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
110	0.009311	0.2778	bsu18230	yngG	-6.09	0.597733	269 -- 285	32 -- 53	hydroxymethylglutaryl-CoA lyase YngG		_____________268____________________286\n_____________\|______________________\|\n5'-AAA...CCCGU_______GCAAC__________AUAAA...GGA-3'\n______________UUGGAUC__________AGAGG\n______________\|:\|\|\|\|\|__________\|\|\|\|\|\n______________AGCCUAG__________UCUCC\n3'-UUU...AAAAA_______AACUAGACUA_____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	269 -- 275	47 -- 53	-12.5955 kcal/mol	5.52332 kcal/mol	0.981755 kcal/mol	268 286@LB@ \| \|@LB@5'-AAA...CCCGU GCAAC AUAAA...GGA-3'@LB@ UUGGAUC AGAGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGCCUAG UCUCC@LB@3'-UUU...AAAAA AACUAGACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -12.5955 kcal/mol@LB@Unfolding Energy - mRNA 5.52332 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 47 -- 53@LB@
180	0.01704	0.3152	bsu28380	gerM	-9.54	0.246988	269 -- 291	32 -- 52	spore germination protein GerM		_____________268______________________292\n_____________\|________________________\|\n5'-AGU...GGAUG___UUU____CA____________CAGCC...AGG-3'\n______________CGG___GUUU__AUCUGAUA_AGG\n______________\|\|\|___:\|:\|__\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC___UAGA__UAGACUAU_UCC\n3'-UUU...AAAAA__________AC________C___CCAAC...AUA-5'\n_____________\|________________________\|\n_____________53_______________________31\n	282 -- 288	36 -- 42	-15.6565 kcal/mol	5.13957 kcal/mol	0.976384 kcal/mol	268 292@LB@ \| \|@LB@5'-AGU...GGAUG UUU CA CAGCC...AGG-3'@LB@ CGG GUUU AUCUGAUA AGG@LB@ \|\|\| :\|:\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC UAGA UAGACUAU UCC@LB@3'-UUU...AAAAA AC C CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -15.6565 kcal/mol@LB@Unfolding Energy - mRNA 5.13957 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 269 -- 291@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 36 -- 42@LB@
190	0.01911	0.3269	bsu05370	ydfD	-12.16	0.099313	269 -- 294	11 -- 36	GntR family transcriptional regulator	bsu10880	_____________268________________________295\n_____________\|__________________________\|\n5'-AAA...AUUAA____AAAAUA__A_____________CGAUUG-3'\n______________AGAG______GG_AAUGGAGAGUGGC\n______________\|\|\|\|______\|\|_\|\|::\|\|\|\|\|\|:\|\|\n______________UCUC______CC_UUGUCUCUCAUCG\n3'-UUU...GACUA____CCCAAC__C_____________AAGAG...AUA-5'\n_____________\|__________________________\|\n_____________37_________________________10\n	288 -- 294	11 -- 17	-24.9379 kcal/mol	3.68177 kcal/mol	9.10067 kcal/mol	268 295@LB@ \| \|@LB@5'-AAA...AUUAA AAAAUA A CGAUUG-3'@LB@ AGAG GG AAUGGAGAGUGGC@LB@ \|\|\|\| \|\| \|\|::\|\|\|\|\|\|:\|\|@LB@ UCUC CC UUGUCUCUCAUCG@LB@3'-UUU...GACUA CCCAAC C AAGAG...AUA-5'@LB@ \| \|@LB@ 37 10@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -24.9379 kcal/mol@LB@Unfolding Energy - mRNA 3.68177 kcal/mol@LB@Unfolding Energy - sRNA 9.10067 kcal/mol@LB@@LB@Position - mRNA 269 -- 294@LB@Position - sRNA 11 -- 36@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 11 -- 17@LB@
133	0.01175	0.2883	bsu11610	ppnK	-12.45	0.088788	273 -- 294	32 -- 53	inorganic polyphosphate/ATP-NAD kinase 1		_____________272____________________295\n_____________\|______________________\|\n5'-CCA...AUUUA____________A___AACU__AUGAAA-3'\n______________UUGGAUUUUGAU_UGG____GG\n______________\|:\|\|\|\|:\|\|\|\|\|_\|\|:____\|\|\n______________AGCCUAGAACUA_ACU____CC\n3'-UUU...AAAAA____________G___AUCU__CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	278 -- 284	42 -- 48	-17.5759 kcal/mol	4.14878 kcal/mol	0.981755 kcal/mol	272 295@LB@ \| \|@LB@5'-CCA...AUUUA A AACU AUGAAA-3'@LB@ UUGGAUUUUGAU UGG GG@LB@ \|:\|\|\|\|:\|\|\|\|\| \|\|: \|\|@LB@ AGCCUAGAACUA ACU CC@LB@3'-UUU...AAAAA G AUCU CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -17.5759 kcal/mol@LB@Unfolding Energy - mRNA 4.14878 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 273 -- 294@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 42 -- 48@LB@
176	0.01673	0.3152	bsu08790	thiC	-9.56	0.245346	273 -- 280	31 -- 38	phosphomethylpyrimidine synthase		_____________272______281\n_____________\|________\|\n5'-GGC...UAUAC________UUCUU...AAG-3'\n______________GUGGAGGG\n______________:\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	274 -- 280	31 -- 37	-12.4867 kcal/mol	2.26991 kcal/mol	0.65488 kcal/mol	272 281@LB@ \| \|@LB@5'-GGC...UAUAC UUCUU...AAG-3'@LB@ GUGGAGGG@LB@ :\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -12.4867 kcal/mol@LB@Unfolding Energy - mRNA 2.26991 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 273 -- 280@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 31 -- 37@LB@
