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	Additional homologs
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein		_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@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@
112	0.02248	0.6177	b2796	sdaC	-8.62	0.078257	115 -- 131	34 -- 50	putative serine transporter		_____________114_______________132\n_____________\|_________________\|\n5'-AUC...CCGAU___CA____________ACGGU...CAA-3'\n______________AGA__GAUUUCAUUUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|\|\|\n______________UCU__UUAAAGUAAAAA\n3'-UUU...CAGUU___CC____________AAUAA...ACA-5'\n_____________\|_________________\|\n_____________51________________33\n	125 -- 131	34 -- 40	-11.667 kcal/mol	1.97198 kcal/mol	1.0739 kcal/mol	114 132@LB@ \| \|@LB@5'-AUC...CCGAU CA ACGGU...CAA-3'@LB@ AGA GAUUUCAUUUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\|\|\|@LB@ UCU UUAAAGUAAAAA@LB@3'-UUU...CAGUU CC AAUAA...ACA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.667 kcal/mol@LB@Unfolding Energy - mRNA 1.97198 kcal/mol@LB@Unfolding Energy - sRNA 1.0739 kcal/mol@LB@@LB@Position - mRNA 115 -- 131@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 34 -- 40@LB@
31	0.005902	0.6127	b1951	rcsA	-8.09	0.100100	163 -- 178	37 -- 51	transcriptional regulator of colanic acid capsular biosynthesis		_____________162______________179\n_____________\|________________\|\n5'-GUU...CAGGU__________A_____ACGCA...UUG-3'\n______________AAGGGGAAUU_UCGUU\n______________\|\|\|:\|\|\|\|\|\|_\|\|:\|\|\n______________UUCUCCUUAA_AGUAA\n3'-UUU...GCAGU________________AAAAA...ACA-5'\n_____________\|________________\|\n_____________52_______________36\n	166 -- 172	42 -- 48	-14.3412 kcal/mol	5.18535 kcal/mol	1.07049 kcal/mol	162 179@LB@ \| \|@LB@5'-GUU...CAGGU A ACGCA...UUG-3'@LB@ AAGGGGAAUU UCGUU@LB@ \|\|\|:\|\|\|\|\|\| \|\|:\|\|@LB@ UUCUCCUUAA AGUAA@LB@3'-UUU...GCAGU AAAAA...ACA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -8.09 kcal/mol@LB@Hybridization Energy -14.3412 kcal/mol@LB@Unfolding Energy - mRNA 5.18535 kcal/mol@LB@Unfolding Energy - sRNA 1.07049 kcal/mol@LB@@LB@Position - mRNA 163 -- 178@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 42 -- 48@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@
110	0.02234	0.6177	b0141	yadN	-8.72	0.074917	179 -- 189	37 -- 47	putative fimbrial-like adhesin protein		_____________178_________190\n_____________\|___________\|\n5'-UUA...CUAAU___________AAAGG...GUG-3'\n______________GGAAUUUUAUU\n______________\|\|\|\|\|\|\|:\|\|\|\n______________CCUUAAAGUAA\n3'-UUU...UUUCU___________AAAAA...ACA-5'\n_____________\|___________\|\n_____________48__________36\n	183 -- 189	37 -- 43	-11.1734 kcal/mol	1.41261 kcal/mol	1.04525 kcal/mol	178 190@LB@ \| \|@LB@5'-UUA...CUAAU AAAGG...GUG-3'@LB@ GGAAUUUUAUU@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ CCUUAAAGUAA@LB@3'-UUU...UUUCU AAAAA...ACA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1734 kcal/mol@LB@Unfolding Energy - mRNA 1.41261 kcal/mol@LB@Unfolding Energy - sRNA 1.04525 kcal/mol@LB@@LB@Position - mRNA 179 -- 189@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 37 -- 43@LB@
