Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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	Additional homologs
142	0.005444	0.1351	b3950	frwB	-10.99	0.063119	13 -- 50	47 -- 86	putative enzyme IIB component of PTS	b3899	_____________12__________________________________________51\n_____________\|___________________________________________\|\n5'-GCA...GGGGU____U__________C__________________C___C____UUAUA...GGG-3'\n______________GGUC_GAUUGUGCUG__CGGUGGUU____GAAGG_AAG_UGGG\n______________::\|\|_:\|\|\|\|\|\|\|\|:__\|:\|\|::\|\|____:\|\|\|\|_\|\|\|_\|::\|\n______________UUAG_UUAACACGAU__GUCAUUAA____UUUCC_UUC_AUUC\n3'-UUU...CAUGC_______________AC________GUUU______________UGUUA...ACG-5'\n_____________\|___________________________________________\|\n_____________87__________________________________________46\n	30 -- 36	63 -- 69	-27.1662 kcal/mol	11.4404 kcal/mol	4.74035 kcal/mol	12 51@LB@ \| \|@LB@5'-GCA...GGGGU U C C C UUAUA...GGG-3'@LB@ GGUC GAUUGUGCUG CGGUGGUU GAAGG AAG UGGG@LB@ ::\|\| :\|\|\|\|\|\|\|\|: \|:\|\|::\|\| :\|\|\|\| \|\|\| \|::\|@LB@ UUAG UUAACACGAU GUCAUUAA UUUCC UUC AUUC@LB@3'-UUU...CAUGC AC GUUU UGUUA...ACG-5'@LB@ \| \|@LB@ 87 46@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -27.1662 kcal/mol@LB@Unfolding Energy - mRNA 11.4404 kcal/mol@LB@Unfolding Energy - sRNA 4.74035 kcal/mol@LB@@LB@Position - mRNA 13 -- 50@LB@Position - sRNA 47 -- 86@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 63 -- 69@LB@
39	0.0003198	0.02889	b3960	argH	-9.38	0.152930	179 -- 221	28 -- 64	argininosuccinate lyase		_____________178__________________________________________222\n_____________\|____________________________________________\|\n5'-GCA...UGAAU_______U_____AACAG___UAU____CUU_____________UUUAC...AUA-3'\n______________UUCAAAA_AAGGA_____AGU___GGCA___UGGGGCG_GGCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|_____\|\|\|___\|:\|\|___\|\|\|:\|\|\|_::\|\|:\n______________AAGUUUU_UUCCU_____UCA___CUGU___ACCUCGC_UUGCG\n3'-UUU...UCAUU_____________________UU_____UAU_______G_____GGUAG...ACG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	210 -- 216	34 -- 40	-30.4591 kcal/mol	8.02766 kcal/mol	13.054 kcal/mol	178 222@LB@ \| \|@LB@5'-GCA...UGAAU U AACAG UAU CUU UUUAC...AUA-3'@LB@ UUCAAAA AAGGA AGU GGCA UGGGGCG GGCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\| \|:\|\| \|\|\|:\|\|\| ::\|\|:@LB@ AAGUUUU UUCCU UCA CUGU ACCUCGC UUGCG@LB@3'-UUU...UCAUU UU UAU G GGUAG...ACG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -30.4591 kcal/mol@LB@Unfolding Energy - mRNA 8.02766 kcal/mol@LB@Unfolding Energy - sRNA 13.054 kcal/mol@LB@@LB@Position - mRNA 179 -- 221@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 34 -- 40@LB@
