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
137	0.02312	0.5385	b2153	folE	-12.97	0.031813	230 -- 265	52 -- 87	GTP cyclohydrolase I	_____________229___________________________________266\n_____________\|_____________________________________\|\n5'-CUG...GCCCU________AA___G_______CG____GACU______ACCGC...ACG-3'\n______________GGUUCAUG___GC_UUAGUUG__CGAG____GGAAAC\n______________:\|\|\|\|\|:\|___\|\|_\|\|\|\|\|\|:__\|\|\|\|____:\|\|\|\|\|\n______________UCAAGUGC___CG_AAUCAAU__GCUC____UCUUUG\n3'-CGC...CGUUU________AAC__A_______AA____AAC_______AGAGC...AAG-5'\n_____________\|_____________________________________\|\n_____________88____________________________________51\n	243 -- 249	67 -- 73	-29.7116 kcal/mol	12.3362 kcal/mol	4.40736 kcal/mol	229 266@LB@ \| \|@LB@5'-CUG...GCCCU AA G CG GACU ACCGC...ACG-3'@LB@ GGUUCAUG GC UUAGUUG CGAG GGAAAC@LB@ :\|\|\|\|\|:\| \|\| \|\|\|\|\|\|: \|\|\|\| :\|\|\|\|\|@LB@ UCAAGUGC CG AAUCAAU GCUC UCUUUG@LB@3'-CGC...CGUUU AAC A AA AAC AGAGC...AAG-5'@LB@ \| \|@LB@ 88 51@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -29.7116 kcal/mol@LB@Unfolding Energy - mRNA 12.3362 kcal/mol@LB@Unfolding Energy - sRNA 4.40736 kcal/mol@LB@@LB@Position - mRNA 230 -- 265@LB@Position - sRNA 52 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 67 -- 73@LB@
189	0.03342	0.5559	b2172	yeiQ	-17.65	0.004645	282 -- 298	70 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________281_______________299\n_____________\|_________________\|\n5'-GAU...GUAUC______U__________AG-3'\n______________GUUCAU_UUGGCUUUGG\n______________\|\|\|\|\|:_\|\|\|\|\|\|\|\|:\|\n______________CAAGUG_AACCGAAAUC\n3'-CGC...GUUUU______C__________AAUAA...AAG-5'\n_____________\|_________________\|\n_____________87________________69\n	292 -- 298	70 -- 76	-21.6632 kcal/mol	3.44897 kcal/mol	0.568254 kcal/mol	281 299@LB@ \| \|@LB@5'-GAU...GUAUC U AG-3'@LB@ GUUCAU UUGGCUUUGG@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|\|:\|@LB@ CAAGUG AACCGAAAUC@LB@3'-CGC...GUUUU C AAUAA...AAG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -17.65 kcal/mol@LB@Hybridization Energy -21.6632 kcal/mol@LB@Unfolding Energy - mRNA 3.44897 kcal/mol@LB@Unfolding Energy - sRNA 0.568254 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 70 -- 76@LB@
7	0.001275	0.5385	b2175	mepS	-13.85	0.022182	178 -- 188	25 -- 35	murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase	_____________177_________189\n_____________\|___________\|\n5'-CAA...UUAAG___________AAAAC...CAA-3'\n______________GACUUCAAGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________CUGAAGUUCCC\n3'-CGC...CGUCA___________AAUUU...AAG-5'\n_____________\|___________\|\n_____________36__________24\n	182 -- 188	25 -- 31	-19.9152 kcal/mol	2.73903 kcal/mol	3.32958 kcal/mol	177 189@LB@ \| \|@LB@5'-CAA...UUAAG AAAAC...CAA-3'@LB@ GACUUCAAGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ CUGAAGUUCCC@LB@3'-CGC...CGUCA AAUUU...AAG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 2.73903 kcal/mol@LB@Unfolding Energy - sRNA 3.32958 kcal/mol@LB@@LB@Position - mRNA 178 -- 188@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 25 -- 31@LB@
