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	Additional homologs
50	0.0006038	0.04249	b3755	yieP	-5.20	0.556147	189 -- 196	25 -- 32	putative transcriptional regulator		_____________188______197\n_____________\|________\|\n5'-UUC...AAAAA________AGUAA...CCG-3'\n______________GGAAGAUA\n______________\|:\|\|\|\|\|\|\n______________CUUUCUAU\n3'-AUU...CCAGA________CUUGU...AUG-5'\n_____________\|________\|\n_____________33_______24\n	190 -- 196	25 -- 31	-8.32385 kcal/mol	1.19727 kcal/mol	1.85262 kcal/mol	188 197@LB@ \| \|@LB@5'-UUC...AAAAA AGUAA...CCG-3'@LB@ GGAAGAUA@LB@ \|:\|\|\|\|\|\|@LB@ CUUUCUAU@LB@3'-AUU...CCAGA CUUGU...AUG-5'@LB@ \| \|@LB@ 33 24@LB@@LB@@LB@Energy -5.20 kcal/mol@LB@Hybridization Energy -8.32385 kcal/mol@LB@Unfolding Energy - mRNA 1.19727 kcal/mol@LB@Unfolding Energy - sRNA 1.85262 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 25 -- 32@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 25 -- 31@LB@
162	0.006534	0.1413	b3771	ilvD	-6.87	0.280008	44 -- 51	49 -- 56	dihydroxyacid dehydratase		_____________43_______52\n_____________\|________\|\n5'-GCG...GUGGC________CAAAC...GUA-3'\n______________CCGGUUAC\n______________\|\|\|:\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	45 -- 51	49 -- 55	-9.72973 kcal/mol	2.55538 kcal/mol	0.317884 kcal/mol	43 52@LB@ \| \|@LB@5'-GCG...GUGGC CAAAC...GUA-3'@LB@ CCGGUUAC@LB@ \|\|\|:\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -6.87 kcal/mol@LB@Hybridization Energy -9.72973 kcal/mol@LB@Unfolding Energy - mRNA 2.55538 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 44 -- 51@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 49 -- 55@LB@
30	0.0002612	0.03063	b3789	rffH	-9.15	0.078548	244 -- 254	48 -- 58	glucose-1-phosphate thymidylyltransferase		_____________243_________255\n_____________\|___________\|\n5'-GGC...AUUGC___________CGCGG...UGA-3'\n______________AUCCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAGGCUAAUGC\n3'-AUU...CGGUU___________ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	248 -- 254	48 -- 54	-15.7126 kcal/mol	4.98099 kcal/mol	1.55987 kcal/mol	243 255@LB@ \| \|@LB@5'-GGC...AUUGC CGCGG...UGA-3'@LB@ AUCCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAGGCUAAUGC@LB@3'-AUU...CGGUU ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.7126 kcal/mol@LB@Unfolding Energy - mRNA 4.98099 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 244 -- 254@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 48 -- 54@LB@
102	0.003218	0.1101	b3816	corA	-9.85	0.049984	130 -- 160	4 -- 37	magnesium/nickel/cobalt transporter		_____________129_________________________________161\n_____________\|___________________________________\|\n5'-ACC...UUAAU_________CCCA________GUU___G_______ACCGA...AAC-3'\n______________GGUCUGAAA________AUUU___UCU_UGUGCCC\n______________\|\|\|\|\|\|\|\|\|________\|\|:\|___:\|\|_\|\|\|:\|\|\|\n______________CCAGACUUU________UAGA___GGA_ACAUGGG\n3'-AUU...AUUUU_________CUAUCUUG____AU____G_______AUG-5'\n_____________\|___________________________________\|\n_____________38__________________________________3\n	154 -- 160	4 -- 10	-28.4013 kcal/mol	7.22925 kcal/mol	11.3428 kcal/mol	129 161@LB@ \| \|@LB@5'-ACC...UUAAU CCCA GUU G ACCGA...AAC-3'@LB@ GGUCUGAAA AUUU UCU UGUGCCC@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| :\|\| \|\|\|:\|\|\|@LB@ CCAGACUUU UAGA GGA ACAUGGG@LB@3'-AUU...AUUUU CUAUCUUG AU G AUG-5'@LB@ \| \|@LB@ 38 3@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -28.4013 kcal/mol@LB@Unfolding Energy - mRNA 7.22925 kcal/mol@LB@Unfolding Energy - sRNA 11.3428 kcal/mol@LB@@LB@Position - mRNA 130 -- 160@LB@Position - sRNA 4 -- 37@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 4 -- 10@LB@
118	0.003907	0.1165	b3827	yigM	-8.32	0.129405	260 -- 268	1 -- 9	putative inner membrane EamA-like transporter		_____________259_______269\n_____________\|_________\|\n5'-GGA...GGCGA_________GGGGC...UGG-3'\n______________GUACCUUGC\n______________\|\|\|\|\|:\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	262 -- 268	1 -- 7	-12.9582 kcal/mol	2.53078 kcal/mol	2.12872 kcal/mol	259 269@LB@ \| \|@LB@5'-GGA...GGCGA GGGGC...UGG-3'@LB@ GUACCUUGC@LB@ \|\|\|\|\|:\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -12.9582 kcal/mol@LB@Unfolding Energy - mRNA 2.53078 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 260 -- 268@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 1 -- 7@LB@
