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
22	0.0004167	0.06318	bsu07570	yflS	-5.44	0.672400	163 -- 208	8 -- 27	malate transporter YflS		_____________162____________________________________________209\n_____________\|______________________________________________\|\n5'-AUG...GAAAA_____U____AAACAAGUAUAUAG___GAGACCUAUUUA_______AGAAA...CUC-3'\n______________GGGGA_CGGA______________GAG____________UGGCUUC\n______________\|\|\|\|\|_\|:\|\|______________\|\|\|____________\|:\|\|\|\|\|\n______________CCCCU_GUCU______________CUC____________AUCGAAG\n3'-UUU...CCCAA_____U________________________________________AGAGAUA-5'\n_____________\|______________________________________________\|\n_____________28_____________________________________________7\n	202 -- 208	8 -- 14	-21.2785 kcal/mol	9.2406 kcal/mol	6.59627 kcal/mol	162 209@LB@ \| \|@LB@5'-AUG...GAAAA U AAACAAGUAUAUAG GAGACCUAUUUA AGAAA...CUC-3'@LB@ GGGGA CGGA GAG UGGCUUC@LB@ \|\|\|\|\| \|:\|\| \|\|\| \|:\|\|\|\|\|@LB@ CCCCU GUCU CUC AUCGAAG@LB@3'-UUU...CCCAA U AGAGAUA-5'@LB@ \| \|@LB@ 28 7@LB@@LB@@LB@Energy -5.44 kcal/mol@LB@Hybridization Energy -21.2785 kcal/mol@LB@Unfolding Energy - mRNA 9.2406 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 163 -- 208@LB@Position - sRNA 8 -- 27@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@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@
135	0.01203	0.2883	bsu09920	yhaN	-10.31	0.192319	8 -- 29	28 -- 47	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16267290; Product type pe : enzyme'		_____________7______________________30\n_____________\|______________________\|\n____5'-AACAAAC_______CUUUUUUU__C____UAUUU...ACG-3'\n______________CUUGAUC________GG_GGUU\n______________\|\|\|\|\|\|\|________\|\|_\|\|\|\|\n______________GAACUAG________CC_CCAA\n3'-UUU...GCCUA_______ACUAUCU________CCCCU...AUA-5'\n_____________\|______________________\|\n_____________48_____________________27\n	8 -- 14	41 -- 47	-14.5368 kcal/mol	3.24797 kcal/mol	0.974663 kcal/mol	7 30@LB@ \| \|@LB@ 5'-AACAAAC CUUUUUUU C UAUUU...ACG-3'@LB@ CUUGAUC GG GGUU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GAACUAG CC CCAA@LB@3'-UUU...GCCUA ACUAUCU CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -14.5368 kcal/mol@LB@Unfolding Energy - mRNA 3.24797 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 8 -- 29@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 41 -- 47@LB@
186	0.01872	0.3269	bsu09880	yhaR	-10.74	0.166509	137 -- 152	16 -- 29	enoyl-CoA hydratase/isomerase YhaR		_____________136______________153\n_____________\|________________\|\n5'-CAG...UUUAU_______UG_______AUGUA...AAU-3'\n______________UUGGGGA__GCGGGGA\n______________\|\|\|\|\|\|\|__:\|:\|:\|\|\n______________AACCCCU__UGUCUCU\n3'-UUU...UCCCC________________CAUCG...AUA-5'\n_____________\|________________\|\n_____________30_______________15\n	146 -- 152	16 -- 22	-19.1675 kcal/mol	2.41685 kcal/mol	6.01276 kcal/mol	136 153@LB@ \| \|@LB@5'-CAG...UUUAU UG AUGUA...AAU-3'@LB@ UUGGGGA GCGGGGA@LB@ \|\|\|\|\|\|\| :\|:\|:\|\|@LB@ AACCCCU UGUCUCU@LB@3'-UUU...UCCCC CAUCG...AUA-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -19.1675 kcal/mol@LB@Unfolding Energy - mRNA 2.41685 kcal/mol@LB@Unfolding Energy - sRNA 6.01276 kcal/mol@LB@@LB@Position - mRNA 137 -- 152@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 16 -- 22@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@
