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
71	0.002326	0.1242	bsu37230	ywjA	-17.78	0.008577	195 -- 260	99 -- 147	ABC transporter ATP-binding protein		_____________194___________________________________________________________261\n_____________\|_____________________________________________________________\|\n5'-UGA...GGGAA____GG__G_________U__UUUUCAUAUUAUAAA________AAC______________GACUU...UUC-3'\n______________GAUA__GU_CUGCGGCAA_UU_______________CCAUAUAA___GUUGUU_CUUUCUC\n______________\|\|:\|__\|\|_\|:\|\|:\|\|\|\|_\|\|_______________\|\|\|\|\|\|\|\|___\|\|\|\|\|:_\|\|\|\|\|\|\|\n______________CUGU__CA_GGCGUCGUU_AA_______________GGUAUAUU___CAACAG_GAAAGAG\n3'-AUU...UGUAA____AA____________C_________________________A________U_______UAGAA...CAA-5'\n_____________\|_____________________________________________________________\|\n_____________148___________________________________________________________98\n	248 -- 254	105 -- 111	-39.3136 kcal/mol	10.514 kcal/mol	13.0974 kcal/mol	194 261@LB@ \| \|@LB@5'-UGA...GGGAA GG G U UUUUCAUAUUAUAAA AAC GACUU...UUC-3'@LB@ GAUA GU CUGCGGCAA UU CCAUAUAA GUUGUU CUUUCUC@LB@ \|\|:\| \|\| \|:\|\|:\|\|\|\| \|\| \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CUGU CA GGCGUCGUU AA GGUAUAUU CAACAG GAAAGAG@LB@3'-AUU...UGUAA AA C A U UAGAA...CAA-5'@LB@ \| \|@LB@ 148 98@LB@@LB@@LB@Energy -17.78 kcal/mol@LB@Hybridization Energy -39.3136 kcal/mol@LB@Unfolding Energy - mRNA 10.514 kcal/mol@LB@Unfolding Energy - sRNA 13.0974 kcal/mol@LB@@LB@Position - mRNA 195 -- 260@LB@Position - sRNA 99 -- 147@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 105 -- 111@LB@
77	0.002638	0.1315	bsu36790	ywmA	-11.30	0.183092	1 -- 48	33 -- 81	Evidence 5: No homology to any previously reported sequences		_____________0_______________49\n_____________\|_______________\|\n5'-CGA...GUUCA_______________AUAUA...GAC-3'\n______________UACCC_UUUCUUAUU\n______________\|\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________AUGGG_AGAGAAUAA\n3'-AUU...UUAGC_____U_________GGGGU...CAA-5'\n_____________\|_______________\|\n_____________82______________32\n	65 -- 71	43 -- 49	-14.8917 kcal/mol	3.00255 kcal/mol	4.80466 kcal/mol	0 49@LB@ \| \|@LB@5'-CGA...GUUCA AUAUA...GAC-3'@LB@ UACCC UUUCUUAUU@LB@ \|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGGG AGAGAAUAA@LB@3'-AUU...UUAGC U GGGGU...CAA-5'@LB@ \| \|@LB@ 82 32@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -14.8917 kcal/mol@LB@Unfolding Energy - mRNA 3.00255 kcal/mol@LB@Unfolding Energy - sRNA 4.80466 kcal/mol@LB@@LB@Position - mRNA 1 -- 48@LB@Position - sRNA 33 -- 81@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 43 -- 49@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@
