Input and runtime details for job 4894743 (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 4894743 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:26 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:36:09 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 05:38:38 CET 2018
	Post-Processing Finished		@ Sat Feb 17 05:38:45 CET 2018
	Job Completed		@ Sat Feb 17 05:39:16 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4894743&toolName=CopraRNA ( 30 days expiry )

Description of the job

SR1

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
161	0.00741	0.1751	bsu24000	bmrU	-16.51	0.015967	115 -- 144	156 -- 183	lipid kinase BmrU		_____________114____________________________________145\n_____________\|______________________________________\|\n5'-GGA...AAUUA___________UC____AA_ACCUC_____________AUCUG...AUU-3'\n______________AAG_UCCAUGU__AAUG__G_____UC_CUUUUUCAUC\n______________\|\|\|_\|\|\|\|\|:\|__\|\|\|\|__\|_____\|\|_\|\|\|\|:\|\|\|\|\|\n______________UUC_AGGUAUA__UUAC__C_____AG_GAAAGAGUAG\n3'-AUU...CGUCG___A_____________AA________U__________AAGUU...CAA-5'\n_____________\|______________________________________\|\n_____________184____________________________________155\n	56 -- 62	102 -- 108	-19.6184 kcal/mol	4.38872 kcal/mol	6.78097 kcal/mol	114 145@LB@ \| \|@LB@5'-GGA...AAUUA UC AA ACCUC AUCUG...AUU-3'@LB@ AAG UCCAUGU AAUG G UC CUUUUUCAUC@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \| \|\| \|\|\|\|:\|\|\|\|\|@LB@ UUC AGGUAUA UUAC C AG GAAAGAGUAG@LB@3'-AUU...CGUCG A AA U AAGUU...CAA-5'@LB@ \| \|@LB@ 184 155@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -19.6184 kcal/mol@LB@Unfolding Energy - mRNA 4.38872 kcal/mol@LB@Unfolding Energy - sRNA 6.78097 kcal/mol@LB@@LB@Position - mRNA 115 -- 144@LB@Position - sRNA 156 -- 183@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 102 -- 108@LB@
181	0.008392	0.1751	bsu19600	yodH	-10.70	0.236480	130 -- 154	156 -- 183	methyltransferase		_____________129______________155\n_____________\|________________\|\n5'-AAC...CUUCU____________A___CUAUG...CCU-3'\n______________UUUGCUUUUCAU_AAC\n______________\|\|\|:\|\|:\|\|\|\|\|_\|\|\|\n______________AAAUGAGAAGUA_UUG\n3'-AUU...AAAAA____________G___UCCUG...CAA-5'\n_____________\|________________\|\n_____________184______________155\n	144 -- 150	160 -- 166	-13.2566 kcal/mol	3.14685 kcal/mol	1.41519 kcal/mol	129 155@LB@ \| \|@LB@5'-AAC...CUUCU A CUAUG...CCU-3'@LB@ UUUGCUUUUCAU AAC@LB@ \|\|\|:\|\|:\|\|\|\|\| \|\|\|@LB@ AAAUGAGAAGUA UUG@LB@3'-AUU...AAAAA G UCCUG...CAA-5'@LB@ \| \|@LB@ 184 155@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -13.2566 kcal/mol@LB@Unfolding Energy - mRNA 3.14685 kcal/mol@LB@Unfolding Energy - sRNA 1.41519 kcal/mol@LB@@LB@Position - mRNA 130 -- 154@LB@Position - sRNA 156 -- 183@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 160 -- 166@LB@
108	0.004583	0.1633	bsu07910	yfkF	-13.96	0.054522	60 -- 82	157 -- 179	MFS transporter		_____________59______________83\n_____________\|_______________\|\n5'-GGC...UUAUU_______________AAACC...CAA-3'\n______________UUUAUUCUUCA_CAA\n______________\|\|\|\|:\|\|\|\|\|\|_\|\|\|\n______________AAAUGAGAAGU_GUU\n3'-AUU...AAAAA___________A___GUCCU...CAA-5'\n_____________\|_______________\|\n_____________180_____________156\n	73 -- 79	161 -- 167	-12.117 kcal/mol	0.967911 kcal/mol	1.36352 kcal/mol	59 83@LB@ \| \|@LB@5'-GGC...UUAUU AAACC...CAA-3'@LB@ UUUAUUCUUCA CAA@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|@LB@ AAAUGAGAAGU GUU@LB@3'-AUU...AAAAA A GUCCU...CAA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -13.96 kcal/mol@LB@Hybridization Energy -12.117 kcal/mol@LB@Unfolding Energy - mRNA 0.967911 kcal/mol@LB@Unfolding Energy - sRNA 1.36352 kcal/mol@LB@@LB@Position - mRNA 60 -- 82@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 161 -- 167@LB@
