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
47	0.002107	0.1496	bsu10620	addB	-16.79	0.012734	176 -- 222	12 -- 44	ATP-dependent helicase/deoxyribonuclease subunit B		_____________175_____________________________________________223\n_____________\|_______________________________________________\|\n5'-UAG...AGAGA___AAAAAG________CUUCUAAUUU__________UUUUU_____GCAGG...AGC-3'\n______________GAU______AGAGGGGU__________GGGAGCAGAG_____AGUAG\n______________\|\|\|______\|\|\|\|\|\|\|\|__________\|\|\|\|:\|\|\|\|\|_____\|\|\|\|\|\n______________CUA______UCUCCCCA__________CCCUUGUCUC_____UCAUC\n3'-UUU...UAGAA___GACUA_________AC____________________________GAAGA...AUA-5'\n_____________\|_______________________________________________\|\n_____________45______________________________________________11\n	206 -- 212	17 -- 23	-35.2405 kcal/mol	8.50165 kcal/mol	9.94637 kcal/mol	175 223@LB@ \| \|@LB@5'-UAG...AGAGA AAAAAG CUUCUAAUUU UUUUU GCAGG...AGC-3'@LB@ GAU AGAGGGGU GGGAGCAGAG AGUAG@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|\|@LB@ CUA UCUCCCCA CCCUUGUCUC UCAUC@LB@3'-UUU...UAGAA GACUA AC GAAGA...AUA-5'@LB@ \| \|@LB@ 45 11@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -35.2405 kcal/mol@LB@Unfolding Energy - mRNA 8.50165 kcal/mol@LB@Unfolding Energy - sRNA 9.94637 kcal/mol@LB@@LB@Position - mRNA 176 -- 222@LB@Position - sRNA 12 -- 44@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 17 -- 23@LB@
195	0.01942	0.3269	bsu00690	ftsH	-11.53	0.125763	258 -- 269	21 -- 33	ATP-dependent zinc metalloprotease FtsH		_____________257___________270\n_____________\|_____________\|\n5'-AGU...UAAUC_______U_____UACUU...AAA-3'\n______________GGGGUUG__GAGC\n______________\|\|\|\|\|\|\|__\|\|:\|\n______________CCCCAAC__CUUG\n3'-UUU...UAUCU_______CC____UCUCU...AUA-5'\n_____________\|_____________\|\n_____________34____________20\n	258 -- 264	27 -- 33	-15.4755 kcal/mol	2.12746 kcal/mol	1.8225 kcal/mol	257 270@LB@ \| \|@LB@5'-AGU...UAAUC U UACUU...AAA-3'@LB@ GGGGUUG GAGC@LB@ \|\|\|\|\|\|\| \|\|:\|@LB@ CCCCAAC CUUG@LB@3'-UUU...UAUCU CC UCUCU...AUA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 2.12746 kcal/mol@LB@Unfolding Energy - sRNA 1.8225 kcal/mol@LB@@LB@Position - mRNA 258 -- 269@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 27 -- 33@LB@
103	0.008788	0.2778	bsu06070	ydiP	-8.66	0.321247	183 -- 194	27 -- 44	BsuMI modification methylase subunit YdiP	bsu20250	_____________182________________195\n_____________\|__________________\|\n5'-GGA...AAAAA__________________AUAUC...UGG-3'\n______________GAUUUGA______GGUUG\n______________\|\|\|:\|\|\|______\|\|\|\|\|\n______________CUAGACU______CCAAC\n3'-UUU...UAGAA_______AUCUCC_____CCCUU...AUA-5'\n_____________\|__________________\|\n_____________45_________________26\n	183 -- 189	38 -- 44	-12.3729 kcal/mol	2.73997 kcal/mol	0.971452 kcal/mol	182 195@LB@ \| \|@LB@5'-GGA...AAAAA AUAUC...UGG-3'@LB@ GAUUUGA GGUUG@LB@ \|\|\|:\|\|\| \|\|\|\|\|@LB@ CUAGACU CCAAC@LB@3'-UUU...UAGAA AUCUCC CCCUU...AUA-5'@LB@ \| \|@LB@ 45 26@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -12.3729 kcal/mol@LB@Unfolding Energy - mRNA 2.73997 kcal/mol@LB@Unfolding Energy - sRNA 0.971452 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 27 -- 44@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 38 -- 44@LB@
