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
121	0.01072	0.2883	bsu28520	etfA	-20.27	0.001775	7 -- 28	32 -- 50	electron transfer flavoprotein subunit alpha	_____________6______________________29\n_____________\|______________________\|\n_____5'-CUUGAU_____________ACGA_____AUGCU...AUG-3'\n______________GAUCUUGAUCUGG____AGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:____\|\|\|\|\|\n______________CUAGAACUAGACU____UCUCC\n3'-UUU...AAAGC_____________A________CCAAC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________31\n	13 -- 19	38 -- 44	-25.4493 kcal/mol	4.21131 kcal/mol	0.970199 kcal/mol	6 29@LB@ \| \|@LB@ 5'-CUUGAU ACGA AUGCU...AUG-3'@LB@ GAUCUUGAUCUGG AGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|: \|\|\|\|\|@LB@ CUAGAACUAGACU UCUCC@LB@3'-UUU...AAAGC A CCAAC...AUA-5'@LB@ \| \|@LB@ 51 31@LB@@LB@@LB@Energy -20.27 kcal/mol@LB@Hybridization Energy -25.4493 kcal/mol@LB@Unfolding Energy - mRNA 4.21131 kcal/mol@LB@Unfolding Energy - sRNA 0.970199 kcal/mol@LB@@LB@Position - mRNA 7 -- 28@LB@Position - sRNA 32 -- 50@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 38 -- 44@LB@
122	0.01077	0.2883	bsu18910	rapK	-11.72	0.116857	189 -- 197	28 -- 36	response regulator aspartate phosphatase K	_____________188_______198\n_____________\|_________\|\n5'-UAU...CAGAA_________UAAAU...CAG-3'\n______________AGAGGGGUU\n______________\|\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-15.633 kcal/mol	3.77416 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UAU...CAGAA UAAAU...CAG-3'@LB@ AGAGGGGUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -15.633 kcal/mol@LB@Unfolding Energy - mRNA 3.77416 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@
123	0.01093	0.2883	bsu22970	ypbH	-15.60	0.022809	254 -- 275	27 -- 45	adapter protein MecA	_____________253____________________276\n_____________\|______________________\|\n5'-GAG...CUCGA________C___CC____A___ACAAA...ACU-3'\n______________UGAUUUGA_AGA__GGGG_UUG\n______________\|\|\|\|:\|\|\|_\|\|\|__\|\|\|\|_\|\|\|\n______________ACUAGACU_UCU__CCCC_AAC\n3'-UUU...CUAGA________A_____________CCCUU...AUA-5'\n_____________\|______________________\|\n_____________46_____________________26\n	255 -- 261	38 -- 44	-20.0369 kcal/mol	3.46393 kcal/mol	0.971562 kcal/mol	253 276@LB@ \| \|@LB@5'-GAG...CUCGA C CC A ACAAA...ACU-3'@LB@ UGAUUUGA AGA GGGG UUG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|@LB@ ACUAGACU UCU CCCC AAC@LB@3'-UUU...CUAGA A CCCUU...AUA-5'@LB@ \| \|@LB@ 46 26@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -20.0369 kcal/mol@LB@Unfolding Energy - mRNA 3.46393 kcal/mol@LB@Unfolding Energy - sRNA 0.971562 kcal/mol@LB@@LB@Position - mRNA 254 -- 275@LB@Position - sRNA 27 -- 45@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 38 -- 44@LB@
124	0.01102	0.2883	bsu36860	atpE	-15.23	0.027175	263 -- 293	30 -- 52	ATP synthase subunit c	_____________262_______________________________294\n_____________\|_________________________________\|\n5'-AAA...GGUAA____________GUUUCACGUAC__________AUUGCCC-3'\n______________CGG__UUUGAUU___________GGUAGAGGGG\n______________\|\|\|__:\|\|\|\|\|:___________\|:\|\|\|\|\|\|\|\|\n______________GCC__GAACUAG___________CUAUCUCCCC\n3'-UUU...AAAAA___UA_______A____________________AACCC...AUA-5'\n_____________\|_________________________________\|\n_____________53________________________________29\n	287 -- 293	30 -- 36	-22.7251 kcal/mol	6.51858 kcal/mol	0.979974 kcal/mol	262 294@LB@ \| \|@LB@5'-AAA...GGUAA GUUUCACGUAC AUUGCCC-3'@LB@ CGG UUUGAUU GGUAGAGGGG@LB@ \|\|\| :\|\|\|\|\|: \|:\|\|\|\|\|\|\|\|@LB@ GCC GAACUAG CUAUCUCCCC@LB@3'-UUU...AAAAA UA A AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.23 kcal/mol@LB@Hybridization Energy -22.7251 kcal/mol@LB@Unfolding Energy - mRNA 6.51858 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 30 -- 36@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@
126	0.0111	0.2883	bsu16220	fliG	-14.68	0.034861	264 -- 293	1 -- 29	flagellar motor switch protein FliG	_____________263_____________________________294\n_____________\|_______________________________\|\n5'-GGG...UUUCC______U_____U_U__C_______G_____AAGCACU-3'\n______________UUGGGG__UAGA_G_GU_AGCUUCU_UCUAU\n______________\|\|\|\|\|\|__:\|\|\|_\|_\|\|_\|\|\|\|\|\|\|_\|\|\|\|\|\n______________AACCCC__GUCU_C_CA_UCGAAGA_AGAUA\n3'-UUU...UCCCC______UU______U__________G_____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	281 -- 287	7 -- 13	-31.0613 kcal/mol	7.38869 kcal/mol	8.9939 kcal/mol	263 294@LB@ \| \|@LB@5'-GGG...UUUCC U U U C G AAGCACU-3'@LB@ UUGGGG UAGA G GU AGCUUCU UCUAU@LB@ \|\|\|\|\|\| :\|\|\| \| \|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AACCCC GUCU C CA UCGAAGA AGAUA@LB@3'-UUU...UCCCC UU U G -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -31.0613 kcal/mol@LB@Unfolding Energy - mRNA 7.38869 kcal/mol@LB@Unfolding Energy - sRNA 8.9939 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@LB@
