Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
34	0.003032	0.2776	b3928	zapB	-12.77	0.066459	230 -- 240	51 -- 61	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________229_________241\n_____________\|___________\|\n5'-UUU...GAGAA___________AAGUA...AAG-3'\n______________ACUGGAAGCAA\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UGACCUUCGUU\n3'-UUU...CAUUA___________ACACU...GCG-5'\n_____________\|___________\|\n_____________62__________50\n	234 -- 240	51 -- 57	-17.959 kcal/mol	2.30162 kcal/mol	2.8896 kcal/mol	229 241@LB@ \| \|@LB@5'-UUU...GAGAA AAGUA...AAG-3'@LB@ ACUGGAAGCAA@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UGACCUUCGUU@LB@3'-UUU...CAUUA ACACU...GCG-5'@LB@ \| \|@LB@ 62 50@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -17.959 kcal/mol@LB@Unfolding Energy - mRNA 2.30162 kcal/mol@LB@Unfolding Energy - sRNA 2.8896 kcal/mol@LB@@LB@Position - mRNA 230 -- 240@LB@Position - sRNA 51 -- 61@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 51 -- 57@LB@
66	0.005808	0.2905	b2016	yeeZ	-14.47	0.034156	261 -- 292	51 -- 85	putative epimerase	_____________260_________________________________293\n_____________\|___________________________________\|\n5'-ACC...CACUU_______GA____________C____C________AACCACAC-3'\n______________UCAGCGC__GGCUGGC_AAGU___AC_GGGAGUAA\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\|_\|\|\|\|___\|\|_\|\|:\|\|:\|\|\n______________GGUCGUG__CCGACCG_UUCA___UG_CCUUCGUU\n______3'-UUUUC_______GG_______A____UUA__A________ACACU...GCG-5'\n_____________\|___________________________________\|\n_____________86__________________________________50\n	286 -- 292	51 -- 57	-40.5662 kcal/mol	11.5945 kcal/mol	14.5012 kcal/mol	260 293@LB@ \| \|@LB@5'-ACC...CACUU GA C C AACCACAC-3'@LB@ UCAGCGC GGCUGGC AAGU AC GGGAGUAA@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|:\|\|:\|\|@LB@ GGUCGUG CCGACCG UUCA UG CCUUCGUU@LB@ 3'-UUUUC GG A UUA A ACACU...GCG-5'@LB@ \| \|@LB@ 86 50@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -40.5662 kcal/mol@LB@Unfolding Energy - mRNA 11.5945 kcal/mol@LB@Unfolding Energy - sRNA 14.5012 kcal/mol@LB@@LB@Position - mRNA 261 -- 292@LB@Position - sRNA 51 -- 85@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 51 -- 57@LB@
76	0.007246	0.3134	b4174	hflK	-10.43	0.160892	249 -- 292	51 -- 90	modulator for HflB protease specific for phage lambda cII repressor	_____________248_____________________________________________293\n_____________\|_______________________________________________\|\n5'-AGA...CGUGG__________AA___________AACUC____GGAAA______A___AGGCGGUC-3'\n______________GGAAG_CAGC__ACCUGGC_GGC_____UGAG______UGGAA_CAA\n______________::\|\|\|_\|\|\|\|__\|\|\|:\|\|\|_\|\|\|_____\|:\|\|______\|\|\|\|\|_\|\|\|\n______________UUUUC_GUCG__UGGGCCG_CCG_____AUUC______ACCUU_GUU\n___________3'-_____G_____________A____________AUUAUG_____C___ACACU...GCG-5'\n______________\|______________________________________________\|\n______________90_____________________________________________50\n	260 -- 266	74 -- 80	-34.0568 kcal/mol	9.12339 kcal/mol	14.5017 kcal/mol	248 293@LB@ \| \|@LB@5'-AGA...CGUGG AA AACUC GGAAA A AGGCGGUC-3'@LB@ GGAAG CAGC ACCUGGC GGC UGAG UGGAA CAA@LB@ ::\|\|\| \|\|\|\| \|\|\|:\|\|\| \|\|\| \|:\|\| \|\|\|\|\| \|\|\|@LB@ UUUUC GUCG UGGGCCG CCG AUUC ACCUU GUU@LB@ 3'- G A AUUAUG C ACACU...GCG-5'@LB@ \| \|@LB@ 90 50@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -34.0568 kcal/mol@LB@Unfolding Energy - mRNA 9.12339 kcal/mol@LB@Unfolding Energy - sRNA 14.5017 kcal/mol@LB@@LB@Position - mRNA 249 -- 292@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 74 -- 80@LB@