193	0.01926	0.3269	bsu04460	dctR	-12.61	0.083358	128 -- 157	20 -- 50	C4-dicarboxylate response regulator DctR		_____________127_____________________________158\n_____________\|_______________________________\|\n5'-CUG...CGAUA__AG______CACAU_C____CA________UCUUU...UCU-3'\n______________GA__UUGAUU_____G_GGGG___GGGGACA\n______________\|\|__\|\|\|\|\|:_____\|_\|\|\|\|___\|\|\|:\|\|\|\n______________CU__AACUAG_____C_CCCC___CCCUUGU\n3'-UUU...AAAGC__AG______ACUAU_U____AAC_______CUCUC...AUA-5'\n_____________\|_______________________________\|\n_____________51______________________________19\n	151 -- 157	20 -- 26	-24.008 kcal/mol	7.17274 kcal/mol	4.22897 kcal/mol	127 158@LB@ \| \|@LB@5'-CUG...CGAUA AG CACAU C CA UCUUU...UCU-3'@LB@ GA UUGAUU G GGGG GGGGACA@LB@ \|\| \|\|\|\|\|: \| \|\|\|\| \|\|\|:\|\|\|@LB@ CU AACUAG C CCCC CCCUUGU@LB@3'-UUU...AAAGC AG ACUAU U AAC CUCUC...AUA-5'@LB@ \| \|@LB@ 51 19@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -24.008 kcal/mol@LB@Unfolding Energy - mRNA 7.17274 kcal/mol@LB@Unfolding Energy - sRNA 4.22897 kcal/mol@LB@@LB@Position - mRNA 128 -- 157@LB@Position - sRNA 20 -- 50@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 20 -- 26@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@
100	0.008436	0.2778	bsu35250	ftsX	-12.75	0.078592	182 -- 188	30 -- 36	cell division protein FtsX		_____________181_____189\n_____________\|_______\|\n5'-UGC...AGUCA_______AGUAU...CGC-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	182 -- 188	30 -- 36	-13.7147 kcal/mol	0.82624 kcal/mol	0.133643 kcal/mol	181 189@LB@ \| \|@LB@5'-UGC...AGUCA AGUAU...CGC-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -13.7147 kcal/mol@LB@Unfolding Energy - mRNA 0.82624 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 182 -- 188@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 30 -- 36@LB@
97	0.008118	0.2778	bsu16450	cheC	-9.97	0.215069	178 -- 195	28 -- 47	Chey-P phosphatase CheC		_____________177__________________196\n_____________\|____________________\|\n5'-CGA...UCAAG___A________A_______AUGAC...UGU-3'\n______________CUU_AUCU__UA_AGGGGUU\n______________\|\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________GAA_UAGA__AU_UCCCCAA\n3'-UUU...GCCUA___C____CU__C_______CCCCU...AUA-5'\n_____________\|____________________\|\n_____________48___________________27\n	189 -- 195	28 -- 34	-14.5799 kcal/mol	3.63028 kcal/mol	0.974663 kcal/mol	177 196@LB@ \| \|@LB@5'-CGA...UCAAG A A AUGAC...UGU-3'@LB@ CUU AUCU UA AGGGGUU@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ GAA UAGA AU UCCCCAA@LB@3'-UUU...GCCUA C CU C CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -14.5799 kcal/mol@LB@Unfolding Energy - mRNA 3.63028 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
87	0.00681	0.2588	bsu29140	citZ	-14.51	0.037644	213 -- 231	27 -- 52	citrate synthase 2		_____________212_________________________232\n_____________\|___________________________\|\n5'-GAG...CGACA__C________________________UAGCA...AUG-3'\n______________CG_GGUCUUGA________AGGGGUUG\n______________\|\|_\|:\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________GC_CUAGAACU________UCCCCAAC\n3'-UUU...AAAAA___________AGACUAUC________CCCUU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________26\n	225 -- 231	27 -- 33	-23.9033 kcal/mol	8.41647 kcal/mol	0.980744 kcal/mol	212 232@LB@ \| \|@LB@5'-GAG...CGACA C UAGCA...AUG-3'@LB@ CG GGUCUUGA AGGGGUUG@LB@ \|\| \|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GC CUAGAACU UCCCCAAC@LB@3'-UUU...AAAAA AGACUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 53 26@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -23.9033 kcal/mol@LB@Unfolding Energy - mRNA 8.41647 kcal/mol@LB@Unfolding Energy - sRNA 0.980744 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 27 -- 52@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
