Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
58	0.002925	0.1727	b0427	yajR	-11.14	0.084219	218 -- 238	54 -- 78	putative transporter		_____________217________________________239\n_____________\|__________________________\|\n5'-CGU...AAAAU_________U________________GACCU...CGG-3'\n______________GACGCCAGG_GAGA____GGC_GCGC\n______________:\|\|:\|\|\|\|\|_\|\|:\|____\|\|\|_\|\|\|\|\n______________UUGUGGUCC_CUUU____CCG_CGCG\n3'-UUU...CGCGG______________AGAA___A____GCAUU...GUG-5'\n_____________\|__________________________\|\n_____________79_________________________53\n	220 -- 226	70 -- 76	-28.7218 kcal/mol	8.65047 kcal/mol	8.92888 kcal/mol	217 239@LB@ \| \|@LB@5'-CGU...AAAAU U GACCU...CGG-3'@LB@ GACGCCAGG GAGA GGC GCGC@LB@ :\|\|:\|\|\|\|\| \|\|:\| \|\|\| \|\|\|\|@LB@ UUGUGGUCC CUUU CCG CGCG@LB@3'-UUU...CGCGG AGAA A GCAUU...GUG-5'@LB@ \| \|@LB@ 79 53@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -28.7218 kcal/mol@LB@Unfolding Energy - mRNA 8.65047 kcal/mol@LB@Unfolding Energy - sRNA 8.92888 kcal/mol@LB@@LB@Position - mRNA 218 -- 238@LB@Position - sRNA 54 -- 78@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 70 -- 76@LB@
7	0.0001601	0.08054	b1864	yebC	-15.40	0.012230	213 -- 249	54 -- 89	UPF0082 family protein		_____________212_____________________________________250\n_____________\|_______________________________________\|\n5'-CGU...GUCAU____AA__G___________AC_____GUAAA_______AGGAU...UAA-3'\n______________AGUA__UG_GCCAACACCAG____AUC_____GCUGCGC\n______________\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|\|\|____\|\|\|_____\|\|\|\|\|\|\|\n______________UUAU__AC_CGGUUGUGGUC____UAG_____CGACGCG\n3'-UUU...CGCGC____G___G___________CCUU___AAC_________GCAUU...GUG-5'\n_____________\|_______________________________________\|\n_____________90______________________________________53\n	243 -- 249	54 -- 60	-38.8431 kcal/mol	7.10336 kcal/mol	16.3388 kcal/mol	212 250@LB@ \| \|@LB@5'-CGU...GUCAU AA G AC GUAAA AGGAU...UAA-3'@LB@ AGUA UG GCCAACACCAG AUC GCUGCGC@LB@ \|:\|\| \|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UUAU AC CGGUUGUGGUC UAG CGACGCG@LB@3'-UUU...CGCGC G G CCUU AAC GCAUU...GUG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -38.8431 kcal/mol@LB@Unfolding Energy - mRNA 7.10336 kcal/mol@LB@Unfolding Energy - sRNA 16.3388 kcal/mol@LB@@LB@Position - mRNA 213 -- 249@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@LB@
59	0.002989	0.1727	b2713	hydN	-12.16	0.053402	276 -- 298	54 -- 76	formate dehydrogenase-H [4Fe-4S] ferredoxin subunit	b3573	_____________275______________________299\n_____________\|________________________\|\n5'-CUU...UUUCU_______A_____A___A______AU-3'\n______________CAUCAGG_AAAUC__GG_CUGUGC\n______________\|\|:\|\|\|\|_\|\|\|\|\|__\|\|_\|\|\|:\|\|\n______________GUGGUCC_UUUAG__CC_GACGCG\n3'-UUU...CGGUU_______C_____AA_________GCAUU...GUG-5'\n_____________\|________________________\|\n_____________77_______________________53\n	276 -- 282	70 -- 76	-25.5609 kcal/mol	4.47784 kcal/mol	8.92391 kcal/mol	275 299@LB@ \| \|@LB@5'-CUU...UUUCU A A A AU-3'@LB@ CAUCAGG AAAUC GG CUGUGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|\|@LB@ GUGGUCC UUUAG CC GACGCG@LB@3'-UUU...CGGUU C AA GCAUU...GUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -25.5609 kcal/mol@LB@Unfolding Energy - mRNA 4.47784 kcal/mol@LB@Unfolding Energy - sRNA 8.92391 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 70 -- 76@LB@
