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
114	0.009837	0.2871	bsu30580	ytmA	-11.73	0.116519	193 -- 212	33 -- 52	peptidase YtmA	_____________192____________________213\n_____________\|______________________\|\n5'-AGA...GGAGG___CU_________________AAAAG...UGG-3'\n______________CGG__GUUUUGAUU__GUAGAG\n______________\|\|\|__:\|:\|\|\|\|\|:__:\|\|\|\|\|\n______________GCC__UAGAACUAG__UAUCUC\n3'-UUU...AAAAA______________AC______CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	200 -- 206	41 -- 47	-17.5653 kcal/mol	4.85678 kcal/mol	0.976367 kcal/mol	192 213@LB@ \| \|@LB@5'-AGA...GGAGG CU AAAAG...UGG-3'@LB@ CGG GUUUUGAUU GUAGAG@LB@ \|\|\| :\|:\|\|\|\|\|: :\|\|\|\|\|@LB@ GCC UAGAACUAG UAUCUC@LB@3'-UUU...AAAAA AC CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.5653 kcal/mol@LB@Unfolding Energy - mRNA 4.85678 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@LB@
65	0.004149	0.2071	bsu25230	yqxD	-11.91	0.108824	196 -- 217	21 -- 43	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 9387153	_____________195_____________________218\n_____________\|_______________________\|\n5'-ACA...CAGGA____A________A____A____UACUC...CAU-3'\n______________GUUU_AUGGAGGG__UGG_GAAU\n______________:\|:\|_\|\|:\|\|\|\|\|__\|\|\|_\|\|\|:\n______________UAGA_UAUCUCCC__ACC_CUUG\n3'-UUU...AGAAC____C________CA___C____UCUCU...AUA-5'\n_____________\|_______________________\|\n_____________44______________________20\n	202 -- 208	31 -- 37	-19.0868 kcal/mol	4.40975 kcal/mol	2.76238 kcal/mol	195 218@LB@ \| \|@LB@5'-ACA...CAGGA A A A UACUC...CAU-3'@LB@ GUUU AUGGAGGG UGG GAAU@LB@ :\|:\| \|\|:\|\|\|\|\| \|\|\| \|\|\|:@LB@ UAGA UAUCUCCC ACC CUUG@LB@3'-UUU...AGAAC C CA C UCUCU...AUA-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -19.0868 kcal/mol@LB@Unfolding Energy - mRNA 4.40975 kcal/mol@LB@Unfolding Energy - sRNA 2.76238 kcal/mol@LB@@LB@Position - mRNA 196 -- 217@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 31 -- 37@LB@
175	0.01672	0.3152	bsu04630	ydcC	-11.64	0.120416	196 -- 203	27 -- 34	sporulation protein YdcC	_____________195______204\n_____________\|________\|\n5'-CCG...GAAAA________AAAAA...UGG-3'\n______________AGGGGUUG\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAAC\n3'-UUU...CUAUC________CCCUU...AUA-5'\n_____________\|________\|\n_____________35_______26\n	197 -- 203	27 -- 33	-14.5305 kcal/mol	2.76844 kcal/mol	0.118612 kcal/mol	195 204@LB@ \| \|@LB@5'-CCG...GAAAA AAAAA...UGG-3'@LB@ AGGGGUUG@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAAC@LB@3'-UUU...CUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -14.5305 kcal/mol@LB@Unfolding Energy - mRNA 2.76844 kcal/mol@LB@Unfolding Energy - sRNA 0.118612 kcal/mol@LB@@LB@Position - mRNA 196 -- 203@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 27 -- 33@LB@
17	0.0003284	0.06216	bsu08690	ygaD	-15.59	0.022949	198 -- 218	30 -- 49	ABC transporter ATP-binding protein	_____________197___________________219\n_____________\|_____________________\|\n5'-UGA...CACAC___A____AAA__G_______GAAUC...UCG-3'\n______________AUC_UGAU___GA_AGAGGGG\n______________\|\|\|_\|\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________UAG_ACUA___CU_UCUCCCC\n3'-UUU...AAGCC___A____GA___A_______AACCC...AUA-5'\n_____________\|_____________________\|\n_____________50____________________29\n	212 -- 218	30 -- 36	-19.3788 kcal/mol	2.8161 kcal/mol	0.974265 kcal/mol	197 219@LB@ \| \|@LB@5'-UGA...CACAC A AAA G GAAUC...UCG-3'@LB@ AUC UGAU GA AGAGGGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UAG ACUA CU UCUCCCC@LB@3'-UUU...AAGCC A GA A AACCC...AUA-5'@LB@ \| \|@LB@ 50 29@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -19.3788 kcal/mol@LB@Unfolding Energy - mRNA 2.8161 kcal/mol@LB@Unfolding Energy - sRNA 0.974265 kcal/mol@LB@@LB@Position - mRNA 198 -- 218@LB@Position - sRNA 30 -- 49@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 30 -- 36@LB@
