Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
198	0.02503	0.4226	b2544	yphB	-11.73	0.099011	68 -- 80	47 -- 61	mutarotase superfamily protein YphB family	_____________67______________81\n_____________\|_______________\|\n5'-CGG...GACGG_______________GCCGC...UAC-3'\n______________ACUGGAAGC__UGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UGACCUUCG__ACAC\n3'-UUU...CAUUA_________UU____UCGUU...GCG-5'\n_____________\|_______________\|\n_____________62______________46\n	70 -- 76	53 -- 59	-17.6322 kcal/mol	2.81046 kcal/mol	3.09217 kcal/mol	67 81@LB@ \| \|@LB@5'-CGG...GACGG GCCGC...UAC-3'@LB@ ACUGGAAGC UGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACCUUCG ACAC@LB@3'-UUU...CAUUA UU UCGUU...GCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.6322 kcal/mol@LB@Unfolding Energy - mRNA 2.81046 kcal/mol@LB@Unfolding Energy - sRNA 3.09217 kcal/mol@LB@@LB@Position - mRNA 68 -- 80@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 53 -- 59@LB@
108	0.01121	0.3489	b4195	ulaC	-11.73	0.099158	148 -- 168	44 -- 62	L-ascorbate-specific enzyme IIA component of PTS	_____________147___________________169\n_____________\|_____________________\|\n5'-GCG...GAAAC_____________CAAA____AUUUC...UGG-3'\n______________UGCUGGAAGUGAU____GAGC\n______________\|:\|\|\|\|\|\|\|::\|\|____\|\|\|\|\n______________AUGACCUUCGUUA____CUCG\n3'-UUU...UCAUU_____________CA______UUACA...GCG-5'\n_____________\|_____________________\|\n_____________63____________________43\n	152 -- 158	52 -- 58	-21.7326 kcal/mol	6.70621 kcal/mol	3.30069 kcal/mol	147 169@LB@ \| \|@LB@5'-GCG...GAAAC CAAA AUUUC...UGG-3'@LB@ UGCUGGAAGUGAU GAGC@LB@ \|:\|\|\|\|\|\|\|::\|\| \|\|\|\|@LB@ AUGACCUUCGUUA CUCG@LB@3'-UUU...UCAUU CA UUACA...GCG-5'@LB@ \| \|@LB@ 63 43@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -21.7326 kcal/mol@LB@Unfolding Energy - mRNA 6.70621 kcal/mol@LB@Unfolding Energy - sRNA 3.30069 kcal/mol@LB@@LB@Position - mRNA 148 -- 168@LB@Position - sRNA 44 -- 62@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 52 -- 58@LB@
82	0.008223	0.3318	b1654	grxD	-11.69	0.100410	189 -- 207	43 -- 58	glutaredoxin-4	_____________188_________________208\n_____________\|___________________\|\n5'-AAA...UUUGA________GACAA______CCACU...CUG-3'\n______________GGAAGCAA_____UGAGCA\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\n______________CCUUCGUU_____ACUCGU\n3'-UUU...UAUGA________AC_________UACAG...GCG-5'\n_____________\|___________________\|\n_____________59__________________42\n	190 -- 196	51 -- 57	-19.1647 kcal/mol	4.26252 kcal/mol	3.20949 kcal/mol	188 208@LB@ \| \|@LB@5'-AAA...UUUGA GACAA CCACU...CUG-3'@LB@ GGAAGCAA UGAGCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CCUUCGUU ACUCGU@LB@3'-UUU...UAUGA AC UACAG...GCG-5'@LB@ \| \|@LB@ 59 42@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -19.1647 kcal/mol@LB@Unfolding Energy - mRNA 4.26252 kcal/mol@LB@Unfolding Energy - sRNA 3.20949 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 43 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 51 -- 57@LB@