177	0.007289	0.1451	b4002	zraP	-14.65	0.005839	172 -- 192	36 -- 54	Zn-dependent periplasmic chaperone		_____________171___________________193\n_____________\|_____________________\|\n5'-AAU...UACCC____________CCAC_____GAUUA...GGC-3'\n______________GAAGUAAGACAA____UGGAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\n______________CUUCAUUCUGUU____ACCUC\n3'-UUU...UUUUC____________AU_______GCGUU...ACG-5'\n_____________\|_____________________\|\n_____________55____________________35\n	177 -- 183	43 -- 49	-21.9873 kcal/mol	3.76916 kcal/mol	3.53499 kcal/mol	171 193@LB@ \| \|@LB@5'-AAU...UACCC CCAC GAUUA...GGC-3'@LB@ GAAGUAAGACAA UGGAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUUCAUUCUGUU ACCUC@LB@3'-UUU...UUUUC AU GCGUU...ACG-5'@LB@ \| \|@LB@ 55 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -21.9873 kcal/mol@LB@Unfolding Energy - mRNA 3.76916 kcal/mol@LB@Unfolding Energy - sRNA 3.53499 kcal/mol@LB@@LB@Position - mRNA 172 -- 192@LB@Position - sRNA 36 -- 54@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 43 -- 49@LB@
74	0.001758	0.08273	b4012	yjaB	-8.69	0.215298	234 -- 243	51 -- 60	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein		_____________233________244\n_____________\|__________\|\n5'-AAG...AUGAG__________AACUC...CAG-3'\n______________GAAGGGGAGG\n______________:\|\|::\|\|\|:\|\n______________UUUUUCCUUC\n3'-UUU...UAAGU__________AUUCU...ACG-5'\n_____________\|__________\|\n_____________61_________50\n	237 -- 243	51 -- 57	-10.2171 kcal/mol	0.810771 kcal/mol	0.715621 kcal/mol	233 244@LB@ \| \|@LB@5'-AAG...AUGAG AACUC...CAG-3'@LB@ GAAGGGGAGG@LB@ :\|\|::\|\|\|:\|@LB@ UUUUUCCUUC@LB@3'-UUU...UAAGU AUUCU...ACG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -10.2171 kcal/mol@LB@Unfolding Energy - mRNA 0.810771 kcal/mol@LB@Unfolding Energy - sRNA 0.715621 kcal/mol@LB@@LB@Position - mRNA 234 -- 243@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
11	1.858e-05	0.005627	b4015	aceA	-14.28	0.007567	72 -- 114	4 -- 39	isocitrate lyase		_____________71___________________________________________115\n_____________\|____________________________________________\|\n5'-UUG...UCCCA_______UUUGAC______G____________GAA__GA_____ACUUC...UGA-3'\n______________GGGGCGU______GAUGCC_CA_CGCUUGAUG___CA__UCACC\n______________\|\|:\|\|\|:______:\|:\|\|\|_\|\|_\|\|\|\|\|\|\|:\|___\|\|__\|\|\|\|\|\n______________CCUCGCG______UUGCGG_GU_GCGAACUGC___GU__AGUGG\n3'-UUU...UUAUA______________________A_________AAC__A______ACG-5'\n_____________\|____________________________________________\|\n_____________40___________________________________________3\n	96 -- 102	15 -- 21	-43.7402 kcal/mol	14.1704 kcal/mol	15.29 kcal/mol	71 115@LB@ \| \|@LB@5'-UUG...UCCCA UUUGAC G GAA GA ACUUC...UGA-3'@LB@ GGGGCGU GAUGCC CA CGCUUGAUG CA UCACC@LB@ \|\|:\|\|\|: :\|:\|\|\| \|\| \|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|@LB@ CCUCGCG UUGCGG GU GCGAACUGC GU AGUGG@LB@3'-UUU...UUAUA A AAC A ACG-5'@LB@ \| \|@LB@ 40 3@LB@@LB@@LB@Energy -14.28 kcal/mol@LB@Hybridization Energy -43.7402 kcal/mol@LB@Unfolding Energy - mRNA 14.1704 kcal/mol@LB@Unfolding Energy - sRNA 15.29 kcal/mol@LB@@LB@Position - mRNA 72 -- 114@LB@Position - sRNA 4 -- 39@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 15 -- 21@LB@