162	0.02022	0.4072	b3354	yheU	-12.65	0.069641	153 -- 196	51 -- 89	UPF0270 family protein	_____________152__________________________________________197\n_____________\|____________________________________________\|\n5'-CUG...UGGCU_______C___UU____A________CAAC___U__________AAUCA...GUA-3'\n______________GGAGUCA_GCA__CCUG_CUGGUUAA____GUA_CUGGAGGCGA\n______________::\|\|:\|\|_\|\|\|__\|\|:\|_\|\|\|\|:\|\|\|____:\|\|_\|\|\|\|\|:\|\|:\|\n______________UUUCGGU_CGU__GGGC_GACCGAUU____UAU_GACCUUCGUU\n__________3'-U_________________C________CAU_______________ACACU...GCG-5'\n_____________\|____________________________________________\|\n_____________90___________________________________________50\n	189 -- 195	52 -- 58	-41.3188 kcal/mol	14.1702 kcal/mol	14.5017 kcal/mol	152 197@LB@ \| \|@LB@5'-CUG...UGGCU C UU A CAAC U AAUCA...GUA-3'@LB@ GGAGUCA GCA CCUG CUGGUUAA GUA CUGGAGGCGA@LB@ ::\|\|:\|\| \|\|\| \|\|:\| \|\|\|\|:\|\|\| :\|\| \|\|\|\|\|:\|\|:\|@LB@ UUUCGGU CGU GGGC GACCGAUU UAU GACCUUCGUU@LB@ 3'-U C CAU ACACU...GCG-5'@LB@ \| \|@LB@ 90 50@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -41.3188 kcal/mol@LB@Unfolding Energy - mRNA 14.1702 kcal/mol@LB@Unfolding Energy - sRNA 14.5017 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 51 -- 89@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@LB@
17	0.001256	0.2406	b2496	hda	-13.91	0.042623	63 -- 79	52 -- 68	ATPase regulatory factor involved in DnaA inactivation	_____________62________________80\n_____________\|_________________\|\n5'-GAC...UGAAG_____________C___GAAGA...CGC-3'\n______________AAGUGGUGCUGGA_GCA\n______________\|\|\|\|::\|:\|\|\|\|\|_\|\|\|\n______________UUCAUUAUGACCU_CGU\n3'-UUU...ACCGA_____________U___UACAC...GCG-5'\n_____________\|_________________\|\n_____________69________________51\n	69 -- 75	56 -- 62	-21.6495 kcal/mol	4.84804 kcal/mol	2.8943 kcal/mol	62 80@LB@ \| \|@LB@5'-GAC...UGAAG C GAAGA...CGC-3'@LB@ AAGUGGUGCUGGA GCA@LB@ \|\|\|\|::\|:\|\|\|\|\| \|\|\|@LB@ UUCAUUAUGACCU CGU@LB@3'-UUU...ACCGA U UACAC...GCG-5'@LB@ \| \|@LB@ 69 51@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -21.6495 kcal/mol@LB@Unfolding Energy - mRNA 4.84804 kcal/mol@LB@Unfolding Energy - sRNA 2.8943 kcal/mol@LB@@LB@Position - mRNA 63 -- 79@LB@Position - sRNA 52 -- 68@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 56 -- 62@LB@
170	0.02096	0.4072	b2283	nuoG	-12.68	0.068788	186 -- 195	52 -- 61	NADH:ubiquinone oxidoreductase chain G	_____________185________196\n_____________\|__________\|\n5'-CUG...AGAAA__________UGCUA...UUU-3'\n______________ACUGGAAGCA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UGACCUUCGU\n3'-UUU...CAUUA__________UACAC...GCG-5'\n_____________\|__________\|\n_____________62_________51\n	189 -- 195	52 -- 58	-16.7738 kcal/mol	1.20687 kcal/mol	2.88813 kcal/mol	185 196@LB@ \| \|@LB@5'-CUG...AGAAA UGCUA...UUU-3'@LB@ ACUGGAAGCA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UGACCUUCGU@LB@3'-UUU...CAUUA UACAC...GCG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -12.68 kcal/mol@LB@Hybridization Energy -16.7738 kcal/mol@LB@Unfolding Energy - mRNA 1.20687 kcal/mol@LB@Unfolding Energy - sRNA 2.88813 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@LB@
