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
135	0.01203	0.2883	bsu09920	yhaN	-10.31	0.192319	8 -- 29	28 -- 47	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16267290; Product type pe : enzyme'	_____________7______________________30\n_____________\|______________________\|\n____5'-AACAAAC_______CUUUUUUU__C____UAUUU...ACG-3'\n______________CUUGAUC________GG_GGUU\n______________\|\|\|\|\|\|\|________\|\|_\|\|\|\|\n______________GAACUAG________CC_CCAA\n3'-UUU...GCCUA_______ACUAUCU________CCCCU...AUA-5'\n_____________\|______________________\|\n_____________48_____________________27\n	8 -- 14	41 -- 47	-14.5368 kcal/mol	3.24797 kcal/mol	0.974663 kcal/mol	7 30@LB@ \| \|@LB@ 5'-AACAAAC CUUUUUUU C UAUUU...ACG-3'@LB@ CUUGAUC GG GGUU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GAACUAG CC CCAA@LB@3'-UUU...GCCUA ACUAUCU CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -14.5368 kcal/mol@LB@Unfolding Energy - mRNA 3.24797 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 8 -- 29@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 41 -- 47@LB@
184	0.01795	0.3254	bsu30470	ytzC	-13.40	0.060457	189 -- 197	28 -- 36	Evidence 4: Homologs of previously reported genes of unknown function	_____________188_______198\n_____________\|_________\|\n5'-UUC...CAAGA_________ACUGU...AUU-3'\n______________GGAGGGGUU\n______________:\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-16.1349 kcal/mol	2.59994 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UUC...CAAGA ACUGU...AUU-3'@LB@ GGAGGGGUU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -13.40 kcal/mol@LB@Hybridization Energy -16.1349 kcal/mol@LB@Unfolding Energy - mRNA 2.59994 kcal/mol@LB@Unfolding Energy - sRNA 0.134381 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 28 -- 36@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
199	0.01988	0.3269	bsu36590	clsA	-10.32	0.192119	169 -- 195	28 -- 48	cardiolipin synthase	_____________168_________________________196\n_____________\|___________________________\|\n5'-UUA...AAUCU_______AAAUA___AUG__C______ACAAA...CUU-3'\n______________UCUUGAU_____UGA___AG_GGGGUU\n______________\|\|\|\|\|\|\|_____\|\|\|___\|\|_\|\|\|\|\|\|\n______________AGAACUA_____ACU___UC_CCCCAA\n3'-UUU...AGCCU_______G_______A____U______CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________49__________________________27\n	169 -- 175	42 -- 48	-17.4562 kcal/mol	6.16425 kcal/mol	0.974701 kcal/mol	168 196@LB@ \| \|@LB@5'-UUA...AAUCU AAAUA AUG C ACAAA...CUU-3'@LB@ UCUUGAU UGA AG GGGGUU@LB@ \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|@LB@ AGAACUA ACU UC CCCCAA@LB@3'-UUU...AGCCU G A U CCCCU...AUA-5'@LB@ \| \|@LB@ 49 27@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.4562 kcal/mol@LB@Unfolding Energy - mRNA 6.16425 kcal/mol@LB@Unfolding Energy - sRNA 0.974701 kcal/mol@LB@@LB@Position - mRNA 169 -- 195@LB@Position - sRNA 28 -- 48@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 42 -- 48@LB@
200	0.01989	0.3269	bsu30150	ytdP	-13.03	0.070310	188 -- 210	28 -- 52	AraC family transcriptional regulator	_____________187________________________211\n_____________\|__________________________\|\n5'-UUU...UGAAG_____G_UA______AAU________UUAUG...UAU-3'\n______________UGGAU_U_____UGA___GGGGGGUU\n______________:\|\|\|\|_\|_____\|\|\|___\|:\|\|\|\|\|\|\n______________GCCUA_A_____ACU___CUCCCCAA\n3'-UUU...AAAAA_____G_ACUAG___AU_________CCCCU...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________27\n	204 -- 210	28 -- 34	-18.7355 kcal/mol	4.72292 kcal/mol	0.980555 kcal/mol	187 211@LB@ \| \|@LB@5'-UUU...UGAAG G UA AAU UUAUG...UAU-3'@LB@ UGGAU U UGA GGGGGGUU@LB@ :\|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|@LB@ GCCUA A ACU CUCCCCAA@LB@3'-UUU...AAAAA G ACUAG AU CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -18.7355 kcal/mol@LB@Unfolding Energy - mRNA 4.72292 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@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@
83	0.006595	0.2588	bsu17210	pksN	-11.93	0.108023	61 -- 115	29 -- 70	polyketide synthase PksN	_____________60_______________________________________________________116\n_____________\|________________________________________________________\|\n5'-AGC...CAAGA____________GAAA__________AA__G_G__CAAAACAUC____A____A__AAAUC...UAU-3'\n______________GGUGGCGCUAGG_____UUGGAUUUU__GA_U_UG_________AUAG_AGGG_GU\n______________\|\|\|:\|\|\|\|:\|:\|_____\|:\|\|\|\|:\|\|__\|\|_\|_\|\|_________\|\|\|\|_\|\|\|\|_\|\|\n______________CCAUCGCGGUUC_____AGCCUAGAA__CU_A_AC_________UAUC_UCCC_CA\n3'-UUU...CGCCC____________AAAAA_______________G_______________________ACCCC...AUA-5'\n_____________\|________________________________________________________\|\n_____________71_______________________________________________________28\n	