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
111	0.009313	0.2778	bsu16780	rnjB	-13.26	0.064171	155 -- 177	29 -- 51	ribonuclease J 2		_____________154_____________________178\n_____________\|_______________________\|\n5'-GCA...UAAUA___ACAAGUGA_______C____AUGAG...UAU-3'\n______________GGA________UGAUGGA_GGGU\n______________\|\|\|________\|\|\|\|:\|\|_\|\|\|\|\n______________CCU________ACUAUCU_CCCA\n3'-UUU...AAAAG___AGAACUAG_______C____ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	166 -- 172	34 -- 40	-18.6769 kcal/mol	4.44629 kcal/mol	0.974539 kcal/mol	154 178@LB@ \| \|@LB@5'-GCA...UAAUA ACAAGUGA C AUGAG...UAU-3'@LB@ GGA UGAUGGA GGGU@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|@LB@ CCU ACUAUCU CCCA@LB@3'-UUU...AAAAG AGAACUAG C ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -18.6769 kcal/mol@LB@Unfolding Energy - mRNA 4.44629 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 155 -- 177@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 34 -- 40@LB@
112	0.009326	0.2778	bsu13200	rsbRB	-15.32	0.026068	265 -- 282	32 -- 51	RsbT co-antagonist protein RsbRB	bsu19450	_____________264__________________283\n_____________\|____________________\|\n5'-CUU...GGAAU_________AAC________AAAGU...CGC-3'\n______________GGAU__UGA___GAUGGAGG\n______________\|\|\|\|__\|\|\|___\|\|\|:\|\|\|\|\n______________CCUA__ACU___CUAUCUCC\n3'-UUU...AAAAG____GA___AGA________CCAAC...AUA-5'\n_____________\|____________________\|\n_____________52___________________31\n	276 -- 282	32 -- 38	-18.0013 kcal/mol	1.71479 kcal/mol	0.97021 kcal/mol	264 283@LB@ \| \|@LB@5'-CUU...GGAAU AAC AAAGU...CGC-3'@LB@ GGAU UGA GAUGGAGG@LB@ \|\|\|\| \|\|\| \|\|\|:\|\|\|\|@LB@ CCUA ACU CUAUCUCC@LB@3'-UUU...AAAAG GA AGA CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -15.32 kcal/mol@LB@Hybridization Energy -18.0013 kcal/mol@LB@Unfolding Energy - mRNA 1.71479 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 265 -- 282@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 32 -- 38@LB@
113	0.00948	0.2799	bsu31960	dhbF	-9.87	0.222399	16 -- 37	32 -- 53	dimodular nonribosomal peptide synthase		_____________15______________________38\n_____________\|_______________________\|\n5'-AGA...CUCGA___U__________C________AUCAU...CAG-3'\n______________UCG_GGUCUUGAUU_GGUA_AGG\n______________\|\|\|_\|:\|\|\|\|\|\|\|:_\|:\|\|_\|\|\|\n______________AGC_CUAGAACUAG_CUAU_UCC\n3'-UUU...AAAAA______________A____C___CCAAC...AUA-5'\n_____________\|_______________________\|\n_____________54______________________31\n	22 -- 28	42 -- 48	-21.9493 kcal/mol	11.0963 kcal/mol	0.981755 kcal/mol	15 38@LB@ \| \|@LB@5'-AGA...CUCGA U C AUCAU...CAG-3'@LB@ UCG GGUCUUGAUU GGUA AGG@LB@ \|\|\| \|:\|\|\|\|\|\|\|: \|:\|\| \|\|\|@LB@ AGC CUAGAACUAG CUAU UCC@LB@3'-UUU...AAAAA A C CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -21.9493 kcal/mol@LB@Unfolding Energy - mRNA 11.0963 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 16 -- 37@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 42 -- 48@LB@
114	0.009837	0.2871	bsu30580	ytmA	-11.73	0.116519	193 -- 212	33 -- 52	peptidase YtmA		_____________192____________________213\n_____________\|______________________\|\n5'-AGA...GGAGG___CU_________________AAAAG...UGG-3'\n______________CGG__GUUUUGAUU__GUAGAG\n______________\|\|\|__:\|:\|\|\|\|\|:__:\|\|\|\|\|\n______________GCC__UAGAACUAG__UAUCUC\n3'-UUU...AAAAA______________AC______CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	200 -- 206	41 -- 47	-17.5653 kcal/mol	4.85678 kcal/mol	0.976367 kcal/mol	192 213@LB@ \| \|@LB@5'-AGA...GGAGG CU AAAAG...UGG-3'@LB@ CGG GUUUUGAUU GUAGAG@LB@ \|\|\| :\|:\|\|\|\|\|: :\|\|\|\|\|@LB@ GCC UAGAACUAG UAUCUC@LB@3'-UUU...AAAAA AC CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.5653 kcal/mol@LB@Unfolding Energy - mRNA 4.85678 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@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@
