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
40	0.001724	0.1438	bsu18440	gltD	-13.77	0.051762	193 -- 208	22 -- 36	glutamate synthase [NADPH] small chain	_____________192______________209\n_____________\|________________\|\n5'-AGA...AGGGG_____AACA_______ACCAA...CUU-3'\n______________AGAGG____UGGGGAA\n______________\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UCUCC____ACCCCUU\n3'-UUU...GACUA_____CCA________GUCUC...AUA-5'\n_____________\|________________\|\n_____________37_______________21\n	202 -- 208	22 -- 28	-17.8722 kcal/mol	3.06294 kcal/mol	1.03819 kcal/mol	192 209@LB@ \| \|@LB@5'-AGA...AGGGG AACA ACCAA...CUU-3'@LB@ AGAGG UGGGGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUCC ACCCCUU@LB@3'-UUU...GACUA CCA GUCUC...AUA-5'@LB@ \| \|@LB@ 37 21@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -17.8722 kcal/mol@LB@Unfolding Energy - mRNA 3.06294 kcal/mol@LB@Unfolding Energy - sRNA 1.03819 kcal/mol@LB@@LB@Position - mRNA 193 -- 208@LB@Position - sRNA 22 -- 36@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
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@
115	0.009897	0.2871	bsu22830	gpsA	-18.23	0.005947	227 -- 241	21 -- 34	glycerol-3-phosphate dehydrogenase	_____________226_____________242\n_____________\|_______________\|\n5'-GGU...GGAGC____A__________AGCAC...GUG-3'\n______________GGGG_GUUGGGGAAC\n______________:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UCCC_CAACCCCUUG\n3'-UUU...CUAUC_______________UCUCU...AUA-5'\n_____________\|_______________\|\n_____________35______________20\n	235 -- 241	21 -- 27	-24.3947 kcal/mol	4.254 kcal/mol	1.91139 kcal/mol	226 242@LB@ \| \|@LB@5'-GGU...GGAGC A AGCAC...GUG-3'@LB@ GGGG GUUGGGGAAC@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UCCC CAACCCCUUG@LB@3'-UUU...CUAUC UCUCU...AUA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -24.3947 kcal/mol@LB@Unfolding Energy - mRNA 4.254 kcal/mol@LB@Unfolding Energy - sRNA 1.91139 kcal/mol@LB@@LB@Position - mRNA 227 -- 241@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
26	0.0005174	0.06638	bsu28170	hemA	-17.53	0.008676	171 -- 186	24 -- 36	glutamyl-tRNA reductase	_____________170______________187\n_____________\|________________\|\n5'-AUG...AAUUA___UU___U_______GUGUA...UGC-3'\n______________AGA__GGG_GUUGGGG\n______________\|\|\|__\|\|\|_\|\|\|\|\|\|\|\n______________UCU__CCC_CAACCCC\n3'-UUU...GACUA________________UUGUC...AUA-5'\n_____________\|________________\|\n_____________37_______________23\n	180 -- 186	24 -- 30	-19.8849 kcal/mol	2.21391 kcal/mol	0.138435 kcal/mol	170 187@LB@ \| \|@LB@5'-AUG...AAUUA UU U GUGUA...UGC-3'@LB@ AGA GGG GUUGGGG@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCU CCC CAACCCC@LB@3'-UUU...GACUA UUGUC...AUA-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -17.53 kcal/mol@LB@Hybridization Energy -19.8849 kcal/mol@LB@Unfolding Energy - mRNA 2.21391 kcal/mol@LB@Unfolding Energy - sRNA 0.138435 kcal/mol@LB@@LB@Position - mRNA 171 -- 186@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 24 -- 30@LB@
158	0.01436	0.3008	bsu10130	hemH	-12.69	0.080628	178 -- 227	6 -- 44	ferrochelatase	_____________177____________________________________________________228\n_____________\|______________________________________________________\|\n5'-GAG...UAUCA____AUUAA______U__A_________U____AGAAAGAAAAUGG________GUGAU...GAA-3'\n______________GAUC_____AGAGGG_GU_____AACAG_GAGU_____________GGCUUCUC\n______________\|\|\|\|_____\|\|\|\|\|\|_\|\|_____\|\|\|\|\|_\|\|\|\|_____________:\|\|\|\|\|\|\|\n______________CUAG_____UCUCCC_CA_____UUGUC_CUCA_____________UCGAAGAG\n3'-UUU...UAGAA____ACUA__________ACCCC_____U_________________________AGAUA-5'\n_____________\|______________________________________________________\|\n_____________45_____________________________________________________5\n	220 -- 226	7 -- 13	-32.766 kcal/mol	10.122 kcal/mol	9.95356 kcal/mol	177 228@LB@ \| \|@LB@5'-GAG...UAUCA AUUAA U A U AGAAAGAAAAUGG GUGAU...GAA-3'@LB@ GAUC AGAGGG GU AACAG GAGU GGCUUCUC@LB@ \|\|\|\| \|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUAG UCUCCC CA UUGUC CUCA UCGAAGAG@LB@3'-UUU...UAGAA ACUA ACCCC U AGAUA-5'@LB@ \| \|@LB@ 45 5@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -32.766 kcal/mol@LB@Unfolding Energy - mRNA 10.122 kcal/mol@LB@Unfolding Energy - sRNA 9.95356 kcal/mol@LB@@LB@Position - mRNA 178 -- 227@LB@Position - sRNA 6 -- 44@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 7 -- 13@LB@
