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
16	0.0007867	0.1666	b2178	yejB	-12.57	0.044336	179 -- 196	66 -- 82	microcin C ABC transporter permease	_____________178________________197\n_____________\|__________________\|\n5'-UGG...CCGUC________AA________GUAGA...GUC-3'\n______________CGCCAGCA__CAGGGAGA\n______________\|\|\|\|\|:\|\|__\|\|\|\|\|\|:\|\n______________GCGGUUGU__GUCCCUUU\n3'-UUU...AUGAC________G_________AGAAC...GUG-5'\n_____________\|__________________\|\n_____________83_________________65\n	190 -- 196	66 -- 72	-25.5869 kcal/mol	5.97553 kcal/mol	7.04029 kcal/mol	178 197@LB@ \| \|@LB@5'-UGG...CCGUC AA GUAGA...GUC-3'@LB@ CGCCAGCA CAGGGAGA@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|\|:\|@LB@ GCGGUUGU GUCCCUUU@LB@3'-UUU...AUGAC G AGAAC...GUG-5'@LB@ \| \|@LB@ 83 65@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -25.5869 kcal/mol@LB@Unfolding Energy - mRNA 5.97553 kcal/mol@LB@Unfolding Energy - sRNA 7.04029 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 66 -- 82@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 66 -- 72@LB@
98	0.005208	0.1855	b4174	hflK	-10.42	0.116019	265 -- 284	65 -- 83	modulator for HflB protease specific for phage lambda cII repressor	_____________264__________________285\n_____________\|____________________\|\n5'-AGA...ACCUG___G____U__G________GGAAA...GUC-3'\n______________GCG_CAAC_CU_AGGGAAAU\n______________\|\|\|_\|\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CGC_GUUG_GG_UCCCUUUA\n3'-UUU...UAUGA___G____U___________GAACC...GUG-5'\n_____________\|____________________\|\n_____________84___________________64\n	278 -- 284	65 -- 71	-24.0318 kcal/mol	6.25533 kcal/mol	7.35968 kcal/mol	264 285@LB@ \| \|@LB@5'-AGA...ACCUG G U G GGAAA...GUC-3'@LB@ GCG CAAC CU AGGGAAAU@LB@ \|\|\| \|\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CGC GUUG GG UCCCUUUA@LB@3'-UUU...UAUGA G U GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -24.0318 kcal/mol@LB@Unfolding Energy - mRNA 6.25533 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 265 -- 284@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 65 -- 71@LB@
118	0.006444	0.1913	b0189	rof	-9.63	0.163299	226 -- 241	29 -- 45	modulator of Rho-dependent transcription termination	_____________225_______________242\n_____________\|_________________\|\n5'-AGG...AAUCA_________________UAAUC...GCG-3'\n______________AUUGUGAUGA_UUACGA\n______________\|\|\|:\|\|\|\|\|\|_\|\|\|\|:\|\n______________UAAUACUACU_AAUGUU\n3'-UUU...UUUAA__________C______CCCGU...GUG-5'\n_____________\|_________________\|\n_____________46________________28\n	229 -- 235	36 -- 42	-15.4032 kcal/mol	3.82623 kcal/mol	1.94966 kcal/mol	225 242@LB@ \| \|@LB@5'-AGG...AAUCA UAAUC...GCG-3'@LB@ AUUGUGAUGA UUACGA@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|:\|@LB@ UAAUACUACU AAUGUU@LB@3'-UUU...UUUAA C CCCGU...GUG-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -15.4032 kcal/mol@LB@Unfolding Energy - mRNA 3.82623 kcal/mol@LB@Unfolding Energy - sRNA 1.94966 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
155	0.009115	0.2059	b1531	marA	-9.94	0.142609	213 -- 231	72 -- 89	multiple antibiotic resistance transcriptional regulator	_____________212_________________232\n_____________\|___________________\|\n5'-AAG...GACGC_______A_____U_____UUCAU...AGC-3'\n______________AAUACUG_CGCUA_UACCA\n______________\|\|\|\|\|\|\|_\|\|\|:\|_:\|\|\|\|\n______________UUAUGAC_GCGGU_GUGGU\n3'-UUU...CGCGC_____________U_____CCCUU...GUG-5'\n_____________\|___________________\|\n_____________90__________________71\n	213 -- 219	83 -- 89	-21.2611 kcal/mol	3.54366 kcal/mol	7.77515 kcal/mol	212 232@LB@ \| \|@LB@5'-AAG...GACGC A U UUCAU...AGC-3'@LB@ AAUACUG CGCUA UACCA@LB@ \|\|\|\|\|\|\| \|\|\|:\| :\|\|\|\|@LB@ UUAUGAC GCGGU GUGGU@LB@3'-UUU...CGCGC U CCCUU...GUG-5'@LB@ \| \|@LB@ 90 71@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -21.2611 kcal/mol@LB@Unfolding Energy - mRNA 3.54366 kcal/mol@LB@Unfolding Energy - sRNA 7.77515 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 72 -- 89@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 83 -- 89@LB@
