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
191	0.009733	0.1776	b0190	yaeQ	-9.83	0.261410	113 -- 128	45 -- 75	PDDEXK superfamily protein	_____________112_____________________________129\n_____________\|_______________________________\|\n5'-UAC...AAGGU_______________________________UUUCU...CUU-3'\n______________GACUAUAC_CA______________CACUCA\n______________\|\|\|\|\|:\|\|_\|\|______________\|\|\|\|\|\|\n______________CUGAUGUG_GU______________GUGAGU\n3'-UUU...CGUUU________U__CGUUAAGCAACAAA______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	114 -- 120	68 -- 74	-15.3898 kcal/mol	1.82074 kcal/mol	3.74078 kcal/mol	112 129@LB@ \| \|@LB@5'-UAC...AAGGU UUUCU...CUU-3'@LB@ GACUAUAC CA CACUCA@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ CUGAUGUG GU GUGAGU@LB@3'-UUU...CGUUU U CGUUAAGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -15.3898 kcal/mol@LB@Unfolding Energy - mRNA 1.82074 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 68 -- 74@LB@
192	0.00979	0.1776	b3879	yihR	-14.50	0.028125	239 -- 282	38 -- 72	putative sulphoquinovose mutarotase	_____________238__________________________________________283\n_____________\|____________________________________________\|\n5'-CAU...ACCAA_______U_____GGACAGACC________UGCCG_________AUCAC...UGA-3'\n______________UAUGCAU_GCAGU_________GUUUCACU_____CGGGGGAUU\n______________\|\|::\|\|:_\|\|\|:\|_________\|\|\|\|\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________AUGUGUG_CGUUA_________CAAAGUGA_____GUCCCCUAA\n3'-UUU...UUCUG_______U_____AGCAA__________________________AGGUA...GCA-5'\n_____________\|____________________________________________\|\n_____________73___________________________________________37\n	276 -- 282	38 -- 44	-32.397 kcal/mol	13.138 kcal/mol	4.76382 kcal/mol	238 283@LB@ \| \|@LB@5'-CAU...ACCAA U GGACAGACC UGCCG AUCAC...UGA-3'@LB@ UAUGCAU GCAGU GUUUCACU CGGGGGAUU@LB@ \|\|::\|\|: \|\|\|:\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGUGUG CGUUA CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUCUG U AGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 73 37@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -32.397 kcal/mol@LB@Unfolding Energy - mRNA 13.138 kcal/mol@LB@Unfolding Energy - sRNA 4.76382 kcal/mol@LB@@LB@Position - mRNA 239 -- 282@LB@Position - sRNA 38 -- 72@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 38 -- 44@LB@
193	0.0098	0.1776	b0757	galK	-12.45	0.083592	134 -- 176	33 -- 76	galactokinase	_____________133____________________________________________177\n_____________\|______________________________________________\|\n5'-CAU...ACCGC________G_______AG__U___CGCG__G____C____A_____UUUCG...GUG-3'\n______________AGA__ACA_GCAGCAG__CG_UUG____CA_UCAG__GAU_UCCAU\n______________\|\|\|__\|\|\|_:\|\|\|\|\|:__\|\|_\|\|\|____\|\|_\|\|\|\|__\|\|\|_\|\|\|\|\|\n______________UCU__UGU_UGUCGUU__GC_AAC____GU_AGUC__CUA_AGGUA\n3'-UUU...CCGUU___GA___G_______AA______AAA___G____CC___A_____CGAAU...GCA-5'\n_____________\|______________________________________________\|\n_____________77_____________________________________________32\n	141 -- 147	61 -- 67	-31.8657 kcal/mol	14.6029 kcal/mol	4.81602 kcal/mol	133 177@LB@ \| \|@LB@5'-CAU...ACCGC G AG U CGCG