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
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@
172	0.03476	0.6177	b3441	yhhY	-9.34	0.055938	185 -- 193	45 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________184_______194\n_____________\|_________\|\n5'-CCC...UACCC_________CAAAG...UGC-3'\n______________CAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	187 -- 193	45 -- 51	-12.8083 kcal/mol	2.54681 kcal/mol	0.917553 kcal/mol	184 194@LB@ \| \|@LB@5'-CCC...UACCC CAAAG...UGC-3'@LB@ CAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -12.8083 kcal/mol@LB@Unfolding Energy - mRNA 2.54681 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 185 -- 193@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
185	0.03847	0.6177	b0621	dcuC	-6.69	0.186516	155 -- 171	26 -- 48	anaerobic C4-dicarboxylate transport	_____________154_____________________172\n_____________\|_______________________\|\n5'-UGC...GCUUU_______________________UACUU...UCG-3'\n______________AGGAAUUUU______UUAUUAUU\n______________\|\|\|\|\|\|\|\|:______\|\|\|\|\|\|\|\|\n______________UCCUUAAAG______AAUAAUAA\n3'-UUU...GUUUC_________UAAAAA________UACGG...ACA-5'\n_____________\|_______________________\|\n_____________49______________________25\n	165 -- 171	26 -- 32	-10.8714 kcal/mol	3.1068 kcal/mol	1.07117 kcal/mol	154 172@LB@ \| \|@LB@5'-UGC...GCUUU UACUU...UCG-3'@LB@ AGGAAUUUU UUAUUAUU@LB@ \|\|\|\|\|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UCCUUAAAG AAUAAUAA@LB@3'-UUU...GUUUC UAAAAA UACGG...ACA-5'@LB@ \| \|@LB@ 49 25@LB@@LB@@LB@Energy -6.69 kcal/mol@LB@Hybridization Energy -10.8714 kcal/mol@LB@Unfolding Energy - mRNA 3.1068 kcal/mol@LB@Unfolding Energy - sRNA 1.07117 kcal/mol@LB@@LB@Position - mRNA 155 -- 171@LB@Position - sRNA 26 -- 48@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 26 -- 32@LB@
61	0.01292	0.6177	b4154	frdA	-9.46	0.053105	187 -- 202	38 -- 54	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit	_____________186_______________203\n_____________\|_________________\|\n5'-UAA...AACAA__U_________G____GCAAA...UCG-3'\n______________UC__GGAGGAAU_UCGU\n______________\|\|__:\|\|\|\|\|\|\|_\|\|:\|\n______________AG__UCUCCUUA_AGUA\n3'-UUU...CGGGC__UU________A____AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	191 -- 197	43 -- 49	-14.1575 kcal/mol	3.5319 kcal/mol	1.17036 kcal/mol	186 203@LB@ \| \|@LB@5'-UAA...AACAA U G GCAAA...UCG-3'@LB@ UC GGAGGAAU UCGU@LB@ \|\| :\|\|\|\|\|\|\| \|\|:\|@LB@ AG UCUCCUUA AGUA@LB@3'-UUU...CGGGC UU A AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -14.1575 kcal/mol@LB@Unfolding Energy - mRNA 3.5319 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 187 -- 202@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
72	0.015	0.6177	b2513	yfgM	-10.40	0.034106	179 -- 190	45 -- 55	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________178__________191\n_____________\|____________\|\n5'-GGC...ACUGG________A___GAAGG...UUG-3'\n______________GUUAAGGA_GGA\n______________\|\|:\|\|:\|\|_\|\|\|\n______________CAGUUUCU_CCU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	180 -- 186	48 -- 54	-12.2699 kcal/mol	0.940443 kcal/mol	0.930875 kcal/mol	178 191@LB@ \| \|@LB@5'-GGC...ACUGG A GAAGG...UUG-3'@LB@ GUUAAGGA GGA@LB@ \|\|:\|\|:\|\| \|\|\|@LB@ CAGUUUCU CCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -12.2699 kcal/mol@LB@Unfolding Energy - mRNA 0.940443 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 190@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 48 -- 54@LB@
176	0.03596	0.6177	b1747	astA	-4.82	0.399998	129 -- 139	46 -- 56	arginine succinyltransferase	_____________128_________140\n_____________\|___________\|\n5'-GGC...GUCAG__AA_______UGACG...AAG-3'\n______________CG__GAAGAGG\n______________\|\|__:\|\|\|\|\|\|\n______________GC__UUUCUCC\n3'-UUU...ACCGG__AG_______UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	133 -- 139	46 -- 52	-9.86744 kcal/mol	4.11365 kcal/mol	0.93204 kcal/mol	128 140@LB@ \| \|@LB@5'-GGC...GUCAG AA UGACG...AAG-3'@LB@ CG GAAGAGG@LB@ \|\| :\|\|\|\|\|\|@LB@ GC UUUCUCC@LB@3'-UUU...ACCGG AG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -4.82 kcal/mol@LB@Hybridization Energy -9.86744 kcal/mol@LB@Unfolding Energy - mRNA 4.11365 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 129 -- 139@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 46 -- 52@LB@
19	0.003501	0.593	b2019	hisG	-12.73	0.011332	183 -- 194	43 -- 54	ATP phosphoribosyltransferase	_____________182__________195\n_____________\|____________\|\n5'-UUU...CAGGU____________AACAA...AUC-3'\n______________UUAAAGAGGAAU\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUUUCUCCUUA\n3'-UUU...CGGGC____________AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	188 -- 194	43 -- 49	-14.9017 kcal/mol	1.23041 kcal/mol	0.944705 kcal/mol	182 195@LB@ \| \|@LB@5'-UUU...CAGGU AACAA...AUC-3'@LB@ UUAAAGAGGAAU@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUUUCUCCUUA@LB@3'-UUU...CGGGC AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -14.9017 kcal/mol@LB@Unfolding Energy - mRNA 1.23041 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
38	0.007716	0.6129	b0480	ushA	-6.97	0.165152	186 -- 197	45 -- 55	bifunctional UDP-sugar hydrolase/5'-nucleotidase	_____________185__________198\n_____________\|____________\|\n5'-AGG...AUCAG_________A__AGUAU...AAA-3'\n______________GUCAGGGAG_GA\n______________\|\|\|\|::\|\|\|_\|\|\n______________CAGUUUCUC_CU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	188 -- 194	47 -- 53	-13.3467 kcal/mol	5.44454 kcal/mol	0.930875 kcal/mol	185 198@LB@ \| \|@LB@5'-AGG...AUCAG A AGUAU...AAA-3'@LB@ GUCAGGGAG GA@LB@ \|\|\|\|::\|\|\| \|\|@LB@ CAGUUUCUC CU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -13.3467 kcal/mol@LB@Unfolding Energy - mRNA 5.44454 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
26	0.004859	0.5992	b1753	ynjA	-8.90	0.068656	186 -- 195	43 -- 52	carboxymuconolactone decarboxylase family protein	_____________185________196\n_____________\|__________\|\n5'-ACU...CGCCA__________GCCUG...GGU-3'\n______________GAAGAGGAAU\n______________:\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	189 -- 195	43 -- 49	-11.6028 kcal/mol	1.83308 kcal/mol	0.865937 kcal/mol	185 196@LB@ \| \|@LB@5'-ACU...CGCCA GCCUG...GGU-3'@LB@ GAAGAGGAAU@LB@ :\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -11.6028 kcal/mol@LB@Unfolding Energy - mRNA 1.83308 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 43 -- 49@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@

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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