Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
91	0.01869	0.6177	b3432	glgB	-9.43	0.053684	93 -- 103	45 -- 56	1 4-alpha-glucan branching enzyme	_____________92___________104\n_____________\|____________\|\n5'-CAU...GACGA____________UGCAC...GAC-3'\n______________CG_CAGAGAGGA\n______________\|\|_\|\|:\|\|\|\|\|\|\n______________GC_GUUUCUCCU\n3'-UUU...ACCGG__A_________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	97 -- 103	45 -- 51	-14.5586 kcal/mol	4.18817 kcal/mol	0.938337 kcal/mol	92 104@LB@ \| \|@LB@5'-CAU...GACGA UGCAC...GAC-3'@LB@ CG CAGAGAGGA@LB@ \|\| \|\|:\|\|\|\|\|\|@LB@ GC GUUUCUCCU@LB@3'-UUU...ACCGG A UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -14.5586 kcal/mol@LB@Unfolding Energy - mRNA 4.18817 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 93 -- 103@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 45 -- 51@LB@
18	0.003456	0.593	b0867	amiD	-11.23	0.023022	276 -- 289	39 -- 52	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________275____________290\n_____________\|______________\|\n5'-GAU...UCGAG__________A___GCUUG...CCC-3'\n______________AAAGAGGGAU_UCA\n______________\|\|\|\|\|\|\|:\|\|_\|\|\|\n______________UUUCUCCUUA_AGU\n3'-UUU...GGCAG__________A___AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	279 -- 285	43 -- 49	-14.4178 kcal/mol	2.13665 kcal/mol	1.05043 kcal/mol	275 290@LB@ \| \|@LB@5'-GAU...UCGAG A GCUUG...CCC-3'@LB@ AAAGAGGGAU UCA@LB@ \|\|\|\|\|\|\|:\|\| \|\|\|@LB@ UUUCUCCUUA AGU@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.4178 kcal/mol@LB@Unfolding Energy - mRNA 2.13665 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 276 -- 289@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 43 -- 49@LB@
151	0.03043	0.6177	b3081	fadH	-8.56	0.080347	290 -- 297	43 -- 50	2 4-dienoyl-CoA reductase NADH and FMN-linked	_____________289______298\n_____________\|________\|\n5'-UGG...GGGCU________ACC-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	291 -- 297	43 -- 49	-10.5858 kcal/mol	1.17616 kcal/mol	0.845564 kcal/mol	289 298@LB@ \| \|@LB@5'-UGG...GGGCU ACC-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -10.5858 kcal/mol@LB@Unfolding Energy - mRNA 1.17616 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
74	0.01569	0.6177	b3012	dkgA	-8.72	0.074604	189 -- 197	44 -- 52	2 5-diketo-D-gluconate reductase A	_____________188_______198\n_____________\|_________\|\n5'-CUG...AUAUA_________CGUAU...CCA-3'\n______________AAGGAGGAA\n______________\|\|:\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.1725 kcal/mol	1.58724 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-CUG...AUAUA CGUAU...CCA-3'@LB@ AAGGAGGAA@LB@ \|\|:\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1725 kcal/mol@LB@Unfolding Energy - mRNA 1.58724 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
87	0.01794	0.6177	b3499	rlmJ	-10.99	0.025859	12 -- 21	46 -- 55	23S rRNA m(6)A2030 methyltransferase SAM-dependent	_____________11_________22\n_____________\|__________\|\n5'-GCG...UCCUG__________UUAAG...AUA-3'\n______________GUUAAAGAGG\n______________\|\|:\|\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	15 -- 21	46 -- 52	-14.3615 kcal/mol	2.45195 kcal/mol	0.924411 kcal/mol	11 22@LB@ \| \|@LB@5'-GCG...UCCUG UUAAG...AUA-3'@LB@ GUUAAAGAGG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -14.3615 kcal/mol@LB@Unfolding Energy - mRNA 2.45195 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 46 -- 52@LB@
45	0.009176	0.6129	b3389	aroB	-8.88	0.069424	203 -- 218	37 -- 52	3-dehydroquinate synthase	_____________202______________219\n_____________\|________________\|\n5'-ACA...GUUAU________UUG_____ACUCU...CGG-3'\n______________GGAGAGGA___UCGUU\n______________::\|\|\|\|\|\|___\|\|:\|\|\n______________UUUCUCCU___AGUAA\n3'-UUU...GGCAG________UAA_____AAAAA...ACA-5'\n_____________\|________________\|\n_____________53_______________36\n	204 -- 210	45 -- 51	-14.6346 kcal/mol	4.67835 kcal/mol	1.07641 kcal/mol	202 219@LB@ \| \|@LB@5'-ACA...GUUAU UUG ACUCU...CGG-3'@LB@ GGAGAGGA UCGUU@LB@ ::\|\|\|\|\|\| \|\|:\|\|@LB@ UUUCUCCU AGUAA@LB@3'-UUU...GGCAG UAA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.6346 kcal/mol@LB@Unfolding Energy - mRNA 4.67835 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 203 -- 218@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 45 -- 51@LB@