134	0.02619	0.6177	b1126	potA	-9.47	0.052791	285 -- 299	37 -- 55	spermidine/putrescine ABC transporter ATPase		_____________284_________________300\n_____________\|___________________\|\n5'-CAA...UUGAU_GU________________C-3'\n______________G__AAAGAGG____UCAUU\n______________\|__\|\|\|\|\|\|\|____\|\|\|\|\|\n______________C__UUUCUCC____AGUAA\n3'-UUU...CCGGG_AG_______UUAA_____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________36\n	288 -- 294	46 -- 52	-11.4861 kcal/mol	0.840334 kcal/mol	1.17789 kcal/mol	284 300@LB@ \| \|@LB@5'-CAA...UUGAU GU C-3'@LB@ G AAAGAGG UCAUU@LB@ \| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ C UUUCUCC AGUAA@LB@3'-UUU...CCGGG AG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 36@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -11.4861 kcal/mol@LB@Unfolding Energy - mRNA 0.840334 kcal/mol@LB@Unfolding Energy - sRNA 1.17789 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 37 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@LB@
183	0.03803	0.6177	b3616	tdh	-7.63	0.122830	33 -- 50	37 -- 52	L-threonine 3-dehydrogenase NAD(P)-binding		_____________32_________________51\n_____________\|__________________\|\n5'-UAG...UGCAA________C____A____ACCGG...GUA-3'\n______________AAAGAGGG_AUUU_CGUU\n______________\|\|\|\|\|\|\|:_\|\|\|\|_\|:\|\|\n______________UUUCUCCU_UAAA_GUAA\n3'-UUU...GGCAG__________________AAAAA...ACA-5'\n_____________\|__________________\|\n_____________53_________________36\n	34 -- 40	45 -- 51	-11.8553 kcal/mol	3.14412 kcal/mol	1.07641 kcal/mol	32 51@LB@ \| \|@LB@5'-UAG...UGCAA C A ACCGG...GUA-3'@LB@ AAAGAGGG AUUU CGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|:\|\|@LB@ UUUCUCCU UAAA GUAA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -11.8553 kcal/mol@LB@Unfolding Energy - mRNA 3.14412 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 33 -- 50@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 45 -- 51@LB@
196	0.04084	0.6177	b3137	kbaY	-7.51	0.129887	187 -- 200	37 -- 51	tagatose 6-phosphate aldolase 1 kbaY subunit	b2096	_____________186_____________201\n_____________\|_______________\|\n5'-CAC...GGCAU_______UCG_____AUGAG...CGA-3'\n______________AAGAGGA____CAUU\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________UUCUCCU____GUAA\n3'-UUU...GCAGU_______UAAA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________52______________36\n	187 -- 193	45 -- 51	-11.4071 kcal/mol	2.82588 kcal/mol	1.07049 kcal/mol	186 201@LB@ \| \|@LB@5'-CAC...GGCAU UCG AUGAG...CGA-3'@LB@ AAGAGGA CAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ UUCUCCU GUAA@LB@3'-UUU...GCAGU UAAA AAAAA...ACA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -11.4071 kcal/mol@LB@Unfolding Energy - mRNA 2.82588 kcal/mol@LB@Unfolding Energy - sRNA 1.07049 kcal/mol@LB@@LB@Position - mRNA 187 -- 200@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
2	6.241e-06	0.01004	b1737	chbC	-18.35	0.000789	134 -- 152	38 -- 56	N N'-diacetylchitobiose-specific enzyme IIC component of PTS		_____________133_________________153\n_____________\|___________________\|\n5'-GUU...UUUCC__________UU_______AAAUC...UUC-3'\n______________CGUCAAAGAG__AUUUCAU\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________GCAGUUUCUC__UAAAGUA\n3'-UUU...ACCGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	146 -- 152	38 -- 44	-21.3647 kcal/mol	1.83077 kcal/mol	1.17918 kcal/mol	133 153@LB@ \| \|@LB@5'-GUU...UUUCC UU AAAUC...UUC-3'@LB@ CGUCAAAGAG AUUUCAU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCAGUUUCUC UAAAGUA@LB@3'-UUU...ACCGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -21.3647 kcal/mol@LB@Unfolding Energy - mRNA 1.83077 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 134 -- 152@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 38 -- 44@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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service.

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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