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
104	0.004338	0.1606	bsu08000	yfjQ	-9.77	0.342120	136 -- 162	103 -- 137	metal ion transporter YfjQ	bsu24740	_____________135_______________163\n_____________\|_________________\|\n5'-CAU...AUUAG____A____A_______CUUUU...AUU-3'\n______________GCAG_GAGU_CCGUAUA\n______________\|\|\|\|_:\|\|\|_\|\|:\|\|\|\|\n______________CGUC_UUCA_GGUAUAU\n3'-AUU...ACAGG____G____A_______UACAA...CAA-5'\n_____________\|_________________\|\n_____________138_______________102\n	146 -- 152	121 -- 127	-16.4629 kcal/mol	4.99509 kcal/mol	3.33887 kcal/mol	135 163@LB@ \| \|@LB@5'-CAU...AUUAG A A CUUUU...AUU-3'@LB@ GCAG GAGU CCGUAUA@LB@ \|\|\|\| :\|\|\| \|\|:\|\|\|\|@LB@ CGUC UUCA GGUAUAU@LB@3'-AUU...ACAGG G A UACAA...CAA-5'@LB@ \| \|@LB@ 138 102@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -16.4629 kcal/mol@LB@Unfolding Energy - mRNA 4.99509 kcal/mol@LB@Unfolding Energy - sRNA 3.33887 kcal/mol@LB@@LB@Position - mRNA 136 -- 162@LB@Position - sRNA 103 -- 137@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 121 -- 127@LB@
25	0.0006626	0.1027	bsu07955	yfkA	-14.87	0.035327	3 -- 70	36 -- 108	radical SAM protein YfkA		_____________2______________71\n_____________\|______________\|\n5'-AGU...GCUAC______________AAUCA...ACG-3'\n______________UUGCGAUCUUGGCA\n______________\|\|\|\|:\|\|\|\|\|\|\|\|\|\n______________AACGUUAGAACCGU\n3'-AUU...GAAGC______________UUGUU...CAA-5'\n_____________\|______________\|\n_____________109____________35\n	130 -- 136	66 -- 72	-22.3996 kcal/mol	5.8798 kcal/mol	4.6863 kcal/mol	2 71@LB@ \| \|@LB@5'-AGU...GCUAC AAUCA...ACG-3'@LB@ UUGCGAUCUUGGCA@LB@ \|\|\|\|:\|\|\|\|\|\|\|\|\|@LB@ AACGUUAGAACCGU@LB@3'-AUU...GAAGC UUGUU...CAA-5'@LB@ \| \|@LB@ 109 35@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -22.3996 kcal/mol@LB@Unfolding Energy - mRNA 5.8798 kcal/mol@LB@Unfolding Energy - sRNA 4.6863 kcal/mol@LB@@LB@Position - mRNA 3 -- 70@LB@Position - sRNA 36 -- 108@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 66 -- 72@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@
76	0.002466	0.1257	bsu07870	yfkK	-15.12	0.031390	12 -- 33	33 -- 55	Evidence 4: Homologs of previously reported genes of unknown function		_____________11______________________34\n_____________\|_______________________\|\n5'-UGU...ACCUC__________UGC__________CUAAA...UCA-3'\n______________CCUA_UUCUU___CCCUAUUUCU\n______________\|\|:\|_:\|\|\|\|___\|\|\|:\|\|\|\|\|\|\n______________GGGU_GAGAA___GGGGUAAAGA\n3'-AUU...AGCAU____A_____UAA__________AACUU...CAA-5'\n_____________\|_______________________\|\n_____________56______________________32\n	27 -- 33	33 -- 39	-21.8682 kcal/mol	0.689294 kcal/mol	9.04338 kcal/mol	11 34@LB@ \| \|@LB@5'-UGU...ACCUC UGC CUAAA...UCA-3'@LB@ CCUA UUCUU CCCUAUUUCU@LB@ \|\|:\| :\|\|\|\| \|\|\|:\|\|\|\|\|\|@LB@ GGGU GAGAA GGGGUAAAGA@LB@3'-AUU...AGCAU A UAA AACUU...CAA-5'@LB@ \| \|@LB@ 56 32@LB@@LB@@LB@Energy -15.12 kcal/mol@LB@Hybridization Energy -21.8682 kcal/mol@LB@Unfolding Energy - mRNA 0.689294 kcal/mol@LB@Unfolding Energy - sRNA 9.04338 kcal/mol@LB@@LB@Position - mRNA 12 -- 33@LB@Position - sRNA 33 -- 55@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 33 -- 39@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@
115	0.005245	0.1741	bsu07690	yflG	-14.30	0.046489	29 -- 56	32 -- 57	methionine aminopeptidase 2		_____________28___________________________57\n_____________\|____________________________\|\n5'-UUC...AAGCA________CCC__C__A____U______CAAAU...GCA-3'\n______________UACCCAUC___CU_AU_CCCU_UUUUUU\n______________\|\|\|\|\|\|\|\|___\|\|_\|\|_\|\|\|:_\|\|\|:\|\|\n______________AUGGGUAG___GA_UA_GGGG_AAAGAA\n3'-AUU...UUAGC________A____A__A____U______ACUUU...CAA-5'\n_____________\|____________________________\|\n_____________58___________________________31\n	30 -- 36	50 -- 56	-21.2542 kcal/mol	0.575621 kcal/mol	9.1585 kcal/mol	28 57@LB@ \| \|@LB@5'-UUC...AAGCA CCC C A U CAAAU...GCA-3'@LB@ UACCCAUC CU AU CCCU UUUUUU@LB@ \|\|\|\|\|\|\|\| \|\| \|\| \|\|\|: \|\|\|:\|\|@LB@ AUGGGUAG GA UA GGGG AAAGAA@LB@3'-AUU...UUAGC A A A U ACUUU...CAA-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -21.2542 kcal/mol@LB@Unfolding Energy - mRNA 0.575621 kcal/mol@LB@Unfolding Energy - sRNA 9.1585 kcal/mol@LB@@LB@Position - mRNA 29 -- 56@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 50 -- 56@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@