90	0.002477	0.09689	b4020	yjbB	-17.01	0.000941	168 -- 222	1 -- 56	putative Na+/Pi-cotransporter		_____________167________________________________________________________223\n_____________\|__________________________________________________________\|\n5'-UCC...GCUUC_____CA__UA______A____AACC___AA______GUUA___C_____________UUUCU...UGC-3'\n______________AGGAA__UA__ACGAUA_GGAG_____UG__C_UCGU____ACG_UGC_UUCACCUGC\n______________\|\|\|\|\|__\|\|__\|\|:\|\|\|_\|\|\|\|_____:\|__\|_\|\|\|:____\|\|\|_\|\|\|_\|\|\|\|\|\|\|\|\|\n______________UCCUU__AU__UGUUAU_CCUC_____GC__G_AGCG____UGC_ACG_AAGUGGACG\n3'-UUU...UUUUU_____C___UC______A____GCGUU__GG_U____AAC____A___U_________-5'\n_____________\|_________________________________________________________\|\n_____________57________________________________________________________1\n	216 -- 222	1 -- 7	-44.3986 kcal/mol	10.5518 kcal/mol	16.8439 kcal/mol	167 223@LB@ \| \|@LB@5'-UCC...GCUUC CA UA A AACC AA GUUA C UUUCU...UGC-3'@LB@ AGGAA UA ACGAUA GGAG UG C UCGU ACG UGC UUCACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\| :\| \| \|\|\|: \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUU AU UGUUAU CCUC GC G AGCG UGC ACG AAGUGGACG@LB@3'-UUU...UUUUU C UC A GCGUU GG U AAC A U -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -44.3986 kcal/mol@LB@Unfolding Energy - mRNA 10.5518 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 168 -- 222@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@LB@
45	0.0004696	0.03623	b4035	malK	-9.83	0.120497	188 -- 201	44 -- 57	maltose ABC transportor ATPase		_____________187____________202\n_____________\|______________\|\n5'-CGC...UUACA_______A______UGGCG...UGU-3'\n______________AAGGGAG_AGGGCA\n______________\|\|\|\|:\|\|_\|:\|:\|\|\n______________UUCCUUC_UUCUGU\n3'-UUU...GUUUU_______A______UAUAC...ACG-5'\n_____________\|______________\|\n_____________58_____________43\n	188 -- 194	51 -- 57	-14.5332 kcal/mol	2.95068 kcal/mol	1.74831 kcal/mol	187 202@LB@ \| \|@LB@5'-CGC...UUACA A UGGCG...UGU-3'@LB@ AAGGGAG AGGGCA@LB@ \|\|\|\|:\|\| \|:\|:\|\|@LB@ UUCCUUC UUCUGU@LB@3'-UUU...GUUUU A UAUAC...ACG-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.5332 kcal/mol@LB@Unfolding Energy - mRNA 2.95068 kcal/mol@LB@Unfolding Energy - sRNA 1.74831 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
21	6.29e-05	0.01049	b4040	ubiA	-12.44	0.026053	187 -- 207	35 -- 59	p-hydroxybenzoate octaprenyltransferase		_____________186_______________________208\n_____________\|_________________________\|\n5'-AGC...GUACU________AAA______________GGAGU...UAU-3'\n______________AAGAGGAA_______AAUAUGGAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|\|\|\|\|\|\|:\n______________UUUUCCUU_______UUAUACCUCG\n3'-UUU...AAGUU________CAUUCUG__________CGUUG...ACG-5'\n_____________\|_________________________\|\n_____________60________________________34\n	201 -- 207	35 -- 41	-18.3412 kcal/mol	1.63668 kcal/mol	4.22714 kcal/mol	186 208@LB@ \| \|@LB@5'-AGC...GUACU AAA GGAGU...UAU-3'@LB@ AAGAGGAA AAUAUGGAGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUUUCCUU UUAUACCUCG@LB@3'-UUU...AAGUU CAUUCUG CGUUG...ACG-5'@LB@ \| \|@LB@ 60 34@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -18.3412 kcal/mol@LB@Unfolding Energy - mRNA 1.63668 kcal/mol@LB@Unfolding Energy - sRNA 4.22714 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 35 -- 59@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 35 -- 41@LB@
