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
30	0.001001	0.1113	bsu08780	ygaJ	-16.90	0.012052	218 -- 231	24 -- 39	peptidase YgaJ	_____________217______________232\n_____________\|________________\|\n5'-UGU...AUUGC_________C______GUUUU...AGC-3'\n______________GAUGGGGGG___GGGG\n______________\|\|\|:\|:\|\|\|___\|\|\|\|\n______________CUAUCUCCC___CCCC\n3'-UUU...CUAGA_________CAA____UUGUC...AUA-5'\n_____________\|________________\|\n_____________40_______________23\n	220 -- 226	31 -- 37	-22.0746 kcal/mol	4.38344 kcal/mol	0.790436 kcal/mol	217 232@LB@ \| \|@LB@5'-UGU...AUUGC C GUUUU...AGC-3'@LB@ GAUGGGGGG GGGG@LB@ \|\|\|:\|:\|\|\| \|\|\|\|@LB@ CUAUCUCCC CCCC@LB@3'-UUU...CUAGA CAA UUGUC...AUA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -22.0746 kcal/mol@LB@Unfolding Energy - mRNA 4.38344 kcal/mol@LB@Unfolding Energy - sRNA 0.790436 kcal/mol@LB@@LB@Position - mRNA 218 -- 231@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 31 -- 37@LB@
177	0.01681	0.3152	bsu00910	ispF	-14.14	0.044127	219 -- 247	31 -- 51	2-D-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________218____________________________248\n_____________\|______________________________\|\n5'-UCG...GACAA__________G__CAUCAAUUA________CCGUC...UUG-3'\n______________GGAUU_UGAU_UG_________GUGGAGGG\n______________\|\|\|\|:_\|\|\|\|_\|\|_________:\|:\|\|\|\|\|\n______________CCUAG_ACUA_AC_________UAUCUCCC\n3'-UUU...AAAAG_____A____G___________________CAACC...AUA-5'\n_____________\|______________________________\|\n_____________52_____________________________30\n	241 -- 247	31 -- 37	-21.3343 kcal/mol	6.22033 kcal/mol	0.970589 kcal/mol	218 248@LB@ \| \|@LB@5'-UCG...GACAA G CAUCAAUUA CCGUC...UUG-3'@LB@ GGAUU UGAU UG GUGGAGGG@LB@ \|\|\|\|: \|\|\|\| \|\| :\|:\|\|\|\|\|@LB@ CCUAG ACUA AC UAUCUCCC@LB@3'-UUU...AAAAG A G CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -21.3343 kcal/mol@LB@Unfolding Energy - mRNA 6.22033 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 219 -- 247@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 31 -- 37@LB@
44	0.001968	0.1492	bsu14940	ylbA	-14.48	0.038144	221 -- 240	24 -- 52	Evidence 4: Homologs of previously reported genes of unknown function	_____________220___________________________241\n_____________\|_____________________________\|\n5'-CAU...GAAAG_________________________AA__CUGAG...AAU-3'\n______________CGGA_CUUGA________AGGGGUU__GG\n______________\|\|\|\|_\|\|\|\|\|________\|\|\|\|\|\|\|__\|\|\n______________GCCU_GAACU________UCCCCAA__CC\n3'-UUU...AAAAA____A_____AGACUAUC_______CC__UUGUC...AUA-5'\n_____________\|_____________________________\|\n_____________53____________________________23\n	230 -- 236	28 -- 34	-22.4266 kcal/mol	6.96942 kcal/mol	0.980851 kcal/mol	220 241@LB@ \| \|@LB@5'-CAU...GAAAG AA CUGAG...AAU-3'@LB@ CGGA CUUGA AGGGGUU GG@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GCCU GAACU UCCCCAA CC@LB@3'-UUU...AAAAA A AGACUAUC CC UUGUC...AUA-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -14.48 kcal/mol@LB@Hybridization Energy -22.4266 kcal/mol@LB@Unfolding Energy - mRNA 6.96942 kcal/mol@LB@Unfolding Energy - sRNA 0.980851 kcal/mol@LB@@LB@Position - mRNA 221 -- 240@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 28 -- 34@LB@
