Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
105	0.009074	0.2778	bsu03220	ycgO	-6.59	0.539508	105 -- 111	67 -- 73	symporter	_____________104_____112\n_____________\|_______\|\n5'-GAA...CCUGC_______UCCAU...GUG-3'\n______________GGGGGUG\n______________\|\|\|\|\|\|:\n______________CCCCCAU\n3'-UUU...AACCG_______CGCGG...AUA-5'\n_____________\|_______\|\n_____________74______66\n	105 -- 111	67 -- 73	-12.2711 kcal/mol	3.65196 kcal/mol	2.02624 kcal/mol	104 112@LB@ \| \|@LB@5'-GAA...CCUGC UCCAU...GUG-3'@LB@ GGGGGUG@LB@ \|\|\|\|\|\|:@LB@ CCCCCAU@LB@3'-UUU...AACCG CGCGG...AUA-5'@LB@ \| \|@LB@ 74 66@LB@@LB@@LB@Energy -6.59 kcal/mol@LB@Hybridization Energy -12.2711 kcal/mol@LB@Unfolding Energy - mRNA 3.65196 kcal/mol@LB@Unfolding Energy - sRNA 2.02624 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 67 -- 73@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 67 -- 73@LB@
108	0.009234	0.2778	bsu12360	exuT	-9.24	0.271038	118 -- 128	32 -- 43	hexuronate transporter	_____________117__________129\n_____________\|____________\|\n5'-AAA...UUCCU____________AUUUA...UUA-3'\n______________GUC_GAUGGAGG\n______________:\|\|_\|\|\|:\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	122 -- 128	32 -- 38	-13.9988 kcal/mol	3.80022 kcal/mol	0.959872 kcal/mol	117 129@LB@ \| \|@LB@5'-AAA...UUCCU AUUUA...UUA-3'@LB@ GUC GAUGGAGG@LB@ :\|\| \|\|\|:\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -13.9988 kcal/mol@LB@Unfolding Energy - mRNA 3.80022 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 118 -- 128@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 32 -- 38@LB@
143	0.01244	0.2883	bsu13980	pbpH	-18.09	0.006437	121 -- 135	29 -- 45	penicillin-binding enzyme for formation of rod-shaped peptidoglycan cell wall	_____________120_______________136\n_____________\|_________________\|\n5'-UUU...UUGAA_________________AACCA...ACG-3'\n______________UGAUUUGA__GAGGGGU\n______________\|\|\|\|:\|\|\|__\|\|\|\|\|\|\|\n______________ACUAGACU__CUCCCCA\n3'-UUU...CUAGA________AU_______ACCCC...AUA-5'\n_____________\|_________________\|\n_____________46________________28\n	129 -- 135	29 -- 35	-21.9726 kcal/mol	2.91712 kcal/mol	0.969832 kcal/mol	120 136@LB@ \| \|@LB@5'-UUU...UUGAA AACCA...ACG-3'@LB@ UGAUUUGA GAGGGGU@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ ACUAGACU CUCCCCA@LB@3'-UUU...CUAGA AU ACCCC...AUA-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -18.09 kcal/mol@LB@Hybridization Energy -21.9726 kcal/mol@LB@Unfolding Energy - mRNA 2.91712 kcal/mol@LB@Unfolding Energy - sRNA 0.969832 kcal/mol@LB@@LB@Position - mRNA 121 -- 135@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 29 -- 35@LB@
185	0.01858	0.3269	bsu27560	hisS	-8.40	0.345340	122 -- 132	25 -- 38	histidine--tRNA ligase	_____________121____________133\n_____________\|______________\|\n5'-GCG...GUAUA_______C______AGUUU...CUU-3'\n______________GUAGGGG____GGG\n______________:\|\|\|:\|\|____\|\|\|\n______________UAUCUCC____CCC\n3'-UUU...UAGAC_______CCAA___CUUGU...AUA-5'\n_____________\|______________\|\n_____________39_____________24\n	122 -- 128	32 -- 38	-11.8618 kcal/mol	2.79445 kcal/mol	0.662893 kcal/mol	121 133@LB@ \| \|@LB@5'-GCG...GUAUA C AGUUU...CUU-3'@LB@ GUAGGGG GGG@LB@ :\|\|\|:\|\| \|\|\|@LB@ UAUCUCC CCC@LB@3'-UUU...UAGAC CCAA CUUGU...AUA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -11.8618 kcal/mol@LB@Unfolding Energy - mRNA 2.79445 kcal/mol@LB@Unfolding Energy - sRNA 0.662893 kcal/mol@LB@@LB@Position - mRNA 122 -- 132@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 32 -- 38@LB@
