Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
185	0.03283	0.5559	b1937	fliE	-12.05	0.046361	209 -- 229	14 -- 35	flagellar basal-body component	_____________208____________________230\n_____________\|______________________\|\n5'-CUG...UCAGC___A_______AUU________UAUCA...GUU-3'\n______________GAU__CAGGGG___GAAGGGGU\n______________\|\|:__\|\|:\|\|\|___:\|\|\|:\|\|\|\n______________CUG__GUUCCC___UUUCUCCA\n3'-CGC...CGUCA___AA______AAU________CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	223 -- 229	14 -- 20	-20.5154 kcal/mol	5.13678 kcal/mol	3.33183 kcal/mol	208 230@LB@ \| \|@LB@5'-CUG...UCAGC A AUU UAUCA...GUU-3'@LB@ GAU CAGGGG GAAGGGGU@LB@ \|\|: \|\|:\|\|\| :\|\|\|:\|\|\|@LB@ CUG GUUCCC UUUCUCCA@LB@3'-CGC...CGUCA AA AAU CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -20.5154 kcal/mol@LB@Unfolding Energy - mRNA 5.13678 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 209 -- 229@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 14 -- 20@LB@
180	0.03162	0.5559	b1941	fliI	-9.97	0.106944	57 -- 70	74 -- 88	flagellum-specific ATP synthase	_____________56______________71\n_____________\|_______________\|\n5'-CUG...ACCUU________A______GGCGC...GCG-3'\n______________AAGUUUGC__UGGCU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\n______________UUCAAGUG__ACCGA\n3'-CGC...GCGUU________CA_____AAUCA...AAG-5'\n_____________\|_______________\|\n_____________89______________73\n	58 -- 64	81 -- 87	-13.0478 kcal/mol	2.55971 kcal/mol	0.516514 kcal/mol	56 71@LB@ \| \|@LB@5'-CUG...ACCUU A GGCGC...GCG-3'@LB@ AAGUUUGC UGGCU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ UUCAAGUG ACCGA@LB@3'-CGC...GCGUU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 89 73@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -13.0478 kcal/mol@LB@Unfolding Energy - mRNA 2.55971 kcal/mol@LB@Unfolding Energy - sRNA 0.516514 kcal/mol@LB@@LB@Position - mRNA 57 -- 70@LB@Position - sRNA 74 -- 88@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 81 -- 87@LB@
114	0.01931	0.5385	b1951	rcsA	-10.71	0.079523	269 -- 285	16 -- 29	transcriptional regulator of colanic acid capsular biosynthesis	_____________268_______________286\n_____________\|_________________\|\n5'-GUU...AGUAG__________AAA____AAAUC...UUG-3'\n______________AGGGGUUAAA___AGAG\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCCAAUUU___UCUC\n3'-CGC...UGAAG_________________CACGG...AAG-5'\n_____________\|_________________\|\n_____________30________________15\n	272 -- 278	20 -- 26	-15.5636 kcal/mol	1.76121 kcal/mol	3.08831 kcal/mol	268 286@LB@ \| \|@LB@5'-GUU...AGUAG AAA AAAUC...UUG-3'@LB@ AGGGGUUAAA AGAG@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCCAAUUU UCUC@LB@3'-CGC...UGAAG CACGG...AAG-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -15.5636 kcal/mol@LB@Unfolding Energy - mRNA 1.76121 kcal/mol@LB@Unfolding Energy - sRNA 3.08831 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 20 -- 26@LB@
187	0.03332	0.5559	b2019	hisG	-10.76	0.077976	170 -- 191	15 -- 34	ATP phosphoribosyltransferase	_____________169____________________192\n_____________\|______________________\|\n5'-UUU...AUAAC_G_____ACA____U_______AAUAA...AUC-3'\n______________G_UUCAG___GGUU_AAAGAGG\n______________:_\|\|\|\|:___\|\|\|\|_\|\|\|\|\|\|\|\n______________U_AAGUU___CCAA_UUUCUCC\n3'-CGC...GUCAC_G_____C______U_______ACGGC...AAG-5'\n_____________\|______________________\|\n_____________35_____________________14\n	185 -- 191	15 -- 21	-17.0816 kcal/mol	2.9882 kcal/mol	3.33044 kcal/mol	169 192@LB@ \| \|@LB@5'-UUU...AUAAC G ACA U AAUAA...AUC-3'@LB@ G UUCAG GGUU AAAGAGG@LB@ : \|\|\|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ U AAGUU CCAA UUUCUCC@LB@3'-CGC...GUCAC G C U ACGGC...AAG-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -17.0816 kcal/mol@LB@Unfolding Energy - mRNA 2.9882 kcal/mol@LB@Unfolding Energy - sRNA 3.33044 kcal/mol@LB@@LB@Position - mRNA 170 -- 191@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 15 -- 21@LB@