106	0.01088	0.3447	b3543	dppB	-11.69	0.100651	144 -- 153	41 -- 50	dipeptide/heme ABC transporter permease	_____________143________154\n_____________\|__________\|\n5'-CGG...UGAUU__________ACAGA...AUC-3'\n______________UGUGAGCAAU\n______________\|\|\|\|\|\|\|\|\|\|\n______________ACACUCGUUA\n3'-UUU...UCGUU__________CAGCA...GCG-5'\n_____________\|__________\|\n_____________51_________40\n	147 -- 153	41 -- 47	-14.8509 kcal/mol	2.00067 kcal/mol	1.16388 kcal/mol	143 154@LB@ \| \|@LB@5'-CGG...UGAUU ACAGA...AUC-3'@LB@ UGUGAGCAAU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ ACACUCGUUA@LB@3'-UUU...UCGUU CAGCA...GCG-5'@LB@ \| \|@LB@ 51 40@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -14.8509 kcal/mol@LB@Unfolding Energy - mRNA 2.00067 kcal/mol@LB@Unfolding Energy - sRNA 1.16388 kcal/mol@LB@@LB@Position - mRNA 144 -- 153@LB@Position - sRNA 41 -- 50@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 41 -- 47@LB@
71	0.00621	0.2939	b0178	skp	-11.69	0.100677	99 -- 118	40 -- 66	periplasmic chaperone	_____________98__________________________119\n_____________\|___________________________\|\n5'-CUC...GGAAU___________________________ACUUU...UCC-3'\n______________GUAGU______GGUAGUGU_AGCGAUG\n______________\|\|\|:\|______:\|:\|:\|\|\|_\|\|\|:\|\|\|\n______________CAUUA______UCGUUACA_UCGUUAC\n3'-UUU...CGAUU_____UGACCU________C_______AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________67__________________________39\n	112 -- 118	40 -- 46	-18.9809 kcal/mol	3.99027 kcal/mol	3.30497 kcal/mol	98 119@LB@ \| \|@LB@5'-CUC...GGAAU ACUUU...UCC-3'@LB@ GUAGU GGUAGUGU AGCGAUG@LB@ \|\|\|:\| :\|:\|:\|\|\| \|\|\|:\|\|\|@LB@ CAUUA UCGUUACA UCGUUAC@LB@3'-UUU...CGAUU UGACCU C AGCAC...GCG-5'@LB@ \| \|@LB@ 67 39@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -18.9809 kcal/mol@LB@Unfolding Energy - mRNA 3.99027 kcal/mol@LB@Unfolding Energy - sRNA 3.30497 kcal/mol@LB@@LB@Position - mRNA 99 -- 118@LB@Position - sRNA 40 -- 66@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 40 -- 46@LB@
62	0.005609	0.2905	b1132	hflD	-11.66	0.101792	188 -- 207	42 -- 58	putative lysogenization regulator	_____________187___________________208\n_____________\|_____________________\|\n5'-ACC...AACAA_________GAAC________AGAAU...CCG-3'\n______________GGAAGCAGU____GUG_GCAA\n______________\|\|\|\|\|\|\|:\|____\|\|\|_\|\|\|\|\n______________CCUUCGUUA____CAC_CGUU\n3'-UUU...UAUGA________________U____ACAGC...GCG-5'\n_____________\|_____________________\|\n_____________59____________________41\n	190 -- 196	50 -- 56	-19.7521 kcal/mol	4.88534 kcal/mol	3.2101 kcal/mol	187 208@LB@ \| \|@LB@5'-ACC...AACAA GAAC AGAAU...CCG-3'@LB@ GGAAGCAGU GUG GCAA@LB@ \|\|\|\|\|\|\|:\| \|\|\| \|\|\|\|@LB@ CCUUCGUUA CAC CGUU@LB@3'-UUU...UAUGA U ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -19.7521 kcal/mol@LB@Unfolding Energy - mRNA 4.88534 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 188 -- 207@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
129	0.01401	0.3627	b0696	kdpC	-11.63	0.102829	282 -- 295	49 -- 63	potassium translocating ATPase subunit C	_____________281_____________296\n_____________\|_______________\|\n5'-GCG...CCACC_______________GUGGU-3'\n______________GUACUGG_GGCAAUG\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\n______________UAUGACC_UCGUUAC\n3'-UUU...UUCAU_______U_______ACUCG...GCG-5'\n_____________\|_______________\|\n_____________64______________48\n	289 -- 295	49 -- 55	-18.0603 kcal/mol	3.42021 kcal/mol	3.01015 kcal/mol	281 296@LB@ \| \|@LB@5'-GCG...CCACC GUGGU-3'@LB@ GUACUGG GGCAAUG@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UAUGACC UCGUUAC@LB@3'-UUU...UUCAU U ACUCG...GCG-5'@LB@ \| \|@LB@ 64 48@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -18.0603 kcal/mol@LB@Unfolding Energy - mRNA 3.42021 kcal/mol@LB@Unfolding Energy - sRNA 3.01015 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 49 -- 63@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 49 -- 55@LB@