110	0.004746	0.1671	bsu09940	yhaL	-13.90	0.056226	141 -- 159	37 -- 56	sporulation protein YhaL		_____________140______________________________________160\n_____________\|________________________________________\|\n5'-GAA...UUUUU____________GUA___U____U___A_GCA________AGCGC...ACC-3'\n______________UCCGUGGUGGGU___UCU_UGUA_UGU_G___UCAUUUUC\n______________\|\|\|\|::\|:::\|\|___\|\|:_\|:\|\|_\|\|\|_\|___\|\|\|:\|\|\|\|\n______________AGGCGUCGUUCA___AGG_AUAU_ACA_C___AGUGAAAG\n3'-AUU...GUAAC__________________U____U___A____________AGUAG...CAA-5'\n_____________\|________________________________________\|\n_____________57_______________________________________36\n	245 -- 251	107 -- 113	-27.9954 kcal/mol	7.44184 kcal/mol	9.97721 kcal/mol	140 160@LB@ \| \|@LB@5'-GAA...UUUUU GUA U U A GCA AGCGC...ACC-3'@LB@ UCCGUGGUGGGU UCU UGUA UGU G UCAUUUUC@LB@ \|\|\|\|::\|:::\|\| \|\|: \|:\|\| \|\|\| \| \|\|\|:\|\|\|\|@LB@ AGGCGUCGUUCA AGG AUAU ACA C AGUGAAAG@LB@3'-AUU...GUAAC U U A AGUAG...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -27.9954 kcal/mol@LB@Unfolding Energy - mRNA 7.44184 kcal/mol@LB@Unfolding Energy - sRNA 9.97721 kcal/mol@LB@@LB@Position - mRNA 141 -- 159@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 107 -- 113@LB@
74	0.002384	0.1242	bsu09450	yhdF	-14.81	0.036487	208 -- 244	132 -- 159	oxidoreductase		_____________207____________________________________245\n_____________\|______________________________________\|\n5'-UCC...GAACC__________GACAAACAGAAG____AGAA________UCAGG...AGG-3'\n______________CAAU_GGACA____________GACA____CCGCAGCA\n______________\|\|\|:_\|\|\|\|\|____________\|\|\|\|____\|\|\|\|\|\|\|\|\n______________GUUG_CCUGU____________CUGU____GGCGUCGU\n3'-AUU...AAGUA____U_____AA______________AACA________UCAAG...CAA-5'\n_____________\|______________________________________\|\n_____________160____________________________________131\n	238 -- 244	132 -- 138	-26.7883 kcal/mol	3.14586 kcal/mol	9.22644 kcal/mol	207 245@LB@ \| \|@LB@5'-UCC...GAACC GACAAACAGAAG AGAA UCAGG...AGG-3'@LB@ CAAU GGACA GACA CCGCAGCA@LB@ \|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUG CCUGU CUGU GGCGUCGU@LB@3'-AUU...AAGUA U AA AACA UCAAG...CAA-5'@LB@ \| \|@LB@ 160 131@LB@@LB@@LB@Energy -14.81 kcal/mol@LB@Hybridization Energy -26.7883 kcal/mol@LB@Unfolding Energy - mRNA 3.14586 kcal/mol@LB@Unfolding Energy - sRNA 9.22644 kcal/mol@LB@@LB@Position - mRNA 208 -- 244@LB@Position - sRNA 132 -- 159@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 132 -- 138@LB@
152	0.006831	0.1741	bsu09480	yhdI	-9.89	0.327778	76 -- 101	102 -- 130	GntR family transcriptional regulator	bsu05240	_____________75__________________________102\n_____________\|___________________________\|\n5'-UCU...UAAUU___________A________C______AUCCC...CAA-3'\n______________GUUUCAUAUGG_____UCAU_UUCUCA\n______________\|\|\|:\|\|\|\|\|::_____\|\|\|:_\|\|\|\|\|\|\n______________CAAGGUAUAUU_____AGUG_AAGAGU\n3'-AUU...UCGUU___________ACAAC____A______AGAAG...CAA-5'\n_____________\|___________________________\|\n_____________131_________________________101\n	79 -- 85	121 -- 127	-18.1477 kcal/mol	2.87073 kcal/mol	6.25825 kcal/mol	75 102@LB@ \| \|@LB@5'-UCU...UAAUU A C AUCCC...CAA-3'@LB@ GUUUCAUAUGG UCAU UUCUCA@LB@ \|\|\|:\|\|\|\|\|:: \|\|\|: \|\|\|\|\|\|@LB@ CAAGGUAUAUU AGUG AAGAGU@LB@3'-AUU...UCGUU ACAAC A AGAAG...CAA-5'@LB@ \| \|@LB@ 131 101@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -18.1477 kcal/mol@LB@Unfolding Energy - mRNA 2.87073 kcal/mol@LB@Unfolding Energy - sRNA 6.25825 kcal/mol@LB@@LB@Position - mRNA 76 -- 101@LB@Position - sRNA 102 -- 130@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 121 -- 127@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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