27	0.005053	0.5385	b2058	wcaB	-11.44	0.059229	168 -- 190	61 -- 82	putative acyl transferase	_____________167______________________191\n_____________\|________________________\|\n5'-ACC...GGCAA____C_____GA____________GGCGC...AGA-3'\n______________ACGU_UGGCU__UGG_UAUUCGGG\n______________\|\|\|\|_\|\|\|\|\|__\|:\|_\|\|\|\|\|\|:\|\n______________UGCA_ACCGA__AUC_AUAAGCUC\n3'-CGC...UCAAG__________A____A________AACUC...AAG-5'\n_____________\|________________________\|\n_____________83_______________________60\n	184 -- 190	61 -- 67	-21.3941 kcal/mol	8.91056 kcal/mol	1.03929 kcal/mol	167 191@LB@ \| \|@LB@5'-ACC...GGCAA C GA GGCGC...AGA-3'@LB@ ACGU UGGCU UGG UAUUCGGG@LB@ \|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|\|:\|@LB@ UGCA ACCGA AUC AUAAGCUC@LB@3'-CGC...UCAAG A A AACUC...AAG-5'@LB@ \| \|@LB@ 83 60@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.3941 kcal/mol@LB@Unfolding Energy - mRNA 8.91056 kcal/mol@LB@Unfolding Energy - sRNA 1.03929 kcal/mol@LB@@LB@Position - mRNA 168 -- 190@LB@Position - sRNA 61 -- 82@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 61 -- 67@LB@
10	0.001846	0.5385	b2099	yegU	-13.29	0.027829	185 -- 270	5 -- 83	ADP-ribosylglycohydrolase family protein	_____________184_________________________________________________________________________________________271\n_____________\|___________________________________________________________________________________________\|\n5'-GUG...GUUGA___AAG__GA_______AA___AAAC____CGU________U__UCUUUAU__________G_______A__C__U____A__________AGCUU...CAC-3'\n______________CAC___GG____AGUUA__UGA____AGAA___AUUCUCGG_GC_______GGGCAG__GC_UUAGGGG_UG_GA_GGGG_UGCC_CUCCG\n______________\|\|\|___\|\|____\|\|\|\|\|__:\|\|____\|\|\|\|___\|:\|\|\|\|\|:_:\|_______\|\|\|\|\|\|__:\|_\|:\|:\|\|\|_\|:_:\|_\|:\|\|_\|\|\|\|_\|\|\|\|\|\n______________GUG___CC____UCAAU__GCU____UCUU___UGAGAGCU_UG_______CCCGUC__UG_AGUUCCC_AU_UU_CUCC_ACGG_GAGGC\n3'-CGC...UUCAA___CAA__GAAA_____AA___CAAC_______________U_______________AC__A_______A__U____________C_____AAAG-5'\n_____________\|___________________________________________________________________________________________\|\n_____________84__________________________________________________________________________________________4\n	243 -- 249	25 -- 31	-60.0716 kcal/mol	25.1194 kcal/mol	21.6578 kcal/mol	184 271@LB@ \| \|@LB@5'-GUG...GUUGA AAG GA AA AAAC CGU U UCUUUAU G A C U A AGCUU...CAC-3'@LB@ CAC GG AGUUA UGA AGAA AUUCUCGG GC GGGCAG GC UUAGGGG UG GA GGGG UGCC CUCCG@LB@ \|\|\| \|\| \|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|: :\| \|\|\|\|\|\| :\| \|:\|:\|\|\| \|: :\| \|:\|\| \|\|\|\| \|\|\|\|\|@LB@ GUG CC UCAAU GCU UCUU UGAGAGCU UG CCCGUC UG AGUUCCC AU UU CUCC ACGG GAGGC@LB@3'-CGC...UUCAA CAA GAAA AA CAAC U AC A A U C AAAG-5'@LB@ \| \|@LB@ 84 4@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -60.0716 kcal/mol@LB@Unfolding Energy - mRNA 25.1194 kcal/mol@LB@Unfolding Energy - sRNA 21.6578 kcal/mol@LB@@LB@Position - mRNA 185 -- 270@LB@Position - sRNA 5 -- 83@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 25 -- 31@LB@
