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
36	0.001118	0.1204	bsu17650	yncE	-8.56	0.524973	291 -- 300	61 -- 70	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type h: extrachromosomal origin'	_____________290_______300\n_____________\|_________\|\n5'-GUA...AUAGG__________-3'\n______________UGGCAAACGA\n______________\|\|\|\|\|\|\|\|:\|\n______________ACCGUUUGUU\n3'-AUU...UUAGA__________AGCAU...CAA-5'\n_____________\|__________\|\n_____________71_________60\n	294 -- 300	61 -- 67	-13.5985 kcal/mol	0.387687 kcal/mol	4.67716 kcal/mol	290 300@LB@ \| \|@LB@5'-GUA...AUAGG -3'@LB@ UGGCAAACGA@LB@ \|\|\|\|\|\|\|\|:\|@LB@ ACCGUUUGUU@LB@3'-AUU...UUAGA AGCAU...CAA-5'@LB@ \| \|@LB@ 71 60@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -13.5985 kcal/mol@LB@Unfolding Energy - mRNA 0.387687 kcal/mol@LB@Unfolding Energy - sRNA 4.67716 kcal/mol@LB@@LB@Position - mRNA 291 -- 300@LB@Position - sRNA 61 -- 70@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 61 -- 67@LB@
150	0.006829	0.1741	bsu17970	cotM	-16.22	0.018442	252 -- 285	70 -- 101	spore coat protein M	_____________251______________________286\n_____________\|________________________\|\n5'-AUG...GUAUG________________________UUGAA...UCG-3'\n______________GAUGAAUGGCUUCG__GCAAUUUU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UUACUUACCGAAGC__CGUUAGAA\n3'-AUU...UUUCA______________AA________CCGUU...CAA-5'\n_____________\|________________________\|\n_____________102______________________69\n	278 -- 284	71 -- 77	-28.716 kcal/mol	7.78723 kcal/mol	6.67697 kcal/mol	251 286@LB@ \| \|@LB@5'-AUG...GUAUG UUGAA...UCG-3'@LB@ GAUGAAUGGCUUCG GCAAUUUU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UUACUUACCGAAGC CGUUAGAA@LB@3'-AUU...UUUCA AA CCGUU...CAA-5'@LB@ \| \|@LB@ 102 69@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -28.716 kcal/mol@LB@Unfolding Energy - mRNA 7.78723 kcal/mol@LB@Unfolding Energy - sRNA 6.67697 kcal/mol@LB@@LB@Position - mRNA 252 -- 285@LB@Position - sRNA 70 -- 101@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 71 -- 77@LB@
61	0.001915	0.1214	bsu19720	yodR	-8.11	0.600668	13 -- 29	71 -- 89	coenzyme A transferase subunit beta	_____________12___________30\n_____________\|____________\|\n5'-GCU...GAAGA____A_______ACCGG...CCU-3'\n______________AAUG_UUGUCAC\n______________\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAC_AACAGUG\n3'-AUU...GUAUA____________AAAGA...CAA-5'\n_____________\|____________\|\n_____________90___________70\n	143 -- 149	111 -- 117	-12.213 kcal/mol	1.50216 kcal/mol	3.63424 kcal/mol	12 30@LB@ \| \|@LB@5'-GCU...GAAGA A ACCGG...CCU-3'@LB@ AAUG UUGUCAC@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ UUAC AACAGUG@LB@3'-AUU...GUAUA AAAGA...CAA-5'@LB@ \| \|@LB@ 90 70@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -12.213 kcal/mol@LB@Unfolding Energy - mRNA 1.50216 kcal/mol@LB@Unfolding Energy - sRNA 3.63424 kcal/mol@LB@@LB@Position - mRNA 13 -- 29@LB@Position - sRNA 71 -- 89@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 111 -- 117@LB@
118	0.005364	0.1741	bsu21980	ypdP	-14.81	0.036422	190 -- 236	72 -- 112	'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'	_____________189_______________________________________________237\n_____________\|_________________________________________________\|\n5'-AAC...AGGAA_____________GUUUAAUAAUUC__UU___________U________AUUCA...GGA-3'\n______________GCUUUUUCAUCUU____________GU__UGGAU__CUUU_UUGCGAUC\n______________:\|\|\|\|:\|\|\|\|\|\|\|____________\|\|__\|\|:\|\|__\|\|\|:_\|\|\|\|:\|\|\|\n______________UGAAAGAGUAGAA____________CA__ACUUA__GAAG_AACGUUAG\n3'-AUU...AACAG_____________GUUU__________UU_____CC____C________AACCG...CAA-5'\n_____________\|_________________________________________________\|\n_____________113_______________________________________________71\n	