185	0.01858	0.3269	bsu27560	hisS	-8.40	0.345340	122 -- 132	25 -- 38	histidine--tRNA ligase	_____________121____________133\n_____________\|______________\|\n5'-GCG...GUAUA_______C______AGUUU...CUU-3'\n______________GUAGGGG____GGG\n______________:\|\|\|:\|\|____\|\|\|\n______________UAUCUCC____CCC\n3'-UUU...UAGAC_______CCAA___CUUGU...AUA-5'\n_____________\|______________\|\n_____________39_____________24\n	122 -- 128	32 -- 38	-11.8618 kcal/mol	2.79445 kcal/mol	0.662893 kcal/mol	121 133@LB@ \| \|@LB@5'-GCG...GUAUA C AGUUU...CUU-3'@LB@ GUAGGGG GGG@LB@ :\|\|\|:\|\| \|\|\|@LB@ UAUCUCC CCC@LB@3'-UUU...UAGAC CCAA CUUGU...AUA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -11.8618 kcal/mol@LB@Unfolding Energy - mRNA 2.79445 kcal/mol@LB@Unfolding Energy - sRNA 0.662893 kcal/mol@LB@@LB@Position - mRNA 122 -- 132@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 32 -- 38@LB@
106	0.009109	0.2778	bsu01390	infA	-12.86	0.075307	175 -- 189	30 -- 45	translation initiation factor IF-1	_____________174______________190\n_____________\|________________\|\n5'-CCA...GUUAC____________A___AGAAC...UGG-3'\n______________UGAUUUGA_AGA_GGG\n______________\|\|\|\|:\|\|\|_\|\|\|_\|\|\|\n______________ACUAGACU_UCU_CCC\n3'-UUU...CUAGA________A___C___AACCC...AUA-5'\n_____________\|________________\|\n_____________46_______________29\n	176 -- 182	38 -- 44	-16.3452 kcal/mol	2.51395 kcal/mol	0.969561 kcal/mol	174 190@LB@ \| \|@LB@5'-CCA...GUUAC A AGAAC...UGG-3'@LB@ UGAUUUGA AGA GGG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ ACUAGACU UCU CCC@LB@3'-UUU...CUAGA A C AACCC...AUA-5'@LB@ \| \|@LB@ 46 29@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -16.3452 kcal/mol@LB@Unfolding Energy - mRNA 2.51395 kcal/mol@LB@Unfolding Energy - sRNA 0.969561 kcal/mol@LB@@LB@Position - mRNA 175 -- 189@LB@Position - sRNA 30 -- 45@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
164	0.01535	0.3122	bsu39720	iolE	-13.03	0.070250	182 -- 189	30 -- 37	inosose dehydratase	_____________181______190\n_____________\|________\|\n5'-GUU...AGUAU________AGGCA...UAA-3'\n______________UAGAGGGG\n______________\|\|\|\|\|\|\|\|\n______________AUCUCCCC\n3'-UUU...AGACU________AACCC...AUA-5'\n_____________\|________\|\n_____________38_______29\n	183 -- 189	30 -- 36	-14.5397 kcal/mol	1.33978 kcal/mol	0.165704 kcal/mol	181 190@LB@ \| \|@LB@5'-GUU...AGUAU AGGCA...UAA-3'@LB@ UAGAGGGG@LB@ \|\|\|\|\|\|\|\|@LB@ AUCUCCCC@LB@3'-UUU...AGACU AACCC...AUA-5'@LB@ \| \|@LB@ 38 29@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -14.5397 kcal/mol@LB@Unfolding Energy - mRNA 1.33978 kcal/mol@LB@Unfolding Energy - sRNA 0.165704 kcal/mol@LB@@LB@Position - mRNA 182 -- 189@LB@Position - sRNA 30 -- 37@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@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@
117	0.0101	0.2881	bsu39670	iolJ	-13.86	0.049938	182 -- 196	29 -- 51	6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase	_____________181_____________________197\n_____________\|_______________________\|\n5'-CCG...GUAAU____AAA________________GAAUA...CGA-3'\n______________GGAU___________GGAGGGGU\n______________\|\|\|\|___________:\|\|\|\|\|\|\|\n______________CCUA___________UCUCCCCA\n3'-UUU...AAAAG____GAACUAGACUA________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	190 -- 196	29 -- 35	-16.9006 kcal/mol	2.07053 kcal/mol	0.974539 kcal/mol	181 197@LB@ \| \|@LB@5'-CCG...GUAAU AAA GAAUA...CGA-3'@LB@ GGAU GGAGGGGU@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ CCUA UCUCCCCA@LB@3'-UUU...AAAAG GAACUAGACUA ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -16.9006 kcal/mol@LB@Unfolding Energy - mRNA 2.07053 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 182 -- 196@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@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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