161	0.006314	0.1377	b4099	phnI	-7.36	0.387929	194 -- 228	46 -- 79	ribophosphonate triphosphate synthase complex putative catalytic subunit		_____________193__________________________________229\n_____________\|____________________________________\|\n5'-AGC...GGAGG______G_____C__UGC___U_________C____AGGCG...GCG-3'\n______________UGUGCU_AUGUA_GU____CG_GAAAGGGGG_GAGA\n______________\|\|\|\|\|\|_\|\|\|:\|_\|\|____\|:_:\|\|\|\|\|::\|_:\|\|\|\n______________ACACGA_UACGU_CA____GU_UUUUCCUUC_UUCU\n3'-UUU...AGUUA_______________UUAA__U_________A____GUUAU...ACG-5'\n_____________\|____________________________________\|\n_____________80___________________________________45\n	217 -- 223	51 -- 57	-26.8268 kcal/mol	14.1464 kcal/mol	5.32077 kcal/mol	193 229@LB@ \| \|@LB@5'-AGC...GGAGG G C UGC U C AGGCG...GCG-3'@LB@ UGUGCU AUGUA GU CG GAAAGGGGG GAGA@LB@ \|\|\|\|\|\| \|\|\|:\| \|\| \|: :\|\|\|\|\|::\| :\|\|\|@LB@ ACACGA UACGU CA GU UUUUCCUUC UUCU@LB@3'-UUU...AGUUA UUAA U A GUUAU...ACG-5'@LB@ \| \|@LB@ 80 45@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -26.8268 kcal/mol@LB@Unfolding Energy - mRNA 14.1464 kcal/mol@LB@Unfolding Energy - sRNA 5.32077 kcal/mol@LB@@LB@Position - mRNA 194 -- 228@LB@Position - sRNA 46 -- 79@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 51 -- 57@LB@
110	0.003505	0.1114	b4111	proP	-11.30	0.052648	186 -- 222	48 -- 93	proline/glycine betaine transporter		_____________185________________________________________________223\n_____________\|__________________________________________________\|\n5'-CAC...CCAAC_________GA_____________U________________AAAA_____AACCG...GUA-3'\n______________UC_UGCGAG__AA____GCUAUGC_________GAAAAGGA____AGUAA\n______________\|\|_\|:\|\|\|:__\|\|____\|\|\|\|\|\|\|_________:\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AG_AUGCUU__UU____CGAUACG_________UUUUUCCU____UCAUU\n3'-UUU...GCCGC__C______AG__AACA_______UCAUUAAGU_________________CUGUU...ACG-5'\n_____________\|__________________________________________________\|\n_____________94_________________________________________________47\n	198 -- 204	70 -- 76	-22.6159 kcal/mol	6.45165 kcal/mol	4.87071 kcal/mol	185 223@LB@ \| \|@LB@5'-CAC...CCAAC GA U AAAA AACCG...GUA-3'@LB@ UC UGCGAG AA GCUAUGC GAAAAGGA AGUAA@LB@ \|\| \|:\|\|\|: \|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|@LB@ AG AUGCUU UU CGAUACG UUUUUCCU UCAUU@LB@3'-UUU...GCCGC C AG AACA UCAUUAAGU CUGUU...ACG-5'@LB@ \| \|@LB@ 94 47@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -22.6159 kcal/mol@LB@Unfolding Energy - mRNA 6.45165 kcal/mol@LB@Unfolding Energy - sRNA 4.87071 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 48 -- 93@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 70 -- 76@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)

Job resubmission

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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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