Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
76	0.002251	0.09621	b0020	nhaR	-13.73	0.025158	90 -- 112	25 -- 46	transcriptional activator of nhaA		_____________89______________________113\n_____________\|_______________________\|\n5'-AUC...UCUUC__C___AA____A__________UACGC...CUC-3'\n______________GG_GGU__UUGG_UACAGCUGGU\n______________\|\|_\|\|\|__:\|\|\|_\|\|\|\|\|\|\|:\|:\n______________CC_CCA__GACC_AUGUCGAUCG\n3'-UUU...UUCCU__A___AG_______________UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________47______________________24\n	106 -- 112	25 -- 31	-27.2836 kcal/mol	8.99906 kcal/mol	4.55673 kcal/mol	89 113@LB@ \| \|@LB@5'-AUC...UCUUC C AA A UACGC...CUC-3'@LB@ GG GGU UUGG UACAGCUGGU@LB@ \|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|:\|:@LB@ CC CCA GACC AUGUCGAUCG@LB@3'-UUU...UUCCU A AG UAAAA...UCG-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -27.2836 kcal/mol@LB@Unfolding Energy - mRNA 8.99906 kcal/mol@LB@Unfolding Energy - sRNA 4.55673 kcal/mol@LB@@LB@Position - mRNA 90 -- 112@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 25 -- 31@LB@
86	0.002806	0.1082	b1107	nagZ	-13.13	0.035629	98 -- 119	25 -- 47	beta N-acetyl-glucosaminidase		_____________97______________________120\n_____________\|_______________________\|\n5'-AUU...AAGCA_________GA_____C______GACAA...CGC-3'\n______________GGGUGGUUU___GUAC_GCUGGC\n______________:\|\|\|\|\|\|\|:___\|\|\|\|_\|\|\|:\|\|\n______________UCCACCAAG___CAUG_CGAUCG\n3'-UUU...AUUCC_________GAC____U______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	100 -- 106	39 -- 45	-29.3426 kcal/mol	11.6523 kcal/mol	4.55753 kcal/mol	97 120@LB@ \| \|@LB@5'-AUU...AAGCA GA C GACAA...CGC-3'@LB@ GGGUGGUUU GUAC GCUGGC@LB@ :\|\|\|\|\|\|\|: \|\|\|\| \|\|\|:\|\|@LB@ UCCACCAAG CAUG CGAUCG@LB@3'-UUU...AUUCC GAC U UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -29.3426 kcal/mol@LB@Unfolding Energy - mRNA 11.6523 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 98 -- 119@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 39 -- 45@LB@
98	0.003416	0.1172	b2024	hisA	-13.42	0.030138	147 -- 168	25 -- 49	N-(5'-phospho-L-ribosyl-formimino)-5-amino-1- (5'-phosphoribosyl)-4-imidazolecarboxamide isomerase		_____________146_______________________169\n_____________\|_________________________\|\n5'-CAG...CACCC____C_____________C______GCUAA...CGC-3'\n______________GGAG___GUU_CUGGUGC_GCUGGU\n______________\|\|\|\|___\|\|\|_\|\|\|\|\|:\|_\|\|\|:\|:\n______________CCUC___CAA_GACCAUG_CGAUCG\n3'-UUU...CGAUU____CAC___G_______U______UAAAA...UCG-5'\n_____________\|_________________________\|\n_____________50________________________24\n	155 -- 161	32 -- 38	-27.4512 kcal/mol	9.47045 kcal/mol	4.5577 kcal/mol	146 169@LB@ \| \|@LB@5'-CAG...CACCC C C GCUAA...CGC-3'@LB@ GGAG GUU CUGGUGC GCUGGU@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\| \|\|\|:\|:@LB@ CCUC CAA GACCAUG CGAUCG@LB@3'-UUU...CGAUU CAC G U UAAAA...UCG-5'@LB@ \| \|@LB@ 50 24@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -27.4512 kcal/mol@LB@Unfolding Energy - mRNA 9.47045 kcal/mol@LB@Unfolding Energy - sRNA 4.5577 kcal/mol@LB@@LB@Position - mRNA 147 -- 168@LB@Position - sRNA 25 -- 49@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 32 -- 38@LB@