6	0.0001378	0.08054	b3860	dsbA	-12.69	0.042007	89 -- 111	55 -- 75	periplasmic protein disulfide isomerase I		_____________88______________________112\n_____________\|_______________________\|\n5'-UUU...GGUUA_______A_____AC________ACAGA...AAC-3'\n______________ACCGGGG_AGAUU__UGGCUGCG\n______________\|\|\|:\|\|\|_\|:\|\|:__\|\|\|\|\|\|\|\|\n______________UGGUCCC_UUUAG__ACCGACGC\n3'-UUU...GGUUG_____________A_________GGCAU...GUG-5'\n_____________\|_______________________\|\n_____________76______________________54\n	105 -- 111	55 -- 61	-30.5184 kcal/mol	9.58616 kcal/mol	8.24199 kcal/mol	88 112@LB@ \| \|@LB@5'-UUU...GGUUA A AC ACAGA...AAC-3'@LB@ ACCGGGG AGAUU UGGCUGCG@LB@ \|\|\|:\|\|\| \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UGGUCCC UUUAG ACCGACGC@LB@3'-UUU...GGUUG A GGCAU...GUG-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -30.5184 kcal/mol@LB@Unfolding Energy - mRNA 9.58616 kcal/mol@LB@Unfolding Energy - sRNA 8.24199 kcal/mol@LB@@LB@Position - mRNA 89 -- 111@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 55 -- 61@LB@
87	0.004792	0.1855	b0476	aes	-9.71	0.157345	34 -- 55	56 -- 76	acetyl esterase		_____________33______________________56\n_____________\|_______________________\|\n5'-CGU...ACGUU______________CA_______UUUUA...CAA-3'\n______________UACC_GGGAAAUUU__UGGUUGU\n______________:\|\|\|_\|\|\|\|\|\|\|:\|__\|\|\|:\|\|:\n______________GUGG_CCCUUUAGA__ACCGACG\n3'-UUU...CGGUU____U__________________CGGCA...GUG-5'\n_____________\|_______________________\|\n_____________77______________________55\n	49 -- 55	56 -- 62	-24.1621 kcal/mol	6.04137 kcal/mol	8.40711 kcal/mol	33 56@LB@ \| \|@LB@5'-CGU...ACGUU CA UUUUA...CAA-3'@LB@ UACC GGGAAAUUU UGGUUGU@LB@ :\|\|\| \|\|\|\|\|\|\|:\| \|\|\|:\|\|:@LB@ GUGG CCCUUUAGA ACCGACG@LB@3'-UUU...CGGUU U CGGCA...GUG-5'@LB@ \| \|@LB@ 77 55@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -24.1621 kcal/mol@LB@Unfolding Energy - mRNA 6.04137 kcal/mol@LB@Unfolding Energy - sRNA 8.40711 kcal/mol@LB@@LB@Position - mRNA 34 -- 55@LB@Position - sRNA 56 -- 76@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 56 -- 62@LB@
198	0.01217	0.2164	b1236	galU	-11.62	0.068156	187 -- 208	56 -- 74	glucose-1-phosphate uridylyltransferase		_____________186____________________209\n_____________\|______________________\|\n5'-CAA...ACAGU_____A______AAA_______CAUUA...UGC-3'\n______________CCAGG_GAAUUU___UGGCUGC\n______________\|\|\|\|\|_:\|\|\|:\|___\|\|\|\|\|\|\|\n______________GGUCC_UUUAGA___ACCGACG\n3'-UUU...GUUGU_____C________________CGGCA...GUG-5'\n_____________\|______________________\|\n_____________75_____________________55\n	202 -- 208	56 -- 62	-24.2568 kcal/mol	4.50323 kcal/mol	8.13729 kcal/mol	186 209@LB@ \| \|@LB@5'-CAA...ACAGU A AAA CAUUA...UGC-3'@LB@ CCAGG GAAUUU UGGCUGC@LB@ \|\|\|\|\| :\|\|\|:\| \|\|\|\|\|\|\|@LB@ GGUCC UUUAGA ACCGACG@LB@3'-UUU...GUUGU C CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -24.2568 kcal/mol@LB@Unfolding Energy - mRNA 4.50323 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 187 -- 208@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 56 -- 62@LB@
100	0.00547	0.1855	b2451	eutA	-10.77	0.099200	8 -- 32	56 -- 86	reactivating factor for ethanolamine ammonia lyase		_____________7_______________________________33\n_____________\|_______________________________\|\n____5'-GUCAUCA________UU______________CC_____UUUCG...UGU-3'\n______________ACUGCGCC__CGCC______GUUU__GCUGC\n______________\|\|\|\|\|\|\|\|__\|:\|\|______:\|:\|__\|\|\|\|\|\n______________UGACGCGG__GUGG______UAGA__CGACG\n3'-UUU...GCUUA________UU____UCCCUU____AC_____CGGCA...GUG-5'\n_____________\|_______________________________\|\n_____________87______________________________55\n	9 -- 15	79 -- 85	-30.9169 kcal/mol	5.09004 kcal/mol	15.0537 kcal/mol	7 33@LB@ \| \|@LB@ 5'-GUCAUCA UU CC UUUCG...UGU-3'@LB@ ACUGCGCC CGCC GUUU GCUGC@LB@ \|\|\|\|\|\|\|\| \|:\|\| :\|:\| \|\|\|\|\|@LB@ UGACGCGG GUGG UAGA CGACG@LB@3'-UUU...GCUUA UU UCCCUU AC CGGCA...GUG-5'@LB@ \| \|@LB@ 87 55@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -30.9169 kcal/mol@LB@Unfolding Energy - mRNA 5.09004 kcal/mol@LB@Unfolding Energy - sRNA 15.0537 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 56 -- 86@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 79 -- 85@LB@