90	0.009279	0.3393	b0817	mntR	-11.60	0.104050	186 -- 211	37 -- 65	Mn(2+)-responsive manganese regulon transcriptional regulator	_____________185___________________________212\n_____________\|_____________________________\|\n5'-CUU...CACCA_____A________CAA_____C______CGCAG...AUC-3'\n______________UAAUG__GGAAGCA___UGAGU___GUCG\n______________\|\|\|\|:__\|\|\|\|\|\|\|___\|\|\|\|:___\|\|\|\|\n______________AUUAU__CCUUCGU___ACUCG___CAGC\n3'-UUU...GAUUC_____GA_______UAC_____UUA____ACGAA...GCG-5'\n_____________\|_____________________________\|\n_____________66____________________________36\n	192 -- 198	52 -- 58	-22.6144 kcal/mol	7.71005 kcal/mol	3.30549 kcal/mol	185 212@LB@ \| \|@LB@5'-CUU...CACCA A CAA C CGCAG...AUC-3'@LB@ UAAUG GGAAGCA UGAGU GUCG@LB@ \|\|\|\|: \|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|@LB@ AUUAU CCUUCGU ACUCG CAGC@LB@3'-UUU...GAUUC GA UAC UUA ACGAA...GCG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -22.6144 kcal/mol@LB@Unfolding Energy - mRNA 7.71005 kcal/mol@LB@Unfolding Energy - sRNA 3.30549 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 52 -- 58@LB@
185	0.02285	0.4113	b0920	elyC	-11.60	0.104081	77 -- 89	66 -- 78	envelope biogenesis factor; DUF218 superfamily protein	_____________76____________90\n_____________\|_____________\|\n5'-UUG...CUCCA_____________ACGUU...GCC-3'\n______________CCGGUUGGCUAAG\n______________\|\|\|\|:\|\|\|\|\|\|\|\|\n______________GGCCGACCGAUUC\n3'-UUU...UCGUG_____________AUUAU...GCG-5'\n_____________\|_____________\|\n_____________79____________65\n	83 -- 89	66 -- 72	-24.3939 kcal/mol	5.56302 kcal/mol	7.23276 kcal/mol	76 90@LB@ \| \|@LB@5'-UUG...CUCCA ACGUU...GCC-3'@LB@ CCGGUUGGCUAAG@LB@ \|\|\|\|:\|\|\|\|\|\|\|\|@LB@ GGCCGACCGAUUC@LB@3'-UUU...UCGUG AUUAU...GCG-5'@LB@ \| \|@LB@ 79 65@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -24.3939 kcal/mol@LB@Unfolding Energy - mRNA 5.56302 kcal/mol@LB@Unfolding Energy - sRNA 7.23276 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 66 -- 78@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 66 -- 72@LB@
186	0.02299	0.4113	b3996	nudC	-11.58	0.104830	175 -- 203	40 -- 67	NADH pyrophosphatase	_____________174____________________________204\n_____________\|______________________________\|\n5'-GAU...AUGCC________AA_________CAA____U___GAUCG...CGG-3'\n______________AGUGAUGC___AGGUAGUG___GAGC_AUG\n______________\|\|\|:\|\|:\|___\|:\|:\|:\|\|___\|\|\|\|_\|\|\|\n______________UCAUUAUG___UUCGUUAC___CUCG_UAC\n3'-UUU...CCGAU________ACC________A______U___AGCAC...GCG-5'\n_____________\|______________________________\|\n_____________68_____________________________39\n	186 -- 192	49 -- 55	-21.6638 kcal/mol	6.77954 kcal/mol	3.30504 kcal/mol	174 204@LB@ \| \|@LB@5'-GAU...AUGCC AA CAA U GAUCG...CGG-3'@LB@ AGUGAUGC AGGUAGUG GAGC AUG@LB@ \|\|\|:\|\|:\| \|:\|:\|:\|\| \|\|\|\| \|\|\|@LB@ UCAUUAUG UUCGUUAC CUCG UAC@LB@3'-UUU...CCGAU ACC A U AGCAC...GCG-5'@LB@ \| \|@LB@ 68 39@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -21.6638 kcal/mol@LB@Unfolding Energy - mRNA 6.77954 kcal/mol@LB@Unfolding Energy - sRNA 3.30504 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 67@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 49 -- 55@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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