113	0.005141	0.1741	bsu36080	ywrF	-10.09	0.302867	265 -- 274	38 -- 47	Evidence 4: Homologs of previously reported genes of unknown function		_____________264________275\n_____________\|__________\|\n5'-UGG...UACCG__________CCCCA...UUU-3'\n______________UUAUUCCCCG\n______________\|\|\|\|\|\|\|\|\|:\n______________AAUAAGGGGU\n3'-AUU...UAGAG__________AAAGA...CAA-5'\n_____________\|__________\|\n_____________48_________37\n	268 -- 274	38 -- 44	-13.6226 kcal/mol	1.45475 kcal/mol	3.86656 kcal/mol	264 275@LB@ \| \|@LB@5'-UGG...UACCG CCCCA...UUU-3'@LB@ UUAUUCCCCG@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AAUAAGGGGU@LB@3'-AUU...UAGAG AAAGA...CAA-5'@LB@ \| \|@LB@ 48 37@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -13.6226 kcal/mol@LB@Unfolding Energy - mRNA 1.45475 kcal/mol@LB@Unfolding Energy - sRNA 3.86656 kcal/mol@LB@@LB@Position - mRNA 265 -- 274@LB@Position - sRNA 38 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 38 -- 44@LB@
13	0.0004662	0.1011	bsu39950	yxaJ	-7.42	0.718209	218 -- 252	31 -- 81	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15743949 15849754 16850406; Product type pm: membrane component'		_____________217_________________________________________253\n_____________\|___________________________________________\|\n5'-CAU...AAUAG___G______A__A_____________________GC______UUUUU...CGG-3'\n______________CGU_GCGAUC_UG_CAA__________CCAUUUCU__GUUUCU\n______________\|\|\|_\|\|:\|\|\|_\|\|_\|\|\|__________\|\|\|\|:\|\|\|__:\|\|:\|:\n______________GCA_CGUUAG_AC_GUU__________GGUAGAGA__UAAGGG\n3'-AUU...CCGAA___A______A__C___UGUUAGCAUG________A_______GUAAA...CAA-5'\n_____________\|___________________________________________\|\n_____________82__________________________________________30\n	236 -- 242	47 -- 53	-25.2058 kcal/mol	7.74885 kcal/mol	10.909 kcal/mol	217 253@LB@ \| \|@LB@5'-CAU...AAUAG G A A GC UUUUU...CGG-3'@LB@ CGU GCGAUC UG CAA CCAUUUCU GUUUCU@LB@ \|\|\| \|\|:\|\|\| \|\| \|\|\| \|\|\|\|:\|\|\| :\|\|:\|:@LB@ GCA CGUUAG AC GUU GGUAGAGA UAAGGG@LB@3'-AUU...CCGAA A A C UGUUAGCAUG A GUAAA...CAA-5'@LB@ \| \|@LB@ 82 30@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.2058 kcal/mol@LB@Unfolding Energy - mRNA 7.74885 kcal/mol@LB@Unfolding Energy - sRNA 10.909 kcal/mol@LB@@LB@Position - mRNA 218 -- 252@LB@Position - sRNA 31 -- 81@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 47 -- 53@LB@
178	0.008149	0.1751	bsu39610	yxeB	-9.68	0.354141	1 -- 23	37 -- 58	iron(3+)-hydroxamate-binding protein YxeB	bsu33320	_____________0_______24\n_____________\|_______\|\n5'-GCA...UGUAA_______AUUUU...CUG-3'\n______________UUCCCAU\n______________\|:\|\|\|\|\|\n______________AGGGGUA\n3'-AUU...GAAUA_______AAGAA...CAA-5'\n_____________\|_______\|\n_____________59______36\n	17 -- 23	37 -- 43	-9.25042 kcal/mol	0.0358808 kcal/mol	2.53706 kcal/mol	0 24@LB@ \| \|@LB@5'-GCA...UGUAA AUUUU...CUG-3'@LB@ UUCCCAU@LB@ \|:\|\|\|\|\|@LB@ AGGGGUA@LB@3'-AUU...GAAUA AAGAA...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -9.68 kcal/mol@LB@Hybridization Energy -9.25042 kcal/mol@LB@Unfolding Energy - mRNA 0.0358808 kcal/mol@LB@Unfolding Energy - sRNA 2.53706 kcal/mol@LB@@LB@Position - mRNA 1 -- 23@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 37 -- 43@LB@
