Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
47	0.001402	0.105	b2297	pta	-18.38	0.002042	9 -- 40	45 -- 75	phosphate acetyltransferase	_____________8__________________________________41\n_____________\|__________________________________\|\n___5'-CGCAACCU_________UUU______A__UG___________ACAAA...GUC-3'\n______________GGCUGCACG___CGGCAA_UC___GUUUCA_UCA\n______________\|:\|\|:\|\|\|:___\|:\|\|\|\|_\|\|___\|\|\|\|\|\|_\|\|\|\n______________CUGAUGUGU___GUCGUU_AG___CAAAGU_AGU\n3'-UUU...CGUUU__________________A__CAA______G___CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________44\n	11 -- 17	67 -- 73	-26.9548 kcal/mol	4.83173 kcal/mol	3.74078 kcal/mol	8 41@LB@ \| \|@LB@ 5'-CGCAACCU UUU A UG ACAAA...GUC-3'@LB@ GGCUGCACG CGGCAA UC GUUUCA UCA@LB@ \|:\|\|:\|\|\|: \|:\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|@LB@ CUGAUGUGU GUCGUU AG CAAAGU AGU@LB@3'-UUU...CGUUU A CAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -18.38 kcal/mol@LB@Hybridization Energy -26.9548 kcal/mol@LB@Unfolding Energy - mRNA 4.83173 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 9 -- 40@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 67 -- 73@LB@
7	1.819e-05	0.009142	b1849	purT	-22.68	0.000026	168 -- 199	33 -- 74	phosphoribosylglycinamide formyltransferase 2	_____________167________________________________________200\n_____________\|__________________________________________\|\n5'-UUU...UUUAU________________AA__________________A_____UAUGA...GUC-3'\n______________ACUGCGCGCGG_AAUU___________UCAGGGGAU_UUCGU\n______________\|\|\|:\|:\|:\|:\|_\|\|\|\|___________\|\|\|\|\|\|\|\|\|_\|:\|:\|\n______________UGAUGUGUGUC_UUAA___________AGUCCCCUA_AGGUA\n3'-UUU...GUUUC___________G____GCAACAAAGUG_________A_____CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	187 -- 193	39 -- 45	-34.2979 kcal/mol	6.80622 kcal/mol	4.81602 kcal/mol	167 200@LB@ \| \|@LB@5'-UUU...UUUAU AA A UAUGA...GUC-3'@LB@ ACUGCGCGCGG AAUU UCAGGGGAU UUCGU@LB@ \|\|\|:\|:\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|\|\| \|:\|:\|@LB@ UGAUGUGUGUC UUAA AGUCCCCUA AGGUA@LB@3'-UUU...GUUUC G GCAACAAAGUG A CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -22.68 kcal/mol@LB@Hybridization Energy -34.2979 kcal/mol@LB@Unfolding Energy - mRNA 6.80622 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 168 -- 199@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 39 -- 45@LB@
71	0.002886	0.1417	b2431	yfeX	-11.26	0.145044	235 -- 277	40 -- 74	porphyrinogen oxidase cytoplasmic	_____________234_________________________________________278\n_____________\|___________________________________________\|\n5'-AUU...AGAAC____C______________GAUCGAA__CAACGUGAA______AGUUG...CCA-3'\n______________AUUG_CGCGCGGCGAUUUG_______GC_________AGGGGA\n______________\|:\|:_\|:\|:\|:\|\|:\|\|\|:\|_______:\|_________\|\|\|\|\|\|\n______________UGAU_GUGUGUCGUUAAGC_______UG_________UCCCCU\n3'-UUU...GUUUC___________________AACAAAG__AG_____________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________75__________________________________________39\n	246 -- 252	58 -- 64	-30.0675 kcal/mol	14.0273 kcal/mol	4.77707 kcal/mol	234 278@LB@ \| \|@LB@5'-AUU...AGAAC C GAUCGAA CAACGUGAA AGUUG...CCA-3'@LB@ AUUG CGCGCGGCGAUUUG GC AGGGGA@LB@ \|:\|: \|:\|:\|:\|\|:\|\|\|:\| :\| \|\|\|\|\|\|@LB@ UGAU GUGUGUCGUUAAGC UG UCCCCU@LB@3'-UUU...GUUUC AACAAAG AG AAAGG...GCA-5'@LB@ \| \|@LB@ 75 39@LB@@LB@@LB@Energy -11.26 kcal/mol@LB@Hybridization Energy -30.0675 kcal/mol@LB@Unfolding Energy - mRNA 14.0273 kcal/mol@LB@Unfolding Energy - sRNA 4.77707 kcal/mol@LB@@LB@Position - mRNA 235 -- 277@LB@Position - sRNA 40 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