79 -- 85	45 -- 51	-37.7722 kcal/mol	10.06 kcal/mol	15.7778 kcal/mol	60 116@LB@ \| \|@LB@5'-AGC...CAAGA GAAA AA G G CAAAACAUC A A AAAUC...UAU-3'@LB@ GGUGGCGCUAGG UUGGAUUUU GA U UG AUAG AGGG GU@LB@ \|\|\|:\|\|\|\|:\|:\| \|:\|\|\|\|:\|\| \|\| \| \|\| \|\|\|\| \|\|\|\| \|\|@LB@ CCAUCGCGGUUC AGCCUAGAA CU A AC UAUC UCCC CA@LB@3'-UUU...CGCCC AAAAA G ACCCC...AUA-5'@LB@ \| \|@LB@ 71 28@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -37.7722 kcal/mol@LB@Unfolding Energy - mRNA 10.06 kcal/mol@LB@Unfolding Energy - sRNA 15.7778 kcal/mol@LB@@LB@Position - mRNA 61 -- 115@LB@Position - sRNA 29 -- 70@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 45 -- 51@LB@
94	0.007849	0.2778	bsu27000	yraB	-9.14	0.279232	183 -- 193	29 -- 39	MerR family transcriptional regulator	_____________182_________194\n_____________\|___________\|\n5'-AGU...UACAG_______A___GAAGA...ACA-3'\n______________GAUAGAG_GGU\n______________\|\|\|\|\|\|\|_\|\|\|\n______________CUAUCUC_CCA\n3'-UUU...CUAGA_______C___ACCCC...AUA-5'\n_____________\|___________\|\n_____________40__________28\n	183 -- 189	33 -- 39	-13.977 kcal/mol	4.05751 kcal/mol	0.779471 kcal/mol	182 194@LB@ \| \|@LB@5'-AGU...UACAG A GAAGA...ACA-3'@LB@ GAUAGAG GGU@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ CUAUCUC CCA@LB@3'-UUU...CUAGA C ACCCC...AUA-5'@LB@ \| \|@LB@ 40 28@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -13.977 kcal/mol@LB@Unfolding Energy - mRNA 4.05751 kcal/mol@LB@Unfolding Energy - sRNA 0.779471 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 29 -- 39@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 33 -- 39@LB@
107	0.009163	0.2778	bsu12780	xepA	-15.86	0.020153	79 -- 99	29 -- 48	phage-like element PBSX protein XepA	_____________78____________________100\n_____________\|_____________________\|\n5'-UUG...UCAAU__AG_______C______U__GAACA...UUU-3'\n______________UC__GAUCUGG_AGAGGG_GU\n______________\|\|__\|\|\|\|\|\|:_\|\|\|\|\|\|_\|\|\n______________AG__CUAGACU_UCUCCC_CA\n3'-UUU...AGCCU__AA_______A_________ACCCC...AUA-5'\n_____________\|_____________________\|\n_____________49____________________28\n	83 -- 89	38 -- 44	-22.9588 kcal/mol	6.12286 kcal/mol	0.974361 kcal/mol	78 100@LB@ \| \|@LB@5'-UUG...UCAAU AG C U GAACA...UUU-3'@LB@ UC GAUCUGG AGAGGG GU@LB@ \|\| \|\|\|\|\|\|: \|\|\|\|\|\| \|\|@LB@ AG CUAGACU UCUCCC CA@LB@3'-UUU...AGCCU AA A ACCCC...AUA-5'@LB@ \| \|@LB@ 49 28@LB@@LB@@LB@Energy -15.86 kcal/mol@LB@Hybridization Energy -22.9588 kcal/mol@LB@Unfolding Energy - mRNA 6.12286 kcal/mol@LB@Unfolding Energy - sRNA 0.974361 kcal/mol@LB@@LB@Position - mRNA 79 -- 99@LB@Position - sRNA 29 -- 48@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 38 -- 44@LB@
111	0.009313	0.2778	bsu16780	rnjB	-13.26	0.064171	155 -- 177	29 -- 51	ribonuclease J 2	_____________154_____________________178\n_____________\|_______________________\|\n5'-GCA...UAAUA___ACAAGUGA_______C____AUGAG...UAU-3'\n______________GGA________UGAUGGA_GGGU\n______________\|\|\|________\|\|\|\|:\|\|_\|\|\|\|\n______________CCU________ACUAUCU_CCCA\n3'-UUU...AAAAG___AGAACUAG_______C____ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	166 -- 172	34 -- 40	-18.6769 kcal/mol	4.44629 kcal/mol	0.974539 kcal/mol	154 178@LB@ \| \|@LB@5'-GCA...UAAUA ACAAGUGA C AUGAG...UAU-3'@LB@ GGA UGAUGGA GGGU@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|@LB@ CCU ACUAUCU CCCA@LB@3'-UUU...AAAAG AGAACUAG C ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -18.6769 kcal/mol@LB@Unfolding Energy - mRNA 4.44629 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 155 -- 177@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 34 -- 40@LB@
117	0.0101	0.2881	bsu39670	iolJ	-13.86	0.049938	182 -- 196	29 -- 51	6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase	_____________181_____________________197\n_____________\|_______________________\|\n5'-CCG...GUAAU____AAA________________GAAUA...CGA-3'\n______________GGAU___________GGAGGGGU\n______________\|\|\|\|___________:\|\|\|\|\|\|\|\n______________CCUA___________UCUCCCCA\n3'-UUU...AAAAG____GAACUAGACUA________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	190 -- 196	29 -- 35	-16.9006 kcal/mol	2.07053 kcal/mol	0.974539 kcal/mol	181 197@LB@ \| \|@LB@5'-CCG...GUAAU AAA GAAUA...CGA-3'@LB@ GGAU GGAGGGGU@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ CCUA UCUCCCCA@LB@3'-UUU...AAAAG GAACUAGACUA ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -16.9006 kcal/mol@LB@Unfolding Energy - mRNA 2.07053 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 182 -- 196@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@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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