53	0.01075	0.5385	b2215	ompC	-12.88	0.032936	67 -- 90	57 -- 76	outer membrane porin protein C	_____________66_______________________91\n_____________\|________________________\|\n5'-AUC...UAAAA________AUCA______U_____AUUAU...AUC-3'\n______________GUUUUAGU____UAUUCG_GUUGG\n______________\|:\|\|\|\|\|\|____\|\|\|\|\|\|_\|\|\|\|:\n______________CGAAAUCA____AUAAGC_CAACU\n3'-CGC...GCAAC__________________U_____CUUUG...AAG-5'\n_____________\|________________________\|\n_____________77_______________________56\n	68 -- 74	69 -- 75	-17.5321 kcal/mol	3.43109 kcal/mol	1.21756 kcal/mol	66 91@LB@ \| \|@LB@5'-AUC...UAAAA AUCA U AUUAU...AUC-3'@LB@ GUUUUAGU UAUUCG GUUGG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|\| \|\|\|\|:@LB@ CGAAAUCA AUAAGC CAACU@LB@3'-CGC...GCAAC U CUUUG...AAG-5'@LB@ \| \|@LB@ 77 56@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -17.5321 kcal/mol@LB@Unfolding Energy - mRNA 3.43109 kcal/mol@LB@Unfolding Energy - sRNA 1.21756 kcal/mol@LB@@LB@Position - mRNA 67 -- 90@LB@Position - sRNA 57 -- 76@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 69 -- 75@LB@
41	0.00828	0.5385	b2246	rhmT	-13.65	0.023999	257 -- 273	69 -- 86	putative L-rhamnonate transporter	_____________256________________274\n_____________\|__________________\|\n5'-ACG...AUUCC____________GCU___AUGUG...CGA-3'\n______________GUUUAUGUUGGC____GU\n______________\|\|\|:\|:\|\|\|\|\|\|____\|\|\n______________CAAGUGCAACCG____CA\n3'-CGC...GUUUU____________AAAU__AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	262 -- 268	75 -- 81	-18.6828 kcal/mol	4.45929 kcal/mol	0.568509 kcal/mol	256 274@LB@ \| \|@LB@5'-ACG...AUUCC GCU AUGUG...CGA-3'@LB@ GUUUAUGUUGGC GU@LB@ \|\|\|:\|:\|\|\|\|\|\| \|\|@LB@ CAAGUGCAACCG CA@LB@3'-CGC...GUUUU AAAU AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -18.6828 kcal/mol@LB@Unfolding Energy - mRNA 4.45929 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 75 -- 81@LB@
95	0.01635	0.5385	b2287	nuoB	-8.27	0.206762	33 -- 42	71 -- 80	NADH:ubiquinone oxidoreductase chain B	_____________32_________43\n_____________\|__________\|\n5'-CAU...GCUGG__A_______UGGAA...UUA-3'\n______________GU_GGCUUUG\n______________\|\|_\|\|\|\|\|\|:\n______________CA_CCGAAAU\n3'-CGC...AAGUG__A_______CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	36 -- 42	71 -- 77	-10.0496 kcal/mol	1.54713 kcal/mol	0.236872 kcal/mol	32 43@LB@ \| \|@LB@5'-CAU...GCUGG A UGGAA...UUA-3'@LB@ GU GGCUUUG@LB@ \|\| \|\|\|\|\|\|:@LB@ CA CCGAAAU@LB@3'-CGC...AAGUG A CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -10.0496 kcal/mol@LB@Unfolding Energy - mRNA 1.54713 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 33 -- 42@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 71 -- 77@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@LB@