105	0.003867	0.1238	b0716	ybgO	-11.28	0.093728	281 -- 296	25 -- 40	putative fimbrial protein	b3048	_____________280______________297\n_____________\|________________\|\n5'-GCC...UGCUA__________U_____GGCG-3'\n______________UUUUGGUACA_CUGGU\n______________\|::\|\|\|\|\|\|\|_\|\|:\|:\n______________AGGACCAUGU_GAUCG\n3'-UUU...CACCA__________C_____UAAAA...UCG-5'\n_____________\|________________\|\n_____________41_______________24\n	284 -- 290	31 -- 37	-18.2853 kcal/mol	2.44789 kcal/mol	4.55365 kcal/mol	280 297@LB@ \| \|@LB@5'-GCC...UGCUA U GGCG-3'@LB@ UUUUGGUACA CUGGU@LB@ \|::\|\|\|\|\|\|\| \|\|:\|:@LB@ AGGACCAUGU GAUCG@LB@3'-UUU...CACCA C UAAAA...UCG-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -18.2853 kcal/mol@LB@Unfolding Energy - mRNA 2.44789 kcal/mol@LB@Unfolding Energy - sRNA 4.55365 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 31 -- 37@LB@
125	0.005266	0.1416	b0957	ompA	-12.88	0.041122	280 -- 293	25 -- 39	outer membrane protein A (3a;II*;G;d)		_____________279_____________294\n_____________\|_______________\|\n5'-CUU...UAACA_______________GCUAAAC-3'\n______________CCUGGUACA_CUGGU\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|:\n______________GGACCAUGU_GAUCG\n3'-UUU...ACCAA_________C_____UAAAA...UCG-5'\n_____________\|_______________\|\n_____________40______________24\n	282 -- 288	31 -- 37	-21.2564 kcal/mol	3.82713 kcal/mol	4.55153 kcal/mol	279 294@LB@ \| \|@LB@5'-CUU...UAACA GCUAAAC-3'@LB@ CCUGGUACA CUGGU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|:@LB@ GGACCAUGU GAUCG@LB@3'-UUU...ACCAA C UAAAA...UCG-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -21.2564 kcal/mol@LB@Unfolding Energy - mRNA 3.82713 kcal/mol@LB@Unfolding Energy - sRNA 4.55153 kcal/mol@LB@@LB@Position - mRNA 280 -- 293@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 31 -- 37@LB@
158	0.007987	0.1694	b0756	galM	-12.34	0.055034	97 -- 122	25 -- 48	aldose 1-epimerase; type-1 mutarotase; galactose mutarotase		_____________96_________________________123\n_____________\|__________________________\|\n5'-CUG...CGGAA___C____G____CC_______A___UGUCG...GGG-3'\n______________GAG_UGGU_CCUG__GUACAGC_AGC\n______________\|\|\|_\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________CUC_ACCA_GGAC__CAUGUCG_UCG\n3'-UUU...GAUUC___C____A_____________A___UAAAA...UCG-5'\n_____________\|__________________________\|\n_____________49_________________________24\n	112 -- 118	29 -- 35	-29.4823 kcal/mol	12.5844 kcal/mol	4.55759 kcal/mol	96 123@LB@ \| \|@LB@5'-CUG...CGGAA C G CC A UGUCG...GGG-3'@LB@ GAG UGGU CCUG GUACAGC AGC@LB@ \|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ CUC ACCA GGAC CAUGUCG UCG@LB@3'-UUU...GAUUC C A A UAAAA...UCG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -12.34 kcal/mol@LB@Hybridization Energy -29.4823 kcal/mol@LB@Unfolding Energy - mRNA 12.5844 kcal/mol@LB@Unfolding Energy - sRNA 4.55759 kcal/mol@LB@@LB@Position - mRNA 97 -- 122@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 29 -- 35@LB@
