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
31	0.001131	0.119	bsu15020	coaD	-13.71	0.053189	186 -- 192	30 -- 36	phosphopantetheine adenylyltransferase	_____________185_____193\n_____________\|_______\|\n5'-UCC...UAAAA_______GUAGU...AUG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-14.3069 kcal/mol	0.46648 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCC...UAAAA GUAGU...AUG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -14.3069 kcal/mol@LB@Unfolding Energy - mRNA 0.46648 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
32	0.001154	0.119	bsu32820	fadE	-9.01	0.290043	236 -- 252	32 -- 52	acyl-CoA dehydrogenase	_____________235____________________253\n_____________\|______________________\|\n5'-AUU...GGCGG________UA____________AUGUC...AGC-3'\n______________CGGAUUUU__AUC_____GAGG\n______________\|\|\|\|\|:\|\|__\|\|\|_____\|\|\|\|\n______________GCCUAGAA__UAG_____CUCC\n3'-UUU...AAAAA________C____ACUAU____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	237 -- 243	45 -- 51	-13.909 kcal/mol	3.91995 kcal/mol	0.976384 kcal/mol	235 253@LB@ \| \|@LB@5'-AUU...GGCGG UA AUGUC...AGC-3'@LB@ CGGAUUUU AUC GAGG@LB@ \|\|\|\|\|:\|\| \|\|\| \|\|\|\|@LB@ GCCUAGAA UAG CUCC@LB@3'-UUU...AAAAA C ACUAU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -13.909 kcal/mol@LB@Unfolding Energy - mRNA 3.91995 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 236 -- 252@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 45 -- 51@LB@
33	0.001178	0.119	bsu14840	ylaN	-15.06	0.029338	181 -- 208	8 -- 28	depletion of this protein in Bacillus subtilis results in defects in cell morphology; crystal structure of Staphylococcus protein shows homodimer; ligand binding protein	_____________180__________________________209\n_____________\|____________________________\|\n5'-GAU...UCGCC______________AUACUUU_______AGAGA...AUA-3'\n______________UGGGGAACGGAGGG_______UGGCUUC\n______________\|\|\|\|\|\|\|\|:\|\|\|:\|_______\|:\|\|\|\|\|\n______________ACCCCUUGUCUCUC_______AUCGAAG\n3'-UUU...CCCCA____________________________AGAGAUA-5'\n_____________\|____________________________\|\n_____________29___________________________7\n	202 -- 208	8 -- 14	-32.8109 kcal/mol	11.1547 kcal/mol	6.59627 kcal/mol	180 209@LB@ \| \|@LB@5'-GAU...UCGCC AUACUUU AGAGA...AUA-3'@LB@ UGGGGAACGGAGGG UGGCUUC@LB@ \|\|\|\|\|\|\|\|:\|\|\|:\| \|:\|\|\|\|\|@LB@ ACCCCUUGUCUCUC AUCGAAG@LB@3'-UUU...CCCCA AGAGAUA-5'@LB@ \| \|@LB@ 29 7@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -32.8109 kcal/mol@LB@Unfolding Energy - mRNA 11.1547 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 181 -- 208@LB@Position - sRNA 8 -- 28@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@LB@
34	0.001327	0.1302	bsu23550	mleA	-19.34	0.003138	3 -- 24	31 -- 51	NAD-dependent malic enzyme 1	_____________2______________________25\n_____________\|______________________\|\n_________5'-AU__U_C____________AU___AUUUA...GGG-3'\n______________GG_U_CUUGGUCUGAUA__GGG\n______________\|\|_\|_\|\|\|\|:\|\|\|\|\|\|\|__\|\|\|\n______________CC_A_GAACUAGACUAU__CCC\n3'-UUU...AAAAG__U______________CU___CAACC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________30\n	13 -- 19	36 -- 42	-24.8934 kcal/mol	4.58077 kcal/mol	0.970589 kcal/mol	2 25@LB@ \| \|@LB@ 5'-AU U C AU AUUUA...GGG-3'@LB@ GG U CUUGGUCUGAUA GGG@LB@ \|\| \| \|\|\|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CC A GAACUAGACUAU CCC@LB@3'-UUU...AAAAG U CU CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -19.34 kcal/mol@LB@Hybridization Energy -24.8934 kcal/mol@LB@Unfolding Energy - mRNA 4.58077 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 3 -- 24@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 36 -- 42@LB@