134	0.01184	0.2883	bsu01450	cbiO	-8.85	0.304208	221 -- 231	32 -- 43	energy-coupling factor transporter ATP-binding protein EcfA1	_____________220__________232\n_____________\|____________\|\n5'-AUA...UUGAU____________AUAUC...AUG-3'\n______________AUC_GGUAGAGG\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	225 -- 231	32 -- 38	-12.7681 kcal/mol	2.95776 kcal/mol	0.959872 kcal/mol	220 232@LB@ \| \|@LB@5'-AUA...UUGAU AUAUC...AUG-3'@LB@ AUC GGUAGAGG@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.7681 kcal/mol@LB@Unfolding Energy - mRNA 2.95776 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 221 -- 231@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 32 -- 38@LB@
12	0.0001633	0.0454	bsu11410	yjbA	-19.25	0.003321	222 -- 243	30 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pf: factor'	_____________221_______________________244\n_____________\|_________________________\|\n5'-GAA...AUGUG______AA_________________AAGAA...UUG-3'\n______________UGGGUC__UUGGUUUGA___AGGGG\n______________:\|\|:\|\|__\|\|\|:\|:\|\|\|___\|\|\|\|\|\n______________GCCUAG__AACUAGACU___UCCCC\n3'-UUU...AAAAA_________________AUC_____AACCC...AUA-5'\n_____________\|_________________________\|\n_____________53________________________29\n	232 -- 238	38 -- 44	-23.9108 kcal/mol	3.6845 kcal/mol	0.979974 kcal/mol	221 244@LB@ \| \|@LB@5'-GAA...AUGUG AA AAGAA...UUG-3'@LB@ UGGGUC UUGGUUUGA AGGGG@LB@ :\|\|:\|\| \|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ GCCUAG AACUAGACU UCCCC@LB@3'-UUU...AAAAA AUC AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -23.9108 kcal/mol@LB@Unfolding Energy - mRNA 3.6845 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 222 -- 243@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 38 -- 44@LB@
36	0.001585	0.1432	bsu03680	yclG	-9.13	0.280303	226 -- 251	29 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'	_____________225________________________252\n_____________\|__________________________\|\n5'-UCA...UGCAG_______C___G_UCC_____AU___AAAAC...UUU-3'\n______________CGGAUUU_GGU_U___UAGAG__GGU\n______________\|\|\|\|\|:\|_\|:\|_\|___\|\|\|\|\|__\|\|\|\n______________GCCUAGA_CUA_A___AUCUC__CCA\n3'-UUU...AAAAA_______A___G_CU______C____ACCCC...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________28\n	226 -- 232	46 -- 52	-18.2294 kcal/mol	8.1219 kcal/mol	0.980233 kcal/mol	225 252@LB@ \| \|@LB@5'-UCA...UGCAG C G UCC AU AAAAC...UUU-3'@LB@ CGGAUUU GGU U UAGAG GGU@LB@ \|\|\|\|\|:\| \|:\| \| \|\|\|\|\| \|\|\|@LB@ GCCUAGA CUA A AUCUC CCA@LB@3'-UUU...AAAAA A G CU C ACCCC...AUA-5'@LB@ \| \|@LB@ 53 28@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -18.2294 kcal/mol@LB@Unfolding Energy - mRNA 8.1219 kcal/mol@LB@Unfolding Energy - sRNA 0.980233 kcal/mol@LB@@LB@Position - mRNA 226 -- 251@LB@Position - sRNA 29 -- 52@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 46 -- 52@LB@
61	0.003607	0.1972	bsu06860	yezE	-12.02	0.104394	226 -- 262	26 -- 52	TetR family transcriptional regulator	_____________225___________________________________263\n_____________\|_____________________________________\|\n5'-AGG...UGAUA___CG____U___UCACAGGGC________UUU____AGAGU...UGC-3'\n______________CGG__CUUG_UCU_________GAUAGAGG___UUGG\n______________\|\|\|__\|\|\|\|_\|\|\|_________\|\|\|\|\|\|\|\|___\|\|\|\|\n______________GCC__GAAC_AGA_________CUAUCUCC___AACC\n3'-UUU...AAAAA___UA____U____________________CC_____CCUUG...AUA-5'\n_____________\|_____________________________________\|\n_____________53____________________________________25\n	249 -- 255	32 -- 38	-24.4528 kcal/mol	11.4473 kcal/mol	0.980817 kcal/mol	225 263@LB@ \| \|@LB@5'-AGG...UGAUA CG U UCACAGGGC UUU AGAGU...UGC-3'@LB@ CGG CUUG UCU GAUAGAGG UUGG@LB@ \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GCC GAAC AGA CUAUCUCC AACC@LB@3'-UUU...AAAAA UA U CC CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -24.4528 kcal/mol@LB@Unfolding Energy - mRNA 11.4473 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 32 -- 38@LB@