58	0.003185	0.1832	bsu24100	bkdR	-13.90	0.048953	199 -- 241	21 -- 51	sigma L-dependent transcriptional regulator YqiR	_____________198_________________________________________242\n_____________\|___________________________________________\|\n5'-AAU...UAUCG____GCAAAA___A_______U___UGCC__CAAAA_______GGCGU...ACA-3'\n______________GGAU______GGU_CUGAUAG_AGG____GG_____GGGGAAC\n______________\|\|\|\|______\|:\|_\|\|\|\|\|\|\|_\|\|\|____\|\|_____\|\|\|\|\|\|\|\n______________CCUA______CUA_GACUAUC_UCC____CC_____CCCCUUG\n3'-UUU...AAAAG____GAA________________________AA__________UCUCU...AUA-5'\n_____________\|___________________________________________\|\n_____________52__________________________________________20\n	235 -- 241	21 -- 27	-28.1295 kcal/mol	11.4588 kcal/mol	2.76846 kcal/mol	198 242@LB@ \| \|@LB@5'-AAU...UAUCG GCAAAA A U UGCC CAAAA GGCGU...ACA-3'@LB@ GGAU GGU CUGAUAG AGG GG GGGGAAC@LB@ \|\|\|\| \|:\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUA CUA GACUAUC UCC CC CCCCUUG@LB@3'-UUU...AAAAG GAA AA UCUCU...AUA-5'@LB@ \| \|@LB@ 52 20@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -28.1295 kcal/mol@LB@Unfolding Energy - mRNA 11.4588 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 21 -- 51@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
4	1.471e-05	0.01227	bsu32200	yutJ	-17.92	0.007061	210 -- 239	21 -- 53	NADH dehydrogenase-like protein YutJ	_____________209_______________________________240\n_____________\|_________________________________\|\n5'-UGA...AAAAA________________C_____UUAC_______AUGCG...UAA-3'\n______________UUGG_UCUUGAUC_GG_GGAGG_____GGGAAC\n______________\|:\|\|_\|\|\|\|\|\|\|\|_\|:_:\|\|\|\|_____\|\|\|\|\|\|\n______________AGCC_AGAACUAG_CU_UCUCC_____CCCUUG\n3'-UUU...AAAAA____U________A__A_____CCAAC______UCUCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________20\n	215 -- 221	41 -- 47	-30.8017 kcal/mol	10.1098 kcal/mol	2.77573 kcal/mol	209 240@LB@ \| \|@LB@5'-UGA...AAAAA C UUAC AUGCG...UAA-3'@LB@ UUGG UCUUGAUC GG GGAGG GGGAAC@LB@ \|:\|\| \|\|\|\|\|\|\|\| \|: :\|\|\|\| \|\|\|\|\|\|@LB@ AGCC AGAACUAG CU UCUCC CCCUUG@LB@3'-UUU...AAAAA U A A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 54 20@LB@@LB@@LB@Energy -17.92 kcal/mol@LB@Hybridization Energy -30.8017 kcal/mol@LB@Unfolding Energy - mRNA 10.1098 kcal/mol@LB@Unfolding Energy - sRNA 2.77573 kcal/mol@LB@@LB@Position - mRNA 210 -- 239@LB@Position - sRNA 21 -- 53@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 41 -- 47@LB@
46	0.002102	0.1496	bsu35160	uvrA	-18.29	0.005742	210 -- 232	21 -- 44	UvrABC system protein A	_____________209______________________233\n_____________\|________________________\|\n5'-CAC...CUAUG____G________UGAA_______CAGGG...GUU-3'\n______________GAUC_GAUAGAGG_____GGGAGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________CUAG_CUAUCUCC_____CCCUUG\n3'-UUU...UAGAA____A________CCAAC______UCUCU...AUA-5'\n_____________\|________________________\|\n_____________45_______________________20\n	216 -- 222	32 -- 38	-26.4443 kcal/mol	5.3846 kcal/mol	2.7671 kcal/mol	209 233@LB@ \| \|@LB@5'-CAC...CUAUG G UGAA CAGGG...GUU-3'@LB@ GAUC GAUAGAGG GGGAGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUAG CUAUCUCC CCCUUG@LB@3'-UUU...UAGAA A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -26.4443 kcal/mol@LB@Unfolding Energy - mRNA 5.3846 kcal/mol@LB@Unfolding Energy - sRNA 2.7671 kcal/mol@LB@@LB@Position - mRNA 210 -- 232@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 32 -- 38@LB@