141	0.008132	0.2031	b3412	bioH	-10.51	0.111302	230 -- 255	56 -- 74	pimeloyl-ACP methyl ester carboxylesterase		_____________229________________________256\n_____________\|__________________________\|\n5'-GGC...AAAGG________AUGUUC______U_____UGCAC...ACG-3'\n______________UCAGGGGA______AUCUUG_GCUGC\n______________:\|\|\|\|\|:\|______\|\|\|\|\|\|_\|\|\|\|\|\n______________GGUCCCUU______UAGAAC_CGACG\n3'-UUU...GUUGU__________________________CGGCA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________55\n	231 -- 237	67 -- 73	-25.2186 kcal/mol	6.56983 kcal/mol	8.13729 kcal/mol	229 256@LB@ \| \|@LB@5'-GGC...AAAGG AUGUUC U UGCAC...ACG-3'@LB@ UCAGGGGA AUCUUG GCUGC@LB@ :\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ GGUCCCUU UAGAAC CGACG@LB@3'-UUU...GUUGU CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -25.2186 kcal/mol@LB@Unfolding Energy - mRNA 6.56983 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 67 -- 73@LB@
146	0.008611	0.2059	b3750	rbsC	-8.88	0.223197	137 -- 159	56 -- 77	D-ribose ABC transporter permease		_____________136_______________________160\n_____________\|_________________________\|\n5'-GAU...AGGCC_____________G_UAA_______CGCUG...UCU-3'\n______________AC_CCA_GGAAGU_U___UGGCUGC\n______________\|\|_\|\|\|_\|\|\|\|:\|_\|___\|\|\|\|\|\|\|\n______________UG_GGU_CCUUUA_A___ACCGACG\n3'-UUU...GCGGU__U___C______G___________CGGCA...GUG-5'\n_____________\|_________________________\|\n_____________78________________________55\n	153 -- 159	56 -- 62	-22.4095 kcal/mol	5.11916 kcal/mol	8.4081 kcal/mol	136 160@LB@ \| \|@LB@5'-GAU...AGGCC G UAA CGCUG...UCU-3'@LB@ AC CCA GGAAGU U UGGCUGC@LB@ \|\| \|\|\| \|\|\|\|:\| \| \|\|\|\|\|\|\|@LB@ UG GGU CCUUUA A ACCGACG@LB@3'-UUU...GCGGU U C G CGGCA...GUG-5'@LB@ \| \|@LB@ 78 55@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -22.4095 kcal/mol@LB@Unfolding Energy - mRNA 5.11916 kcal/mol@LB@Unfolding Energy - sRNA 8.4081 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 56 -- 77@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 56 -- 62@LB@
134	0.007678	0.1993	b3139	agaC	-7.83	0.338422	255 -- 275	57 -- 74	N-acetylgalactosamine-specific enzyme IIC component of PTS		_____________254___________________276\n_____________\|_____________________\|\n5'-AAC...UUGUU_______UUGAU_________GAAGC...CGA-3'\n______________CUGGGGA_____UUUUGGCUG\n______________\|::\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________GGUCCCU_____AGAACCGAC\n3'-UUU...GUUGU_______UU____________GCGGC...GUG-5'\n_____________\|_____________________\|\n_____________75____________________56\n	269 -- 275	57 -- 63	-21.9136 kcal/mol	6.09668 kcal/mol	7.9843 kcal/mol	254 276@LB@ \| \|@LB@5'-AAC...UUGUU UUGAU GAAGC...CGA-3'@LB@ CUGGGGA UUUUGGCUG@LB@ \|::\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GGUCCCU AGAACCGAC@LB@3'-UUU...GUUGU UU GCGGC...GUG-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -21.9136 kcal/mol@LB@Unfolding Energy - mRNA 6.09668 kcal/mol@LB@Unfolding Energy - sRNA 7.9843 kcal/mol@LB@@LB@Position - mRNA 255 -- 275@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 57 -- 63@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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