127	0.01117	0.2883	bsu05980	tatAY	-16.78	0.012784	171 -- 194	21 -- 43	Sec-independent protein translocase protein TatAy	_____________170______________________195\n_____________\|________________________\|\n5'-CCG...AGGAA___GA________AAA__A_____CCAAA...ACA-3'\n______________AUC__AUAGAGGG___GG_GGAGC\n______________\|\|\|__\|\|\|\|\|\|\|\|___\|\|_\|\|\|:\|\n______________UAG__UAUCUCCC___CC_CCUUG\n3'-UUU...AGAAC___AC________CAA________UCUCU...AUA-5'\n_____________\|________________________\|\n_____________44_______________________20\n	177 -- 183	31 -- 37	-24.2003 kcal/mol	4.65314 kcal/mol	2.76238 kcal/mol	170 195@LB@ \| \|@LB@5'-CCG...AGGAA GA AAA A CCAAA...ACA-3'@LB@ AUC AUAGAGGG GG GGAGC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\| \|\|\|:\|@LB@ UAG UAUCUCCC CC CCUUG@LB@3'-UUU...AGAAC AC CAA UCUCU...AUA-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -16.78 kcal/mol@LB@Hybridization Energy -24.2003 kcal/mol@LB@Unfolding Energy - mRNA 4.65314 kcal/mol@LB@Unfolding Energy - sRNA 2.76238 kcal/mol@LB@@LB@Position - mRNA 171 -- 194@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 31 -- 37@LB@
128	0.01143	0.2883	bsu29690	acuA	-15.81	0.020690	248 -- 269	30 -- 52	acetoin utilization protein AcuA	_____________247_____________________270\n_____________\|_______________________\|\n5'-UAU...GCAAC___C____UA_________A___CCUGU...AUG-3'\n______________CGG_UCUU___CUGAUAGA_GGG\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC_AGAA___GACUAUCU_CCC\n3'-UUU...AAAAA___U____CUA________C___AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	259 -- 265	34 -- 40	-22.8929 kcal/mol	6.10629 kcal/mol	0.979974 kcal/mol	247 270@LB@ \| \|@LB@5'-UAU...GCAAC C UA A CCUGU...AUG-3'@LB@ CGG UCUU CUGAUAGA GGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC AGAA GACUAUCU CCC@LB@3'-UUU...AAAAA U CUA C AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.81 kcal/mol@LB@Hybridization Energy -22.8929 kcal/mol@LB@Unfolding Energy - mRNA 6.10629 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 34 -- 40@LB@
129	0.01144	0.2883	bsu36230	ywqF	-11.45	0.129133	185 -- 195	31 -- 41	UDP-glucose 6-dehydrogenase YwqF	_____________184_________196\n_____________\|___________\|\n5'-UUU...UUUAA___U_______AAACA...CUC-3'\n______________CUG_UGGAGGG\n______________\|\|\|_\|:\|\|\|\|\|\n______________GAC_AUCUCCC\n3'-UUU...AACUA___U_______CAACC...AUA-5'\n_____________\|___________\|\n_____________42__________30\n	189 -- 195	31 -- 37	-16.042 kcal/mol	3.66073 kcal/mol	0.928126 kcal/mol	184 196@LB@ \| \|@LB@5'-UUU...UUUAA U AAACA...CUC-3'@LB@ CUG UGGAGGG@LB@ \|\|\| \|:\|\|\|\|\|@LB@ GAC AUCUCCC@LB@3'-UUU...AACUA U CAACC...AUA-5'@LB@ \| \|@LB@ 42 30@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -16.042 kcal/mol@LB@Unfolding Energy - mRNA 3.66073 kcal/mol@LB@Unfolding Energy - sRNA 0.928126 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 31 -- 41@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 31 -- 37@LB@
130	0.01149	0.2883	bsu02620	phoD	-13.55	0.056825	174 -- 193	30 -- 50	alkaline phosphatase D	_____________173____________________194\n_____________\|______________________\|\n5'-GCC...GAGAC____AA___G____G_______AUCUU...CGG-3'\n______________GAUC__UGA___GA_AGAGGGG\n______________\|\|\|\|__\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________CUAG__ACU___CU_UCUCCCC\n3'-UUU...AAAGC____A____AGA__A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	187 -- 193	30 -- 36	-18.9864 kcal/mol	4.46268 kcal/mol	0.974272 kcal/mol	173 194@LB@ \| \|@LB@5'-GCC...GAGAC AA G G AUCUU...CGG-3'@LB@ GAUC UGA GA AGAGGGG@LB@ \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CUAG ACU CU UCUCCCC@LB@3'-UUU...AAAGC A AGA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -18.9864 kcal/mol@LB@Unfolding Energy - mRNA 4.46268 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 187 -- 193@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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