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
169	0.01639	0.3152	bsu07850	yfkM	-11.33	0.135062	186 -- 208	22 -- 34	general stress protein 18	_____________185_____________________209\n_____________\|_______________________\|\n5'-UGU...AAAGC___A___UAUGAAUCA_______AAAAA...CUG-3'\n______________GGG_GGU_________UGGGGAA\n______________:\|\|_\|\|\|_________\|\|\|\|\|\|\|\n______________UCC_CCA_________ACCCCUU\n3'-UUU...CUAUC_______________________GUCUC...AUA-5'\n_____________\|_______________________\|\n_____________35______________________21\n	202 -- 208	22 -- 28	-15.0114 kcal/mol	2.66027 kcal/mol	1.02154 kcal/mol	185 209@LB@ \| \|@LB@5'-UGU...AAAGC A UAUGAAUCA AAAAA...CUG-3'@LB@ GGG GGU UGGGGAA@LB@ :\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCC CCA ACCCCUU@LB@3'-UUU...CUAUC GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -15.0114 kcal/mol@LB@Unfolding Energy - mRNA 2.66027 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
109	0.009307	0.2778	bsu07880	yfkJ	-15.70	0.021808	288 -- 299	30 -- 51	low molecular weight protein-tyrosine-phosphatase YfkJ	_____________287____________________300\n_____________\|______________________\|\n5'-GGU...AAAAA______________________A-3'\n______________GGAU__________UAGAGGGG\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\n______________CCUA__________AUCUCCCC\n3'-UUU...AAAAG____GAACUAGACU________AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	293 -- 299	30 -- 36	-17.0834 kcal/mol	0.412933 kcal/mol	0.974282 kcal/mol	287 300@LB@ \| \|@LB@5'-GGU...AAAAA A-3'@LB@ GGAU UAGAGGGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCUA AUCUCCCC@LB@3'-UUU...AAAAG GAACUAGACU AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -17.0834 kcal/mol@LB@Unfolding Energy - mRNA 0.412933 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 288 -- 299@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 30 -- 36@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@
179	0.01703	0.3152	bsu08425	mprF	-11.09	0.146985	133 -- 167	22 -- 52	phosphatidylglycerol lysyltransferase	_____________132__________________________________168\n_____________\|____________________________________\|\n5'-ACU...AAUAA___UAG___UAUAA___GU_____AUUA________GAGGA...AUC-3'\n______________CGG____UG_____UGA__UGGAG____UUGGGGGA\n______________\|\|\|____\|\|_____\|\|\|__\|:\|\|\|____\|\|\|\|\|\|:\|\n______________GCC____AC_____ACU__AUCUC____AACCCCUU\n3'-UUU...AAAAA___UAGA__UAG____________CCC_________GUCUC...AUA-5'\n_____________\|____________________________________\|\n_____________53___________________________________21\n	161 -- 167	22 -- 28	-20.3953 kcal/mol	7.42087 kcal/mol	1.8808 kcal/mol	132 168@LB@ \| \|@LB@5'-ACU...AAUAA UAG UAUAA GU AUUA GAGGA...AUC-3'@LB@ CGG UG UGA UGGAG UUGGGGGA@LB@ \|\|\| \|\| \|\|\| \|:\|\|\| \|\|\|\|\|\|:\|@LB@ GCC AC ACU AUCUC AACCCCUU@LB@3'-UUU...AAAAA UAGA UAG CCC GUCUC...AUA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -20.3953 kcal/mol@LB@Unfolding Energy - mRNA 7.42087 kcal/mol@LB@Unfolding Energy - sRNA 1.8808 kcal/mol@LB@@LB@Position - mRNA 133 -- 167@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 22 -- 28@LB@
183	0.01776	0.3237	bsu08550	sspK	-13.38	0.060997	172 -- 193	31 -- 48	small acid-soluble spore protein K	_____________171____________________194\n_____________\|______________________\|\n5'-UUU...CAACU_________C__ACC_______AUAUG...ACG-3'\n______________UUUUGAUCU_GA___UAGGGGG\n______________\|:\|\|\|\|\|\|\|_\|\|___\|\|\|:\|\|\|\n______________AGAACUAGA_CU___AUCUCCC\n3'-UUU...AGCCU______________________CAACC...AUA-5'\n_____________\|______________________\|\n_____________49_____________________30\n	187 -- 193	31 -- 37	-20.1262 kcal/mol	5.7766 kcal/mol	0.970395 kcal/mol	171 194@LB@ \| \|@LB@5'-UUU...CAACU C ACC AUAUG...ACG-3'@LB@ UUUUGAUCU GA UAGGGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ AGAACUAGA CU AUCUCCC@LB@3'-UUU...AGCCU CAACC...AUA-5'@LB@ \| \|@LB@ 49 30@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -20.1262 kcal/mol@LB@Unfolding Energy - mRNA 5.7766 kcal/mol@LB@Unfolding Energy - sRNA 0.970395 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 31 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
