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
191	0.01913	0.3269	bsu37760	rocC	-14.43	0.038902	267 -- 280	26 -- 36	amino acid permease RocC		_____________266____________281\n_____________\|______________\|\n5'-CCG...CUUUG________GAU___CACUG...GCU-3'\n______________GGAGGGGU___UGG\n______________:\|\|\|\|\|\|\|___\|\|\|\n______________UCUCCCCA___ACC\n3'-UUU...GACUA______________CCUUG...AUA-5'\n_____________\|______________\|\n_____________37_____________25\n	268 -- 274	29 -- 35	-16.8756 kcal/mol	2.30826 kcal/mol	0.135623 kcal/mol	266 281@LB@ \| \|@LB@5'-CCG...CUUUG GAU CACUG...GCU-3'@LB@ GGAGGGGU UGG@LB@ :\|\|\|\|\|\|\| \|\|\|@LB@ UCUCCCCA ACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -16.8756 kcal/mol@LB@Unfolding Energy - mRNA 2.30826 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 267 -- 280@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 29 -- 35@LB@
192	0.01921	0.3269	bsu12649	ykzM	-11.69	0.118448	82 -- 103	11 -- 32	Evidence 4: Homologs of previously reported genes of unknown function	bsu26089	_____________81______________________104\n_____________\|_______________________\|\n5'-AAG...GACAA____A____________C_A___GGCCA...UCG-3'\n______________GGGU__GGGGACAGGGG_G_GGC\n______________\|\|\|\|__\|\|\|:\|\|\|\|:\|:_\|_:\|\|\n______________CCCA__CCCUUGUCUCU_C_UCG\n3'-UUU...AUCUC____AC_____________A___AAGAG...AUA-5'\n_____________\|_______________________\|\n_____________33______________________10\n	88 -- 94	19 -- 25	-26.088 kcal/mol	7.89329 kcal/mol	6.50677 kcal/mol	81 104@LB@ \| \|@LB@5'-AAG...GACAA A C A GGCCA...UCG-3'@LB@ GGGU GGGGACAGGGG G GGC@LB@ \|\|\|\| \|\|\|:\|\|\|\|:\|: \| :\|\|@LB@ CCCA CCCUUGUCUCU C UCG@LB@3'-UUU...AUCUC AC A AAGAG...AUA-5'@LB@ \| \|@LB@ 33 10@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -26.088 kcal/mol@LB@Unfolding Energy - mRNA 7.89329 kcal/mol@LB@Unfolding Energy - sRNA 6.50677 kcal/mol@LB@@LB@Position - mRNA 82 -- 103@LB@Position - sRNA 11 -- 32@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 19 -- 25@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@
194	0.01929	0.3269	bsu14860	pycA	-10.87	0.159030	149 -- 193	23 -- 51	pyruvate carboxylase		_____________148___________________________________________194\n_____________\|_____________________________________________\|\n5'-GGG...GGGAA____AUUCCGCUA_______UUAUAUUCCAUUC____AAG_____GAAAA...UUG-3'\n______________GGAU_________UGAUAGA_____________GGGU___GGGGA\n______________\|\|\|\|_________\|\|\|\|\|\|\|_____________\|\|\|\|___\|\|\|\|\|\n______________CCUA_________ACUAUCU_____________CCCA___CCCCU\n3'-UUU...AAAAG____GAACUAG_________C________________A_______UGUCU...AUA-5'\n_____________\|_____________________________________________\|\n_____________52____________________________________________22\n	162 -- 168	34 -- 40	-22.9068 kcal/mol	11.0566 kcal/mol	0.980049 kcal/mol	148 194@LB@ \| \|@LB@5'-GGG...GGGAA AUUCCGCUA UUAUAUUCCAUUC AAG GAAAA...UUG-3'@LB@ GGAU UGAUAGA GGGU GGGGA@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ CCUA ACUAUCU CCCA CCCCU@LB@3'-UUU...AAAAG GAACUAG C A UGUCU...AUA-5'@LB@ \| \|@LB@ 52 22@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -22.9068 kcal/mol@LB@Unfolding Energy - mRNA 11.0566 kcal/mol@LB@Unfolding Energy - sRNA 0.980049 kcal/mol@LB@@LB@Position - mRNA 149 -- 193@LB@Position - sRNA 23 -- 51@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 34 -- 40@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@
196	0.01947	0.3269	bsu15810	spoVM	-12.63	0.082660	188 -- 194	30 -- 36	stage V sporulation protein M		_____________187_____195\n_____________\|_______\|\n5'-AAA...UUAUA_______ACAAA...GCC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.8815 kcal/mol	1.12038 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-AAA...UUAUA ACAAA...GCC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8815 kcal/mol@LB@Unfolding Energy - mRNA 1.12038 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
197	0.0195	0.3269	bsu04670	rsbRA	-10.67	0.170227	19 -- 37	34 -- 52	RsbT co-antagonist protein RsbRA		_____________18__________________38\n_____________\|___________________\|\n5'-CGG...UCAUC_____GA___AA_______UAAGG...AAU-3'\n______________UGGAU__UGA__UGAUGGA\n______________:\|\|\|\|__\|\|\|__\|\|\|\|:\|\|\n______________GCCUA__ACU__ACUAUCU\n3'-UUU...AAAAA_____GA___AG_______CCCCA...AUA-5'\n_____________\|___________________\|\n_____________53__________________33\n	31 -- 37	34 -- 40	-17.5102 kcal/mol	5.86002 kcal/mol	0.976339 kcal/mol	18 38@LB@ \| \|@LB@5'-CGG...UCAUC GA AA UAAGG...AAU-3'@LB@ UGGAU UGA UGAUGGA@LB@ :\|\|\|\| \|\|\| \|\|\|\|:\|\|@LB@ GCCUA ACU ACUAUCU@LB@3'-UUU...AAAAA GA AG CCCCA...AUA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -10.67 kcal/mol@LB@Hybridization Energy -17.5102 kcal/mol@LB@Unfolding Energy - mRNA 5.86002 kcal/mol@LB@Unfolding Energy - sRNA 0.976339 kcal/mol@LB@@LB@Position - mRNA 19 -- 37@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 34 -- 40@LB@
198	0.0197	0.3269	bsu08980	yhbH	-11.85	0.111658	189 -- 195	30 -- 36	stress response UPF0229 protein YhbH		_____________188_____196\n_____________\|_______\|\n5'-GGC...GUUAA_______AAUUC...UGC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	189 -- 195	30 -- 36	-13.8096 kcal/mol	1.82966 kcal/mol	0.133643 kcal/mol	188 196@LB@ \| \|@LB@5'-GGC...GUUAA AAUUC...UGC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -13.8096 kcal/mol@LB@Unfolding Energy - mRNA 1.82966 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@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@

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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