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
98	0.0193	0.6177	b2705	srlD	-10.75	0.028892	101 -- 114	40 -- 53	sorbitol-6-phosphate dehydrogenase	_____________100____________115\n_____________\|______________\|\n5'-CAC...UUAAA_____C________CGGGC...AUA-3'\n______________CGAAG_GGAAUUUC\n______________\|:\|\|\|_\|\|\|\|\|\|\|\|\n______________GUUUC_CCUUAAAG\n3'-UUU...GGGCA_____U________UAAAA...ACA-5'\n_____________\|______________\|\n_____________54_____________39\n	108 -- 114	40 -- 46	-15.1517 kcal/mol	3.39572 kcal/mol	1.00568 kcal/mol	100 115@LB@ \| \|@LB@5'-CAC...UUAAA C CGGGC...AUA-3'@LB@ CGAAG GGAAUUUC@LB@ \|:\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUUC CCUUAAAG@LB@3'-UUU...GGGCA U UAAAA...ACA-5'@LB@ \| \|@LB@ 54 39@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -15.1517 kcal/mol@LB@Unfolding Energy - mRNA 3.39572 kcal/mol@LB@Unfolding Energy - sRNA 1.00568 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 40 -- 53@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 40 -- 46@LB@
103	0.02062	0.6177	b1332	ynaJ	-7.81	0.113347	36 -- 54	40 -- 55	DUF2534 family putative inner membrane protein	_____________35__________________55\n_____________\|___________________\|\n5'-AAA...ACUGA____GCC____A_______CCCGC...CCA-3'\n______________GUCA___GAGA_GAAUUUC\n______________\|\|\|\|___:\|\|\|_\|\|\|\|\|\|\|\n______________CAGU___UUCU_CUUAAAG\n3'-UUU...CCGGG___________C_______UAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________39\n	48 -- 54	40 -- 46	-13.2524 kcal/mol	4.4222 kcal/mol	1.01784 kcal/mol	35 55@LB@ \| \|@LB@5'-AAA...ACUGA GCC A CCCGC...CCA-3'@LB@ GUCA GAGA GAAUUUC@LB@ \|\|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ CAGU UUCU CUUAAAG@LB@3'-UUU...CCGGG C UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -13.2524 kcal/mol@LB@Unfolding Energy - mRNA 4.4222 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 40 -- 46@LB@
125	0.02442	0.6177	b3181	greA	-6.11	0.239901	243 -- 260	40 -- 56	transcript cleavage factor	_____________242_________________261\n_____________\|___________________\|\n5'-CGC...AAUUA__________CU_______CUGAA...UCG-3'\n______________CG_CGAAGAG__GGAUUUU\n______________\|\|_\|:\|\|\|\|\|__\|:\|\|\|\|:\n______________GC_GUUUCUC__CUUAAAG\n3'-UUU...ACCGG__A________________UAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________39\n	245 -- 251	47 -- 53	-12.1125 kcal/mol	4.98158 kcal/mol	1.02557 kcal/mol	242 261@LB@ \| \|@LB@5'-CGC...AAUUA CU CUGAA...UCG-3'@LB@ CG CGAAGAG GGAUUUU@LB@ \|\| \|:\|\|\|\|\| \|:\|\|\|\|:@LB@ GC GUUUCUC CUUAAAG@LB@3'-UUU...ACCGG A UAAAA...ACA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -6.11 kcal/mol@LB@Hybridization Energy -12.1125 kcal/mol@LB@Unfolding Energy - mRNA 4.98158 kcal/mol@LB@Unfolding Energy - sRNA 1.02557 kcal/mol@LB@@LB@Position - mRNA 243 -- 260@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 47 -- 53@LB@