169	0.009174	0.1803	b1467	narY	-12.55	0.049142	183 -- 194	25 -- 36	nitrate reductase 2 (NRZ) beta subunit		_____________182__________195\n_____________\|____________\|\n5'-CGC...GAUCA_______GA___GAAAA...GCG-3'\n______________GGUACAG__GGC\n______________\|\|\|\|\|\|\|__:\|\|\n______________CCAUGUC__UCG\n3'-UUU...AAGGA_______GA___UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	183 -- 189	30 -- 36	-16.0252 kcal/mol	2.04549 kcal/mol	1.42738 kcal/mol	182 195@LB@ \| \|@LB@5'-CGC...GAUCA GA GAAAA...GCG-3'@LB@ GGUACAG GGC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ CCAUGUC UCG@LB@3'-UUU...AAGGA GA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -16.0252 kcal/mol@LB@Unfolding Energy - mRNA 2.04549 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
182	0.01043	0.1919	b1235	rssB	-12.59	0.048266	47 -- 57	25 -- 36	PcnB-degradosome interaction factor; response regulator		_____________46___________58\n_____________\|____________\|\n5'-AAU...CGGCC____________AGUGG...CAA-3'\n______________GG_ACAGCUGGC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________CC_UGUCGAUCG\n3'-UUU...AAGGA__A_________UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	51 -- 57	25 -- 31	-17.7308 kcal/mol	3.71782 kcal/mol	1.42738 kcal/mol	46 58@LB@ \| \|@LB@5'-AAU...CGGCC AGUGG...CAA-3'@LB@ GG ACAGCUGGC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ CC UGUCGAUCG@LB@3'-UUU...AAGGA A UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -17.7308 kcal/mol@LB@Unfolding Energy - mRNA 3.71782 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 47 -- 57@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 25 -- 31@LB@
187	0.01074	0.1919	b2536	hcaT	-7.74	0.383266	275 -- 291	25 -- 41	putative 3-phenylpropionic transporter		_____________274_______________292\n_____________\|_________________\|\n5'-UCG...CUACC_______A___U_____UUAAA...GGA-3'\n______________UUUCUGG_GCG_CUGGC\n______________\|\|:\|\|\|\|_:\|:_\|\|:\|\|\n______________AAGGACC_UGU_GAUCG\n3'-UUU...CCACC_______A___C_____UAAAA...UCG-5'\n_____________\|_________________\|\n_____________42________________24\n	275 -- 281	35 -- 41	-17.8602 kcal/mol	5.56231 kcal/mol	4.55428 kcal/mol	274 292@LB@ \| \|@LB@5'-UCG...CUACC A U UUAAA...GGA-3'@LB@ UUUCUGG GCG CUGGC@LB@ \|\|:\|\|\|\| :\|: \|\|:\|\|@LB@ AAGGACC UGU GAUCG@LB@3'-UUU...CCACC A C UAAAA...UCG-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -17.8602 kcal/mol@LB@Unfolding Energy - mRNA 5.56231 kcal/mol@LB@Unfolding Energy - sRNA 4.55428 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 35 -- 41@LB@
192	0.01101	0.1919	b2478	dapA	-6.78	0.505920	248 -- 269	25 -- 47	dihydrodipicolinate synthase		_____________247_____________________270\n_____________\|_______________________\|\n5'-GGC...GAAAA____AAUG____UCG________UUGAA...CCA-3'\n______________AGGU____UCUG____GGCUAGC\n______________\|\|\|\|____:\|\|\|____:\|\|\|\|\|\|\n______________UCCA____GGAC____UCGAUCG\n3'-UUU...AUUCC____CCAA____CAUG_______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	263 -- 269	25 -- 31	-19.6963 kcal/mol	8.35751 kcal/mol	4.55753 kcal/mol	247 270@LB@ \| \|@LB@5'-GGC...GAAAA AAUG UCG UUGAA...CCA-3'@LB@ AGGU UCUG GGCUAGC@LB@ \|\|\|\| :\|\|\| :\|\|\|\|\|\|@LB@ UCCA GGAC UCGAUCG@LB@3'-UUU...AUUCC CCAA CAUG UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -19.6963 kcal/mol@LB@Unfolding Energy - mRNA 8.35751 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 25 -- 31@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)

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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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