35	0.001389	0.1324	bsu24570	gcvT	-12.27	0.095214	256 -- 273	25 -- 46	aminomethyltransferase	_____________255____________________274\n_____________\|______________________\|\n5'-CUC...AACGA_______C_______C______AGCUU...UAA-3'\n______________UUGAUUU___GGAGG___UGGG\n______________\|\|\|\|\|:\|___:\|\|\|\|___\|\|\|\|\n______________AACUAGA___UCUCC___ACCC\n3'-UUU...CCUAG_______CUA_____CCA____CUUGU...AUA-5'\n_____________\|______________________\|\n_____________47_____________________24\n	256 -- 262	40 -- 46	-17.62 kcal/mol	4.38211 kcal/mol	0.972727 kcal/mol	255 274@LB@ \| \|@LB@5'-CUC...AACGA C C AGCUU...UAA-3'@LB@ UUGAUUU GGAGG UGGG@LB@ \|\|\|\|\|:\| :\|\|\|\| \|\|\|\|@LB@ AACUAGA UCUCC ACCC@LB@3'-UUU...CCUAG CUA CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -17.62 kcal/mol@LB@Unfolding Energy - mRNA 4.38211 kcal/mol@LB@Unfolding Energy - sRNA 0.972727 kcal/mol@LB@@LB@Position - mRNA 256 -- 273@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 40 -- 46@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@
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@
38	0.001645	0.1432	bsu19540	yodB	-7.66	0.420262	259 -- 271	37 -- 51	ArsR family transcriptional regulator	_____________258_____________272\n_____________\|_______________\|\n5'-GAG...ACGAU___AC__________CAUCC...AAC-3'\n______________GGA____GGUCUGAU\n______________\|\|\|____\|:\|\|\|\|\|\|\n______________CCU____CUAGACUA\n3'-UUU...AAAAG___AGAA________UCUCC...AUA-5'\n_____________\|_______________\|\n_____________52______________36\n	265 -- 271	37 -- 43	-11.6813 kcal/mol	3.05786 kcal/mol	0.959935 kcal/mol	258 272@LB@ \| \|@LB@5'-GAG...ACGAU AC CAUCC...AAC-3'@LB@ GGA GGUCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CCU CUAGACUA@LB@3'-UUU...AAAAG AGAA UCUCC...AUA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -11.6813 kcal/mol@LB@Unfolding Energy - mRNA 3.05786 kcal/mol@LB@Unfolding Energy - sRNA 0.959935 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 37 -- 43@LB@
39	0.001675	0.1432	bsu23240	ypzK	-16.45	0.015090	173 -- 197	28 -- 52	riboflavin biosynthesis protein RibT	_____________172_________________________198\n_____________\|___________________________\|\n5'-GCG...CAGAC____CA______AU_____________UUUAU...UUA-3'\n______________UGGA__UUUUGG____AUAGAGGGGUU\n______________:\|\|\|__\|:\|\|\|:____\|\|\|\|\|\|\|\|\|\|\|\n______________GCCU__AGAACU____UAUCUCCCCAA\n3'-UUU...AAAAA____________AGAC___________CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________27\n	191 -- 197	28 -- 34	-23.4842 kcal/mol	6.04944 kcal/mol	0.980555 kcal/mol	172 198@LB@ \| \|@LB@5'-GCG...CAGAC CA AU UUUAU...UUA-3'@LB@ UGGA UUUUGG AUAGAGGGGUU@LB@ :\|\|\| \|:\|\|\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ GCCU AGAACU UAUCUCCCCAA@LB@3'-UUU...AAAAA AGAC CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -23.4842 kcal/mol@LB@Unfolding Energy - mRNA 6.04944 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 173 -- 197@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
40	0.001724	0.1438	bsu18440	gltD	-13.77	0.051762	193 -- 208	22 -- 36	glutamate synthase [NADPH] small chain	_____________192______________209\n_____________\|________________\|\n5'-AGA...AGGGG_____AACA_______ACCAA...CUU-3'\n______________AGAGG____UGGGGAA\n______________\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UCUCC____ACCCCUU\n3'-UUU...GACUA_____CCA________GUCUC...AUA-5'\n_____________\|________________\|\n_____________37_______________21\n	202 -- 208	22 -- 28	-17.8722 kcal/mol	3.06294 kcal/mol	1.03819 kcal/mol	192 209@LB@ \| \|@LB@5'-AGA...AGGGG AACA ACCAA...CUU-3'@LB@ AGAGG UGGGGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUCC ACCCCUU@LB@3'-UUU...GACUA CCA GUCUC...AUA-5'@LB@ \| \|@LB@ 37 21@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -17.8722 kcal/mol@LB@Unfolding Energy - mRNA 3.06294 kcal/mol@LB@Unfolding Energy - sRNA 1.03819 kcal/mol@LB@@LB@Position - mRNA 193 -- 208@LB@Position - sRNA 22 -- 36@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@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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