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
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@
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@
25	0.0005172	0.06638	bsu30210	bioD	-10.94	0.155183	179 -- 210	28 -- 53	ATP-dependent dethiobiotin synthetase BioD	_____________178_______________________________211\n_____________\|_________________________________\|\n5'-GUC...UUCAA_____AAG___G___CACAUCAUUU________UUUUU...UCG-3'\n______________UCGGA____GA_CUG__________GAGGGGUU\n______________\|\|\|\|\|____\|\|_\|\|\|__________\|\|\|\|\|\|\|\|\n______________AGCCU____CU_GAC__________CUCCCCAA\n3'-UUU...AAAAA_____AGAA__A___UAU_______________CCCCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________27\n	204 -- 210	28 -- 34	-21.1469 kcal/mol	9.22099 kcal/mol	0.985925 kcal/mol	178 211@LB@ \| \|@LB@5'-GUC...UUCAA AAG G CACAUCAUUU UUUUU...UCG-3'@LB@ UCGGA GA CUG GAGGGGUU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU CU GAC CUCCCCAA@LB@3'-UUU...AAAAA AGAA A UAU CCCCU...AUA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -10.94 kcal/mol@LB@Hybridization Energy -21.1469 kcal/mol@LB@Unfolding Energy - mRNA 9.22099 kcal/mol@LB@Unfolding Energy - sRNA 0.985925 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
88	0.006855	0.2588	bsu03770	rapC	-14.27	0.041792	179 -- 211	12 -- 42	response regulator aspartate phosphatase C	_____________178_______________________________212\n_____________\|_________________________________\|\n5'-UCA...CAGUU______G____A____GAA______A_______GGUAA...UAA-3'\n______________UUUGAU_GGAG_GGGU___GGAAUG_AGAGUGG\n______________\|:\|\|\|\|_:\|\|\|_\|\|\|\|___\|\|\|\|::_\|\|\|\|\|:\|\n______________AGACUA_UCUC_CCCA___CCUUGU_UCUCAUC\n3'-UUU...GAACU________________ACC______C_______GAAGA...AUA-5'\n_____________\|_________________________________\|\n_____________43________________________________11\n	205 -- 211	12 -- 18	-33.0113 kcal/mol	8.84839 kcal/mol	9.89449 kcal/mol	178 212@LB@ \| \|@LB@5'-UCA...CAGUU G A GAA A GGUAA...UAA-3'@LB@ UUUGAU GGAG GGGU GGAAUG AGAGUGG@LB@ \|:\|\|\|\| :\|\|\| \|\|\|\| \|\|\|\|:: \|\|\|\|\|:\|@LB@ AGACUA UCUC CCCA CCUUGU UCUCAUC@LB@3'-UUU...GAACU ACC C GAAGA...AUA-5'@LB@ \| \|@LB@ 43 11@LB@@LB@@LB@Energy -14.27 kcal/mol@LB@Hybridization Energy -33.0113 kcal/mol@LB@Unfolding Energy - mRNA 8.84839 kcal/mol@LB@Unfolding Energy - sRNA 9.89449 kcal/mol@LB@@LB@Position - mRNA 179 -- 211@LB@Position - sRNA 12 -- 42@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 12 -- 18@LB@
181	0.0171	0.3152	bsu32040	yuiF	-15.17	0.027943	179 -- 194	29 -- 51	amino acid transporter YuiF	_____________178_____________________195\n_____________\|_______________________\|\n5'-ACA...CUAAA_______________________AUCAU...GGU-3'\n______________GGAUUUU_______UGGAGGGGU\n______________\|\|\|\|:\|\|_______\|:\|\|\|\|\|\|\|\n______________CCUAGAA_______AUCUCCCCA\n3'-UUU...AAAAG_______CUAGACU_________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	188 -- 194	29 -- 35	-21.3957 kcal/mol	5.25498 kcal/mol	0.974539 kcal/mol	178 195@LB@ \| \|@LB@5'-ACA...CUAAA AUCAU...GGU-3'@LB@ GGAUUUU UGGAGGGGU@LB@ \|\|\|\|:\|\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA AUCUCCCCA@LB@3'-UUU...AAAAG CUAGACU ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -21.3957 kcal/mol@LB@Unfolding Energy - mRNA 5.25498 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 179 -- 194@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 29 -- 35@LB@
33	0.001178	0.119	bsu14840	ylaN	-15.06	0.029338	181 -- 208	8 -- 28	depletion of this protein in Bacillus subtilis results in defects in cell morphology; crystal structure of Staphylococcus protein shows homodimer; ligand binding protein	_____________180__________________________209\n_____________\|____________________________\|\n5'-GAU...UCGCC______________AUACUUU_______AGAGA...AUA-3'\n______________UGGGGAACGGAGGG_______UGGCUUC\n______________\|\|\|\|\|\|\|\|:\|\|\|:\|_______\|:\|\|\|\|\|\n______________ACCCCUUGUCUCUC_______AUCGAAG\n3'-UUU...CCCCA____________________________AGAGAUA-5'\n_____________\|____________________________\|\n_____________29___________________________7\n	202 -- 208	8 -- 14	-32.8109 kcal/mol	11.1547 kcal/mol	6.59627 kcal/mol	180 209@LB@ \| \|@LB@5'-GAU...UCGCC AUACUUU AGAGA...AUA-3'@LB@ UGGGGAACGGAGGG UGGCUUC@LB@ \|\|\|\|\|\|\|\|:\|\|\|:\| \|:\|\|\|\|\|@LB@ ACCCCUUGUCUCUC AUCGAAG@LB@3'-UUU...CCCCA AGAGAUA-5'@LB@ \| \|@LB@ 29 7@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -32.8109 kcal/mol@LB@Unfolding Energy - mRNA 11.1547 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 181 -- 208@LB@Position - sRNA 8 -- 28@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@LB@
9	8.212e-05	0.03044	bsu07800	treP	-22.21	0.000470	182 -- 210	21 -- 52	PTS system-trehalose-specific transporter subunit EIIBC	_____________181____________________________________211\n_____________\|______________________________________\|\n5'-UUA...AAAAA_____AC__________________GGCAUG_______UGAAC...UUG-3'\n______________CGGAU___________GGAGGGGUU______GGGGAAC\n______________\|\|\|\|\|___________:\|\|\|\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GCCUA___________UCUCCCCAA______CCCCUUG\n3'-UUU...AAAAA_____GAACUAGACUA______________________UCUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________20\n	204 -- 210	21 -- 27	-29.9746 kcal/mol	4.99416 kcal/mol	2.77037 kcal/mol	181 211@LB@ \| \|@LB@5'-UUA...AAAAA AC GGCAUG UGAAC...UUG-3'@LB@ CGGAU GGAGGGGUU GGGGAAC@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCCUA UCUCCCCAA CCCCUUG@LB@3'-UUU...AAAAA GAACUAGACUA UCUCU...AUA-5'@LB@ \| \|@LB@ 53 20@LB@@LB@@LB@Energy -22.21 kcal/mol@LB@Hybridization Energy -29.9746 kcal/mol@LB@Unfolding Energy - mRNA 4.99416 kcal/mol@LB@Unfolding Energy - sRNA 2.77037 kcal/mol@LB@@LB@Position - mRNA 182 -- 210@LB@Position - sRNA 21 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 21 -- 27@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@
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@
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@

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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