157	0.01433	0.3008	bsu38150	qoxC	-14.65	0.035334	274 -- 297	30 -- 53	quinol oxidase subunit 3		_____________273_______________________298\n_____________\|_________________________\|\n5'-ACC...UAUUC__________G____UUUU______CAG-3'\n______________UCGGGUUUUG_AUCU_____AGGGG\n______________\|\|\|\|:\|:\|\|\|_\|\|\|\|_____\|\|\|\|\|\n______________AGCCUAGAAC_UAGA_____UCCCC\n3'-UUU...AAAAA_______________CUAUC_____AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	277 -- 283	44 -- 50	-24.1532 kcal/mol	8.5194 kcal/mol	0.985344 kcal/mol	273 298@LB@ \| \|@LB@5'-ACC...UAUUC G UUUU CAG-3'@LB@ UCGGGUUUUG AUCU AGGGG@LB@ \|\|\|\|:\|:\|\|\| \|\|\|\| \|\|\|\|\|@LB@ AGCCUAGAAC UAGA UCCCC@LB@3'-UUU...AAAAA CUAUC AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -24.1532 kcal/mol@LB@Unfolding Energy - mRNA 8.5194 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 274 -- 297@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 44 -- 50@LB@
160	0.01451	0.3008	bsu30080	yteV	-11.71	0.117611	279 -- 298	34 -- 53	sporulation protein cse60		_____________278__________________299\n_____________\|____________________\|\n5'-UUU...GGAUA_____GGAGCAG________UA-3'\n______________UCGGA_______CUGAUAGA\n______________\|\|\|\|\|_______\|\|\|\|\|\|\|\|\n______________AGCCU_______GACUAUCU\n3'-UUU...AAAAA_____AGAACUA________CCCCA...AUA-5'\n_____________\|____________________\|\n_____________54___________________33\n	292 -- 298	34 -- 40	-18.1644 kcal/mol	5.47565 kcal/mol	0.98171 kcal/mol	278 299@LB@ \| \|@LB@5'-UUU...GGAUA GGAGCAG UA-3'@LB@ UCGGA CUGAUAGA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU GACUAUCU@LB@3'-UUU...AAAAA AGAACUA CCCCA...AUA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -18.1644 kcal/mol@LB@Unfolding Energy - mRNA 5.47565 kcal/mol@LB@Unfolding Energy - sRNA 0.98171 kcal/mol@LB@@LB@Position - mRNA 279 -- 298@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 34 -- 40@LB@
146	0.01275	0.2913	bsu00450	sspF	-8.40	0.345478	283 -- 295	24 -- 38	small acid-soluble spore protein SspF		_____________282_____________296\n_____________\|_______________\|\n5'-UGA...AAAAA_______C_______UGAAA-3'\n______________AUGGAGG___UGGGG\n______________\|\|:\|\|\|\|___\|\|\|\|\|\n______________UAUCUCC___ACCCC\n3'-UUU...UAGAC_______CCA_____UUGUC...AUA-5'\n_____________\|_______________\|\n_____________39______________23\n	283 -- 289	32 -- 38	-17.1295 kcal/mol	8.05792 kcal/mol	0.668509 kcal/mol	282 296@LB@ \| \|@LB@5'-UGA...AAAAA C UGAAA-3'@LB@ AUGGAGG UGGGG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UAUCUCC ACCCC@LB@3'-UUU...UAGAC CCA UUGUC...AUA-5'@LB@ \| \|@LB@ 39 23@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -17.1295 kcal/mol@LB@Unfolding Energy - mRNA 8.05792 kcal/mol@LB@Unfolding Energy - sRNA 0.668509 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 24 -- 38@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 32 -- 38@LB@
125	0.01105	0.2883	bsu27350	yrrN	-18.26	0.005831	285 -- 299	16 -- 30	protease YrrN		_____________284_____________300\n_____________\|_______________\|\n5'-GGG...UUUUA_______________U-3'\n______________GUUGGGGAACAGAGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________CAACCCCUUGUCUCU\n3'-UUU...CUCCC_______________CAUCG...AUA-5'\n_____________\|_______________\|\n_____________31______________15\n	293 -- 299	16 -- 22	-28.5342 kcal/mol	4.24145 kcal/mol	6.02784 kcal/mol	284 300@LB@ \| \|@LB@5'-GGG...UUUUA U-3'@LB@ GUUGGGGAACAGAGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CAACCCCUUGUCUCU@LB@3'-UUU...CUCCC CAUCG...AUA-5'@LB@ \| \|@LB@ 31 15@LB@@LB@@LB@Energy -18.26 kcal/mol@LB@Hybridization Energy -28.5342 kcal/mol@LB@Unfolding Energy - mRNA 4.24145 kcal/mol@LB@Unfolding Energy - sRNA 6.02784 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 16 -- 30@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 16 -- 22@LB@
109	0.009307	0.2778	bsu07880	yfkJ	-15.70	0.021808	288 -- 299	30 -- 51	low molecular weight protein-tyrosine-phosphatase YfkJ		_____________287____________________300\n_____________\|______________________\|\n5'-GGU...AAAAA______________________A-3'\n______________GGAU__________UAGAGGGG\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\n______________CCUA__________AUCUCCCC\n3'-UUU...AAAAG____GAACUAGACU________AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	293 -- 299	30 -- 36	-17.0834 kcal/mol	0.412933 kcal/mol	0.974282 kcal/mol	287 300@LB@ \| \|@LB@5'-GGU...AAAAA A-3'@LB@ GGAU UAGAGGGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCUA AUCUCCCC@LB@3'-UUU...AAAAG GAACUAGACU AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -17.0834 kcal/mol@LB@Unfolding Energy - mRNA 0.412933 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 288 -- 299@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 30 -- 36@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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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

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