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
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@
66	0.01414	0.6177	b0440	hupB	-10.30	0.035643	184 -- 193	44 -- 53	HU DNA-binding transcriptional regulator beta subunit	_____________183________194\n_____________\|__________\|\n5'-CGC...AAUUA__________GAGAA...CUG-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	187 -- 193	44 -- 50	-11.552 kcal/mol	0.319105 kcal/mol	0.927997 kcal/mol	183 194@LB@ \| \|@LB@5'-CGC...AAUUA GAGAA...CUG-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -11.552 kcal/mol@LB@Unfolding Energy - mRNA 0.319105 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
71	0.01472	0.6177	b0846	rcdA	-10.28	0.035999	187 -- 195	44 -- 52	transcriptional regulator of csgD and ybiJI; autoregulator	_____________186_______196\n_____________\|_________\|\n5'-GCG...UGCAG_________AUGAC...AAA-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-11.6116 kcal/mol	0.46711 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-GCG...UGCAG AUGAC...AAA-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -11.6116 kcal/mol@LB@Unfolding Energy - mRNA 0.46711 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
64	0.01382	0.6177	b3250	mreC	-10.24	0.036759	206 -- 229	53 -- 75	cell wall structural complex MreBCD transmembrane component MreC	_____________205_______________________230\n_____________\|_________________________\|\n5'-GAC...AUGAA______UUUUA__CG__________GCUAC...GGA-3'\n______________GCCAAU_____GC___UGGCCCGUC\n______________\|\|\|\|\|\|_____\|\|___\|\|\|\|\|\|\|\|\|\n______________CGGUUA_____CG___ACCGGGCAG\n3'-UUU...UUUAC______UAG____AUA_________UUUCU...ACA-5'\n_____________\|_________________________\|\n_____________76________________________52\n	223 -- 229	53 -- 59	-27.5071 kcal/mol	5.94491 kcal/mol	11.3228 kcal/mol	205 230@LB@ \| \|@LB@5'-GAC...AUGAA UUUUA CG GCUAC...GGA-3'@LB@ GCCAAU GC UGGCCCGUC@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ CGGUUA CG ACCGGGCAG@LB@3'-UUU...UUUAC UAG AUA UUUCU...ACA-5'@LB@ \| \|@LB@ 76 52@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -27.5071 kcal/mol@LB@Unfolding Energy - mRNA 5.94491 kcal/mol@LB@Unfolding Energy - sRNA 11.3228 kcal/mol@LB@@LB@Position - mRNA 206 -- 229@LB@Position - sRNA 53 -- 75@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 53 -- 59@LB@
9	0.001801	0.593	b1276	acnA	-10.22	0.037037	184 -- 198	44 -- 55	aconitate hydratase 1; aconitase A	_____________183_____________199\n_____________\|_______________\|\n5'-CUU...ACCCU____UUA________CUAUG...GCG-3'\n______________GUCA___AGGAGGAG\n______________\|\|\|\|___\|:\|\|\|\|\|:\n______________CAGU___UUCUCCUU\n3'-UUU...CCGGG_______________AAAGU...ACA-5'\n_____________\|_______________\|\n_____________56______________43\n	192 -- 198	44 -- 50	-13.3918 kcal/mol	2.22696 kcal/mol	0.941432 kcal/mol	183 199@LB@ \| \|@LB@5'-CUU...ACCCU UUA CUAUG...GCG-3'@LB@ GUCA AGGAGGAG@LB@ \|\|\|\| \|:\|\|\|\|\|:@LB@ CAGU UUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -13.3918 kcal/mol@LB@Unfolding Energy - mRNA 2.22696 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
23	0.004411	0.5992	b3390	aroK	-10.22	0.037117	283 -- 298	39 -- 54	shikimate kinase I	_____________282______________299\n_____________\|________________\|\n5'-UGG...ACAAC____UAU_________CG-3'\n______________UCAA___GGAAUUUUA\n______________\|\|\|\|___\|\|\|\|\|\|\|:\|\n______________AGUU___CCUUAAAGU\n3'-UUU...CGGGC____UCU_________AAAAA...ACA-5'\n_____________\|________________\|\n_____________55_______________38\n	292 -- 298	39 -- 45	-11.8677 kcal/mol	0.499768 kcal/mol	1.1491 kcal/mol	282 299@LB@ \| \|@LB@5'-UGG...ACAAC UAU CG-3'@LB@ UCAA GGAAUUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|:\|@LB@ AGUU CCUUAAAGU@LB@3'-UUU...CGGGC UCU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -11.8677 kcal/mol@LB@Unfolding Energy - mRNA 0.499768 kcal/mol@LB@Unfolding Energy - sRNA 1.1491 kcal/mol@LB@@LB@Position - mRNA 283 -- 298@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@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@
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@
120	0.02398	0.6177	b0283	paoD	-10.02	0.040757	188 -- 198	44 -- 54	moco insertion factor for PaoABC aldehyde oxidoreductase	_____________187_________199\n_____________\|___________\|\n5'-AGG...GUGGU___________CAAUG...AGG-3'\n______________UUAAGGAGGAA\n______________\|:\|\|:\|\|\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	192 -- 198	44 -- 50	-12.5456 kcal/mol	1.58604 kcal/mol	0.939671 kcal/mol	187 199@LB@ \| \|@LB@5'-AGG...GUGGU CAAUG...AGG-3'@LB@ UUAAGGAGGAA@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.5456 kcal/mol@LB@Unfolding Energy - mRNA 1.58604 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 188 -- 198@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
115	0.02287	0.6177	b3621	waaC	-10.02	0.040839	179 -- 191	44 -- 55	ADP-heptose:LPS heptosyl transferase I	_____________178___________192\n_____________\|_____________\|\n5'-UUG...CUAUU____C________GCCUG...UUG-3'\n______________GUUA_AAGAGGAA\n______________\|\|:\|_\|\|\|\|\|\|\|\|\n______________CAGU_UUCUCCUU\n3'-UUU...CCGGG_____________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	185 -- 191	44 -- 50	-12.6771 kcal/mol	1.72007 kcal/mol	0.941432 kcal/mol	178 192@LB@ \| \|@LB@5'-UUG...CUAUU C GCCUG...UUG-3'@LB@ GUUA AAGAGGAA@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ CAGU UUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.6771 kcal/mol@LB@Unfolding Energy - mRNA 1.72007 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 179 -- 191@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 44 -- 50@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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