96	0.01001	0.3393	b2714	ascG	-11.75	0.098239	209 -- 220	53 -- 64	asc operon transcriptional repressor; prpBC operon repressor	_____________208__________221\n_____________\|____________\|\n5'-AAA...ACGAC____________GGCGA...AAG-3'\n______________GAUGCUGGAAGU\n______________:\|\|:\|\|\|\|\|\|\|:\n______________UUAUGACCUUCG\n3'-UUU...AUUCA____________UUACA...GCG-5'\n_____________\|____________\|\n_____________65___________52\n	214 -- 220	53 -- 59	-16.9486 kcal/mol	2.31342 kcal/mol	2.88502 kcal/mol	208 221@LB@ \| \|@LB@5'-AAA...ACGAC GGCGA...AAG-3'@LB@ GAUGCUGGAAGU@LB@ :\|\|:\|\|\|\|\|\|\|:@LB@ UUAUGACCUUCG@LB@3'-UUU...AUUCA UUACA...GCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -16.9486 kcal/mol@LB@Unfolding Energy - mRNA 2.31342 kcal/mol@LB@Unfolding Energy - sRNA 2.88502 kcal/mol@LB@@LB@Position - mRNA 209 -- 220@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 53 -- 59@LB@
30	0.002864	0.2776	b1863	ruvC	-10.04	0.185852	89 -- 98	54 -- 63	component of RuvABC resolvasome endonuclease	_____________88_________99\n_____________\|__________\|\n5'-AGC...UCGAU__________AUUGC...GCA-3'\n______________AUGCUGGAAG\n______________\|\|:\|\|\|\|\|\|\|\n______________UAUGACCUUC\n3'-UUU...UUCAU__________GUUAC...GCG-5'\n_____________\|__________\|\n_____________64_________53\n	92 -- 98	54 -- 60	-14.3659 kcal/mol	1.62427 kcal/mol	2.70635 kcal/mol	88 99@LB@ \| \|@LB@5'-AGC...UCGAU AUUGC...GCA-3'@LB@ AUGCUGGAAG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ UAUGACCUUC@LB@3'-UUU...UUCAU GUUAC...GCG-5'@LB@ \| \|@LB@ 64 53@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -14.3659 kcal/mol@LB@Unfolding Energy - mRNA 1.62427 kcal/mol@LB@Unfolding Energy - sRNA 2.70635 kcal/mol@LB@@LB@Position - mRNA 89 -- 98@LB@Position - sRNA 54 -- 63@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 54 -- 60@LB@
142	0.01677	0.3964	b3208	mtgA	-9.50	0.224857	30 -- 43	54 -- 67	biosynthetic peptidoglycan transglycosylase	_____________29_____________44\n_____________\|______________\|\n5'-UUG...ACCGC__A___________AGAUG...UGU-3'\n______________AG_AGUGCUGGAAG\n______________\|\|_\|:\|:\|\|\|\|\|\|\|\n______________UC_UUAUGACCUUC\n3'-UUU...CCGAU__A___________GUUAC...GCG-5'\n_____________\|______________\|\n_____________68_____________53\n	37 -- 43	54 -- 60	-16.1342 kcal/mol	3.92242 kcal/mol	2.71077 kcal/mol	29 44@LB@ \| \|@LB@5'-UUG...ACCGC A AGAUG...UGU-3'@LB@ AG AGUGCUGGAAG@LB@ \|\| \|:\|:\|\|\|\|\|\|\|@LB@ UC UUAUGACCUUC@LB@3'-UUU...CCGAU A GUUAC...GCG-5'@LB@ \| \|@LB@ 68 53@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -16.1342 kcal/mol@LB@Unfolding Energy - mRNA 3.92242 kcal/mol@LB@Unfolding Energy - sRNA 2.71077 kcal/mol@LB@@LB@Position - mRNA 30 -- 43@LB@Position - sRNA 54 -- 67@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 54 -- 60@LB@
156	0.0192	0.4072	b0472	recR	-11.39	0.112512	68 -- 82	54 -- 68	gap repair protein	_____________67______________83\n_____________\|_______________\|\n5'-GUG...CGACA___A___________ACCUG...UUC-3'\n______________AAG_GAUGCUGGAAG\n______________\|\|\|_:\|\|:\|\|\|\|\|\|\|\n______________UUC_UUAUGACCUUC\n3'-UUU...ACCGA___A___________GUUAC...GCG-5'\n_____________\|_______________\|\n_____________69______________53\n	76 -- 82	54 -- 60	-16.6291 kcal/mol	2.52602 kcal/mol	2.71091 kcal/mol	67 83@LB@ \| \|@LB@5'-GUG...CGACA A ACCUG...UUC-3'@LB@ AAG GAUGCUGGAAG@LB@ \|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UUC UUAUGACCUUC@LB@3'-UUU...ACCGA A GUUAC...GCG-5'@LB@ \| \|@LB@ 69 53@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -16.6291 kcal/mol@LB@Unfolding Energy - mRNA 2.52602 kcal/mol@LB@Unfolding Energy - sRNA 2.71091 kcal/mol@LB@@LB@Position - mRNA 68 -- 82@LB@Position - sRNA 54 -- 68@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 54 -- 60@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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