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
27	0.001616	0.2012	b0085	murE	-13.53	0.018874	165 -- 198	1 -- 33	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase	_____________164_________________________________199\n_____________\|___________________________________\|\n5'-UGC...CGAUA_________________U___C______AGGG___AGGUG...CGG-3'\n______________AAAAU_GAAUUUGUGAU_AAU_AAGGCG____GAC\n______________\|\|\|\|\|_:\|\|\|:\|\|\|\|\|:_\|\|\|_\|\|\|\|\|:____:\|\|\n______________UUUUA_UUUAGACACUG_UUA_UUCCGU____UUG\n3'-UUU...UUGUC_____U_______________U______AUA____-5'\n_____________\|__________________________________\|\n_____________34_________________________________1\n	174 -- 180	17 -- 23	-22.2929 kcal/mol	3.71145 kcal/mol	5.04823 kcal/mol	164 199@LB@ \| \|@LB@5'-UGC...CGAUA U C AGGG AGGUG...CGG-3'@LB@ AAAAU GAAUUUGUGAU AAU AAGGCG GAC@LB@ \|\|\|\|\| :\|\|\|:\|\|\|\|\|: \|\|\| \|\|\|\|\|: :\|\|@LB@ UUUUA UUUAGACACUG UUA UUCCGU UUG@LB@3'-UUU...UUGUC U U AUA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.2929 kcal/mol@LB@Unfolding Energy - mRNA 3.71145 kcal/mol@LB@Unfolding Energy - sRNA 5.04823 kcal/mol@LB@@LB@Position - mRNA 165 -- 198@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 17 -- 23@LB@
28	0.001683	0.2021	b0166	dapD	-9.25	0.172213	119 -- 166	9 -- 65	2 3 4 5-tetrahydropyridine-2-carboxylate N-succinyltransferase	_____________118___________________________________________________________167\n_____________\|_____________________________________________________________\|\n5'-UUG...CAGCA_____UGC_____C_______A___A_____UC______________CAA___________GUGAU...AGG-3'\n______________GGAAG___AUCAG_GGU__UG_CAG_GGCCC____________AAUC____ACGAUAAAGG\n______________\|\|\|\|:___\|\|\|\|\|_\|\|:__\|\|_\|\|:_\|\|\|\|\|____________\|\|\|\|____\|\|:\|\|\|\|\|\|\|\n______________CCUUU___UAGUC_CCG__AC_GUU_CCGGG____________UUAG____UGUUAUUUCC\n3'-UUU...UACAA_____________A___UU______A_____UUGUCUUUUAUU____ACAC__________GUAUAUUG-5'\n_____________\|_____________________________________________________________\|\n_____________66____________________________________________________________8\n	160 -- 166	9 -- 15	-36.4613 kcal/mol	16.0785 kcal/mol	11.1365 kcal/mol	118 167@LB@ \| \|@LB@5'-UUG...CAGCA UGC C A A UC CAA GUGAU...AGG-3'@LB@ GGAAG AUCAG GGU UG CAG GGCCC AAUC ACGAUAAAGG@LB@ \|\|\|\|: \|\|\|\|\| \|\|: \|\| \|\|: \|\|\|\|\| \|\|\|\| \|\|:\|\|\|\|\|\|\|@LB@ CCUUU UAGUC CCG AC GUU CCGGG UUAG UGUUAUUUCC@LB@3'-UUU...UACAA A UU A UUGUCUUUUAUU ACAC GUAUAUUG-5'@LB@ \| \|@LB@ 66 8@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -36.4613 kcal/mol@LB@Unfolding Energy - mRNA 16.0785 kcal/mol@LB@Unfolding Energy - sRNA 11.1365 kcal/mol@LB@@LB@Position - mRNA 119 -- 166@LB@Position - sRNA 9 -- 65@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 9 -- 15@LB@
29	0.001819	0.2065	b3648	gmk	-8.89	0.201842	236 -- 243	51 -- 58	guanylate kinase	_____________235______244\n_____________\|________\|\n5'-GUG...GCCCC________CGGGU...CCC-3'\n______________CAGUGGCG\n______________\|\|\|\|\|\|\|:\n______________GUCACCGU\n3'-UUU...UUUUA________UACGU...UUG-5'\n_____________\|________\|\n_____________59_______50\n	237 -- 243	51 -- 57	-13.8917 kcal/mol	2.3096 kcal/mol	2.69685 kcal/mol	235 244@LB@ \| \|@LB@5'-GUG...GCCCC CGGGU...CCC-3'@LB@ CAGUGGCG@LB@ \|\|\|\|\|\|\|:@LB@ GUCACCGU@LB@3'-UUU...UUUUA UACGU...UUG-5'@LB@ \| \|@LB@ 59 50@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -13.8917 kcal/mol@LB@Unfolding Energy - mRNA 2.3096 kcal/mol@LB@Unfolding Energy - sRNA 2.69685 kcal/mol@LB@@LB@Position - mRNA 236 -- 243@LB@Position - sRNA 51 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
30	0.001842	0.2065	b3574	yiaJ	-8.97	0.194276	228 -- 279	20 -- 64	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________227_____________________________________________________280\n_____________\|_______________________________________________________\|\n5'-CCC...AAAAA_____CG__A___________GAAAAAGAGC______C______CC_________UUCGC...UUG-3'\n______________GAGAA__AG_UGGC___GCAG__________GUCCAG_CGGAAG__AGAGUCUGU\n______________\|\|:\|\|__\|\|_\|\|\|\|___\|\|\|:__________\|:\|\|\|:_\|:\|\|\|:__\|:\|:\|\|\|\|\|\n______________CUUUU__UC_ACCG___CGUU__________CGGGUU_GUCUUU__UUUUAGACA\n3'-UUU...ACAAC_____AG_______UUA____AC_____________________UA_________CUGUU...UUG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________19\n	273 -- 279	20 -- 26	-33.3994 kcal/mol	13.3805 kcal/mol	11.0456 kcal/mol	227 280@LB@ \| \|@LB@5'-CCC...AAAAA CG A GAAAAAGAGC C CC UUCGC...UUG-3'@LB@ GAGAA AG UGGC GCAG GUCCAG CGGAAG AGAGUCUGU@LB@ \|\|:\|\| \|\| \|\|\|\| \|\|\|: \|:\|\|\|: \|:\|\|\|: \|:\|:\|\|\|\|\|@LB@ CUUUU UC ACCG CGUU CGGGUU GUCUUU UUUUAGACA@LB@3'-UUU...ACAAC AG UUA AC UA CUGUU...UUG-5'@LB@ \| \|@LB@ 65 19@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -33.3994 kcal/mol@LB@Unfolding Energy - mRNA 13.3805 kcal/mol@LB@Unfolding Energy - sRNA 11.0456 kcal/mol@LB@@LB@Position - mRNA 228 -- 279@LB@Position - sRNA 20 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 20 -- 26@LB@
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@
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@

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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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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