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
106	0.003365	0.1101	b0955	ycbZ	-10.52	0.031644	269 -- 288	48 -- 66	putative peptidase	_____________268__________________289\n_____________\|____________________\|\n5'-UUG...UUUGC_______C_________A__AAAAC...CUU-3'\n______________UCAGCCA_AUUUGAUUG_CG\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|:_\|\|\n______________AGUCGGU_UAGGCUAAU_GC\n3'-AUU...UUAUA_______U____________ACUUC...AUG-5'\n_____________\|____________________\|\n_____________67___________________47\n	279 -- 285	50 -- 56	-21.5915 kcal/mol	3.60671 kcal/mol	7.48271 kcal/mol	268 289@LB@ \| \|@LB@5'-UUG...UUUGC C A AAAAC...CUU-3'@LB@ UCAGCCA AUUUGAUUG CG@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|: \|\|@LB@ AGUCGGU UAGGCUAAU GC@LB@3'-AUU...UUAUA U ACUUC...AUG-5'@LB@ \| \|@LB@ 67 47@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -21.5915 kcal/mol@LB@Unfolding Energy - mRNA 3.60671 kcal/mol@LB@Unfolding Energy - sRNA 7.48271 kcal/mol@LB@@LB@Position - mRNA 269 -- 288@LB@Position - sRNA 48 -- 66@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 50 -- 56@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@
108	0.003398	0.1101	b0973	hyaB	-11.40	0.016694	267 -- 275	48 -- 56	hydrogenase 1 large subunit	_____________266_______276\n_____________\|_________\|\n5'-GGU...UCGAC_________CGCAU...GCG-3'\n______________CCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	269 -- 275	48 -- 54	-14.3171 kcal/mol	1.33562 kcal/mol	1.55919 kcal/mol	266 276@LB@ \| \|@LB@5'-GGU...UCGAC CGCAU...GCG-3'@LB@ CCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -14.3171 kcal/mol@LB@Unfolding Energy - mRNA 1.33562 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 267 -- 275@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
109	0.003426	0.1101	b2280	nuoJ	-6.41	0.346318	31 -- 43	48 -- 59	NADH:ubiquinone oxidoreductase membrane subunit J	_____________30____________44\n_____________\|_____________\|\n5'-GAU...GCCAG_________U___AGAAA...UUA-3'\n______________GAUCUGGUU_ACG\n______________:\|\|\|:\|:\|\|_\|\|\|\n______________UUAGGCUAA_UGC\n3'-AUU...UCGGU_____________ACUUC...AUG-5'\n_____________\|_____________\|\n_____________60____________47\n	33 -- 39	51 -- 57	-11.2654 kcal/mol	3.27917 kcal/mol	1.55995 kcal/mol	30 44@LB@ \| \|@LB@5'-GAU...GCCAG U AGAAA...UUA-3'@LB@ GAUCUGGUU ACG@LB@ :\|\|\|:\|:\|\| \|\|\|@LB@ UUAGGCUAA UGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -11.2654 kcal/mol@LB@Unfolding Energy - mRNA 3.27917 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 31 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 51 -- 57@LB@
110	0.003442	0.1101	b0528	ybcJ	-8.36	0.126664	258 -- 272	21 -- 34	ribosome-associated protein; putative RNA-binding protein	_____________257_____________273\n_____________\|_______________\|\n5'-AGG...UGAAA________C______GAAAG...CGA-3'\n______________CUGGAAGG_UGGAGC\n______________\|\|\|:\|\|\|:_\|:\|\|:\|\n______________GACUUUCU_AUCUUG\n3'-AUU...UUCCA_______________UAGAA...AUG-5'\n_____________\|_______________\|\n_____________35______________20\n	259 -- 265	27 -- 33	-15.4755 kcal/mol	3.05057 kcal/mol	4.02417 kcal/mol	257 273@LB@ \| \|@LB@5'-AGG...UGAAA C GAAAG...CGA-3'@LB@ CUGGAAGG UGGAGC@LB@ \|\|\|:\|\|\|: \|:\|\|:\|@LB@ GACUUUCU AUCUUG@LB@3'-AUU...UUCCA UAGAA...AUG-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 3.05057 kcal/mol@LB@Unfolding Energy - sRNA 4.02417 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 27 -- 33@LB@