37	0.00164	0.1432	bsu32390	yunF	-13.99	0.047070	211 -- 231	31 -- 53	Evidence 4: Homologs of previously reported genes of unknown function	_____________210_____________________232\n_____________\|_______________________\|\n5'-UGU...UUAUA___________CGG_________AUCAU...UUC-3'\n______________UCGGA_C_UGA___GAUGGGGGG\n______________\|\|\|\|\|_\|_\|\|\|___\|\|\|:\|:\|\|\|\n______________AGCCU_G_ACU___CUAUCUCCC\n3'-UUU...AAAAA_____A_A___AGA_________CAACC...AUA-5'\n_____________\|_______________________\|\n_____________54______________________30\n	225 -- 231	31 -- 37	-23.274 kcal/mol	8.29838 kcal/mol	0.981784 kcal/mol	210 232@LB@ \| \|@LB@5'-UGU...UUAUA CGG AUCAU...UUC-3'@LB@ UCGGA C UGA GAUGGGGGG@LB@ \|\|\|\|\| \| \|\|\| \|\|\|:\|:\|\|\|@LB@ AGCCU G ACU CUAUCUCCC@LB@3'-UUU...AAAAA A A AGA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -23.274 kcal/mol@LB@Unfolding Energy - mRNA 8.29838 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 31 -- 37@LB@
147	0.013	0.2949	bsu12910	proG	-10.46	0.183122	211 -- 241	23 -- 53	pyrroline-5-carboxylate reductase 3	_____________210________________________________242\n_____________\|__________________________________\|\n5'-UUC...ACAGA_____________G____U___CAGCA___C___UAUGA...UUG-3'\n______________UUGGAUU__GAUU_GAUA__GG_____UGG_GGA\n______________\|:\|\|\|\|:__\|\|\|:_\|\|\|\|__\|\|_____\|\|\|_\|\|\|\n______________AGCCUAG__CUAG_CUAU__CC_____ACC_CCU\n3'-UUU...AAAAA_______AA____A____CU__CCA_________UGUCU...AUA-5'\n_____________\|__________________________________\|\n_____________54_________________________________22\n	211 -- 217	47 -- 53	-18.7228 kcal/mol	7.27559 kcal/mol	0.987321 kcal/mol	210 242@LB@ \| \|@LB@5'-UUC...ACAGA G U CAGCA C UAUGA...UUG-3'@LB@ UUGGAUU GAUU GAUA GG UGG GGA@LB@ \|:\|\|\|\|: \|\|\|: \|\|\|\| \|\| \|\|\| \|\|\|@LB@ AGCCUAG CUAG CUAU CC ACC CCU@LB@3'-UUU...AAAAA AA A CU CCA UGUCU...AUA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -18.7228 kcal/mol@LB@Unfolding Energy - mRNA 7.27559 kcal/mol@LB@Unfolding Energy - sRNA 0.987321 kcal/mol@LB@@LB@Position - mRNA 211 -- 241@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 47 -- 53@LB@
87	0.00681	0.2588	bsu29140	citZ	-14.51	0.037644	213 -- 231	27 -- 52	citrate synthase 2	_____________212_________________________232\n_____________\|___________________________\|\n5'-GAG...CGACA__C________________________UAGCA...AUG-3'\n______________CG_GGUCUUGA________AGGGGUUG\n______________\|\|_\|:\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________GC_CUAGAACU________UCCCCAAC\n3'-UUU...AAAAA___________AGACUAUC________CCCUU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________26\n	225 -- 231	27 -- 33	-23.9033 kcal/mol	8.41647 kcal/mol	0.980744 kcal/mol	212 232@LB@ \| \|@LB@5'-GAG...CGACA C UAGCA...AUG-3'@LB@ CG GGUCUUGA AGGGGUUG@LB@ \|\| \|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GC CUAGAACU UCCCCAAC@LB@3'-UUU...AAAAA AGACUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 53 26@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -23.9033 kcal/mol@LB@Unfolding Energy - mRNA 8.41647 kcal/mol@LB@Unfolding Energy - sRNA 0.980744 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 27 -- 52@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@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:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching