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
144	0.006569	0.1605	b2900	yqfB	-12.46	0.083290	200 -- 238	34 -- 70	UPF0267 family protein	_____________199_______________________________________239\n_____________\|_________________________________________\|\n5'-UUC...AGUAC________CAAA__ACA________UUUUUCAAC_______GGAUG...UCA-3'\n______________CAUGCAGC____CG_____UCACUU_________GUUUCCA\n______________\|\|::\|\|\|\|____\|\|_____\|\|\|\|\|:_________:\|\|\|\|\|\|\n______________GUGUGUCG____GC_____AGUGAG_________UAAAGGU\n3'-UUU...CUGAU________UUAA__AACAA______UCCCC___________ACGAA...GCA-5'\n_____________\|_________________________________________\|\n_____________71________________________________________33\n	232 -- 238	34 -- 40	-21.1736 kcal/mol	3.92715 kcal/mol	4.79237 kcal/mol	199 239@LB@ \| \|@LB@5'-UUC...AGUAC CAAA ACA UUUUUCAAC GGAUG...UCA-3'@LB@ CAUGCAGC CG UCACUU GUUUCCA@LB@ \|\|::\|\|\|\| \|\| \|\|\|\|\|: :\|\|\|\|\|\|@LB@ GUGUGUCG GC AGUGAG UAAAGGU@LB@3'-UUU...CUGAU UUAA AACAA UCCCC ACGAA...GCA-5'@LB@ \| \|@LB@ 71 33@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.1736 kcal/mol@LB@Unfolding Energy - mRNA 3.92715 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 200 -- 238@LB@Position - sRNA 34 -- 70@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 34 -- 40@LB@
195	0.009901	0.1776	b1098	tmk	-15.44	0.015998	201 -- 230	41 -- 71	thymidylate kinase	_____________200_____________________________231\n_____________\|_______________________________\|\n5'-UAA...AAAAA___________GUAUAUCG______G_____CUGGA...GCG-3'\n______________AUGCGCAGUAA_________UCAUU_AGGGG\n______________\|::\|:\|\|\|:\|\|_________\|\|\|:\|_\|\|\|\|\|\n______________UGUGUGUCGUU_________AGUGA_UCCCC\n3'-UUU...UCUGA___________AAGCAACAA_____G_____UAAAG...GCA-5'\n_____________\|_______________________________\|\n_____________72______________________________40\n	205 -- 211	61 -- 67	-28.5877 kcal/mol	8.40445 kcal/mol	4.74226 kcal/mol	200 231@LB@ \| \|@LB@5'-UAA...AAAAA GUAUAUCG G CUGGA...GCG-3'@LB@ AUGCGCAGUAA UCAUU AGGGG@LB@ \|::\|:\|\|\|:\|\| \|\|\|:\| \|\|\|\|\|@LB@ UGUGUGUCGUU AGUGA UCCCC@LB@3'-UUU...UCUGA AAGCAACAA G UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -28.5877 kcal/mol@LB@Unfolding Energy - mRNA 8.40445 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 201 -- 230@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 61 -- 67@LB@
16	0.00012	0.02638	b3089	sstT	-15.87	0.012233	203 -- 224	42 -- 75	sodium:serine/threonine symporter	_____________202________________________________225\n_____________\|__________________________________\|\n5'-CAC...AAAAU_________ACG______________________CUAUU...CAU-3'\n______________GACUACGCA______________UUCAC_CGGGG\n______________\|\|\|\|\|\|:\|\|______________\|\|\|\|\|_\|:\|\|\|\n______________CUGAUGUGU______________AAGUG_GUCCC\n3'-UUU...CGUUU_________GUCGUUAAGCAACA_____A_____CUAAA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________41\n	205 -- 211	67 -- 73	-24.6329 kcal/mol	4.00159 kcal/mol	4.76397 kcal/mol	202 225@LB@ \| \|@LB@5'-CAC...AAAAU ACG CUAUU...CAU-3'@LB@ GACUACGCA UUCAC CGGGG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\| \|:\|\|\|@LB@ CUGAUGUGU AAGUG GUCCC@LB@3'-UUU...CGUUU GUCGUUAAGCAACA A CUAAA...GCA-5'@LB@ \| \|@LB@ 76 41@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.6329 kcal/mol@LB@Unfolding Energy - mRNA 4.00159 kcal/mol@LB@Unfolding Energy - sRNA 4.76397 kcal/mol@LB@@LB@Position - mRNA 203 -- 224@LB@Position - sRNA 42 -- 75@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 67 -- 73@LB@
