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	Additional homologs
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@
162	0.01461	0.3008	bsu28700	ysfE	-18.20	0.006050	31 -- 59	26 -- 51	Evidence 5: No homology to any previously reported sequences	bsu26940	_____________30____________________________60\n_____________\|_____________________________\|\n5'-AAG...UAGAA___CUA____AAA__CUG___________CAAUG...AAA-3'\n______________GGA___UUGA___UG___AGAGGGGUUGG\n______________\|\|\|___\|\|\|\|___\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________CCU___AACU___AC___UCUCCCCAACC\n3'-UUU...AAAAG___AG_____AG___UA____________CCUUG...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________25\n	53 -- 59	26 -- 32	-27.3955 kcal/mol	8.22133 kcal/mol	0.975822 kcal/mol	30 60@LB@ \| \|@LB@5'-AAG...UAGAA CUA AAA CUG CAAUG...AAA-3'@LB@ GGA UUGA UG AGAGGGGUUGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CCU AACU AC UCUCCCCAACC@LB@3'-UUU...AAAAG AG AG UA CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -18.20 kcal/mol@LB@Hybridization Energy -27.3955 kcal/mol@LB@Unfolding Energy - mRNA 8.22133 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 31 -- 59@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 26 -- 32@LB@
163	0.01533	0.3122	bsu19639	yoyE	-15.95	0.019304	185 -- 198	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function		_____________184_____________199\n_____________\|_______________\|\n5'-UCA...CGCAG__A____________ACAUG...AAU-3'\n______________GA_GGAGGGGU_GGG\n______________\|\|_:\|\|\|\|\|\|\|_\|\|\|\n______________CU_UCUCCCCA_CCC\n3'-UUU...CUAGA__A________A___CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	189 -- 195	29 -- 35	-22.4813 kcal/mol	5.74668 kcal/mol	0.783603 kcal/mol	184 199@LB@ \| \|@LB@5'-UCA...CGCAG A ACAUG...AAU-3'@LB@ GA GGAGGGGU GGG@LB@ \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CU UCUCCCCA CCC@LB@3'-UUU...CUAGA A A CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -22.4813 kcal/mol@LB@Unfolding Energy - mRNA 5.74668 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 185 -- 198@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 29 -- 35@LB@
164	0.01535	0.3122	bsu39720	iolE	-13.03	0.070250	182 -- 189	30 -- 37	inosose dehydratase		_____________181______190\n_____________\|________\|\n5'-GUU...AGUAU________AGGCA...UAA-3'\n______________UAGAGGGG\n______________\|\|\|\|\|\|\|\|\n______________AUCUCCCC\n3'-UUU...AGACU________AACCC...AUA-5'\n_____________\|________\|\n_____________38_______29\n	183 -- 189	30 -- 36	-14.5397 kcal/mol	1.33978 kcal/mol	0.165704 kcal/mol	181 190@LB@ \| \|@LB@5'-GUU...AGUAU AGGCA...UAA-3'@LB@ UAGAGGGG@LB@ \|\|\|\|\|\|\|\|@LB@ AUCUCCCC@LB@3'-UUU...AGACU AACCC...AUA-5'@LB@ \| \|@LB@ 38 29@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -14.5397 kcal/mol@LB@Unfolding Energy - mRNA 1.33978 kcal/mol@LB@Unfolding Energy - sRNA 0.165704 kcal/mol@LB@@LB@Position - mRNA 182 -- 189@LB@Position - sRNA 30 -- 37@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
165	0.01546	0.3127	bsu02230	purT	-12.11	0.100898	185 -- 195	30 -- 39	phosphoribosylglycinamide formyltransferase		_____________184_________196\n_____________\|___________\|\n5'-GAU...GAACA___A_______CAAAG...UUG-3'\n______________GAU_GGAGGGG\n______________\|\|\|_:\|\|\|\|\|\|\n______________CUA_UCUCCCC\n3'-UUU...CUAGA___________AACCC...AUA-5'\n_____________\|___________\|\n_____________40__________29\n	189 -- 195	30 -- 36	-15.5568 kcal/mol	2.66346 kcal/mol	0.779184 kcal/mol	184 196@LB@ \| \|@LB@5'-GAU...GAACA A CAAAG...UUG-3'@LB@ GAU GGAGGGG@LB@ \|\|\| :\|\|\|\|\|\|@LB@ CUA UCUCCCC@LB@3'-UUU...CUAGA AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.5568 kcal/mol@LB@Unfolding Energy - mRNA 2.66346 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
166	0.01583	0.3152	bsu38190	galT	-8.42	0.343831	170 -- 181	16 -- 26	galactose-1-phosphate uridylyltransferase		_____________169__________182\n_____________\|____________\|\n5'-GGG...GGAGA_______A____ACUAA...AUG-3'\n______________GGGAGCG_GAGA\n______________\|\|\|\|:\|:_\|\|\|\|\n______________CCCUUGU_CUCU\n3'-UUU...CCAAC____________CAUCG...AUA-5'\n_____________\|____________\|\n_____________27___________15\n	170 -- 176	20 -- 26	-15.5563 kcal/mol	1.12924 kcal/mol	6.00672 kcal/mol	169 182@LB@ \| \|@LB@5'-GGG...GGAGA A ACUAA...AUG-3'@LB@ GGGAGCG GAGA@LB@ \|\|\|\|:\|: \|\|\|\|@LB@ CCCUUGU CUCU@LB@3'-UUU...CCAAC CAUCG...AUA-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -15.5563 kcal/mol@LB@Unfolding Energy - mRNA 1.12924 kcal/mol@LB@Unfolding Energy - sRNA 6.00672 kcal/mol@LB@@LB@Position - mRNA 170 -- 181@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 20 -- 26@LB@