43	0.00194	0.1492	bsu01370	adk	-12.74	0.079154	128 -- 149	32 -- 52	adenylate kinase	_____________127____________________150\n_____________\|______________________\|\n5'-UUU...UACCG_______A___AAAAC______AAAUG...AUA-3'\n______________UGGAUUU_UGA_____UAGAGG\n______________:\|\|\|\|:\|_\|\|\|_____\|\|\|\|\|\|\n______________GCCUAGA_ACU_____AUCUCC\n3'-UUU...AAAAA___________AGACU______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	128 -- 134	46 -- 52	-16.4639 kcal/mol	2.75066 kcal/mol	0.976384 kcal/mol	127 150@LB@ \| \|@LB@5'-UUU...UACCG A AAAAC AAAUG...AUA-3'@LB@ UGGAUUU UGA UAGAGG@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|\|\|@LB@ GCCUAGA ACU AUCUCC@LB@3'-UUU...AAAAA AGACU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -16.4639 kcal/mol@LB@Unfolding Energy - mRNA 2.75066 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 128 -- 149@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 46 -- 52@LB@
193	0.01926	0.3269	bsu04460	dctR	-12.61	0.083358	128 -- 157	20 -- 50	C4-dicarboxylate response regulator DctR	_____________127_____________________________158\n_____________\|_______________________________\|\n5'-CUG...CGAUA__AG______CACAU_C____CA________UCUUU...UCU-3'\n______________GA__UUGAUU_____G_GGGG___GGGGACA\n______________\|\|__\|\|\|\|\|:_____\|_\|\|\|\|___\|\|\|:\|\|\|\n______________CU__AACUAG_____C_CCCC___CCCUUGU\n3'-UUU...AAAGC__AG______ACUAU_U____AAC_______CUCUC...AUA-5'\n_____________\|_______________________________\|\n_____________51______________________________19\n	151 -- 157	20 -- 26	-24.008 kcal/mol	7.17274 kcal/mol	4.22897 kcal/mol	127 158@LB@ \| \|@LB@5'-CUG...CGAUA AG CACAU C CA UCUUU...UCU-3'@LB@ GA UUGAUU G GGGG GGGGACA@LB@ \|\| \|\|\|\|\|: \| \|\|\|\| \|\|\|:\|\|\|@LB@ CU AACUAG C CCCC CCCUUGU@LB@3'-UUU...AAAGC AG ACUAU U AAC CUCUC...AUA-5'@LB@ \| \|@LB@ 51 19@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -24.008 kcal/mol@LB@Unfolding Energy - mRNA 7.17274 kcal/mol@LB@Unfolding Energy - sRNA 4.22897 kcal/mol@LB@@LB@Position - mRNA 128 -- 157@LB@Position - sRNA 20 -- 50@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 20 -- 26@LB@
179	0.01703	0.3152	bsu08425	mprF	-11.09	0.146985	133 -- 167	22 -- 52	phosphatidylglycerol lysyltransferase	_____________132__________________________________168\n_____________\|____________________________________\|\n5'-ACU...AAUAA___UAG___UAUAA___GU_____AUUA________GAGGA...AUC-3'\n______________CGG____UG_____UGA__UGGAG____UUGGGGGA\n______________\|\|\|____\|\|_____\|\|\|__\|:\|\|\|____\|\|\|\|\|\|:\|\n______________GCC____AC_____ACU__AUCUC____AACCCCUU\n3'-UUU...AAAAA___UAGA__UAG____________CCC_________GUCUC...AUA-5'\n_____________\|____________________________________\|\n_____________53___________________________________21\n	161 -- 167	22 -- 28	-20.3953 kcal/mol	7.42087 kcal/mol	1.8808 kcal/mol	132 168@LB@ \| \|@LB@5'-ACU...AAUAA UAG UAUAA GU AUUA GAGGA...AUC-3'@LB@ CGG UG UGA UGGAG UUGGGGGA@LB@ \|\|\| \|\| \|\|\| \|:\|\|\| \|\|\|\|\|\|:\|@LB@ GCC AC ACU AUCUC AACCCCUU@LB@3'-UUU...AAAAA UAGA UAG CCC GUCUC...AUA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -20.3953 kcal/mol@LB@Unfolding Energy - mRNA 7.42087 kcal/mol@LB@Unfolding Energy - sRNA 1.8808 kcal/mol@LB@@LB@Position - mRNA 133 -- 167@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 22 -- 28@LB@