30	0.0004324	0.05073	b3364	tsgA	-16.38	0.008733	203 -- 236	38 -- 75	putative transporter	_____________202_____________________________________237\n_____________\|_______________________________________\|\n5'-CCA...AUCAU___________________CAUCAA______CAU_____AGCUU...AUA-3'\n______________GACUA___ACAGCAAU_CG_______GCUCA___GGAUU\n______________\|\|\|\|\|___\|\|\|\|\|\|\|\|_\|\|_______:\|\|\|\|___\|\|\|\|\|\n______________CUGAU___UGUCGUUA_GC_______UGAGU___CCUAA\n3'-UUU...CGUUU_____GUG________A__AACAAAG_____CC______AGGUA...GCA-5'\n_____________\|_______________________________________\|\n_____________76______________________________________37\n	209 -- 215	60 -- 66	-26.4683 kcal/mol	5.30565 kcal/mol	4.77946 kcal/mol	202 237@LB@ \| \|@LB@5'-CCA...AUCAU CAUCAA CAU AGCUU...AUA-3'@LB@ GACUA ACAGCAAU CG GCUCA GGAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\| :\|\|\|\| \|\|\|\|\|@LB@ CUGAU UGUCGUUA GC UGAGU CCUAA@LB@3'-UUU...CGUUU GUG A AACAAAG CC AGGUA...GCA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -26.4683 kcal/mol@LB@Unfolding Energy - mRNA 5.30565 kcal/mol@LB@Unfolding Energy - sRNA 4.77946 kcal/mol@LB@@LB@Position - mRNA 203 -- 236@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 60 -- 66@LB@
78	0.003218	0.1452	b1641	slyB	-13.21	0.056987	203 -- 235	43 -- 75	outer membrane lipoprotein	_____________202_________________________________236\n_____________\|___________________________________\|\n5'-CCG...UCAAU_____A___________G_________AUGG____UCUGU...AAG-3'\n______________GAUUA_ACGC_GU_AUU_GUUGUUUCA____UAGG\n______________\|\|:\|\|_\|\|:\|_\|:_\|\|\|_\|\|\|\|\|\|\|\|\|____:\|\|\|\n______________CUGAU_UGUG_CG_UAA_CAACAAAGU____GUCC\n3'-UUU...CGUUU_____G____U__U___G_________GA______CCUAA...GCA-5'\n_____________\|___________________________________\|\n_____________76__________________________________42\n	221 -- 227	49 -- 55	-26.1882 kcal/mol	8.63028 kcal/mol	4.35266 kcal/mol	202 236@LB@ \| \|@LB@5'-CCG...UCAAU A G AUGG UCUGU...AAG-3'@LB@ GAUUA ACGC GU AUU GUUGUUUCA UAGG@LB@ \|\|:\|\| \|\|:\| \|: \|\|\| \|\|\|\|\|\|\|\|\| :\|\|\|@LB@ CUGAU UGUG CG UAA CAACAAAGU GUCC@LB@3'-UUU...CGUUU G U U G GA CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.1882 kcal/mol@LB@Unfolding Energy - mRNA 8.63028 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 203 -- 235@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 49 -- 55@LB@
118	0.005291	0.1553	b0481	ybaK	-9.02	0.349126	203 -- 225	45 -- 75	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase	_____________202_____________________________226\n_____________\|_______________________________\|\n5'-AAU...ACCAU______C______UAAA______________AAAAA...UCG-3'\n______________GAC_AC_CGCAGU___________UUACUCG\n______________\|\|\|_\|\|_\|:\|\|\|:___________\|:\|\|\|\|:\n______________CUG_UG_GUGUCG___________AGUGAGU\n3'-UUU...CGUUU___A__U______UUAAGCAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	219 -- 225	45 -- 51	-15.8984 kcal/mol	3.13427 kcal/mol	3.74078 kcal/mol	202 226@LB@ \| \|@LB@5'-AAU...ACCAU C UAAA AAAAA...UCG-3'@LB@ GAC AC CGCAGU UUACUCG@LB@ \|\|\| \|\| \|:\|\|\|: \|:\|\|\|\|:@LB@ CUG UG GUGUCG AGUGAGU@LB@3'-UUU...CGUUU A U UUAAGCAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.8984 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 225@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 45 -- 51@LB@
139	0.006425	0.1605	b0924	mukB	-11.72	0.118276	203 -- 227	45 -- 75	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________202_____________________________228\n_____________\|_______________________________\|\n5'-UGG...AUAAU_____A_________A_______________CUGAC...CUG-3'\n______________GAUUG_ACGCGGUAA_______UUUCGCUCA\n______________\|\|:\|:_\|\|:\|:\|:\|\|_______\|\|\|\|:\|\|\|\|\n______________CUGAU_UGUGUCGUU_______AAAGUGAGU\n3'-UUU...CGUUU_____G_________AAGCAAC_________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	221 -- 227	45 -- 51	-22.3255 kcal/mol	6.8688 kcal/mol	3.74078 kcal/mol	202 228@LB@ \| \|@LB@5'-UGG...AUAAU A A CUGAC...CUG-3'@LB@ GAUUG ACGCGGUAA UUUCGCUCA@LB@ \|\|:\|: \|\|:\|:\|:\|\| \|\|\|\|:\|\|\|\|@LB@ CUGAU UGUGUCGUU AAAGUGAGU@LB@3'-UUU...CGUUU G AAGCAAC CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -22.3255 kcal/mol@LB@Unfolding Energy - mRNA 6.8688 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 45 -- 51@LB@