12	0.0004488	0.1198	b3133	agaV	-20.63	0.001136	94 -- 118	64 -- 86	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________93________________________119\n_____________\|_________________________\|\n5'-UCA...GGCGA_____A__________C_____C__AUUAU...UAG-3'\n______________GCUGC_GCCAACGCCA_GGGAA_UC\n______________:\|\|\|\|_\|\|\|\|\|\|:\|\|\|_\|\|\|\|\|_\|\|\n______________UGACG_CGGUUGUGGU_CCCUU_AG\n3'-UUU...GCUUA______________________U__AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	103 -- 109	72 -- 78	-36.2121 kcal/mol	8.19626 kcal/mol	7.38435 kcal/mol	93 119@LB@ \| \|@LB@5'-UCA...GGCGA A C C AUUAU...UAG-3'@LB@ GCUGC GCCAACGCCA GGGAA UC@LB@ :\|\|\|\| \|\|\|\|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UGACG CGGUUGUGGU CCCUU AG@LB@3'-UUU...GCUUA U AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -36.2121 kcal/mol@LB@Unfolding Energy - mRNA 8.19626 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 94 -- 118@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 72 -- 78@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@
18	0.001002	0.1727	b2284	nuoF	-9.91	0.144715	4 -- 28	1 -- 36	NADH:ubiquinone oxidoreductase chain F	_____________3____________________________________29\n_____________\|____________________________________\|\n________5'-AAC______C________________________G____UCGAG...ACG-3'\n______________GGUUAU_AGGGUAU___________UCAGGC_GCGC\n______________:\|\|\|\|:_\|\|\|\|:\|:___________\|\|\|\|\|\|_\|\|:\|\n______________UCAAUG_UCCCGUG___________AGUCCG_CGUG\n3'-UUU...ACUAC______U_______UCGUGACAAAA______G____-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	11 -- 17	23 -- 29	-32.4986 kcal/mol	7.53826 kcal/mol	15.052 kcal/mol	3 29@LB@ \| \|@LB@ 5'-AAC C G UCGAG...ACG-3'@LB@ GGUUAU AGGGUAU UCAGGC GCGC@LB@ :\|\|\|\|: \|\|\|\|:\|: \|\|\|\|\|\| \|\|:\|@LB@ UCAAUG UCCCGUG AGUCCG CGUG@LB@3'-UUU...ACUAC U UCGUGACAAAA G -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -32.4986 kcal/mol@LB@Unfolding Energy - mRNA 7.53826 kcal/mol@LB@Unfolding Energy - sRNA 15.052 kcal/mol@LB@@LB@Position - mRNA 4 -- 28@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 23 -- 29@LB@
14	0.0004762	0.1198	b2286	nuoC	-13.55	0.028468	156 -- 179	68 -- 87	NADH:ubiquinone oxidoreductase fused CD subunit	_____________155______________________180\n_____________\|________________________\|\n5'-AGG...AAGCU_____________GUCA___C___CCAUU...CCU-3'\n______________UACUGCGCCGACA____CCA_GGA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|____\|\|\|_\|\|\|\n______________AUGACGCGGUUGU____GGU_CCU\n3'-UUU...CGCUU____________________C___UUAGA...GUG-5'\n_____________\|________________________\|\n_____________88_______________________67\n	162 -- 168	75 -- 81	-29.2495 kcal/mol	8.32219 kcal/mol	7.38006 kcal/mol	155 180@LB@ \| \|@LB@5'-AGG...AAGCU GUCA C CCAUU...CCU-3'@LB@ UACUGCGCCGACA CCA GGA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ AUGACGCGGUUGU GGU CCU@LB@3'-UUU...CGCUU C UUAGA...GUG-5'@LB@ \| \|@LB@ 88 67@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -29.2495 kcal/mol@LB@Unfolding Energy - mRNA 8.32219 kcal/mol@LB@Unfolding Energy - sRNA 7.38006 kcal/mol@LB@@LB@Position - mRNA 156 -- 179@LB@Position - sRNA 68 -- 87@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 75 -- 81@LB@
26	0.001553	0.1727	b0853	ybjN	-8.94	0.217650	161 -- 169	52 -- 60	negative regulator of motility; multicopy suppressor of coaA(Ts)	_____________160_______170\n_____________\|_________\|\n5'-CGC...CGUAA_________GUCUU...AUC-3'\n______________GCUGUGCCG\n______________\|\|\|\|:\|\|\|\|\n______________CGACGCGGC\n3'-UUU...AGAAC_________AUUUA...GUG-5'\n_____________\|_________\|\n_____________61________51\n	163 -- 169	52 -- 58	-18.9448 kcal/mol	5.13325 kcal/mol	4.86882 kcal/mol	160 170@LB@ \| \|@LB@5'-CGC...CGUAA GUCUU...AUC-3'@LB@ GCUGUGCCG@LB@ \|\|\|\|:\|\|\|\|@LB@ CGACGCGGC@LB@3'-UUU...AGAAC AUUUA...GUG-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -18.9448 kcal/mol@LB@Unfolding Energy - mRNA 5.13325 kcal/mol@LB@Unfolding Energy - sRNA 4.86882 kcal/mol@LB@@LB@Position - mRNA 161 -- 169@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
8	0.000265	0.1166	b1244	oppB	-12.83	0.039495	280 -- 295	70 -- 84	oligopeptide ABC transporter permease	_____________279______________296\n_____________\|________________\|\n5'-UCC...UAUGA______UC________AAGCC-3'\n______________UGCGCC__GCGCCGGG\n______________\|\|\|\|\|\|__:\|:\|\|:\|\|\n______________ACGCGG__UGUGGUCC\n3'-UUU...UUAUG______U_________CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	289 -- 295	70 -- 76	-25.4509 kcal/mol	5.37602 kcal/mol	7.24859 kcal/mol	279 296@LB@ \| \|@LB@5'-UCC...UAUGA UC AAGCC-3'@LB@ UGCGCC GCGCCGGG@LB@ \|\|\|\|\|\| :\|:\|\|:\|\|@LB@ ACGCGG UGUGGUCC@LB@3'-UUU...UUAUG U CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -25.4509 kcal/mol@LB@Unfolding Energy - mRNA 5.37602 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@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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