137	0.006339	0.1741	bsu39320	yxiB	-11.20	0.191268	188 -- 222	111 -- 147	Evidence 4: Homologs of previously reported genes of unknown function		_____________187_________________________223\n_____________\|___________________________\|\n5'-UAA...GUGUU______UGCAUA___A___________AUUCG...AAA-3'\n______________GCGGCA______GUG_AAUGUUGUUAC\n______________\|\|:\|\|\|______:\|:_\|\|\|\|\|\|\|\|:\|\|\n______________CGUCGU______UAU_UUACAACAGUG\n3'-AUU...ACAGG______UCAAGG___A___________AAAGA...CAA-5'\n_____________\|___________________________\|\n_____________148_________________________110\n	216 -- 222	111 -- 117	-23.3412 kcal/mol	7.76229 kcal/mol	5.28835 kcal/mol	187 223@LB@ \| \|@LB@5'-UAA...GUGUU UGCAUA A AUUCG...AAA-3'@LB@ GCGGCA GUG AAUGUUGUUAC@LB@ \|\|:\|\|\| :\|: \|\|\|\|\|\|\|\|:\|\|@LB@ CGUCGU UAU UUACAACAGUG@LB@3'-AUU...ACAGG UCAAGG A AAAGA...CAA-5'@LB@ \| \|@LB@ 148 110@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -23.3412 kcal/mol@LB@Unfolding Energy - mRNA 7.76229 kcal/mol@LB@Unfolding Energy - sRNA 5.28835 kcal/mol@LB@@LB@Position - mRNA 188 -- 222@LB@Position - sRNA 111 -- 147@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 111 -- 117@LB@
157	0.007221	0.1751	bsu40660	yybF	-12.55	0.105157	243 -- 270	125 -- 152	MFS transporter		_____________242__________________________271\n_____________\|____________________________\|\n5'-UGU...AAAUU_____U__U__C_____U__________AUACA...AGC-3'\n______________ACGUU_GC_UU_UUCGC_GCGGGUUUCA\n______________\|\|:\|\|_:\|_\|\|_\|:\|\|\|_\|\|::\|\|\|:\|\|\n______________UGUAA_UG_AA_AGGCG_CGUUCAAGGU\n3'-AUU...UGUCC_____C__U__C_____U__________AUAUU...CAA-5'\n_____________\|____________________________\|\n_____________153__________________________124\n	264 -- 270	125 -- 131	-24.436 kcal/mol	4.92439 kcal/mol	8.98549 kcal/mol	242 271@LB@ \| \|@LB@5'-UGU...AAAUU U U C U AUACA...AGC-3'@LB@ ACGUU GC UU UUCGC GCGGGUUUCA@LB@ \|\|:\|\| :\| \|\| \|:\|\|\| \|\|::\|\|\|:\|\|@LB@ UGUAA UG AA AGGCG CGUUCAAGGU@LB@3'-AUU...UGUCC C U C U AUAUU...CAA-5'@LB@ \| \|@LB@ 153 124@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -24.436 kcal/mol@LB@Unfolding Energy - mRNA 4.92439 kcal/mol@LB@Unfolding Energy - sRNA 8.98549 kcal/mol@LB@@LB@Position - mRNA 243 -- 270@LB@Position - sRNA 125 -- 152@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 125 -- 131@LB@