111	0.003555	0.1127	b2938	speA	-9.18	0.077057	36 -- 48	46 -- 58	biosynthetic arginine decarboxylase PLP-binding	_____________35____________49\n_____________\|_____________\|\n5'-GUU...CUUAC_____________CUUAA...GCA-3'\n______________GUUCGGUUAUGUG\n______________:\|:\|\|:\|\|\|:\|\|\|\n______________UAGGCUAAUGCAC\n3'-AUU...CGGUU_____________UUCAU...AUG-5'\n_____________\|_____________\|\n_____________59____________45\n	42 -- 48	46 -- 52	-14.853 kcal/mol	3.8258 kcal/mol	1.8625 kcal/mol	35 49@LB@ \| \|@LB@5'-GUU...CUUAC CUUAA...GCA-3'@LB@ GUUCGGUUAUGUG@LB@ :\|:\|\|:\|\|\|:\|\|\|@LB@ UAGGCUAAUGCAC@LB@3'-AUU...CGGUU UUCAU...AUG-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -14.853 kcal/mol@LB@Unfolding Energy - mRNA 3.8258 kcal/mol@LB@Unfolding Energy - sRNA 1.8625 kcal/mol@LB@@LB@Position - mRNA 36 -- 48@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 46 -- 52@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@
113	0.003703	0.1147	b1728	ydjM	-2.69	0.937889	161 -- 167	1 -- 7	inner membrane protein regulated by LexA	_____________160_____168\n_____________\|_______\|\n5'-CGC...UAAAA_______ACUGU...AUA-3'\n______________AUCCUAU\n______________\|:\|\|\|\|:\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-7.15055 kcal/mol	2.44298 kcal/mol	2.03949 kcal/mol	160 168@LB@ \| \|@LB@5'-CGC...UAAAA ACUGU...AUA-3'@LB@ AUCCUAU@LB@ \|:\|\|\|\|:@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -2.69 kcal/mol@LB@Hybridization Energy -7.15055 kcal/mol@LB@Unfolding Energy - mRNA 2.44298 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
114	0.003723	0.1147	b2327	yfcA	-8.38	0.125082	22 -- 29	1 -- 8	TauE/TSUP family inner membrane protein	_____________21_______30\n_____________\|________\|\n5'-CAU...UACGU________CGAUA...GUG-3'\n______________UGCCCUGC\n______________\|:\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	23 -- 29	1 -- 7	-12.241 kcal/mol	1.76759 kcal/mol	2.11603 kcal/mol	21 30@LB@ \| \|@LB@5'-CAU...UACGU CGAUA...GUG-3'@LB@ UGCCCUGC@LB@ \|:\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -12.241 kcal/mol@LB@Unfolding Energy - mRNA 1.76759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 1 -- 7@LB@
115	0.00375	0.1147	b1057	yceJ	-5.38	0.522888	37 -- 59	1 -- 23	putative cytochrome b561	_____________36_______________________60\n_____________\|________________________\|\n5'-UGA...CACCA_______C__AUG___A_______UAAAC...UGU-3'\n______________GACAUCU_UG___CUG_ACCC_AC\n______________:\|\|\|\|\|\|_\|:___\|\|\|_\|\|\|\|_\|\|\n______________UUGUAGA_AU___GAC_UGGG_UG\n3'-AUU...CUAUC__________GGA___A____A__-5'\n_____________\|_______________________\|\n_____________24______________________1\n	37 -- 43	17 -- 23	-17.2281 kcal/mol	3.85652 kcal/mol	8.01506 kcal/mol	36 60@LB@ \| \|@LB@5'-UGA...CACCA C AUG A UAAAC...UGU-3'@LB@ GACAUCU UG CUG ACCC AC@LB@ :\|\|\|\|\|\| \|: \|\|\| \|\|\|\| \|\|@LB@ UUGUAGA AU GAC UGGG UG@LB@3'-AUU...CUAUC GGA A A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -5.38 kcal/mol@LB@Hybridization Energy -17.2281 kcal/mol@LB@Unfolding Energy - mRNA 3.85652 kcal/mol@LB@Unfolding Energy - sRNA 8.01506 kcal/mol@LB@@LB@Position - mRNA 37 -- 59@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 17 -- 23@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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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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