125	0.005556	0.1564	b3384	trpS	-12.26	0.091693	207 -- 244	40 -- 100	tryptophanyl-tRNA synthetase	_____________206___________________________________________________________245\n_____________\|_____________________________________________________________\|\n5'-ACA...UGACU___________UUUUA__________________________________________U__AUUGA...AUG-3'\n______________AAGCCCAUCGU_____GUGG__________CGCACAGC____________C_CUCAGG_GA\n______________\|\|\|\|\|\|\|\|\|\|\|_____:\|\|\|__________\|:\|\|\|\|\|\|____________\|_\|\|\|\|\|\|_\|\|\n______________UUCGGGUAGCA_____UACC__________GUGUGUCG____________G_GAGUCC_CU\n______3'-UUUUU___________CCCUC____CGUUUCUGAU________UUAAGCAACAAA_U______C__AAAGG...GCA-5'\n_____________\|_____________________________________________________________\|\n_____________101___________________________________________________________39\n	228 -- 234	63 -- 69	-41.2838 kcal/mol	11.4457 kcal/mol	17.5818 kcal/mol	206 245@LB@ \| \|@LB@5'-ACA...UGACU UUUUA U AUUGA...AUG-3'@LB@ AAGCCCAUCGU GUGG CGCACAGC C CUCAGG GA@LB@ \|\|\|\|\|\|\|\|\|\|\| :\|\|\| \|:\|\|\|\|\|\| \| \|\|\|\|\|\| \|\|@LB@ UUCGGGUAGCA UACC GUGUGUCG G GAGUCC CU@LB@ 3'-UUUUU CCCUC CGUUUCUGAU UUAAGCAACAAA U C AAAGG...GCA-5'@LB@ \| \|@LB@ 101 39@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -41.2838 kcal/mol@LB@Unfolding Energy - mRNA 11.4457 kcal/mol@LB@Unfolding Energy - sRNA 17.5818 kcal/mol@LB@@LB@Position - mRNA 207 -- 244@LB@Position - sRNA 40 -- 100@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 63 -- 69@LB@
65	0.002677	0.1417	b0584	fepA	-11.47	0.132508	209 -- 249	37 -- 78	ferrienterobactin outer membrane transporter	_____________208___________________________________________250\n_____________\|_____________________________________________\|\n5'-GAA...AACAA___________U_CCU___C________G____A__U________AUGGG...ACG-3'\n______________GAAGAUU_CAU_C___GGC___UUGUUG__UCA_UC_GGGGAUUU\n______________:\|\|\|\|:\|_\|\|:_\|___:\|\|___\|:\|\|\|\|__\|\|\|_\|\|_\|\|\|\|\|\|\|\|\n______________UUUCUGA_GUG_G___UCG___AGCAAC__AGU_AG_CCCCUAAA\n3'-UUU...ACCCG_______U___U_______UUA______AA___G__U________GGUAC...GCA-5'\n_____________\|_____________________________________________\|\n_____________79____________________________________________36\n	243 -- 249	37 -- 43	-30.6633 kcal/mol	14.4176 kcal/mol	4.77973 kcal/mol	208 250@LB@ \| \|@LB@5'-GAA...AACAA U CCU C G A U AUGGG...ACG-3'@LB@ GAAGAUU CAU C GGC UUGUUG UCA UC GGGGAUUU@LB@ :\|\|\|\|:\| \|\|: \| :\|\| \|:\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UUUCUGA GUG G UCG AGCAAC AGU AG CCCCUAAA@LB@3'-UUU...ACCCG U U UUA AA G U GGUAC...GCA-5'@LB@ \| \|@LB@ 79 36@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -30.6633 kcal/mol@LB@Unfolding Energy - mRNA 14.4176 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 209 -- 249@LB@Position - sRNA 37 -- 78@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 37 -- 43@LB@
113	0.004991	0.1545	b0888	trxB	-9.59	0.285839	209 -- 223	61 -- 75	thioredoxin reductase FAD/NAD(P)-binding	_____________208_____________224\n_____________\|_______________\|\n5'-AAC...GGCAC___CAA_________ACUGC...UGC-3'\n______________GAC___ACACAGUAA\n______________\|\|\|___\|\|\|\|\|\|:\|\|\n______________CUG___UGUGUCGUU\n3'-UUU...CGUUU___AUG_________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	217 -- 223	61 -- 67	-15.4977 kcal/mol	2.65453 kcal/mol	3.25399 kcal/mol	208 224@LB@ \| \|@LB@5'-AAC...GGCAC CAA ACUGC...UGC-3'@LB@ GAC ACACAGUAA@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UGUGUCGUU@LB@3'-UUU...CGUUU AUG AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4977 kcal/mol@LB@Unfolding Energy - mRNA 2.65453 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 209 -- 223@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 61 -- 67@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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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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