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
95	0.007929	0.2778	bsu40080	gntZ	-7.93	0.392252	74 -- 93	34 -- 54	6-phosphogluconate dehydrogenase	_____________73____________________94\n_____________\|_____________________\|\n5'-ACU...AAUAC________AAGCA____A___AACAU...ACA-3'\n______________UUCGGAUU______UGA_AGA\n______________\|\|\|\|\|\|\|:______\|\|\|_\|\|\|\n______________AAGCCUAG______ACU_UCU\n3'-UUU...CAAAA________AACUAG___A___CCCCA...AUA-5'\n_____________\|_____________________\|\n_____________55____________________33\n	75 -- 81	47 -- 53	-13.3211 kcal/mol	3.78785 kcal/mol	1.60142 kcal/mol	73 94@LB@ \| \|@LB@5'-ACU...AAUAC AAGCA A AACAU...ACA-3'@LB@ UUCGGAUU UGA AGA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\|@LB@ AAGCCUAG ACU UCU@LB@3'-UUU...CAAAA AACUAG A CCCCA...AUA-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -7.93 kcal/mol@LB@Hybridization Energy -13.3211 kcal/mol@LB@Unfolding Energy - mRNA 3.78785 kcal/mol@LB@Unfolding Energy - sRNA 1.60142 kcal/mol@LB@@LB@Position - mRNA 74 -- 93@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 47 -- 53@LB@
96	0.00803	0.2778	bsu39710	iolF	-10.11	0.206009	172 -- 191	30 -- 53	minor myo-inositol transporter IolF	_____________171______________________192\n_____________\|________________________\|\n5'-GGC...AGUUG__________________AU____AAUGA...CCG-3'\n______________UUGGAUCU_GG_CU__UA__GGGG\n______________\|:\|\|\|\|\|\|_\|:_\|\|__\|\|__\|\|\|\|\n______________AGCCUAGA_CU_GA__AU__CCCC\n3'-UUU...AAAAA________A__A__CU__CU____AACCC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________29\n	173 -- 179	46 -- 52	-17.6548 kcal/mol	6.56277 kcal/mol	0.985344 kcal/mol	171 192@LB@ \| \|@LB@5'-GGC...AGUUG AU AAUGA...CCG-3'@LB@ UUGGAUCU GG CU UA GGGG@LB@ \|:\|\|\|\|\|\| \|: \|\| \|\| \|\|\|\|@LB@ AGCCUAGA CU GA AU CCCC@LB@3'-UUU...AAAAA A A CU CU AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -10.11 kcal/mol@LB@Hybridization Energy -17.6548 kcal/mol@LB@Unfolding Energy - mRNA 6.56277 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 172 -- 191@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 46 -- 52@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@
98	0.008247	0.2778	bsu19360	odhB	-11.30	0.136272	146 -- 191	23 -- 51	dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex	_____________145____________________________________________192\n_____________\|______________________________________________\|\n5'-AAG...GAACA___ACGUA___U_________CUU_ACUCGCAAAAACUAAG_____AAUGA...AAU-3'\n______________GGA_____UUG_AUCUGAUAG___G________________GGGGA\n______________\|\|\|_____\|\|\|_\|\|\|\|\|\|\|\|\|___\|________________\|\|\|\|\|\n______________CCU_____AAC_UAGACUAUC___C________________CCCCU\n3'-UUU...AAAAG___AG________________UCC_CAA__________________UGUCU...AUA-5'\n_____________\|______________________________________________\|\n_____________52_____________________________________________22\n	160 -- 166	35 -- 41	-19.511 kcal/mol	7.22607 kcal/mol	0.980049 kcal/mol	145 192@LB@ \| \|@LB@5'-AAG...GAACA ACGUA U CUU ACUCGCAAAAACUAAG AAUGA...AAU-3'@LB@ GGA UUG AUCUGAUAG G GGGGA@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ CCU AAC UAGACUAUC C CCCCU@LB@3'-UUU...AAAAG AG UCC CAA UGUCU...AUA-5'@LB@ \| \|@LB@ 52 22@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -19.511 kcal/mol@LB@Unfolding Energy - mRNA 7.22607 kcal/mol@LB@Unfolding Energy - sRNA 0.980049 kcal/mol@LB@@LB@Position - mRNA 146 -- 191@LB@Position - sRNA 23 -- 51@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 35 -- 41@LB@