230 -- 236	72 -- 78	-29.9578 kcal/mol	5.88063 kcal/mol	12.3236 kcal/mol	189 237@LB@ \| \|@LB@5'-AAC...AGGAA GUUUAAUAAUUC UU U AUUCA...GGA-3'@LB@ GCUUUUUCAUCUU GU UGGAU CUUU UUGCGAUC@LB@ :\|\|\|\|:\|\|\|\|\|\|\| \|\| \|\|:\|\| \|\|\|: \|\|\|\|:\|\|\|@LB@ UGAAAGAGUAGAA CA ACUUA GAAG AACGUUAG@LB@3'-AUU...AACAG GUUU UU CC C AACCG...CAA-5'@LB@ \| \|@LB@ 113 71@LB@@LB@@LB@Energy -14.81 kcal/mol@LB@Hybridization Energy -29.9578 kcal/mol@LB@Unfolding Energy - mRNA 5.88063 kcal/mol@LB@Unfolding Energy - sRNA 12.3236 kcal/mol@LB@@LB@Position - mRNA 190 -- 236@LB@Position - sRNA 72 -- 112@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 72 -- 78@LB@
89	0.003315	0.1443	bsu30460	ytrA	-11.86	0.143485	75 -- 137	74 -- 137	GntR family transcriptional regulator	_____________74__________________________________________________________________138\n_____________\|___________________________________________________________________\|\n5'-UUU...UGAUU_______________AUCGC_____CU_______U_G___UU________UC_______AAUG____AAAAG...AUA-3'\n______________GCGGCA___UCUGUG_____UUGUU__UUUUUUC_U_UUC___GUGAUGA__GGUUUUG____GCAA\n______________\|\|:\|\|\|___\|\|::\|:_____\|\|\|\|:__:\|\|\|:\|\|_\|_\|\|\|___\|\|:\|\|\|\|__\|\|:\|\|:\|____\|\|\|\|\n______________CGUCGU___AGGUAU_____AACAG__GAAAGAG_A_AAG___CAUUACU__CCGAAGC____CGUU\n3'-AUU...ACAGG______UCA______AUUAC_____U________U_G___UUU_______UA_______AA______AGAAC...CAA-5'\n_____________\|___________________________________________________________________\|\n_____________138_________________________________________________________________73\n	123 -- 129	80 -- 86	-41.3024 kcal/mol	16.5538 kcal/mol	14.8582 kcal/mol	74 138@LB@ \| \|@LB@5'-UUU...UGAUU AUCGC CU U G UU UC AAUG AAAAG...AUA-3'@LB@ GCGGCA UCUGUG UUGUU UUUUUUC U UUC GUGAUGA GGUUUUG GCAA@LB@ \|\|:\|\|\| \|\|::\|: \|\|\|\|: :\|\|\|:\|\| \| \|\|\| \|\|:\|\|\|\| \|\|:\|\|:\| \|\|\|\|@LB@ CGUCGU AGGUAU AACAG GAAAGAG A AAG CAUUACU CCGAAGC CGUU@LB@3'-AUU...ACAGG UCA AUUAC U U G UUU UA AA AGAAC...CAA-5'@LB@ \| \|@LB@ 138 73@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -41.3024 kcal/mol@LB@Unfolding Energy - mRNA 16.5538 kcal/mol@LB@Unfolding Energy - sRNA 14.8582 kcal/mol@LB@@LB@Position - mRNA 75 -- 137@LB@Position - sRNA 74 -- 137@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 80 -- 86@LB@
133	0.006226	0.1741	bsu14430	ykpA	-10.78	0.228396	48 -- 105	75 -- 129	ABC transporter ATP-binding protein	_____________47____________106\n_____________\|_____________\|\n5'-GUA...AAGUU_____________AAUAU...UUG-3'\n______________AUUUGAAGAUGUU\n______________\|\|\|\|\|\|\|:\|:\|:\|\n______________UAAACUUUUGCGA\n3'-AUU...AACUU_____________AUUAA...CAA-5'\n_____________\|_____________\|\n_____________130___________74\n	254 -- 260	15 -- 21	-11.9489 kcal/mol	0.844332 kcal/mol	3.96844 kcal/mol	47 106@LB@ \| \|@LB@5'-GUA...AAGUU AAUAU...UUG-3'@LB@ AUUUGAAGAUGUU@LB@ \|\|\|\|\|\|\|:\|:\|:\|@LB@ UAAACUUUUGCGA@LB@3'-AUU...AACUU AUUAA...CAA-5'@LB@ \| \|@LB@ 130 74@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -11.9489 kcal/mol@LB@Unfolding Energy - mRNA 0.844332 kcal/mol@LB@Unfolding Energy - sRNA 3.96844 kcal/mol@LB@@LB@Position - mRNA 48 -- 105@LB@Position - sRNA 75 -- 129@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 15 -- 21@LB@
180	0.008222	0.1751	bsu14560	def	-9.11	0.436669	135 -- 145	75 -- 85	peptide deformylase	_____________134_________146\n_____________\|___________\|\n5'-UGG...CAUUC___________CCUUU...AGC-3'\n______________GUUUCGUUGCA\n______________\|:\|\|\|\|\|\|\|\|\|\n______________CGAAGCAACGU\n3'-AUU...CUUAC___________UAGAA...CAA-5'\n_____________\|___________\|\n_____________86__________74\n	139 -- 145	75 -- 81	-16.022 kcal/mol	4.21993 kcal/mol	4.54464 kcal/mol	134 146@LB@ \| \|@LB@5'-UGG...CAUUC CCUUU...AGC-3'@LB@ GUUUCGUUGCA@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ CGAAGCAACGU@LB@3'-AUU...CUUAC UAGAA...CAA-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -9.11 kcal/mol@LB@Hybridization Energy -16.022 kcal/mol@LB@Unfolding Energy - mRNA 4.21993 kcal/mol@LB@Unfolding Energy - sRNA 4.54464 kcal/mol@LB@@LB@Position - mRNA 135 -- 145@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 75 -- 81@LB@