194	0.008808	0.1751	bsu16370	fliR	-9.70	0.351361	227 -- 250	157 -- 179	flagellar biosynthetic protein FliR		_____________226____________________________________251\n_____________\|______________________________________\|\n5'-UAU...CGACA____AA____CAGG________U________UAU____AAAAU...UGC-3'\n______________ACUC___AUC____AACA_GAC_UUGGCGUU___UCCG\n______________\|\|\|\|___\|\|\|____\|\|\|\|_\|\|\|_\|\|\|:\|:\|\|___\|\|\|\|\n______________UGAG___UAG____UUGU_CUG_AACUGUAA___AGGC\n3'-AUU...AAAAA____AAG___________C___U________C______GUCGU...CAA-5'\n_____________\|______________________________________\|\n_____________180____________________________________156\n	69 -- 75	142 -- 148	-23.642 kcal/mol	8.17018 kcal/mol	7.49537 kcal/mol	226 251@LB@ \| \|@LB@5'-UAU...CGACA AA CAGG U UAU AAAAU...UGC-3'@LB@ ACUC AUC AACA GAC UUGGCGUU UCCG@LB@ \|\|\|\| \|\|\| \|\|\|\| \|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ UGAG UAG UUGU CUG AACUGUAA AGGC@LB@3'-AUU...AAAAA AAG C U C GUCGU...CAA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -23.642 kcal/mol@LB@Unfolding Energy - mRNA 8.17018 kcal/mol@LB@Unfolding Energy - sRNA 7.49537 kcal/mol@LB@@LB@Position - mRNA 227 -- 250@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 142 -- 148@LB@
154	0.00707	0.1751	bsu07830	yfkO	-12.90	0.089530	138 -- 152	158 -- 172	NAD(P)H nitroreductase YfkO		_____________137____________153\n_____________\|______________\|\n5'-GGA...GUACU______________UAAUG...AAU-3'\n______________UUUACUUUUUAUCA\n______________\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________AAAUGAGAAGUAGU\n3'-AUU...AAAAA______________UGUCC...CAA-5'\n_____________\|______________\|\n_____________173____________157\n	146 -- 152	158 -- 164	-13.59 kcal/mol	1.38023 kcal/mol	1.02713 kcal/mol	137 153@LB@ \| \|@LB@5'-GGA...GUACU UAAUG...AAU-3'@LB@ UUUACUUUUUAUCA@LB@ \|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ AAAUGAGAAGUAGU@LB@3'-AUU...AAAAA UGUCC...CAA-5'@LB@ \| \|@LB@ 173 157@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -13.59 kcal/mol@LB@Unfolding Energy - mRNA 1.38023 kcal/mol@LB@Unfolding Energy - sRNA 1.02713 kcal/mol@LB@@LB@Position - mRNA 138 -- 152@LB@Position - sRNA 158 -- 172@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 158 -- 164@LB@
171	0.007883	0.1751	bsu38330	lrgB	-10.47	0.260275	28 -- 48	159 -- 187	'Evidence 2a: Function of homologous gene experimentally demonstrated in an other organism; PubMedId: 15659658 15849754 16850406; Product type r : regulator'		_____________27____________49\n_____________\|_____________\|\n5'-GAG...CUGCU_____________CCGUC...UAU-3'\n______________UUUAUUUUUUAUC\n______________\|\|\|\|:\|:\|\|:\|\|\|\n______________AAAUGAGAAGUAG\n3'-AUU...AAAAA_____________UUGUC...CAA-5'\n_____________\|_____________\|\n_____________188___________158\n	42 -- 48	159 -- 165	-9.66314 kcal/mol	1.00478 kcal/mol	0.734181 kcal/mol	27 49@LB@ \| \|@LB@5'-GAG...CUGCU CCGUC...UAU-3'@LB@ UUUAUUUUUUAUC@LB@ \|\|\|\|:\|:\|\|:\|\|\|@LB@ AAAUGAGAAGUAG@LB@3'-AUU...AAAAA UUGUC...CAA-5'@LB@ \| \|@LB@ 188 158@LB@@LB@@LB@Energy -10.47 kcal/mol@LB@Hybridization Energy -9.66314 kcal/mol@LB@Unfolding Energy - mRNA 1.00478 kcal/mol@LB@Unfolding Energy - sRNA 0.734181 kcal/mol@LB@@LB@Position - mRNA 28 -- 48@LB@Position - sRNA 159 -- 187@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 159 -- 165@LB@