188	0.01873	0.3269	bsu10750	yisK	-12.58	0.084103	165 -- 222	21 -- 51	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'		_____________164_________________________________________________________223\n_____________\|___________________________________________________________\|\n5'-UCC...AUGAA___GCAU________UAAAAGA_________AAUAACAUGAAAUUU_C_ACA_______UUUAC...UGU-3'\n______________GGA____UC_UGAUU_______UGAUGGAGG_______________G_G___GGGGAAC\n______________\|\|\|____\|\|_\|\|\|\|:_______\|\|\|\|:\|\|\|\|_______________\|_\|___\|\|\|\|\|\|\|\n______________CCU____AG_ACUAG_______ACUAUCUCC_______________C_C___CCCCUUG\n3'-UUU...AAAAG_________A_______________________________________AA________UCUCU...AUA-5'\n_____________\|___________________________________________________________\|\n_____________52__________________________________________________________20\n	216 -- 222	21 -- 27	-23.7404 kcal/mol	8.38838 kcal/mol	2.76846 kcal/mol	164 223@LB@ \| \|@LB@5'-UCC...AUGAA GCAU UAAAAGA AAUAACAUGAAAUUU C ACA UUUAC...UGU-3'@LB@ GGA UC UGAUU UGAUGGAGG G G GGGGAAC@LB@ \|\|\| \|\| \|\|\|\|: \|\|\|\|:\|\|\|\| \| \| \|\|\|\|\|\|\|@LB@ CCU AG ACUAG ACUAUCUCC C C CCCCUUG@LB@3'-UUU...AAAAG A AA UCUCU...AUA-5'@LB@ \| \|@LB@ 52 20@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -23.7404 kcal/mol@LB@Unfolding Energy - mRNA 8.38838 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 165 -- 222@LB@Position - sRNA 21 -- 51@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 21 -- 27@LB@
2	2.736e-07	0.0004564	bsu10760	yisL	-18.52	0.005045	172 -- 193	31 -- 51	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15849754 16850406; Product type pm: membrane component'		_____________171____________________194\n_____________\|______________________\|\n5'-UAC...AAGUG____AAUUU_____________AACAU...UCA-3'\n______________GGGU_____AUCUGAUAGGGGG\n______________\|\|:\|_____\|\|\|\|\|\|\|\|\|:\|\|\|\n______________CCUA_____UAGACUAUCUCCC\n3'-UUU...AAAAG____GAAC______________CAACC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________30\n	187 -- 193	31 -- 37	-25.2722 kcal/mol	5.77834 kcal/mol	0.970589 kcal/mol	171 194@LB@ \| \|@LB@5'-UAC...AAGUG AAUUU AACAU...UCA-3'@LB@ GGGU AUCUGAUAGGGGG@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ CCUA UAGACUAUCUCCC@LB@3'-UUU...AAAAG GAAC CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -18.52 kcal/mol@LB@Hybridization Energy -25.2722 kcal/mol@LB@Unfolding Energy - mRNA 5.77834 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
12	0.0001633	0.0454	bsu11410	yjbA	-19.25	0.003321	222 -- 243	30 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pf: factor'		_____________221_______________________244\n_____________\|_________________________\|\n5'-GAA...AUGUG______AA_________________AAGAA...UUG-3'\n______________UGGGUC__UUGGUUUGA___AGGGG\n______________:\|\|:\|\|__\|\|\|:\|:\|\|\|___\|\|\|\|\|\n______________GCCUAG__AACUAGACU___UCCCC\n3'-UUU...AAAAA_________________AUC_____AACCC...AUA-5'\n_____________\|_________________________\|\n_____________53________________________29\n	232 -- 238	38 -- 44	-23.9108 kcal/mol	3.6845 kcal/mol	0.979974 kcal/mol	221 244@LB@ \| \|@LB@5'-GAA...AUGUG AA AAGAA...UUG-3'@LB@ UGGGUC UUGGUUUGA AGGGG@LB@ :\|\|:\|\| \|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ GCCUAG AACUAGACU UCCCC@LB@3'-UUU...AAAAA AUC AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -23.9108 kcal/mol@LB@Unfolding Energy - mRNA 3.6845 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 222 -- 243@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 38 -- 44@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@

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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