42	0.0009586	0.08031	b3747	kup	-11.44	0.134185	159 -- 185	49 -- 77	potassium transporter	_____________158___________________________186\n_____________\|_____________________________\|\n5'-AAA...GCCAA_______A________U___AUA______ACGAA...GUG-3'\n______________GGGACUA_GCACA_CA_UUC____UUUCA\n______________::\|\|\|\|\|_:\|\|\|\|_\|\|_\|\|\|____\|\|\|\|\|\n______________UUCUGAU_UGUGU_GU_AAG____AAAGU\n3'-UUU...CCCGU_______G_____C__U___CAAC_____GAGUC...GCA-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	159 -- 165	71 -- 77	-19.3471 kcal/mol	4.22429 kcal/mol	3.68465 kcal/mol	158 186@LB@ \| \|@LB@5'-AAA...GCCAA A U AUA ACGAA...GUG-3'@LB@ GGGACUA GCACA CA UUC UUUCA@LB@ ::\|\|\|\|\| :\|\|\|\| \|\| \|\|\| \|\|\|\|\|@LB@ UUCUGAU UGUGU GU AAG AAAGU@LB@3'-UUU...CCCGU G C U CAAC GAGUC...GCA-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -19.3471 kcal/mol@LB@Unfolding Energy - mRNA 4.22429 kcal/mol@LB@Unfolding Energy - sRNA 3.68465 kcal/mol@LB@@LB@Position - mRNA 159 -- 185@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 71 -- 77@LB@
110	0.004806	0.1538	b1429	tehA	-12.16	0.096068	32 -- 62	44 -- 75	potassium-tellurite ethidium and proflavin transporter	_____________31_________________________________63\n_____________\|__________________________________\|\n5'-AAU...UUCCU___A__UAAA_________C___UC_________ACGAU...UUU-3'\n______________GAU_AC____GGC___UCG_UGU__UUCACUUAG\n______________\|\|:_\|\|____:\|\|___\|\|\|_\|\|\|__\|\|\|\|\|\|:\|\|\n______________CUG_UG____UCG___AGC_ACA__AAGUGAGUC\n3'-UUU...CGUUU___A__UGUG___UUA___A______________CCCUA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________43\n	56 -- 62	44 -- 50	-20.5577 kcal/mol	4.26011 kcal/mol	4.13839 kcal/mol	31 63@LB@ \| \|@LB@5'-AAU...UUCCU A UAAA C UC ACGAU...UUU-3'@LB@ GAU AC GGC UCG UGU UUCACUUAG@LB@ \|\|: \|\| :\|\| \|\|\| \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UG UCG AGC ACA AAGUGAGUC@LB@3'-UUU...CGUUU A UGUG UUA A CCCUA...GCA-5'@LB@ \| \|@LB@ 76 43@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -20.5577 kcal/mol@LB@Unfolding Energy - mRNA 4.26011 kcal/mol@LB@Unfolding Energy - sRNA 4.13839 kcal/mol@LB@@LB@Position - mRNA 32 -- 62@LB@Position - sRNA 44 -- 75@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 44 -- 50@LB@
74	0.003066	0.1452	b0467	priC	-11.71	0.118543	157 -- 193	43 -- 75	primosomal replication protein N''	_____________156___________________________________194\n_____________\|_____________________________________\|\n5'-GGG...AGAGU______UUUA_____A_____AUCAU_______G___UCUUA...GUU-3'\n______________GGCUAC____GCAUA_CAAUU_____UUUCAUU_AGG\n______________\|:\|\|\|\|____:\|\|:\|_\|\|\|\|\|_____\|\|\|\|\|:\|_\|\|\|\n______________CUGAUG____UGUGU_GUUAA_____AAAGUGA_UCC\n3'-UUU...CGUUU_______________C_____GCAAC_______G___CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________76____________________________________42\n	183 -- 189	47 -- 53	-24.815 kcal/mol	8.75149 kcal/mol	4.35266 kcal/mol	156 194@LB@ \| \|@LB@5'-GGG...AGAGU UUUA A AUCAU G UCUUA...GUU-3'@LB@ GGCUAC GCAUA CAAUU UUUCAUU AGG@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|@LB@ CUGAUG UGUGU GUUAA AAAGUGA UCC@LB@3'-UUU...CGUUU C GCAAC G CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -24.815 kcal/mol@LB@Unfolding Energy - mRNA 8.75149 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 157 -- 193@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 47 -- 53@LB@