192	0.03364	0.5559	b2333	yfcP	-8.48	0.190877	22 -- 36	61 -- 77	putative fimbrial-like adhesin protein	_____________21________________37\n_____________\|_________________\|\n5'-GCA...UACCC_________A_______CUUCA...AUU-3'\n______________GGUUUUGGU___UCGAG\n______________\|\|:\|\|\|:\|\|___\|\|\|\|\|\n______________CCGAAAUCA___AGCUC\n3'-CGC...UGCAA_________AUA_____AACUC...AAG-5'\n_____________\|_________________\|\n_____________78________________60\n	23 -- 29	70 -- 76	-16.4218 kcal/mol	7.14733 kcal/mol	0.796269 kcal/mol	21 37@LB@ \| \|@LB@5'-GCA...UACCC A CUUCA...AUU-3'@LB@ GGUUUUGGU UCGAG@LB@ \|\|:\|\|\|:\|\| \|\|\|\|\|@LB@ CCGAAAUCA AGCUC@LB@3'-CGC...UGCAA AUA AACUC...AAG-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -16.4218 kcal/mol@LB@Unfolding Energy - mRNA 7.14733 kcal/mol@LB@Unfolding Energy - sRNA 0.796269 kcal/mol@LB@@LB@Position - mRNA 22 -- 36@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 70 -- 76@LB@
35	0.006586	0.5385	b2351	gtrB	-12.36	0.040837	174 -- 213	48 -- 89	CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase	_____________173________________________________________214\n_____________\|__________________________________________\|\n5'-GCA...UAUUC_____________U______GG__G___AA___A__UA____UUGUA...AAG-3'\n______________AAAGUUCAU__UG_CUUUAG__AU_CGA__UGA_GA__UCUC\n______________\|\|\|\|\|\|\|\|:__\|\|_\|\|\|\|\|\|__\|\|_\|\|\|__\|\|\|_:\|__\|\|\|\|\n______________UUUCAAGUG__AC_GAAAUC__UA_GCU__ACU_UU__AGAG\n3'-CGC...GGCGU_________CA__C______AA__A___CA___C__UG____CUUUG...AAG-5'\n_____________\|__________________________________________\|\n_____________90_________________________________________47\n	176 -- 182	81 -- 87	-27.281 kcal/mol	10.5075 kcal/mol	4.41572 kcal/mol	173 214@LB@ \| \|@LB@5'-GCA...UAUUC U GG G AA A UA UUGUA...AAG-3'@LB@ AAAGUUCAU UG CUUUAG AU CGA UGA GA UCUC@LB@ \|\|\|\|\|\|\|\|: \|\| \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|\|@LB@ UUUCAAGUG AC GAAAUC UA GCU ACU UU AGAG@LB@3'-CGC...GGCGU CA C AA A CA C UG CUUUG...AAG-5'@LB@ \| \|@LB@ 90 47@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -27.281 kcal/mol@LB@Unfolding Energy - mRNA 10.5075 kcal/mol@LB@Unfolding Energy - sRNA 4.41572 kcal/mol@LB@@LB@Position - mRNA 174 -- 213@LB@Position - sRNA 48 -- 89@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 81 -- 87@LB@
60	0.01169	0.5385	b2441	eutB	-14.17	0.019414	238 -- 261	12 -- 34	ethanolamine ammonia-lyase large subunit heavy chain	_____________237______________________262\n_____________\|________________________\|\n5'-CUG...AUAUC_G_______AUG____________UGGCU...UGG-3'\n______________A_UUUAAGG___UAAAAGAGGUGC\n______________\|_\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\n______________U_AAGUUCC___AUUUUCUCCACG\n3'-CGC...GUCAC_G_______CA_____________GCGAG...AAG-5'\n_____________\|________________________\|\n_____________35_______________________11\n	255 -- 261	12 -- 18	-24.3693 kcal/mol	4.39141 kcal/mol	5.80707 kcal/mol	237 262@LB@ \| \|@LB@5'-CUG...AUAUC G AUG UGGCU...UGG-3'@LB@ A UUUAAGG UAAAAGAGGUGC@LB@ \| \|\|:\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ U AAGUUCC AUUUUCUCCACG@LB@3'-CGC...GUCAC G CA GCGAG...AAG-5'@LB@ \| \|@LB@ 35 11@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -24.3693 kcal/mol@LB@Unfolding Energy - mRNA 4.39141 kcal/mol@LB@Unfolding Energy - sRNA 5.80707 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 12 -- 34@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 12 -- 18@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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