6	1.448e-05	0.00754	b3863	polA	-11.40	0.016745	236 -- 262	1 -- 29	5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease		_____________235___________________________263\n_____________\|_____________________________\|\n5'-AGA...CUUGU______UU_________________GC__AUAUC...GCG-3'\n______________AGAUGG__CAUCUUAUCUU__UAUC__GC\n______________\|\|\|\|:\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|__:\|\n______________UCUAUC__GUAGAAUGGAG__AUGG__UG\n3'-AUU...GACUU______UU___________AC____GA__-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	244 -- 250	15 -- 21	-25.0693 kcal/mol	5.64295 kcal/mol	8.05079 kcal/mol	235 263@LB@ \| \|@LB@5'-AGA...CUUGU UU GC AUAUC...GCG-3'@LB@ AGAUGG CAUCUUAUCUU UAUC GC@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|:\|\|: \|\|:\| :\|@LB@ UCUAUC GUAGAAUGGAG AUGG UG@LB@3'-AUU...GACUU UU AC GA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -25.0693 kcal/mol@LB@Unfolding Energy - mRNA 5.64295 kcal/mol@LB@Unfolding Energy - sRNA 8.05079 kcal/mol@LB@@LB@Position - mRNA 236 -- 262@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 15 -- 21@LB@
112	0.003594	0.1129	b3866	yihI	-3.87	0.795256	171 -- 194	53 -- 75	activator of Der GTPase		_____________170______________________195\n_____________\|________________________\|\n5'-GAA...CUAUA_____UAAAA________AGA___ACCAU...GUC-3'\n______________CUGAA_____CGGCUAAA___CGA\n______________\|\|:\|\|_____\|:\|\|:\|\|\|___\|\|\|\n______________GAUUU_____GUCGGUUU___GCU\n3'-AUU...CCGCC_____UAUAA________AG____AAUGC...AUG-5'\n_____________\|________________________\|\n_____________76_______________________52\n	181 -- 187	59 -- 65	-14.4152 kcal/mol	4.20142 kcal/mol	6.36326 kcal/mol	170 195@LB@ \| \|@LB@5'-GAA...CUAUA UAAAA AGA ACCAU...GUC-3'@LB@ CUGAA CGGCUAAA CGA@LB@ \|\|:\|\| \|:\|\|:\|\|\| \|\|\|@LB@ GAUUU GUCGGUUU GCU@LB@3'-AUU...CCGCC UAUAA AG AAUGC...AUG-5'@LB@ \| \|@LB@ 76 52@LB@@LB@@LB@Energy -3.87 kcal/mol@LB@Hybridization Energy -14.4152 kcal/mol@LB@Unfolding Energy - mRNA 4.20142 kcal/mol@LB@Unfolding Energy - sRNA 6.36326 kcal/mol@LB@@LB@Position - mRNA 171 -- 194@LB@Position - sRNA 53 -- 75@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 59 -- 65@LB@
107	0.003396	0.1101	b3871	typA	-9.79	0.052081	283 -- 294	47 -- 59	GTP-binding protein		_____________282___________295\n_____________\|_____________\|\n5'-UGC...CCAAC_____________UCGACU-3'\n______________AAUCCGGU_ACGU\n______________\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUAGGCUA_UGCA\n3'-AUU...UCGGU________A____CUUCA...AUG-5'\n_____________\|_____________\|\n_____________60____________46\n	284 -- 290	52 -- 58	-13.0383 kcal/mol	1.68034 kcal/mol	1.56852 kcal/mol	282 295@LB@ \| \|@LB@5'-UGC...CCAAC UCGACU-3'@LB@ AAUCCGGU ACGU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ UUAGGCUA UGCA@LB@3'-AUU...UCGGU A CUUCA...AUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -13.0383 kcal/mol@LB@Unfolding Energy - mRNA 1.68034 kcal/mol@LB@Unfolding Energy - sRNA 1.56852 kcal/mol@LB@@LB@Position - mRNA 283 -- 294@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 52 -- 58@LB@
88	0.002339	0.09349	b3878	yihQ	-11.00	0.022508	260 -- 267	1 -- 8	putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase	b3656	_____________259______268\n_____________\|________\|\n5'-AAC...AGUUU________AUUUU...GCA-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	261 -- 267	1 -- 7	-13.427 kcal/mol	0.33456 kcal/mol	2.11603 kcal/mol	259 268@LB@ \| \|@LB@5'-AAC...AGUUU AUUUU...GCA-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -13.427 kcal/mol@LB@Unfolding Energy - mRNA 0.33456 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 260 -- 267@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 1 -- 7@LB@
62	0.001059	0.05856	b3927	glpF	-11.40	0.016677	192 -- 203	48 -- 59	glycerol facilitator		_____________191__________204\n_____________\|____________\|\n5'-GAU...UUCAG____________AGUCA...AAG-3'\n______________GAUCCGAUUAUG\n______________:\|\|\|\|\|\|\|\|\|:\|\n______________UUAGGCUAAUGC\n3'-AUU...UCGGU____________ACUUC...AUG-5'\n_____________\|____________\|\n_____________60___________47\n	197 -- 203	48 -- 54	-15.6898 kcal/mol	2.7066 kcal/mol	1.55995 kcal/mol	191 204@LB@ \| \|@LB@5'-GAU...UUCAG AGUCA...AAG-3'@LB@ GAUCCGAUUAUG@LB@ :\|\|\|\|\|\|\|\|\|:\|@LB@ UUAGGCUAAUGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -15.6898 kcal/mol@LB@Unfolding Energy - mRNA 2.7066 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 192 -- 203@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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