57	0.003091	0.1809	bsu19720	yodR	-13.42	0.059995	155 -- 217	11 -- 51	coenzyme A transferase subunit beta		_____________154_________________________________________________________________218\n_____________\|___________________________________________________________________\|\n5'-GCU...ACCGG_______UG________________UACGAAGCGA____GUGAAGUGGAAAUGG__UU_________AGAAA...CCU-3'\n______________GGGUUUU___UUGA___GGGGGUUG__________GGGA_______________GC__GGGAGUAGC\n______________\|\|:\|:\|\|___:\|\|\|___:\|\|\|\|\|\|\|__________\|\|\|\|_______________:\|__\|:\|\|\|\|\|\|\|\n______________CCUAGAA___GACU___UCCCCAAC__________CCCU_______________UG__CUCUCAUCG\n3'-UUU...AAAAG_______CUA____AUC_______________________________________U__________AAGAG...AUA-5'\n_____________\|___________________________________________________________________\|\n_____________52__________________________________________________________________10\n	211 -- 217	11 -- 17	-37.5623 kcal/mol	14.1868 kcal/mol	9.95641 kcal/mol	154 218@LB@ \| \|@LB@5'-GCU...ACCGG UG UACGAAGCGA GUGAAGUGGAAAUGG UU AGAAA...CCU-3'@LB@ GGGUUUU UUGA GGGGGUUG GGGA GC GGGAGUAGC@LB@ \|\|:\|:\|\| :\|\|\| :\|\|\|\|\|\|\| \|\|\|\| :\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA GACU UCCCCAAC CCCU UG CUCUCAUCG@LB@3'-UUU...AAAAG CUA AUC U AAGAG...AUA-5'@LB@ \| \|@LB@ 52 10@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -37.5623 kcal/mol@LB@Unfolding Energy - mRNA 14.1868 kcal/mol@LB@Unfolding Energy - sRNA 9.95641 kcal/mol@LB@@LB@Position - mRNA 155 -- 217@LB@Position - sRNA 11 -- 51@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
151	0.01347	0.2966	bsu25570	comEC	-9.44	0.254651	59 -- 89	9 -- 50	ComE operon protein 3		_____________58__________________________________________90\n_____________\|___________________________________________\|\n5'-CGC...GAAAU____G_________AA____________________AA_____UCAUU...UCU-3'\n______________GAUC_UUGAUCUGA______________AACAGAGA__AGCUU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAG_AACUAGACU______________UUGUCUCU__UCGAA\n3'-UUU...AAAGC______________AUCUCCCCAACCCC________CA_____GAGAGAUA-5'\n_____________\|___________________________________________\|\n_____________51__________________________________________8\n	76 -- 82	16 -- 22	-28.9501 kcal/mol	9.55134 kcal/mol	9.9565 kcal/mol	58 90@LB@ \| \|@LB@5'-CGC...GAAAU G AA AA UCAUU...UCU-3'@LB@ GAUC UUGAUCUGA AACAGAGA AGCUU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAG AACUAGACU UUGUCUCU UCGAA@LB@3'-UUU...AAAGC AUCUCCCCAACCCC CA GAGAGAUA-5'@LB@ \| \|@LB@ 51 8@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -28.9501 kcal/mol@LB@Unfolding Energy - mRNA 9.55134 kcal/mol@LB@Unfolding Energy - sRNA 9.9565 kcal/mol@LB@@LB@Position - mRNA 59 -- 89@LB@Position - sRNA 9 -- 50@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 16 -- 22@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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