79	0.00332	0.1462	b1845	ptrB	-10.90	0.169644	42 -- 70	35 -- 70	protease II	_____________41____________________________________71\n_____________\|_____________________________________\|\n5'-UCU...AGAAU________C_____AA____________CU_______UCUGU...AGC-3'\n______________CGCACAGC_AUUUG__________CAGG__GAUUUUC\n______________\|:\|\|\|\|\|\|_\|\|\|:\|__________\|\|\|\|__\|\|\|\|\|:\|\n______________GUGUGUCG_UAAGC__________GUCC__CUAAAGG\n3'-UUU...CUGAU________U_____AACAAAGUGA____C________UACGA...GCA-5'\n_____________\|_____________________________________\|\n_____________71____________________________________34\n	64 -- 70	35 -- 41	-24.5069 kcal/mol	8.82337 kcal/mol	4.7817 kcal/mol	41 71@LB@ \| \|@LB@5'-UCU...AGAAU C AA CU UCUGU...AGC-3'@LB@ CGCACAGC AUUUG CAGG GAUUUUC@LB@ \|:\|\|\|\|\|\| \|\|\|:\| \|\|\|\| \|\|\|\|\|:\|@LB@ GUGUGUCG UAAGC GUCC CUAAAGG@LB@3'-UUU...CUGAU U AACAAAGUGA C UACGA...GCA-5'@LB@ \| \|@LB@ 71 34@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -24.5069 kcal/mol@LB@Unfolding Energy - mRNA 8.82337 kcal/mol@LB@Unfolding Energy - sRNA 4.7817 kcal/mol@LB@@LB@Position - mRNA 42 -- 70@LB@Position - sRNA 35 -- 70@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 35 -- 41@LB@
50	0.001668	0.1153	b2821	ptrA	-10.19	0.227412	3 -- 12	46 -- 55	protease III	_____________2__________13\n_____________\|__________\|\n_________5'-GC__________UAAUC...CCA-3'\n______________UGUUUCGCUU\n______________\|\|\|\|\|\|:\|\|:\n______________ACAAAGUGAG\n3'-UUU...AAGCA__________UCCCC...GCA-5'\n_____________\|__________\|\n_____________56_________45\n	6 -- 12	46 -- 52	-11.8599 kcal/mol	0.772948 kcal/mol	0.89782 kcal/mol	2 13@LB@ \| \|@LB@ 5'-GC UAAUC...CCA-3'@LB@ UGUUUCGCUU@LB@ \|\|\|\|\|\|:\|\|:@LB@ ACAAAGUGAG@LB@3'-UUU...AAGCA UCCCC...GCA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -11.8599 kcal/mol@LB@Unfolding Energy - mRNA 0.772948 kcal/mol@LB@Unfolding Energy - sRNA 0.89782 kcal/mol@LB@@LB@Position - mRNA 3 -- 12@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 46 -- 52@LB@
39	0.0006857	0.06187	b1305	pspB	-16.08	0.010660	268 -- 296	48 -- 75	psp operon transcription co-activator	_____________267____________________________297\n_____________\|______________________________\|\n5'-AUU...GUUAU_______U______________CUGG____AGUG-3'\n______________GGCUGCA_UACAGCAAU_CGUU____UCGC\n______________\|:\|\|:\|\|_:\|\|\|\|\|\|\|\|_\|\|\|\|____\|\|:\|\n______________CUGAUGU_GUGUCGUUA_GCAA____AGUG\n3'-UUU...CGUUU_________________A____CAA_____AGUCC...GCA-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	278 -- 284	60 -- 66	-29.5086 kcal/mol	9.74074 kcal/mol	3.68696 kcal/mol	267 297@LB@ \| \|@LB@5'-AUU...GUUAU U CUGG AGUG-3'@LB@ GGCUGCA UACAGCAAU CGUU UCGC@LB@ \|:\|\|:\|\| :\|\|\|\|\|\|\|\| \|\|\|\| \|\|:\|@LB@ CUGAUGU GUGUCGUUA GCAA AGUG@LB@3'-UUU...CGUUU A CAA AGUCC...GCA-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -16.08 kcal/mol@LB@Hybridization Energy -29.5086 kcal/mol@LB@Unfolding Energy - mRNA 9.74074 kcal/mol@LB@Unfolding Energy - sRNA 3.68696 kcal/mol@LB@@LB@Position - mRNA 268 -- 296@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 60 -- 66@LB@
66	0.002697	0.1417	b1306	pspC	-11.06	0.158336	44 -- 64	55 -- 75	psp operon transcription co-activator	_____________43_____________________65\n_____________\|______________________\|\n5'-CCG...GUUAU_______U______________CUGGU...CGG-3'\n______________GGCUGCA_UACAGCAAU_CGUU\n______________\|:\|\|:\|\|_:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUGAUGU_GUGUCGUUA_GCAA\n3'-UUU...CGUUU_________________A____CAAAG...GCA-5'\n_____________\|______________________\|\n_____________76_____________________54\n	54 -- 60	60 -- 66	-24.9269 kcal/mol	10.2549 kcal/mol	3.6092 kcal/mol	43 65@LB@ \| \|@LB@5'-CCG...GUUAU U CUGGU...CGG-3'@LB@ GGCUGCA UACAGCAAU CGUU@LB@ \|:\|\|:\|\| :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGAUGU GUGUCGUUA GCAA@LB@3'-UUU...CGUUU A CAAAG...GCA-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -24.9269 kcal/mol@LB@Unfolding Energy - mRNA 10.2549 kcal/mol@LB@Unfolding Energy - sRNA 3.6092 kcal/mol@LB@@LB@Position - mRNA 44 -- 64@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 60 -- 66@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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service.

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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