129	0.02539	0.6177	b0129	yadI	-10.21	0.037333	124 -- 136	40 -- 52	putative PTS Enzyme IIA	_____________123___________137\n_____________\|_____________\|\n5'-CUG...UUGGG_____________GACGG...UGA-3'\n______________GGAGAGGAGUUUU\n______________::\|\|\|\|\|\|:\|\|\|:\n______________UUUCUCCUUAAAG\n3'-UUU...GGCAG_____________UAAAA...ACA-5'\n_____________\|_____________\|\n_____________53____________39\n	130 -- 136	40 -- 46	-14.8894 kcal/mol	3.74683 kcal/mol	0.936082 kcal/mol	123 137@LB@ \| \|@LB@5'-CUG...UUGGG GACGG...UGA-3'@LB@ GGAGAGGAGUUUU@LB@ ::\|\|\|\|\|\|:\|\|\|:@LB@ UUUCUCCUUAAAG@LB@3'-UUU...GGCAG UAAAA...ACA-5'@LB@ \| \|@LB@ 53 39@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -14.8894 kcal/mol@LB@Unfolding Energy - mRNA 3.74683 kcal/mol@LB@Unfolding Energy - sRNA 0.936082 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 40 -- 52@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 40 -- 46@LB@
154	0.03071	0.6177	b0368	tauD	-7.18	0.150437	69 -- 85	40 -- 55	taurine dioxygenase 2-oxoglutarate-dependent	_____________68________________86\n_____________\|_________________\|\n5'-GUG...GUUCA_____C___U_______UCGCA...AAC-3'\n______________GUCAG_GGG_GAAUUUC\n______________\|\|\|\|:_\|:\|_\|\|\|\|\|\|\|\n______________CAGUU_CUC_CUUAAAG\n3'-UUU...CCGGG_____U___________UAAAA...ACA-5'\n_____________\|_________________\|\n_____________56________________39\n	79 -- 85	40 -- 46	-16.0696 kcal/mol	7.86965 kcal/mol	1.01784 kcal/mol	68 86@LB@ \| \|@LB@5'-GUG...GUUCA C U UCGCA...AAC-3'@LB@ GUCAG GGG GAAUUUC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|\|@LB@ CAGUU CUC CUUAAAG@LB@3'-UUU...CCGGG U UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.0696 kcal/mol@LB@Unfolding Energy - mRNA 7.86965 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 40 -- 46@LB@
22	0.004195	0.5992	b3715	yieH	-7.44	0.134211	287 -- 299	41 -- 55	phosphoenolpyruvate and 6-phosphogluconate phosphatase	_____________286_____________300\n_____________\|_______________\|\n5'-CUG...ACGAU___UC__________G-3'\n______________GUU____AGGAAUUU\n______________\|\|:____\|\|\|\|\|\|\|\|\n______________CAG____UCCUUAAA\n3'-UUU...CCGGG___UUUC________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	293 -- 299	41 -- 47	-8.9861 kcal/mol	0.60049 kcal/mol	0.947844 kcal/mol	286 300@LB@ \| \|@LB@5'-CUG...ACGAU UC G-3'@LB@ GUU AGGAAUUU@LB@ \|\|: \|\|\|\|\|\|\|\|@LB@ CAG UCCUUAAA@LB@3'-UUU...CCGGG UUUC GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -8.9861 kcal/mol@LB@Unfolding Energy - mRNA 0.60049 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 41 -- 47@LB@
24	0.004602	0.5992	b0526	cysS	-10.20	0.037463	234 -- 245	41 -- 52	cysteinyl-tRNA synthetase	_____________233__________246\n_____________\|____________\|\n5'-GCC...GCCAA____________AAGCC...ACG-3'\n______________AAAGAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUUAAA\n3'-UUU...GGCAG____________GUAAA...ACA-5'\n_____________\|____________\|\n_____________53___________40\n	239 -- 245	41 -- 47	-14.6017 kcal/mol	3.53507 kcal/mol	0.867487 kcal/mol	233 246@LB@ \| \|@LB@5'-GCC...GCCAA AAGCC...ACG-3'@LB@ AAAGAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUUAAA@LB@3'-UUU...GGCAG GUAAA...ACA-5'@LB@ \| \|@LB@ 53 40@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6017 kcal/mol@LB@Unfolding Energy - mRNA 3.53507 kcal/mol@LB@Unfolding Energy - sRNA 0.867487 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 41 -- 52@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 41 -- 47@LB@