17	0.0003284	0.06216	bsu08690	ygaD	-15.59	0.022949	198 -- 218	30 -- 49	ABC transporter ATP-binding protein	_____________197___________________219\n_____________\|_____________________\|\n5'-UGA...CACAC___A____AAA__G_______GAAUC...UCG-3'\n______________AUC_UGAU___GA_AGAGGGG\n______________\|\|\|_\|\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________UAG_ACUA___CU_UCUCCCC\n3'-UUU...AAGCC___A____GA___A_______AACCC...AUA-5'\n_____________\|_____________________\|\n_____________50____________________29\n	212 -- 218	30 -- 36	-19.3788 kcal/mol	2.8161 kcal/mol	0.974265 kcal/mol	197 219@LB@ \| \|@LB@5'-UGA...CACAC A AAA G GAAUC...UCG-3'@LB@ AUC UGAU GA AGAGGGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UAG ACUA CU UCUCCCC@LB@3'-UUU...AAGCC A GA A AACCC...AUA-5'@LB@ \| \|@LB@ 50 29@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -19.3788 kcal/mol@LB@Unfolding Energy - mRNA 2.8161 kcal/mol@LB@Unfolding Energy - sRNA 0.974265 kcal/mol@LB@@LB@Position - mRNA 198 -- 218@LB@Position - sRNA 30 -- 49@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 30 -- 36@LB@
30	0.001001	0.1113	bsu08780	ygaJ	-16.90	0.012052	218 -- 231	24 -- 39	peptidase YgaJ	_____________217______________232\n_____________\|________________\|\n5'-UGU...AUUGC_________C______GUUUU...AGC-3'\n______________GAUGGGGGG___GGGG\n______________\|\|\|:\|:\|\|\|___\|\|\|\|\n______________CUAUCUCCC___CCCC\n3'-UUU...CUAGA_________CAA____UUGUC...AUA-5'\n_____________\|________________\|\n_____________40_______________23\n	220 -- 226	31 -- 37	-22.0746 kcal/mol	4.38344 kcal/mol	0.790436 kcal/mol	217 232@LB@ \| \|@LB@5'-UGU...AUUGC C GUUUU...AGC-3'@LB@ GAUGGGGGG GGGG@LB@ \|\|\|:\|:\|\|\| \|\|\|\|@LB@ CUAUCUCCC CCCC@LB@3'-UUU...CUAGA CAA UUGUC...AUA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -22.0746 kcal/mol@LB@Unfolding Energy - mRNA 4.38344 kcal/mol@LB@Unfolding Energy - sRNA 0.790436 kcal/mol@LB@@LB@Position - mRNA 218 -- 231@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 31 -- 37@LB@
176	0.01673	0.3152	bsu08790	thiC	-9.56	0.245346	273 -- 280	31 -- 38	phosphomethylpyrimidine synthase	_____________272______281\n_____________\|________\|\n5'-GGC...UAUAC________UUCUU...AAG-3'\n______________GUGGAGGG\n______________:\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	274 -- 280	31 -- 37	-12.4867 kcal/mol	2.26991 kcal/mol	0.65488 kcal/mol	272 281@LB@ \| \|@LB@5'-GGC...UAUAC UUCUU...AAG-3'@LB@ GUGGAGGG@LB@ :\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -12.4867 kcal/mol@LB@Unfolding Energy - mRNA 2.26991 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 273 -- 280@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 31 -- 37@LB@
198	0.0197	0.3269	bsu08980	yhbH	-11.85	0.111658	189 -- 195	30 -- 36	stress response UPF0229 protein YhbH	_____________188_____196\n_____________\|_______\|\n5'-GGC...GUUAA_______AAUUC...UGC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	189 -- 195	30 -- 36	-13.8096 kcal/mol	1.82966 kcal/mol	0.133643 kcal/mol	188 196@LB@ \| \|@LB@5'-GGC...GUUAA AAUUC...UGC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -13.8096 kcal/mol@LB@Unfolding Energy - mRNA 1.82966 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
178	0.01684	0.3152	bsu09460	ctrA	-17.20	0.010320	182 -- 213	20 -- 50	amino acid permease	_____________181_________________________________214\n_____________\|___________________________________\|\n5'-CAA...UAGAU____GG__G____________AA__AAA_______UUUUU...UAA-3'\n______________GAUC__GA_UUGA___AGGGG__UG___GGGAGCG\n______________\|\|\|\|__\|\|_:\|\|\|___\|\|\|\|\|__\|\|___\|\|\|\|:\|:\n______________CUAG__CU_GACU___UCCCC__AC___CCCUUGU\n3'-UUU...AAAGC____AA__A____AUC_____A_____________CUCUC...AUA-5'\n_____________\|___________________________________\|\n_____________51__________________________________19\n	207 -- 213	20 -- 26	-25.5851 kcal/mol	4.15406 kcal/mol	4.22897 kcal/mol	181 214@LB@ \| \|@LB@5'-CAA...UAGAU GG G AA AAA UUUUU...UAA-3'@LB@ GAUC GA UUGA AGGGG UG GGGAGCG@LB@ \|\|\|\| \|\| :\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:@LB@ CUAG CU GACU UCCCC AC CCCUUGU@LB@3'-UUU...AAAGC AA A AUC A CUCUC...AUA-5'@LB@ \| \|@LB@ 51 19@LB@@LB@@LB@Energy -17.20 kcal/mol@LB@Hybridization Energy -25.5851 kcal/mol@LB@Unfolding Energy - mRNA 4.15406 kcal/mol@LB@Unfolding Energy - sRNA 4.22897 kcal/mol@LB@@LB@Position - mRNA 182 -- 213@LB@Position - sRNA 20 -- 50@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 20 -- 26@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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