Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
31	0.001906	0.2067	b0198	metI	-9.82	0.132421	237 -- 257	48 -- 68	DL-methionine transporter subunit		_____________236____________________258\n_____________\|______________________\|\n5'-UCA...GUGGC__A__________C________ACCUU...CGG-3'\n______________GU_UGGGAAA_CG_UGGCAAUG\n______________\|\|_\|\|\|:\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CA_ACCUUUU_GU_ACCGUUAC\n3'-UUU...AUAUA__________A__C________GUUAC...UUG-5'\n_____________\|______________________\|\n_____________69_____________________47\n	251 -- 257	48 -- 54	-20.2902 kcal/mol	6.26471 kcal/mol	4.20468 kcal/mol	236 258@LB@ \| \|@LB@5'-UCA...GUGGC A C ACCUU...CGG-3'@LB@ GU UGGGAAA CG UGGCAAUG@LB@ \|\| \|\|\|:\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CA ACCUUUU GU ACCGUUAC@LB@3'-UUU...AUAUA A C GUUAC...UUG-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -20.2902 kcal/mol@LB@Unfolding Energy - mRNA 6.26471 kcal/mol@LB@Unfolding Energy - sRNA 4.20468 kcal/mol@LB@@LB@Position - mRNA 237 -- 257@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 48 -- 54@LB@
32	0.002002	0.2088	b0423	thiI	-12.47	0.034301	40 -- 74	41 -- 65	tRNA s(4)U8 sulfurtransferase		_____________39_____________________________________75\n_____________\|______________________________________\|\n5'-AUG...GUAAC___C____________AUAGCAAAUAACGC________AAGGU...UUU-3'\n______________GGA___UCAG_GGCAA______________GCAAUGGU\n______________\|\|\|___\|\|\|\|_\|\|\|\|\|______________\|\|\|\|\|\|\|:\n______________CCU___AGUC_CCGUU______________CGUUACCG\n3'-UUU...UACAA___UUU____A_____A_____________________GGUUG...UUG-5'\n_____________\|______________________________________\|\n_____________66_____________________________________40\n	68 -- 74	41 -- 47	-23.8518 kcal/mol	5.56921 kcal/mol	5.80973 kcal/mol	39 75@LB@ \| \|@LB@5'-AUG...GUAAC C AUAGCAAAUAACGC AAGGU...UUU-3'@LB@ GGA UCAG GGCAA GCAAUGGU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ CCU AGUC CCGUU CGUUACCG@LB@3'-UUU...UACAA UUU A A GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -23.8518 kcal/mol@LB@Unfolding Energy - mRNA 5.56921 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 40 -- 74@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 41 -- 47@LB@
33	0.002101	0.2088	b1300	puuC	-8.92	0.198515	81 -- 101	2 -- 20	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase	b0312	_____________80____________________102\n_____________\|_____________________\|\n5'-GGC...CGGCU___AG_______U________AGAAU...AAA-3'\n______________UGA__GAUGAAG_GUAUAUAA\n______________\|\|\|__:\|\|:\|\|\|_\|:\|\|\|\|\|\|\n______________ACU__UUAUUUC_CGUAUAUU\n3'-UUU...UAGAC___G_________________G-5'\n_____________\|_____________________\|\n_____________21____________________1\n	94 -- 100	3 -- 9	-14.4968 kcal/mol	1.34672 kcal/mol	4.22649 kcal/mol	80 102@LB@ \| \|@LB@5'-GGC...CGGCU AG U AGAAU...AAA-3'@LB@ UGA GAUGAAG GUAUAUAA@LB@ \|\|\| :\|\|:\|\|\| \|:\|\|\|\|\|\|@LB@ ACU UUAUUUC CGUAUAUU@LB@3'-UUU...UAGAC G G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.92 kcal/mol@LB@Hybridization Energy -14.4968 kcal/mol@LB@Unfolding Energy - mRNA 1.34672 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 3 -- 9@LB@
34	0.002116	0.2088	b0081	mraZ	-11.86	0.047767	154 -- 189	9 -- 59	RsmH methytransferase inhibitor		_____________153___________________________________________________190\n_____________\|_____________________________________________________\|\n5'-GAU...UCCUU_______G__AU_________AA_____________________G________GUGAG...AAA-3'\n______________UCAGUGG_AA__UGUGG_GGC__A________________GUGG_AAUAAGGG\n______________\|\|\|\|\|\|\|_\|\|__\|\|:::_\|\|\|__\|________________\|\|\|:_\|\|\|\|\|:\|\|\n______________AGUCACC_UU__ACGUU_CCG__U________________CACU_UUAUUUCC\n3'-UUU...CUUUU_______G_________A___GG_UGUCUUUUAUUUUAGA____G________GUAUAUUG-5'\n_____________\|_____________________________________________________\|\n_____________60____________________________________________________8\n	