119	0.005369	0.1741	bsu33250	yvrL	-8.38	0.555183	10 -- 36	76 -- 105	membrane-bound negative regulator YvrL	_____________9__________37\n_____________\|__________\|\n5'-AUG...CCUUC__________UUGCG...AUA-3'\n______________AAAACGCUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUUUGCGAAU\n3'-AUU...UAAAC__________UAAAG...CAA-5'\n_____________\|__________\|\n_____________106________75\n	224 -- 230	13 -- 19	-10.8458 kcal/mol	2.09283 kcal/mol	3.31287 kcal/mol	9 37@LB@ \| \|@LB@5'-AUG...CCUUC UUGCG...AUA-3'@LB@ AAAACGCUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUUUGCGAAU@LB@3'-AUU...UAAAC UAAAG...CAA-5'@LB@ \| \|@LB@ 106 75@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -10.8458 kcal/mol@LB@Unfolding Energy - mRNA 2.09283 kcal/mol@LB@Unfolding Energy - sRNA 3.31287 kcal/mol@LB@@LB@Position - mRNA 10 -- 36@LB@Position - sRNA 76 -- 105@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 13 -- 19@LB@
174	0.008073	0.1751	bsu36350	ywpD	-6.29	0.883503	121 -- 192	80 -- 160	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16740923; Product type prc : receptor'	_____________120___________________________________193\n_____________\|_____________________________________\|\n5'-GAC...UCGUU______AAA_______________CGGU_____G___UGAAG...GAG-3'\n______________UCAACA___GCGU____AUUGUCC____GCAAG__CC\n______________\|\|\|\|\|\|___:\|:\|____\|\|\|\|\|\|\|____\|\|\|\|\|__\|\|\n______________AGUUGU___UGUA____UAACAGG____CGUUC__GG\n3'-AUU...GAAGU______CC_____ACUG_______CGU______AA__UAUAU...CAA-5'\n_____________\|_____________________________________\|\n_____________161___________________________________79\n	134 -- 140	138 -- 144	-24.1445 kcal/mol	6.42035 kcal/mol	10.3237 kcal/mol	120 193@LB@ \| \|@LB@5'-GAC...UCGUU AAA CGGU G UGAAG...GAG-3'@LB@ UCAACA GCGU AUUGUCC GCAAG CC@LB@ \|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\| \|\|\|\|\| \|\|@LB@ AGUUGU UGUA UAACAGG CGUUC GG@LB@3'-AUU...GAAGU CC ACUG CGU AA UAUAU...CAA-5'@LB@ \| \|@LB@ 161 79@LB@@LB@@LB@Energy -6.29 kcal/mol@LB@Hybridization Energy -24.1445 kcal/mol@LB@Unfolding Energy - mRNA 6.42035 kcal/mol@LB@Unfolding Energy - sRNA 10.3237 kcal/mol@LB@@LB@Position - mRNA 121 -- 192@LB@Position - sRNA 80 -- 160@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 138 -- 144@LB@
88	0.003231	0.1423	bsu34620	mdxD	-9.76	0.344052	128 -- 173	81 -- 130	glucan 1 4-alpha-maltohexaosidase	_____________127____________174\n_____________\|______________\|\n5'-GUU...AUGCA__GA_______C__GCCAU...GUG-3'\n______________GC__UUCAUCA_CA\n______________:\|__\|\|\|\|\|\|\|_\|\|\n______________UG__AAGUAGU_GU\n3'-AUU...AAAAA__AG_______U__CCUGU...CAA-5'\n_____________\|______________\|\n_____________131____________80\n	220 -- 226	158 -- 164	-10.4913 kcal/mol	1.73429 kcal/mol	1.41528 kcal/mol	127 174@LB@ \| \|@LB@5'-GUU...AUGCA GA C GCCAU...GUG-3'@LB@ GC UUCAUCA CA@LB@ :\| \|\|\|\|\|\|\| \|\|@LB@ UG AAGUAGU GU@LB@3'-AUU...AAAAA AG U CCUGU...CAA-5'@LB@ \| \|@LB@ 131 80@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -10.4913 kcal/mol@LB@Unfolding Energy - mRNA 1.73429 kcal/mol@LB@Unfolding Energy - sRNA 1.41528 kcal/mol@LB@@LB@Position - mRNA 128 -- 173@LB@Position - sRNA 81 -- 130@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 158 -- 164@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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