83	0.01501	0.5385	b2114	metG	-6.55	0.379655	47 -- 64	63 -- 79	methionyl-tRNA synthetase	_____________46_________________65\n_____________\|__________________\|\n5'-AUU...GUGAU_____CUG__A_______UUCAU...AUG-3'\n______________UUGGC___GG_UUGUUCG\n______________\|\|\|\|\|___:\|_\|\|:\|\|\|\|\n______________AACCG___UC_AAUAAGC\n3'-CGC...AGUGC_____AAA__________UCAAC...AAG-5'\n_____________\|__________________\|\n_____________80_________________62\n	58 -- 64	63 -- 69	-14.0866 kcal/mol	6.80006 kcal/mol	0.735636 kcal/mol	46 65@LB@ \| \|@LB@5'-AUU...GUGAU CUG A UUCAU...AUG-3'@LB@ UUGGC GG UUGUUCG@LB@ \|\|\|\|\| :\| \|\|:\|\|\|\|@LB@ AACCG UC AAUAAGC@LB@3'-CGC...AGUGC AAA UCAAC...AAG-5'@LB@ \| \|@LB@ 80 62@LB@@LB@@LB@Energy -6.55 kcal/mol@LB@Hybridization Energy -14.0866 kcal/mol@LB@Unfolding Energy - mRNA 6.80006 kcal/mol@LB@Unfolding Energy - sRNA 0.735636 kcal/mol@LB@@LB@Position - mRNA 47 -- 64@LB@Position - sRNA 63 -- 79@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 63 -- 69@LB@
191	0.03353	0.5559	b2129	yehX	-7.36	0.287226	59 -- 67	69 -- 77	putative ABC transporter ATPase	_____________58________68\n_____________\|_________\|\n5'-GGU...CAGGC_________GCGCU...UUG-3'\n______________GGUUUUGGU\n______________\|\|:\|\|\|:\|\|\n______________CCGAAAUCA\n3'-CGC...UGCAA_________AUAAG...AAG-5'\n_____________\|_________\|\n_____________78________68\n	61 -- 67	69 -- 75	-10.3561 kcal/mol	2.74802 kcal/mol	0.243235 kcal/mol	58 68@LB@ \| \|@LB@5'-GGU...CAGGC GCGCU...UUG-3'@LB@ GGUUUUGGU@LB@ \|\|:\|\|\|:\|\|@LB@ CCGAAAUCA@LB@3'-CGC...UGCAA AUAAG...AAG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -10.3561 kcal/mol@LB@Unfolding Energy - mRNA 2.74802 kcal/mol@LB@Unfolding Energy - sRNA 0.243235 kcal/mol@LB@@LB@Position - mRNA 59 -- 67@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 69 -- 75@LB@
148	0.0249	0.5467	b2131	osmF	-10.26	0.095288	236 -- 244	75 -- 83	putative ABC transporter periplasmic binding protein	_____________235_______245\n_____________\|_________\|\n5'-AGG...CUGGU_________AGCCG...UCG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	238 -- 244	75 -- 81	-12.6611 kcal/mol	1.90691 kcal/mol	0.492259 kcal/mol	235 245@LB@ \| \|@LB@5'-AGG...CUGGU AGCCG...UCG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -12.6611 kcal/mol@LB@Unfolding Energy - mRNA 1.90691 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 236 -- 244@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@LB@
175	0.03099	0.5559	b2149	mglA	-9.34	0.136967	92 -- 105	70 -- 84	methyl-galactoside ABC transporter ATPase	_____________91______________106\n_____________\|_______________\|\n5'-CGA...GUACC__________G____AUAAA...AUU-3'\n______________UUAUGUUGGC__UAG\n______________\|:\|:\|\|\|\|\|\|__\|\|\|\n______________AGUGCAACCG__AUC\n3'-CGC...UUUCA__________AA___AAUAA...AAG-5'\n_____________\|_______________\|\n_____________85______________69\n	95 -- 101	75 -- 81	-15.5186 kcal/mol	5.61316 kcal/mol	0.563314 kcal/mol	91 106@LB@ \| \|@LB@5'-CGA...GUACC G AUAAA...AUU-3'@LB@ UUAUGUUGGC UAG@LB@ \|:\|:\|\|\|\|\|\| \|\|\|@LB@ AGUGCAACCG AUC@LB@3'-CGC...UUUCA AA AAUAA...AAG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -15.5186 kcal/mol@LB@Unfolding Energy - mRNA 5.61316 kcal/mol@LB@Unfolding Energy - sRNA 0.563314 kcal/mol@LB@@LB@Position - mRNA 92 -- 105@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 75 -- 81@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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