G C A UUUCG...GUG-3'@LB@ AGA ACA GCAGCAG CG UUG CA UCAG GAU UCCAU@LB@ \|\|\| \|\|\| :\|\|\|\|\|: \|\| \|\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ UCU UGU UGUCGUU GC AAC GU AGUC CUA AGGUA@LB@3'-UUU...CCGUU GA G AA AAA G CC A CGAAU...GCA-5'@LB@ \| \|@LB@ 77 32@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -31.8657 kcal/mol@LB@Unfolding Energy - mRNA 14.6029 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 134 -- 176@LB@Position - sRNA 33 -- 76@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 61 -- 67@LB@
194	0.009812	0.1776	b2687	luxS	-7.90	0.495572	99 -- 106	42 -- 49	S-ribosylhomocysteine lyase	_____________98_______107\n_____________\|________\|\n5'-GAA...UCUGA________AUGAU...UCA-3'\n______________AUUCAGGG\n______________\|:\|\|\|\|\|\|\n______________UGAGUCCC\n3'-UUU...CAAAG________CUAAA...GCA-5'\n_____________\|________\|\n_____________50_______41\n	100 -- 106	42 -- 48	-12.5942 kcal/mol	3.05922 kcal/mol	1.63991 kcal/mol	98 107@LB@ \| \|@LB@5'-GAA...UCUGA AUGAU...UCA-3'@LB@ AUUCAGGG@LB@ \|:\|\|\|\|\|\|@LB@ UGAGUCCC@LB@3'-UUU...CAAAG CUAAA...GCA-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -12.5942 kcal/mol@LB@Unfolding Energy - mRNA 3.05922 kcal/mol@LB@Unfolding Energy - sRNA 1.63991 kcal/mol@LB@@LB@Position - mRNA 99 -- 106@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 42 -- 48@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@
196	0.01003	0.1776	b0344	lacZ	-8.86	0.369200	215 -- 237	48 -- 76	beta-D-galactosidase	_____________214___________________________238\n_____________\|_____________________________\|\n5'-ACC...AUUAC_____________________C_______AACGU...CUU-3'\n______________GGAUU_CAC_UGGC____CGU_GUUUUAC\n______________:\|\|:\|_\|\|\|_::\|\|____\|\|\|_\|\|\|\|:\|\|\n______________UCUGA_GUG_GUCG____GCA_CAAAGUG\n3'-UUU...CCGUU_____U___U____UUAA___A_______AGUCC...GCA-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	231 -- 237	48 -- 54	-17.9156 kcal/mol	5.37156 kcal/mol	3.68714 kcal/mol	214 238@LB@ \| \|@LB@5'-ACC...AUUAC C AACGU...CUU-3'@LB@ GGAUU CAC UGGC CGU GUUUUAC@LB@ :\|\|:\| \|\|\| ::\|\| \|\|\| \|\|\|\|:\|\|@LB@ UCUGA GUG GUCG GCA CAAAGUG@LB@3'-UUU...CCGUU U U UUAA A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -17.9156 kcal/mol@LB@Unfolding Energy - mRNA 5.37156 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 215 -- 237@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 48 -- 54@LB@
197	0.01006	0.1776	b0069	sgrR	-8.41	0.425671	7 -- 22	58 -- 74	transcriptional DNA-binding transcriptional activator of sgrS sRNA	_____________6_________________23\n_____________\|_________________\|\n_____5'-CAUCCC____________CC___AAGCA...UGA-3'\n______________ACUGCAU_CAGU__UUC\n______________\|\|\|:\|\|:_\|\|\|:__\|\|\|\n______________UGAUGUG_GUCG__AAG\n3'-UUU...GUUUC_______U____UU___CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	7 -- 13	68 -- 74	-13.3461 kcal/mol	1.63335 kcal/mol	3.3008 kcal/mol	6 23@LB@ \| \|@LB@ 5'-CAUCCC CC AAGCA...UGA-3'@LB@ ACUGCAU CAGU UUC@LB@ \|\|\|:\|\|: \|\|\|: \|\|\|@LB@ UGAUGUG GUCG AAG@LB@3'-UUU...GUUUC U UU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3461 kcal/mol@LB@Unfolding Energy - mRNA 1.63335 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 7 -- 22@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 68 -- 74@LB@