49	0.001587	0.1212	bsu40240	yycS	-16.07	0.019817	5 -- 79	35 -- 113	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type h: extrachromosomal origin'		_____________4_________________________________________________________________________________80\n_____________\|_________________________________________________________________________________\|\n_______5'-AAUA_____G______G______UCCUCC____U_______C__U_____________A___U___U____AA___AA_______AUUCA...GCA-3'\n______________CGCUU_UUUCAU_UUCAAA______GAUG_UUUC_UU_CA_UUUU_____ACAA_UGU_CUC_UCUC__UAU__CCUAUUU\n______________\|:\|\|\|_\|:\|\|\|\|_\|\|\|\|\|\|______:\|\|\|_:\|\|\|_\|\|_\|\|_\|:\|\|_____\|\|\|\|_:\|\|_\|:\|_\|\|\|\|__\|\|\|__\|\|:\|\|\|\|\n______________GUGAA_AGAGUA_AAGUUU______UUAC_GAAG_AA_GU_AGAA_____UGUU_GCA_GGG_AGAG__AUA__GGGUAAA\n3'-AUU...CAACA____________G______CAUUAC____C____C__C__U____CCGUU____A___U___U____A____AG_______GAAAC...CAA-5'\n_____________\|_________________________________________________________________________________\|\n_____________114_______________________________________________________________________________34\n	73 -- 79	35 -- 41	-40.7208 kcal/mol	6.49365 kcal/mol	21.9183 kcal/mol	4 80@LB@ \| \|@LB@ 5'-AAUA G G UCCUCC U C U A U U AA AA AUUCA...GCA-3'@LB@ CGCUU UUUCAU UUCAAA GAUG UUUC UU CA UUUU ACAA UGU CUC UCUC UAU CCUAUUU@LB@ \|:\|\|\| \|:\|\|\|\| \|\|\|\|\|\| :\|\|\| :\|\|\| \|\| \|\| \|:\|\| \|\|\|\| :\|\| \|:\| \|\|\|\| \|\|\| \|\|:\|\|\|\|@LB@ GUGAA AGAGUA AAGUUU UUAC GAAG AA GU AGAA UGUU GCA GGG AGAG AUA GGGUAAA@LB@3'-AUU...CAACA G CAUUAC C C C U CCGUU A U U A AG GAAAC...CAA-5'@LB@ \| \|@LB@ 114 34@LB@@LB@@LB@Energy -16.07 kcal/mol@LB@Hybridization Energy -40.7208 kcal/mol@LB@Unfolding Energy - mRNA 6.49365 kcal/mol@LB@Unfolding Energy - sRNA 21.9183 kcal/mol@LB@@LB@Position - mRNA 5 -- 79@LB@Position - sRNA 35 -- 113@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 35 -- 41@LB@
94	0.003675	0.1515	bsu40130	yydK	-17.16	0.011624	17 -- 47	34 -- 60	HTH-type transcriptional regulator YydK		_____________16___________________________________48\n_____________\|____________________________________\|\n__________5'-A_____UUU__U___C_________CUC_________CCCGA...UGG-3'\n______________UGUCU___GC_AGU_UCGUAUAAU____UCACUUUC\n______________\|\|\|\|:___\|\|_\|\|\|_:\|:\|\|\|\|\|\|____\|\|\|\|\|\|\|\|\n______________ACAGG___CG_UCA_GGUAUAUUA____AGUGAAAG\n3'-AUU...CUGUA_____CGU__U___A_________CAAC________AGUAG...CAA-5'\n_____________\|____________________________________\|\n_____________61___________________________________33\n	30 -- 36	107 -- 113	-26.8798 kcal/mol	2.26958 kcal/mol	10.0128 kcal/mol	16 48@LB@ \| \|@LB@ 5'-A UUU U C CUC CCCGA...UGG-3'@LB@ UGUCU GC AGU UCGUAUAAU UCACUUUC@LB@ \|\|\|\|: \|\| \|\|\| :\|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACAGG CG UCA GGUAUAUUA AGUGAAAG@LB@3'-AUU...CUGUA CGU U A CAAC AGUAG...CAA-5'@LB@ \| \|@LB@ 61 33@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -26.8798 kcal/mol@LB@Unfolding Energy - mRNA 2.26958 kcal/mol@LB@Unfolding Energy - sRNA 10.0128 kcal/mol@LB@@LB@Position - mRNA 17 -- 47@LB@Position - sRNA 34 -- 60@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 107 -- 113@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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