167	0.01619	0.3152	bsu31500	yuxK	-13.98	0.047449	182 -- 199	26 -- 51	Evidence 4: Homologs of previously reported genes of unknown function		_____________181__________________________200\n_____________\|____________________________\|\n5'-UAC...UUAAA______________________AUA___AGUGA...ACG-3'\n______________GGAUC__________GGAGGGG___UGG\n______________\|\|\|\|\|__________:\|\|\|\|\|\|___\|\|\|\n______________CCUAG__________UCUCCCC___ACC\n3'-UUU...AAAAG_____AACUAGACUA_______A_____CCUUG...AUA-5'\n_____________\|____________________________\|\n_____________52___________________________25\n	187 -- 193	30 -- 36	-20.9361 kcal/mol	5.98517 kcal/mol	0.975822 kcal/mol	181 200@LB@ \| \|@LB@5'-UAC...UUAAA AUA AGUGA...ACG-3'@LB@ GGAUC GGAGGGG UGG@LB@ \|\|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ CCUAG UCUCCCC ACC@LB@3'-UUU...AAAAG AACUAGACUA A CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -13.98 kcal/mol@LB@Hybridization Energy -20.9361 kcal/mol@LB@Unfolding Energy - mRNA 5.98517 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
168	0.01631	0.3152	bsu14170	ykuP	-12.43	0.089417	80 -- 100	11 -- 27	flavodoxin-2		_____________79____________________101\n_____________\|_____________________\|\n5'-CAC...AUUAA___ACAU______________CAAUC...UAG-3'\n______________GGG____GGAUGGAGAGUGGC\n______________\|\|\|____\|:\|::\|\|\|\|\|\|:\|\|\n______________CCC____CUUGUCUCUCAUCG\n3'-UUU...CCCAA_____________________AAGAG...AUA-5'\n_____________\|_____________________\|\n_____________28____________________10\n	94 -- 100	11 -- 17	-24.7716 kcal/mol	6.31596 kcal/mol	6.0284 kcal/mol	79 101@LB@ \| \|@LB@5'-CAC...AUUAA ACAU CAAUC...UAG-3'@LB@ GGG GGAUGGAGAGUGGC@LB@ \|\|\| \|:\|::\|\|\|\|\|\|:\|\|@LB@ CCC CUUGUCUCUCAUCG@LB@3'-UUU...CCCAA AAGAG...AUA-5'@LB@ \| \|@LB@ 28 10@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -24.7716 kcal/mol@LB@Unfolding Energy - mRNA 6.31596 kcal/mol@LB@Unfolding Energy - sRNA 6.0284 kcal/mol@LB@@LB@Position - mRNA 80 -- 100@LB@Position - sRNA 11 -- 27@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 11 -- 17@LB@
169	0.01639	0.3152	bsu07850	yfkM	-11.33	0.135062	186 -- 208	22 -- 34	general stress protein 18		_____________185_____________________209\n_____________\|_______________________\|\n5'-UGU...AAAGC___A___UAUGAAUCA_______AAAAA...CUG-3'\n______________GGG_GGU_________UGGGGAA\n______________:\|\|_\|\|\|_________\|\|\|\|\|\|\|\n______________UCC_CCA_________ACCCCUU\n3'-UUU...CUAUC_______________________GUCUC...AUA-5'\n_____________\|_______________________\|\n_____________35______________________21\n	202 -- 208	22 -- 28	-15.0114 kcal/mol	2.66027 kcal/mol	1.02154 kcal/mol	185 209@LB@ \| \|@LB@5'-UGU...AAAGC A UAUGAAUCA AAAAA...CUG-3'@LB@ GGG GGU UGGGGAA@LB@ :\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCC CCA ACCCCUU@LB@3'-UUU...CUAUC GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -15.0114 kcal/mol@LB@Unfolding Energy - mRNA 2.66027 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
170	0.0164	0.3152	bsu13090	ykkC	-8.27	0.358617	162 -- 212	23 -- 55	multidrug resistance protein		_____________161__________________________________________________213\n_____________\|____________________________________________________\|\n5'-UCA...UUUGU_______GAA____A__A_______AA__AAUGACUCAAAAU_AAA______UUGGU...CCA-3'\n______________UUUCGGA___UCUU_AU__GAUAGA__GG_____________G___UGGGGA\n______________\|\|\|\|\|\|\|___\|\|\|\|_\|\|__\|\|\|\|\|\|__\|\|_____________\|___\|\|\|\|\|\|\n______________AAAGCCU___AGAA_UA__CUAUCU__CC_____________C___ACCCCU\n3'-UUU...UCAAA______________C__GA______C_________________A________UGUCU...AUA-5'\n_____________\|____________________________________________________\|\n_____________56___________________________________________________22\n	162 -- 168	49 -- 55	-21.902 kcal/mol	11.1231 kcal/mol	2.51158 kcal/mol	161 213@LB@ \| \|@LB@5'-UCA...UUUGU GAA A A AA AAUGACUCAAAAU AAA UUGGU...CCA-3'@LB@ UUUCGGA UCUU AU GAUAGA GG G UGGGGA@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\| \|\| \| \|\|\|\|\|\|@LB@ AAAGCCU AGAA UA CUAUCU CC C ACCCCU@LB@3'-UUU...UCAAA C GA C A UGUCU...AUA-5'@LB@ \| \|@LB@ 56 22@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -21.902 kcal/mol@LB@Unfolding Energy - mRNA 11.1231 kcal/mol@LB@Unfolding Energy - sRNA 2.51158 kcal/mol@LB@@LB@Position - mRNA 162 -- 212@LB@Position - sRNA 23 -- 55@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 49 -- 55@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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