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
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@
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@
165	0.01546	0.3127	bsu02230	purT	-12.11	0.100898	185 -- 195	30 -- 39	phosphoribosylglycinamide formyltransferase	_____________184_________196\n_____________\|___________\|\n5'-GAU...GAACA___A_______CAAAG...UUG-3'\n______________GAU_GGAGGGG\n______________\|\|\|_:\|\|\|\|\|\|\n______________CUA_UCUCCCC\n3'-UUU...CUAGA___________AACCC...AUA-5'\n_____________\|___________\|\n_____________40__________29\n	189 -- 195	30 -- 36	-15.5568 kcal/mol	2.66346 kcal/mol	0.779184 kcal/mol	184 196@LB@ \| \|@LB@5'-GAU...GAACA A CAAAG...UUG-3'@LB@ GAU GGAGGGG@LB@ \|\|\| :\|\|\|\|\|\|@LB@ CUA UCUCCCC@LB@3'-UUU...CUAGA AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.5568 kcal/mol@LB@Unfolding Energy - mRNA 2.66346 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
161	0.01452	0.3008	bsu04700	rsbU	-15.42	0.024826	142 -- 163	16 -- 38	phosphoserine phosphatase RsbU	_____________141_____________________164\n_____________\|_______________________\|\n5'-CUG...AUUCC____C____GAA___________UACAA...UCA-3'\n______________GUAG_GGGG____GGAACAGAGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________UAUC_CCCC____CCUUGUCUCU\n3'-UUU...UAGAC____U____AACC__________CAUCG...AUA-5'\n_____________\|_______________________\|\n_____________39______________________15\n	157 -- 163	16 -- 22	-28.36 kcal/mol	3.46196 kcal/mol	9.47701 kcal/mol	141 164@LB@ \| \|@LB@5'-CUG...AUUCC C GAA UACAA...UCA-3'@LB@ GUAG GGGG GGAACAGAGA@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UAUC CCCC CCUUGUCUCU@LB@3'-UUU...UAGAC U AACC CAUCG...AUA-5'@LB@ \| \|@LB@ 39 15@LB@@LB@@LB@Energy -15.42 kcal/mol@LB@Hybridization Energy -28.36 kcal/mol@LB@Unfolding Energy - mRNA 3.46196 kcal/mol@LB@Unfolding Energy - sRNA 9.47701 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 16 -- 38@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 16 -- 22@LB@
19	0.0003652	0.06216	bsu29920	ytmP	-16.30	0.016289	3 -- 31	25 -- 51	phosphotransferase YtmP	_____________2_____________________________32\n_____________\|_____________________________\|\n_________5'-AU_____GAACA______U__ACU_______ACAAU...GUA-3'\n______________GGGUU_____UUGAUA_GA___GGUUGGG\n______________\|\|:\|:_____:\|\|\|\|\|_\|\|___\|\|\|\|\|\|\|\n______________CCUAG_____GACUAU_CU___CCAACCC\n3'-UUU...AAAAG_____AACUA_________CC________CUUGU...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________24\n	25 -- 31	25 -- 31	-23.4751 kcal/mol	6.19942 kcal/mol	0.976067 kcal/mol	2 32@LB@ \| \|@LB@ 5'-AU GAACA U ACU ACAAU...GUA-3'@LB@ GGGUU UUGAUA GA GGUUGGG@LB@ \|\|:\|: :\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUAG GACUAU CU CCAACCC@LB@3'-UUU...AAAAG AACUA CC CUUGU...AUA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -23.4751 kcal/mol@LB@Unfolding Energy - mRNA 6.19942 kcal/mol@LB@Unfolding Energy - sRNA 0.976067 kcal/mol@LB@@LB@Position - mRNA 3 -- 31@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 25 -- 31@LB@
138	0.01215	0.2883	bsu17940	yneI	-15.06	0.029368	176 -- 197	30 -- 52	plasmid maintenance protein CcdB	_____________175_____________________198\n_____________\|_______________________\|\n5'-GAA...AUCUG____AA_C____GU_________AAUAU...CGG-3'\n______________UGGA__U_GAUU___UGGAGGGG\n______________:\|\|\|__\|_\|\|\|:___\|:\|\|\|\|\|\|\n______________GCCU__A_CUAG___AUCUCCCC\n3'-UUU...AAAAA____AG_A____ACU________AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	191 -- 197	30 -- 36	-21.3361 kcal/mol	5.29839 kcal/mol	0.979974 kcal/mol	175 198@LB@ \| \|@LB@5'-GAA...AUCUG AA C GU AAUAU...CGG-3'@LB@ UGGA U GAUU UGGAGGGG@LB@ :\|\|\| \| \|\|\|: \|:\|\|\|\|\|\|@LB@ GCCU A CUAG AUCUCCCC@LB@3'-UUU...AAAAA AG A ACU AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -21.3361 kcal/mol@LB@Unfolding Energy - mRNA 5.29839 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 30 -- 36@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@
101	0.008451	0.2778	bsu32150	paiA	-11.07	0.148459	77 -- 92	23 -- 39	protease synthase and sporulation negative regulatory protein PAI 1	_____________76________________93\n_____________\|_________________\|\n5'-AUU...AUCAC_______A______U__UGAAG...CAC-3'\n______________GAUAGGG__GUUGG_GA\n______________\|\|\|\|\|:\|__\|\|\|\|\|_\|\|\n______________CUAUCUC__CAACC_CU\n3'-UUU...CUAGA_______CC_____C__UGUCU...AUA-5'\n_____________\|_________________\|\n_____________40________________22\n	77 -- 83	33 -- 39	-14.8457 kcal/mol	2.98855 kcal/mol	0.791731 kcal/mol	76 93@LB@ \| \|@LB@5'-AUU...AUCAC A U UGAAG...CAC-3'@LB@ GAUAGGG GUUGG GA@LB@ \|\|\|\|\|:\| \|\|\|\|\| \|\|@LB@ CUAUCUC CAACC CU@LB@3'-UUU...CUAGA CC C UGUCU...AUA-5'@LB@ \| \|@LB@ 40 22@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -14.8457 kcal/mol@LB@Unfolding Energy - mRNA 2.98855 kcal/mol@LB@Unfolding Energy - sRNA 0.791731 kcal/mol@LB@@LB@Position - mRNA 77 -- 92@LB@Position - sRNA 23 -- 39@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 33 -- 39@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@
41	0.001775	0.1444	bsu36710	fdhD	-11.37	0.133163	186 -- 192	30 -- 36	protein FdhD	_____________185_____193\n_____________\|_______\|\n5'-UCG...AUUGC_______AAGAG...CAG-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-13.1021 kcal/mol	1.59974 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCG...AUUGC AAGAG...CAG-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -13.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.59974 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@

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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