121	0.02422	0.6177	b0754	aroG	-7.67	0.121074	238 -- 245	47 -- 54	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase phenylalanine repressible	_____________237______246\n_____________\|________\|\n5'-CUU...AGAAA________UUACU...CGA-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	239 -- 245	47 -- 53	-9.80538 kcal/mol	1.24089 kcal/mol	0.897871 kcal/mol	237 246@LB@ \| \|@LB@5'-CUU...AGAAA UUACU...CGA-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -9.80538 kcal/mol@LB@Unfolding Energy - mRNA 1.24089 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 238 -- 245@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 47 -- 53@LB@
25	0.004737	0.5992	b1093	fabG	-11.25	0.022809	188 -- 202	38 -- 52	3-oxoacyl-[acyl-carrier-protein] reductase	_____________187_____________203\n_____________\|_______________\|\n5'-UAC...CUUUA_________AA____GAAUU...UUG-3'\n______________AAAGAGGAA__UCAU\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UUUCUCCUU__AGUA\n3'-UUU...GGCAG_________AA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	190 -- 196	44 -- 50	-14.2885 kcal/mol	1.96871 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-UAC...CUUUA AA GAAUU...UUG-3'@LB@ AAAGAGGAA UCAU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUCCUU AGUA@LB@3'-UUU...GGCAG AA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -14.2885 kcal/mol@LB@Unfolding Energy - mRNA 1.96871 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
118	0.0238	0.6177	b3321	rpsJ	-9.75	0.046314	151 -- 177	30 -- 55	30S ribosomal subunit protein S10	_____________150___________________________178\n_____________\|_____________________________\|\n5'-UUC...AAUGG___U_________AA_______CG_____AAAAU...GUG-3'\n______________GUC___GAGGAGU__UCAUUUU__UUUAU\n______________\|\|\|___\|\|\|\|\|:\|__\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CAG___CUCCUUA__AGUAAAA__AAAUA\n3'-UUU...CCGGG___UUU_______A_______________AUAAU...ACA-5'\n_____________\|_____________________________\|\n_____________56____________________________29\n	164 -- 170	35 -- 41	-16.2369 kcal/mol	5.30163 kcal/mol	1.18773 kcal/mol	150 178@LB@ \| \|@LB@5'-UUC...AAUGG U AA CG AAAAU...GUG-3'@LB@ GUC GAGGAGU UCAUUUU UUUAU@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ CAG CUCCUUA AGUAAAA AAAUA@LB@3'-UUU...CCGGG UUU A AUAAU...ACA-5'@LB@ \| \|@LB@ 56 29@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -16.2369 kcal/mol@LB@Unfolding Energy - mRNA 5.30163 kcal/mol@LB@Unfolding Energy - sRNA 1.18773 kcal/mol@LB@@LB@Position - mRNA 151 -- 177@LB@Position - sRNA 30 -- 55@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 35 -- 41@LB@
152	0.03059	0.6177	b2609	rpsP	-6.70	0.186060	187 -- 203	23 -- 53	30S ribosomal subunit protein S16	_____________186______________________________204\n_____________\|________________________________\|\n5'-UCA...AUUCA__C_____________________________GUAAC...UCG-3'\n______________CA_AAGAGGA_______________UGUUAUG\n______________\|\|_\|\|\|\|\|\|\|_______________\|:\|\|\|\|\|\n______________GU_UUCUCCU_______________AUAAUAC\n3'-UUU...GGGCA__________UAAAGUAAAAAAAUA_______GGCAG...ACA-5'\n_____________\|________________________________\|\n_____________54_______________________________22\n	197 -- 203	23 -- 29	-10.7305 kcal/mol	2.84664 kcal/mol	1.18482 kcal/mol	186 204@LB@ \| \|@LB@5'-UCA...AUUCA C GUAAC...UCG-3'@LB@ CA AAGAGGA UGUUAUG@LB@ \|\| \|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GU UUCUCCU AUAAUAC@LB@3'-UUU...GGGCA UAAAGUAAAAAAAUA GGCAG...ACA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -10.7305 kcal/mol@LB@Unfolding Energy - mRNA 2.84664 kcal/mol@LB@Unfolding Energy - sRNA 1.18482 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 23 -- 29@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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