183 -- 189	9 -- 15	-29.7093 kcal/mol	6.7157 kcal/mol	11.1344 kcal/mol	153 190@LB@ \| \|@LB@5'-GAU...UCCUU G AU AA G GUGAG...AAA-3'@LB@ UCAGUGG AA UGUGG GGC A GUGG AAUAAGGG@LB@ \|\|\|\|\|\|\| \|\| \|\|::: \|\|\| \| \|\|\|: \|\|\|\|\|:\|\|@LB@ AGUCACC UU ACGUU CCG U CACU UUAUUUCC@LB@3'-UUU...CUUUU G A GG UGUCUUUUAUUUUAGA G GUAUAUUG-5'@LB@ \| \|@LB@ 60 8@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -29.7093 kcal/mol@LB@Unfolding Energy - mRNA 6.7157 kcal/mol@LB@Unfolding Energy - sRNA 11.1344 kcal/mol@LB@@LB@Position - mRNA 154 -- 189@LB@Position - sRNA 9 -- 59@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 9 -- 15@LB@
35	0.002227	0.2088	b1482	osmC	-7.15	0.399399	183 -- 208	14 -- 42	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin		_____________182___________________________209\n_____________\|_____________________________\|\n5'-UAG...UUUAA_____________GCAACAA_________CCAUA...CGU-3'\n______________GCCC_ACAGGAGA_________UGACAAU\n______________\|\|\|\|_\|\|\|\|:\|:\|_________\|\|\|\|\|\|\|\n______________CGGG_UGUCUUUU_________ACUGUUA\n3'-UUU...GUUAC____U________AUUUUAGAC_______UUUCC...UUG-5'\n_____________\|_____________________________\|\n_____________43____________________________13\n	202 -- 208	14 -- 20	-22.1887 kcal/mol	4.46968 kcal/mol	10.5676 kcal/mol	182 209@LB@ \| \|@LB@5'-UAG...UUUAA GCAACAA CCAUA...CGU-3'@LB@ GCCC ACAGGAGA UGACAAU@LB@ \|\|\|\| \|\|\|\|:\|:\| \|\|\|\|\|\|\|@LB@ CGGG UGUCUUUU ACUGUUA@LB@3'-UUU...GUUAC U AUUUUAGAC UUUCC...UUG-5'@LB@ \| \|@LB@ 43 13@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -22.1887 kcal/mol@LB@Unfolding Energy - mRNA 4.46968 kcal/mol@LB@Unfolding Energy - sRNA 10.5676 kcal/mol@LB@@LB@Position - mRNA 183 -- 208@LB@Position - sRNA 14 -- 42@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 14 -- 20@LB@
36	0.002273	0.2088	b4138	dcuA	-11.14	0.069498	259 -- 284	41 -- 65	C4-dicarboxylate antiporter		_____________258__________________________285\n_____________\|____________________________\|\n5'-AAC...AUUGG_______A___AUU___UU_________GGAUU...UGG-3'\n______________GGGGAAU_GGU___GGU__UGCA__GGC\n______________\|\|::\|\|\|_:\|\|___\|\|:__\|\|\|\|__\|\|\|\n______________CCUUUUA_UCA___CCG__ACGU__CCG\n3'-UUU...UACAA_______G_________UU____UA___GGUUG...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________40\n	259 -- 265	59 -- 65	-20.3442 kcal/mol	3.39574 kcal/mol	5.80973 kcal/mol	258 285@LB@ \| \|@LB@5'-AAC...AUUGG A AUU UU GGAUU...UGG-3'@LB@ GGGGAAU GGU GGU UGCA GGC@LB@ \|\|::\|\|\| :\|\| \|\|: \|\|\|\| \|\|\|@LB@ CCUUUUA UCA CCG ACGU CCG@LB@3'-UUU...UACAA G UU UA GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -20.3442 kcal/mol@LB@Unfolding Energy - mRNA 3.39574 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 59 -- 65@LB@
37	0.002433	0.2088	b2825	ppdB	-7.88	0.305516	133 -- 146	40 -- 54	putative prepilin peptidase-dependent protein		_____________132_____________147\n_____________\|_______________\|\n5'-CAU...CAACG_______________GGUGG...CGU-3'\n______________GGCGA_GUGGUGGCU\n______________\|\|\|:\|_\|:::\|\|\|\|:\n______________CCGUU_CGUUACCGG\n3'-UUU...AGUCA_____A_________GUUGU...UUG-5'\n_____________\|_______________\|\n_____________55______________39\n	140 -- 146	40 -- 46	-19.4494 kcal/mol	6.98652 kcal/mol	4.58617 kcal/mol	132 147@LB@ \| \|@LB@5'-CAU...CAACG GGUGG...CGU-3'@LB@ GGCGA GUGGUGGCU@LB@ \|\|\|:\| \|:::\|\|\|\|:@LB@ CCGUU CGUUACCGG@LB@3'-UUU...AGUCA A GUUGU...UUG-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -19.4494 kcal/mol@LB@Unfolding Energy - mRNA 6.98652 kcal/mol@LB@Unfolding Energy - sRNA 4.58617 kcal/mol@LB@@LB@Position - mRNA 133 -- 146@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 40 -- 46@LB@