54	0.001793	0.1212	bsu21030	yonP	-11.11	0.198660	20 -- 36	161 -- 178	Evidence 5: No homology to any previously reported sequences		_____________19_______37\n_____________\|________\|\n5'-AAU...UUUAA________AUAUU...ACA-3'\n______________ACUCUUUA\n______________\|\|\|\|\|\|:\|\n______________UGAGAAGU\n3'-AUU...AAAAA________AGUUG...CAA-5'\n_____________\|________\|\n_____________179______160\n	30 -- 36	161 -- 167	-8.6372 kcal/mol	0.252156 kcal/mol	0.576912 kcal/mol	19 37@LB@ \| \|@LB@5'-AAU...UUUAA AUAUU...ACA-3'@LB@ ACUCUUUA@LB@ \|\|\|\|\|\|:\|@LB@ UGAGAAGU@LB@3'-AUU...AAAAA AGUUG...CAA-5'@LB@ \| \|@LB@ 179 160@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -8.6372 kcal/mol@LB@Unfolding Energy - mRNA 0.252156 kcal/mol@LB@Unfolding Energy - sRNA 0.576912 kcal/mol@LB@@LB@Position - mRNA 20 -- 36@LB@Position - sRNA 161 -- 178@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 161 -- 167@LB@
44	0.001404	0.1206	bsu30660	ytkA	-11.27	0.185588	215 -- 238	164 -- 186	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type lp: lipoprotein'		_____________214_________239\n_____________\|___________\|\n5'-CAU...GCGCU___________GCGUU...UUU-3'\n______________AAACGUUUAAU\n______________\|\|\|\|\|:\|\|\|\|\|\n______________UUUGCGAAUUA\n3'-AUU...AAACU___________AAGAA...CAA-5'\n_____________\|___________\|\n_____________187_________163\n	23 -- 29	11 -- 17	-8.86173 kcal/mol	2.03186 kcal/mol	2.83264 kcal/mol	214 239@LB@ \| \|@LB@5'-CAU...GCGCU GCGUU...UUU-3'@LB@ AAACGUUUAAU@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ UUUGCGAAUUA@LB@3'-AUU...AAACU AAGAA...CAA-5'@LB@ \| \|@LB@ 187 163@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -8.86173 kcal/mol@LB@Unfolding Energy - mRNA 2.03186 kcal/mol@LB@Unfolding Energy - sRNA 2.83264 kcal/mol@LB@@LB@Position - mRNA 215 -- 238@LB@Position - sRNA 164 -- 186@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 11 -- 17@LB@
22	0.0005922	0.1011	bsu09965	yhaJ	-9.39	0.394896	264 -- 275	174 -- 185	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16845009; Product type pf : factor'		_____________263___________276\n_____________\|_____________\|\n5'-ACU...AACCC___AU________UUGUU...CCU-3'\n______________CAU__UUCGCAGU\n______________\|\|\|__\|:\|\|\|\|\|:\n______________GUA__AGGCGUCG\n3'-AUU...UAACU___AC________UUCAA...CAA-5'\n_____________\|_____________\|\n_____________186___________173\n	68 -- 74	133 -- 139	-12.4018 kcal/mol	1.72698 kcal/mol	5.12932 kcal/mol	263 276@LB@ \| \|@LB@5'-ACU...AACCC AU UUGUU...CCU-3'@LB@ CAU UUCGCAGU@LB@ \|\|\| \|:\|\|\|\|\|:@LB@ GUA AGGCGUCG@LB@3'-AUU...UAACU AC UUCAA...CAA-5'@LB@ \| \|@LB@ 186 173@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.4018 kcal/mol@LB@Unfolding Energy - mRNA 1.72698 kcal/mol@LB@Unfolding Energy - sRNA 5.12932 kcal/mol@LB@@LB@Position - mRNA 264 -- 275@LB@Position - sRNA 174 -- 185@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 133 -- 139@LB@
109	0.004595	0.1633	bsu02700	estA	-7.85	0.646397	289 -- 295	181 -- 187	lipase EstA	bsu08350	_____________288_______296\n_____________\|_________\|\n5'-AUC...CUUAA_________AAAAA...AAC-3'\n______________AAUUUCUUU\n______________\|\|\|\|\|\|\|\|\|\n______________UUAAAGAAA\n3'-AUU...GCGAA_________ACAA-5'\n_____________\|_________\|\n_____________188_______180\n	109 -- 115	5 -- 11	-6.84044 kcal/mol	1.42932 kcal/mol	0.176622 kcal/mol	288 296@LB@ \| \|@LB@5'-AUC...CUUAA AAAAA...AAC-3'@LB@ AAUUUCUUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUAAAGAAA@LB@3'-AUU...GCGAA ACAA-5'@LB@ \| \|@LB@ 188 180@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -6.84044 kcal/mol@LB@Unfolding Energy - mRNA 1.42932 kcal/mol@LB@Unfolding Energy - sRNA 0.176622 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 181 -- 187@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 5 -- 11@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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