55	0.01149	0.6177	b3287	def	-9.61	0.049470	133 -- 146	41 -- 54	peptide deformylase	_____________132____________147\n_____________\|______________\|\n5'-AUA...GUCAA______________GUCUA...AUG-3'\n______________UCAGAGGGGGAUUU\n______________\|\|\|:\|\|:\|\|:\|\|\|\|\n______________AGUUUCUCCUUAAA\n3'-UUU...CGGGC______________GUAAA...ACA-5'\n_____________\|______________\|\n_____________55_____________40\n	140 -- 146	41 -- 47	-17.2173 kcal/mol	6.66439 kcal/mol	0.946064 kcal/mol	132 147@LB@ \| \|@LB@5'-AUA...GUCAA GUCUA...AUG-3'@LB@ UCAGAGGGGGAUUU@LB@ \|\|\|:\|\|:\|\|:\|\|\|\|@LB@ AGUUUCUCCUUAAA@LB@3'-UUU...CGGGC GUAAA...ACA-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -17.2173 kcal/mol@LB@Unfolding Energy - mRNA 6.66439 kcal/mol@LB@Unfolding Energy - sRNA 0.946064 kcal/mol@LB@@LB@Position - mRNA 133 -- 146@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 41 -- 47@LB@
111	0.02245	0.6177	b3413	gntX	-10.38	0.034336	253 -- 267	41 -- 55	DNA catabolic protein	_____________252_____________268\n_____________\|_______________\|\n5'-CCC...GUUAG____UU_________GUUCG...AUA-3'\n______________GUCA__GGGGGAUUU\n______________\|\|\|\|__\|:\|\|:\|\|\|\|\n______________CAGU__CUCCUUAAA\n3'-UUU...CCGGG____UU_________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	261 -- 267	41 -- 47	-16.783 kcal/mol	5.45091 kcal/mol	0.947844 kcal/mol	252 268@LB@ \| \|@LB@5'-CCC...GUUAG UU GUUCG...AUA-3'@LB@ GUCA GGGGGAUUU@LB@ \|\|\|\| \|:\|\|:\|\|\|\|@LB@ CAGU CUCCUUAAA@LB@3'-UUU...CCGGG UU GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.783 kcal/mol@LB@Unfolding Energy - mRNA 5.45091 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 253 -- 267@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 41 -- 47@LB@
144	0.02798	0.6177	b0682	chiQ	-9.70	0.047426	184 -- 197	41 -- 56	chitosugar-induced verified lipoprotein	_____________183______________198\n_____________\|________________\|\n5'-CGG...CCGCA____U___________GCUAU...ACA-3'\n______________CGUU___GAGGAAUUU\n______________\|\|\|:___\|\|\|\|\|\|\|\|\|\n______________GCAG___CUCCUUAAA\n3'-UUU...ACCGG____UUU_________GUAAA...ACA-5'\n_____________\|________________\|\n_____________57_______________40\n	191 -- 197	41 -- 47	-13.1137 kcal/mol	2.46147 kcal/mol	0.955312 kcal/mol	183 198@LB@ \| \|@LB@5'-CGG...CCGCA U GCUAU...ACA-3'@LB@ CGUU GAGGAAUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GCAG CUCCUUAAA@LB@3'-UUU...ACCGG UUU GUAAA...ACA-5'@LB@ \| \|@LB@ 57 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.1137 kcal/mol@LB@Unfolding Energy - mRNA 2.46147 kcal/mol@LB@Unfolding Energy - sRNA 0.955312 kcal/mol@LB@@LB@Position - mRNA 184 -- 197@LB@Position - sRNA 41 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@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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