38	0.00253	0.2088	b3789	rffH	-8.84	0.205897	98 -- 106	51 -- 59	glucose-1-phosphate thymidylyltransferase		_____________97________107\n_____________\|_________\|\n5'-GGC...ACGGU_________UCUGG...UGA-3'\n______________UCAGUGGUA\n______________\|\|\|\|\|\|\|:\|\n______________AGUCACCGU\n3'-UUU...CUUUU_________UACGU...UUG-5'\n_____________\|_________\|\n_____________60________50\n	100 -- 106	51 -- 57	-13.9039 kcal/mol	2.34576 kcal/mol	2.71896 kcal/mol	97 107@LB@ \| \|@LB@5'-GGC...ACGGU UCUGG...UGA-3'@LB@ UCAGUGGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ AGUCACCGU@LB@3'-UUU...CUUUU UACGU...UUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.9039 kcal/mol@LB@Unfolding Energy - mRNA 2.34576 kcal/mol@LB@Unfolding Energy - sRNA 2.71896 kcal/mol@LB@@LB@Position - mRNA 98 -- 106@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 51 -- 57@LB@
39	0.002581	0.2088	b3991	thiG	-13.93	0.014953	9 -- 37	40 -- 69	thiamine biosynthesis ThiGH complex subunit		_____________8_______________________________38\n_____________\|_______________________________\|\n___5'-GCAGAUCC____UAAC_____A_____________C___GCCGG...CCG-3'\n______________UGUU____GAUCA___GCGAUGCAGUG_GCC\n______________\|\|\|\|____:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|_\|\|\|\n______________ACAA____UUAGU___CGUUACGUUAC_CGG\n3'-UUU...AAUAU____CCUU_____CAC_______________GUUGU...UUG-5'\n_____________\|_______________________________\|\n_____________70______________________________39\n	27 -- 33	43 -- 49	-27.0914 kcal/mol	6.322 kcal/mol	6.83756 kcal/mol	8 38@LB@ \| \|@LB@ 5'-GCAGAUCC UAAC A C GCCGG...CCG-3'@LB@ UGUU GAUCA GCGAUGCAGUG GCC@LB@ \|\|\|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\| \|\|\|@LB@ ACAA UUAGU CGUUACGUUAC CGG@LB@3'-UUU...AAUAU CCUU CAC GUUGU...UUG-5'@LB@ \| \|@LB@ 70 39@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -27.0914 kcal/mol@LB@Unfolding Energy - mRNA 6.322 kcal/mol@LB@Unfolding Energy - sRNA 6.83756 kcal/mol@LB@@LB@Position - mRNA 9 -- 37@LB@Position - sRNA 40 -- 69@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 43 -- 49@LB@
40	0.00261	0.2088	b3008	metC	-11.48	0.058180	224 -- 274	11 -- 59	cystathionine beta-lyase PLP-dependent		_____________223___________________________________________________275\n_____________\|_____________________________________________________\|\n5'-CGA...GAUAC___AC____G__________A_G_____A______CAC___C_GC________UAGCG...CGC-3'\n______________UCA__UGGU_AAUGCA__GG_C_CAGCA_AAAAUA___UCU_G__GCGGUAAA\n______________\|\|\|__\|\|\|:_\|\|\|\|\|\|__\|\|_\|_\|\|:\|\|_\|\|\|\|\|\|___\|\|\|_\|__:\|::\|\|\|\|\n______________AGU__ACCG_UUACGU__CC_G_GUUGU_UUUUAU___AGA_C__UGUUAUUU\n3'-UUU...CUUUU___C____________UA____G_____C______UUU_____AC________CCGUA...UUG-5'\n_____________\|_____________________________________________________\|\n_____________60____________________________________________________10\n	268 -- 274	11 -- 17	-31.6805 kcal/mol	9.07324 kcal/mol	11.1233 kcal/mol	223 275@LB@ \| \|@LB@5'-CGA...GAUAC AC G A G A CAC C GC UAGCG...CGC-3'@LB@ UCA UGGU AAUGCA GG C CAGCA AAAAUA UCU G GCGGUAAA@LB@ \|\|\| \|\|\|: \|\|\|\|\|\| \|\| \| \|\|:\|\| \|\|\|\|\|\| \|\|\| \| :\|::\|\|\|\|@LB@ AGU ACCG UUACGU CC G GUUGU UUUUAU AGA C UGUUAUUU@LB@3'-UUU...CUUUU C UA G C UUU AC CCGUA...UUG-5'@LB@ \| \|@LB@ 60 10@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -31.6805 kcal/mol@LB@Unfolding Energy - mRNA 9.07324 kcal/mol@LB@Unfolding Energy - sRNA 11.1233 kcal/mol@LB@@LB@Position - mRNA 224 -- 274@LB@Position - sRNA 11 -- 59@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 11 -- 17@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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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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