99	0.00842	0.2778	bsu19470	yojF	-13.80	0.051174	184 -- 193	30 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183________194\n_____________\|__________\|\n5'-GAA...AAGAA__A_______AGCAA...CAG-3'\n______________GA_AGAGGGG\n______________\|\|_\|\|\|\|\|\|\|\n______________CU_UCUCCCC\n3'-UUU...CUAGA__A_______AACCC...AUA-5'\n_____________\|__________\|\n_____________40_________29\n	187 -- 193	30 -- 36	-15.454 kcal/mol	0.87683 kcal/mol	0.779184 kcal/mol	183 194@LB@ \| \|@LB@5'-GAA...AAGAA A AGCAA...CAG-3'@LB@ GA AGAGGGG@LB@ \|\| \|\|\|\|\|\|\|@LB@ CU UCUCCCC@LB@3'-UUU...CUAGA A AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -15.454 kcal/mol@LB@Unfolding Energy - mRNA 0.87683 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@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@
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@
102	0.008773	0.2778	bsu06170	ydjE	-10.58	0.175640	264 -- 284	30 -- 50	sugar kinase YdjE	_____________263___________________285\n_____________\|_____________________\|\n5'-GGG...AUGUU__CG_______A_____A___CGCCA...AAA-3'\n______________GA__UUGAUUU_AUGGA_GGG\n______________\|\|__\|\|\|\|\|:\|_\|\|:\|\|_\|\|\|\n______________CU__AACUAGA_UAUCU_CCC\n3'-UUU...AAAGC__AG_______C_____C___AACCC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________29\n	268 -- 274	40 -- 46	-17.5575 kcal/mol	6.00068 kcal/mol	0.974272 kcal/mol	263 285@LB@ \| \|@LB@5'-GGG...AUGUU CG A A CGCCA...AAA-3'@LB@ GA UUGAUUU AUGGA GGG@LB@ \|\| \|\|\|\|\|:\| \|\|:\|\| \|\|\|@LB@ CU AACUAGA UAUCU CCC@LB@3'-UUU...AAAGC AG C C AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -17.5575 kcal/mol@LB@Unfolding Energy - mRNA 6.00068 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 264 -- 284@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 40 -- 46@LB@
104	0.009018	0.2778	bsu08080	acoC	-12.10	0.101314	188 -- 194	30 -- 36	dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system	_____________187_____195\n_____________\|_______\|\n5'-UGC...AUUAA_______ACACA...GAG-3'\n______________AGGGGGG\n______________\|\|:\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.004 kcal/mol	0.767034 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGC...AUUAA ACACA...GAG-3'@LB@ AGGGGGG@LB@ \|\|:\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -13.004 kcal/mol@LB@Unfolding Energy - mRNA 0.767034 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@
105	0.009074	0.2778	bsu03220	ycgO	-6.59	0.539508	105 -- 111	67 -- 73	symporter	_____________104_____112\n_____________\|_______\|\n5'-GAA...CCUGC_______UCCAU...GUG-3'\n______________GGGGGUG\n______________\|\|\|\|\|\|:\n______________CCCCCAU\n3'-UUU...AACCG_______CGCGG...AUA-5'\n_____________\|_______\|\n_____________74______66\n	105 -- 111	67 -- 73	-12.2711 kcal/mol	3.65196 kcal/mol	2.02624 kcal/mol	104 112@LB@ \| \|@LB@5'-GAA...CCUGC UCCAU...GUG-3'@LB@ GGGGGUG@LB@ \|\|\|\|\|\|:@LB@ CCCCCAU@LB@3'-UUU...AACCG CGCGG...AUA-5'@LB@ \| \|@LB@ 74 66@LB@@LB@@LB@Energy -6.59 kcal/mol@LB@Hybridization Energy -12.2711 kcal/mol@LB@Unfolding Energy - mRNA 3.65196 kcal/mol@LB@Unfolding Energy - sRNA 2.02624 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 67 -- 73@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 67 -- 73@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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