186	0.01872	0.3269	bsu09880	yhaR	-10.74	0.166509	137 -- 152	16 -- 29	enoyl-CoA hydratase/isomerase YhaR	_____________136______________153\n_____________\|________________\|\n5'-CAG...UUUAU_______UG_______AUGUA...AAU-3'\n______________UUGGGGA__GCGGGGA\n______________\|\|\|\|\|\|\|__:\|:\|:\|\|\n______________AACCCCU__UGUCUCU\n3'-UUU...UCCCC________________CAUCG...AUA-5'\n_____________\|________________\|\n_____________30_______________15\n	146 -- 152	16 -- 22	-19.1675 kcal/mol	2.41685 kcal/mol	6.01276 kcal/mol	136 153@LB@ \| \|@LB@5'-CAG...UUUAU UG AUGUA...AAU-3'@LB@ UUGGGGA GCGGGGA@LB@ \|\|\|\|\|\|\| :\|:\|:\|\|@LB@ AACCCCU UGUCUCU@LB@3'-UUU...UCCCC CAUCG...AUA-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -19.1675 kcal/mol@LB@Unfolding Energy - mRNA 2.41685 kcal/mol@LB@Unfolding Energy - sRNA 6.01276 kcal/mol@LB@@LB@Position - mRNA 137 -- 152@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 16 -- 22@LB@
72	0.005249	0.2402	bsu31470	kapD	-7.49	0.439018	141 -- 147	21 -- 27	3'-5' exonuclease KapD	_____________140_____148\n_____________\|_______\|\n5'-UUU...GAGAA_______UGAUA...GAA-3'\n______________GGGGAAU\n______________\|\|\|\|\|\|:\n______________CCCCUUG\n3'-UUU...CCCAA_______UCUCU...AUA-5'\n_____________\|_______\|\n_____________28______20\n	141 -- 147	21 -- 27	-11.5159 kcal/mol	2.2254 kcal/mol	1.80207 kcal/mol	140 148@LB@ \| \|@LB@5'-UUU...GAGAA UGAUA...GAA-3'@LB@ GGGGAAU@LB@ \|\|\|\|\|\|:@LB@ CCCCUUG@LB@3'-UUU...CCCAA UCUCU...AUA-5'@LB@ \| \|@LB@ 28 20@LB@@LB@@LB@Energy -7.49 kcal/mol@LB@Hybridization Energy -11.5159 kcal/mol@LB@Unfolding Energy - mRNA 2.2254 kcal/mol@LB@Unfolding Energy - sRNA 1.80207 kcal/mol@LB@@LB@Position - mRNA 141 -- 147@LB@Position - sRNA 21 -- 27@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 21 -- 27@LB@
161	0.01452	0.3008	bsu04700	rsbU	-15.42	0.024826	142 -- 163	16 -- 38	phosphoserine phosphatase RsbU	_____________141_____________________164\n_____________\|_______________________\|\n5'-CUG...AUUCC____C____GAA___________UACAA...UCA-3'\n______________GUAG_GGGG____GGAACAGAGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________UAUC_CCCC____CCUUGUCUCU\n3'-UUU...UAGAC____U____AACC__________CAUCG...AUA-5'\n_____________\|_______________________\|\n_____________39______________________15\n	157 -- 163	16 -- 22	-28.36 kcal/mol	3.46196 kcal/mol	9.47701 kcal/mol	141 164@LB@ \| \|@LB@5'-CUG...AUUCC C GAA UACAA...UCA-3'@LB@ GUAG GGGG GGAACAGAGA@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UAUC CCCC CCUUGUCUCU@LB@3'-UUU...UAGAC U AACC CAUCG...AUA-5'@LB@ \| \|@LB@ 39 15@LB@@LB@@LB@Energy -15.42 kcal/mol@LB@Hybridization Energy -28.36 kcal/mol@LB@Unfolding Energy - mRNA 3.46196 kcal/mol@LB@Unfolding Energy - sRNA 9.47701 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 16 -- 38@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 16 -- 22@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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