115	0.009897	0.2871	bsu22830	gpsA	-18.23	0.005947	227 -- 241	21 -- 34	glycerol-3-phosphate dehydrogenase	_____________226_____________242\n_____________\|_______________\|\n5'-GGU...GGAGC____A__________AGCAC...GUG-3'\n______________GGGG_GUUGGGGAAC\n______________:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UCCC_CAACCCCUUG\n3'-UUU...CUAUC_______________UCUCU...AUA-5'\n_____________\|_______________\|\n_____________35______________20\n	235 -- 241	21 -- 27	-24.3947 kcal/mol	4.254 kcal/mol	1.91139 kcal/mol	226 242@LB@ \| \|@LB@5'-GGU...GGAGC A AGCAC...GUG-3'@LB@ GGGG GUUGGGGAAC@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UCCC CAACCCCUUG@LB@3'-UUU...CUAUC UCUCU...AUA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -24.3947 kcal/mol@LB@Unfolding Energy - mRNA 4.254 kcal/mol@LB@Unfolding Energy - sRNA 1.91139 kcal/mol@LB@@LB@Position - mRNA 227 -- 241@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
75	0.005596	0.2441	bsu19669	yoyF	-14.84	0.032440	230 -- 255	26 -- 52	Evidence 5: No homology to any previously reported sequences	_____________229_________________________256\n_____________\|___________________________\|\n5'-GUA...CUGGA____GAAA_________UCAUAA____AAAAA...GUC-3'\n______________CGGA____GAUUUGAUA_______UGG\n______________\|\|\|\|____\|\|\|:\|\|\|\|\|_______\|\|\|\n______________GCCU____CUAGACUAU_______ACC\n3'-UUU...AAAAA____AGAA_________CUCCCCA___CCUUG...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________25\n	240 -- 246	36 -- 42	-17.4265 kcal/mol	1.6069 kcal/mol	0.980817 kcal/mol	229 256@LB@ \| \|@LB@5'-GUA...CUGGA GAAA UCAUAA AAAAA...GUC-3'@LB@ CGGA GAUUUGAUA UGG@LB@ \|\|\|\| \|\|\|:\|\|\|\|\| \|\|\|@LB@ GCCU CUAGACUAU ACC@LB@3'-UUU...AAAAA AGAA CUCCCCA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -17.4265 kcal/mol@LB@Unfolding Energy - mRNA 1.6069 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 36 -- 42@LB@
7	4.152e-05	0.01979	bsu05670	ydgJ	-17.13	0.010734	234 -- 258	25 -- 49	MarR family transcriptional regulator	_____________233_______________________259\n_____________\|_________________________\|\n5'-AAG...UAAUA_______CAG__A___A___A____UUUUG...AUC-3'\n______________GUUUUGA___GA_AGA_GGG_UGGG\n______________:\|:\|\|\|\|___\|\|_\|\|\|_\|\|\|_\|\|\|\|\n______________UAGAACU___CU_UCU_CCC_ACCC\n3'-UUU...AAGCC_______AGA__A___C___A____CUUGU...AUA-5'\n_____________\|_________________________\|\n_____________50________________________24\n	234 -- 240	43 -- 49	-20.9262 kcal/mol	2.82407 kcal/mol	0.976049 kcal/mol	233 259@LB@ \| \|@LB@5'-AAG...UAAUA CAG A A A UUUUG...AUC-3'@LB@ GUUUUGA GA AGA GGG UGGG@LB@ :\|:\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|@LB@ UAGAACU CU UCU CCC ACCC@LB@3'-UUU...AAGCC AGA A C A CUUGU...AUA-5'@LB@ \| \|@LB@ 50 24@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -20.9262 kcal/mol@LB@Unfolding Energy - mRNA 2.82407 kcal/mol@LB@Unfolding Energy - sRNA 0.976049 kcal/mol@LB@@LB@Position - mRNA 234 -- 258@LB@Position - sRNA 25 -- 49@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 43 -- 49@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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