198	0.01016	0.1776	b1764	selD	-10.66	0.187945	118 -- 146	45 -- 71	selenophosphate synthase	_____________117___________________________147\n_____________\|_____________________________\|\n5'-UUU...AGCAA_G______G_____AGACACUC_______UCACU...AGC-3'\n______________A_GCGCAG_AAUUC________UCACUUA\n______________\|_:\|:\|\|\|_\|\|\|\|\|________\|\|\|\|\|:\|\n______________U_UGUGUC_UUAAG________AGUGAGU\n3'-UUU...UCUGA_G______G_____CAACAA_________CCCCU...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________44\n	140 -- 146	45 -- 51	-20.1282 kcal/mol	5.75637 kcal/mol	3.71323 kcal/mol	117 147@LB@ \| \|@LB@5'-UUU...AGCAA G G AGACACUC UCACU...AGC-3'@LB@ A GCGCAG AAUUC UCACUUA@LB@ \| :\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|@LB@ U UGUGUC UUAAG AGUGAGU@LB@3'-UUU...UCUGA G G CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 72 44@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -20.1282 kcal/mol@LB@Unfolding Energy - mRNA 5.75637 kcal/mol@LB@Unfolding Energy - sRNA 3.71323 kcal/mol@LB@@LB@Position - mRNA 118 -- 146@LB@Position - sRNA 45 -- 71@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 45 -- 51@LB@
199	0.01026	0.1776	b2324	mnmC	-11.15	0.152427	29 -- 45	45 -- 74	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme	_____________28_____________________________46\n_____________\|______________________________\|\n5'-GCU...UAAUC______________________________AUACC...ACG-3'\n______________ACUGCAC_____________GUUUCAUUCA\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|:\|\|\|\n______________UGAUGUG_____________CAAAGUGAGU\n3'-UUU...GUUUC_______UGUCGUUAAGCAA__________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	39 -- 45	45 -- 51	-17.885 kcal/mol	2.99426 kcal/mol	3.74056 kcal/mol	28 46@LB@ \| \|@LB@5'-GCU...UAAUC AUACC...ACG-3'@LB@ ACUGCAC GUUUCAUUCA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|:\|\|\|@LB@ UGAUGUG CAAAGUGAGU@LB@3'-UUU...GUUUC UGUCGUUAAGCAA CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -17.885 kcal/mol@LB@Unfolding Energy - mRNA 2.99426 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 29 -- 45@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 45 -- 51@LB@
200	0.01028	0.1776	b2803	fucK	-15.72	0.013449	16 -- 30	62 -- 76	L-fuculokinase	_____________15______________31\n_____________\|_______________\|\n5'-AUC...UGCCU_______________UGGAU...CGC-3'\n______________GGGCUGCGCACGGCA\n______________:\|:\|\|:\|:\|\|\|:\|\|\|\n______________UCUGAUGUGUGUCGU\n3'-UUU...CCGUU_______________UAAGC...GCA-5'\n_____________\|_______________\|\n_____________77______________61\n	24 -- 30	62 -- 68	-24.6836 kcal/mol	5.71098 kcal/mol	3.25371 kcal/mol	15 31@LB@ \| \|@LB@5'-AUC...UGCCU UGGAU...CGC-3'@LB@ GGGCUGCGCACGGCA@LB@ :\|:\|\|:\|:\|\|\|:\|\|\|@LB@ UCUGAUGUGUGUCGU@LB@3'-UUU...CCGUU UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -24.6836 kcal/mol@LB@Unfolding Energy - mRNA 5.71098 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 16 -- 30@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 62 -- 68@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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