116	0.01008	0.2881	bsu32800	yusH	-9.74	0.231897	187 -- 194	31 -- 38	glycine cleavage system H protein		_____________186______195\n_____________\|________\|\n5'-AUC...AAAAA________AUUCA...CCG-3'\n______________AUGGAGGG\n______________\|\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	188 -- 194	31 -- 37	-12.574 kcal/mol	2.17853 kcal/mol	0.65488 kcal/mol	186 195@LB@ \| \|@LB@5'-AUC...AAAAA AUUCA...CCG-3'@LB@ AUGGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.574 kcal/mol@LB@Unfolding Energy - mRNA 2.17853 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@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@
118	0.01022	0.2883	bsu19370	sucA	-9.59	0.243554	183 -- 190	23 -- 30	2-oxoglutarate dehydrogenase subunit E1		_____________182______191\n_____________\|________\|\n5'-UUU...UUUAA________UAAUA...AUC-3'\n______________GUUGGGGG\n______________\|\|\|\|\|\|\|:\n______________CAACCCCU\n3'-UUU...CUCCC________UGUCU...AUA-5'\n_____________\|________\|\n_____________31_______22\n	184 -- 190	23 -- 29	-13.0923 kcal/mol	3.48895 kcal/mol	0.018115 kcal/mol	182 191@LB@ \| \|@LB@5'-UUU...UUUAA UAAUA...AUC-3'@LB@ GUUGGGGG@LB@ \|\|\|\|\|\|\|:@LB@ CAACCCCU@LB@3'-UUU...CUCCC UGUCU...AUA-5'@LB@ \| \|@LB@ 31 22@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0923 kcal/mol@LB@Unfolding Energy - mRNA 3.48895 kcal/mol@LB@Unfolding Energy - sRNA 0.018115 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 23 -- 30@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 23 -- 29@LB@
119	0.01041	0.2883	bsu11480	yjbB	-12.30	0.094041	10 -- 19	22 -- 31	MFS transporter	bsu07460	_____________9__________20\n_____________\|__________\|\n5'-UCA...UUAAA__A_______ACGAU...GGA-3'\n______________GG_UGGGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________CC_ACCCCUU\n3'-UUU...UCUCC__A_______GUCUC...AUA-5'\n_____________\|__________\|\n_____________32_________21\n	13 -- 19	22 -- 28	-13.9571 kcal/mol	0.741777 kcal/mol	0.918006 kcal/mol	9 20@LB@ \| \|@LB@5'-UCA...UUAAA A ACGAU...GGA-3'@LB@ GG UGGGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ CC ACCCCUU@LB@3'-UUU...UCUCC A GUCUC...AUA-5'@LB@ \| \|@LB@ 32 21@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -13.9571 kcal/mol@LB@Unfolding Energy - mRNA 0.741777 kcal/mol@LB@Unfolding Energy - sRNA 0.918006 kcal/mol@LB@@LB@Position - mRNA 10 -- 19@LB@Position - sRNA 22 -- 31@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 22 -- 28@LB@
120	0.01063	0.2883	bsu25190	cccA	-10.44	0.184184	169 -- 199	18 -- 38	cytochrome c-550		_____________168_____________________________200\n_____________\|_______________________________\|\n5'-CCA...UUUAC________AAGGAUCAAAAAG______G___AAUGA...AGA-3'\n______________AUAGGGGG_____________GGGGAA_GGA\n______________\|\|\|\|:\|\|\|_____________\|\|\|\|\|\|_:\|\|\n______________UAUCUCCC_____________CCCCUU_UCU\n3'-UUU...UAGAC________CAA________________G___CUCAU...AUA-5'\n_____________\|_______________________________\|\n_____________39______________________________17\n	170 -- 176	31 -- 37	-23.3565 kcal/mol	5.07512 kcal/mol	7.8385 kcal/mol	168 200@LB@ \| \|@LB@5'-CCA...UUUAC AAGGAUCAAAAAG G AAUGA...AGA-3'@LB@ AUAGGGGG GGGGAA GGA@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\| :\|\|@LB@ UAUCUCCC CCCCUU UCU@LB@3'-UUU...UAGAC CAA G CUCAU...AUA-5'@LB@ \| \|@LB@ 39 17@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -23.3565 kcal/mol@LB@Unfolding Energy - mRNA 5.07512 kcal/mol@LB@Unfolding Energy - sRNA 7.8385 kcal/mol@LB@@LB@Position - mRNA 169 -- 199@LB@Position - sRNA 18 -- 38@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 31 -- 37@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)

Job resubmission

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service.

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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