\n______________GAGCAUU_UAUCUC______UACCCUGC\n______________\|\|:\|\|\|:_\|\|:\|\|\|______\|\|\|\|\|\|:\|\n______________CUUGUAG_AUGGAG______AUGGGAUG\n3'-AUU...UCUAU_______A______AC____________-5'\n_____________\|___________________________\|\n_____________25__________________________1\n	173 -- 179	1 -- 7	-24.5136 kcal/mol	6.27388 kcal/mol	8.02158 kcal/mol	152 180@LB@ \| \|@LB@5'-GUA...CCGCC AAGCAC AUAAG...AUA-3'@LB@ GAGCAUU UAUCUC UACCCUGC@LB@ \|\|:\|\|\|: \|\|:\|\|\| \|\|\|\|\|\|:\|@LB@ CUUGUAG AUGGAG AUGGGAUG@LB@3'-AUU...UCUAU A AC -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -24.5136 kcal/mol@LB@Unfolding Energy - mRNA 6.27388 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
200	0.009019	0.1567	b3343	tusB	-6.18	0.382258	145 -- 152	1 -- 8	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________144______153\n_____________\|________\|\n5'-GCU...GCAGA________GCCGC...GCG-3'\n______________UGCCUUAC\n______________\|:\|\|:\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	146 -- 152	1 -- 7	-9.97017 kcal/mol	1.6972 kcal/mol	2.11603 kcal/mol	144 153@LB@ \| \|@LB@5'-GCU...GCAGA GCCGC...GCG-3'@LB@ UGCCUUAC@LB@ \|:\|\|:\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -9.97017 kcal/mol@LB@Unfolding Energy - mRNA 1.6972 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 145 -- 152@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor	_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
142	0.005204	0.1284	b3931	hslU	-6.88	0.277791	3 -- 17	52 -- 65	molecular chaperone and ATPase component of HslUV protease	_____________2_______________18\n_____________\|_______________\|\n_________5'-UG________AAA____CUUAU...ACC-3'\n______________CAGCCAGA___CGAU\n______________\|\|\|\|\|\|:\|___\|\|\|\|\n______________GUCGGUUU___GCUA\n3'-AUU...UAUAA________AG_____AUGCA...AUG-5'\n_____________\|_______________\|\n_____________66______________51\n	4 -- 10	58 -- 64	-14.8174 kcal/mol	1.78514 kcal/mol	6.17277 kcal/mol	2 18@LB@ \| \|@LB@ 5'-UG AAA CUUAU...ACC-3'@LB@ CAGCCAGA CGAU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ GUCGGUUU GCUA@LB@3'-AUU...UAUAA AG AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -6.88 kcal/mol@LB@Hybridization Energy -14.8174 kcal/mol@LB@Unfolding Energy - mRNA 1.78514 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 3 -- 17@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 58 -- 64@LB@
125	0.004186	0.1178	b0781	moaA	-8.90	0.091954	79 -- 99	4 -- 23	molybdopterin biosynthesis protein A	_____________78____________________100\n_____________\|_____________________\|\n5'-ACG...CACUA____C___A_______C____GGGUC...CGG-3'\n______________AACA_UCU_GCCUCUG_ACCU\n______________\|\|\|\|_\|\|\|_:\|\|\|\|\|\|_\|\|\|:\n______________UUGU_AGA_UGGAGAC_UGGG\n3'-AUU...CUAUC________A_______A____AUG-5'\n_____________\|_____________________\|\n_____________24____________________3\n	88 -- 94	9 -- 15	-21.7522 kcal/mol	4.86496 kcal/mol	8.01134 kcal/mol	78 100@LB@ \| \|@LB@5'-ACG...CACUA C A C GGGUC...CGG-3'@LB@ AACA UCU GCCUCUG ACCU@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\| \|\|\|:@LB@ UUGU AGA UGGAGAC UGGG@LB@3'-AUU...CUAUC A A AUG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -21.7522 kcal/mol@LB@Unfolding Energy - mRNA 4.86496 kcal/mol@LB@Unfolding Energy - sRNA 8.01134 kcal/mol@LB@@LB@Position - mRNA 79 -- 99@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 9 -- 15@LB@
187	0.008276	0.1556	b0827	moeA	-6.51	0.330510	82 -- 91	23 -- 32	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________81_________92\n_____________\|__________\|\n5'-AUU...AUAUA__________UAUGG...UAC-3'\n______________GAAAGAUGGA\n______________\|\|\|\|\|\|\|:\|\|\n______________CUUUCUAUCU\n3'-AUU...CCAGA__________UGUAG...AUG-5'\n_____________\|__________\|\n_____________33_________22\n	85 -- 91	23 -- 29	-12.1772 kcal/mol	2.37895 kcal/mol	3.23951 kcal/mol	81 92@LB@ \| \|@LB@5'-AUU...AUAUA UAUGG...UAC-3'@LB@ GAAAGAUGGA@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUUUCUAUCU@LB@3'-AUU...CCAGA UGUAG...AUG-5'@LB@ \| \|@LB@ 33 22@LB@@LB@@LB@Energy -6.51 kcal/mol@LB@Hybridization Energy -12.1772 kcal/mol@LB@Unfolding Energy - mRNA 2.37895 kcal/mol@LB@Unfolding Energy - sRNA 3.23951 kcal/mol@LB@@LB@Position - mRNA 82 -- 91@LB@Position - sRNA 23 -- 32@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 23 -- 29@LB@
134	0.004727	0.1241	b1655	mepH	-9.70	0.055155	231 -- 243	1 -- 13	murein DD-endopeptidase space-maker hydrolase	_____________230___________244\n_____________\|_____________\|\n5'-CGU...UCACG_____________UUUUU...AGA-3'\n______________CUCUGUGCUUUAC\n______________\|\|\|\|\|\|:\|::\|\|\|\n______________GAGACAUGGGAUG\n3'-AUU...GAAUG_____________-5'\n_____________\|____________\|\n_____________14___________1\n	237 -- 243	1 -- 7	-18.9465 kcal/mol	4.13106 kcal/mol	5.13393 kcal/mol	230 244@LB@ \| \|@LB@5'-CGU...UCACG UUUUU...AGA-3'@LB@ CUCUGUGCUUUAC@LB@ \|\|\|\|\|\|:\|::\|\|\|@LB@ GAGACAUGGGAUG@LB@3'-AUU...GAAUG -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -18.9465 kcal/mol@LB@Unfolding Energy - mRNA 4.13106 kcal/mol@LB@Unfolding Energy - sRNA 5.13393 kcal/mol@LB@@LB@Position - mRNA 231 -- 243@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@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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service.

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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