Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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	0.009659	0.2693	b0155	clcA	-5.80	0.214551	108 -- 124	25 -- 40	H(+)/Cl(-) exchange transporter	_____________107_______________125\n_____________\|_________________\|\n5'-AGU...UUUGU__________C___A__CUUUG...UAG-3'\n______________GCAUUUGAAA_AUU_CG\n______________\|\|\|:\|\|:\|\|\|_\|\|\|_\|\|\n______________CGUGAAUUUU_UAA_GC\n3'-UUU...UUCUU__________U______AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	109 -- 115	33 -- 39	-11.0899 kcal/mol	3.63771 kcal/mol	1.64821 kcal/mol	107 125@LB@ \| \|@LB@5'-AGU...UUUGU C A CUUUG...UAG-3'@LB@ GCAUUUGAAA AUU CG@LB@ \|\|\|:\|\|:\|\|\| \|\|\| \|\|@LB@ CGUGAAUUUU UAA GC@LB@3'-UUU...UUCUU U AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -5.80 kcal/mol@LB@Hybridization Energy -11.0899 kcal/mol@LB@Unfolding Energy - mRNA 3.63771 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 108 -- 124@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 33 -- 39@LB@
55	0.002761	0.1597	b0238	gpt	-5.76	0.219641	15 -- 42	30 -- 59	xanthine phosphoribosyltransferase; xanthine-guanine phosphoribosyltransferase	_____________14_____________________________43\n_____________\|______________________________\|\n5'-AUG...ACACA____AG____________UAUG________UACCA...UUG-3'\n______________AGAC__GCUU__GCGAGA____UUUGAGAA\n______________\|:\|\|__\|\|\|\|__\|\|:\|\|\|____:\|\|:\|:\|\|\n______________UUUG__CGAA__CGUUCU____GAAUUUUU\n3'-UUU...CCUAC____AA____UU______UCGU________UAAGC...CAA-5'\n_____________\|______________________________\|\n_____________60_____________________________29\n	36 -- 42	30 -- 36	-17.3334 kcal/mol	5.3037 kcal/mol	6.27042 kcal/mol	14 43@LB@ \| \|@LB@5'-AUG...ACACA AG UAUG UACCA...UUG-3'@LB@ AGAC GCUU GCGAGA UUUGAGAA@LB@ \|:\|\| \|\|\|\| \|\|:\|\|\| :\|\|:\|:\|\|@LB@ UUUG CGAA CGUUCU GAAUUUUU@LB@3'-UUU...CCUAC AA UU UCGU UAAGC...CAA-5'@LB@ \| \|@LB@ 60 29@LB@@LB@@LB@Energy -5.76 kcal/mol@LB@Hybridization Energy -17.3334 kcal/mol@LB@Unfolding Energy - mRNA 5.3037 kcal/mol@LB@Unfolding Energy - sRNA 6.27042 kcal/mol@LB@@LB@Position - mRNA 15 -- 42@LB@Position - sRNA 30 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 30 -- 36@LB@
130	0.01234	0.3033	b2958	yggN	-5.61	0.236844	227 -- 233	35 -- 41	DUF2884 family putative periplasmic protein	_____________226_____234\n_____________\|_______\|\n5'-ACG...GCGGC_______UCAGU...UUG-3'\n______________AGCACUU\n______________\|\|\|\|\|\|\|\n______________UCGUGAA\n3'-UUU...GUUCU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________42______34\n	227 -- 233	35 -- 41	-8.1936 kcal/mol	0.976472 kcal/mol	1.6033 kcal/mol	226 234@LB@ \| \|@LB@5'-ACG...GCGGC UCAGU...UUG-3'@LB@ AGCACUU@LB@ \|\|\|\|\|\|\|@LB@ UCGUGAA@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 34@LB@@LB@@LB@Energy -5.61 kcal/mol@LB@Hybridization Energy -8.1936 kcal/mol@LB@Unfolding Energy - mRNA 0.976472 kcal/mol@LB@Unfolding Energy - sRNA 1.6033 kcal/mol@LB@@LB@Position - mRNA 227 -- 233@LB@Position - sRNA 35 -- 41@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 35 -- 41@LB@
169	0.01902	0.3625	b0858	ybjO	-5.59	0.239654	140 -- 156	25 -- 43	DUF2593 family inner membrane protein	_____________139__________________157\n_____________\|____________________\|\n5'-AUG...UGGCU____A_______________CCAAC...UUA-3'\n______________GAAG_CACU___AAAAUUUG\n______________\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|:\|\n______________CUUC_GUGA___UUUUAAGC\n3'-UUU...UCGUU_________AUU________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________44___________________24\n	150 -- 156	25 -- 31	-11.6219 kcal/mol	2.26879 kcal/mol	3.76226 kcal/mol	139 157@LB@ \| \|@LB@5'-AUG...UGGCU A CCAAC...UUA-3'@LB@ GAAG CACU AAAAUUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ CUUC GUGA UUUUAAGC@LB@3'-UUU...UCGUU AUU AAUGU...CAA-5'@LB@ \| \|@LB@ 44 24@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -11.6219 kcal/mol@LB@Unfolding Energy - mRNA 2.26879 kcal/mol@LB@Unfolding Energy - sRNA 3.76226 kcal/mol@LB@@LB@Position - mRNA 140 -- 156@LB@Position - sRNA 25 -- 43@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 25 -- 31@LB@
176	0.02022	0.37	b0495	ybbA	-5.55	0.244939	212 -- 247	24 -- 59	putative ABC transporter ATPase	_____________211___________________________________248\n_____________\|_____________________________________\|\n5'-GCC...GCGGA____A_____G____UCAUCAU___________C___CGGUC...UCA-3'\n______________AAAC_UUGUU_AAGU________CUUAAGAAGU_CGU\n______________\|\|\|\|_\|\|\|:\|_\|\|\|:________\|\|\|\|\|:\|\|:\|_\|\|\|\n______________UUUG_AACGA_UUCG________GAAUUUUUUA_GCA\n3'-UUU...CCUAC__________A____UUCUUCGU__________A___AUGUG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________23\n	235 -- 241	30 -- 36	-18.4731 kcal/mol	6.64875 kcal/mol	6.27609 kcal/mol	211 248@LB@ \| \|@LB@5'-GCC...GCGGA A G UCAUCAU C CGGUC...UCA-3'@LB@ AAAC UUGUU AAGU CUUAAGAAGU CGU@LB@ \|\|\|\| \|\|\|:\| \|\|\|: \|\|\|\|\|:\|\|:\| \|\|\|@LB@ UUUG AACGA UUCG GAAUUUUUUA GCA@LB@3'-UUU...CCUAC A UUCUUCGU A AUGUG...CAA-5'@LB@ \| \|@LB@ 60 23@LB@@LB@@LB@Energy -5.55 kcal/mol@LB@Hybridization Energy -18.4731 kcal/mol@LB@Unfolding Energy - mRNA 6.64875 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 212 -- 247@LB@Position - sRNA 24 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 30 -- 36@LB@
73	0.004067	0.1794	b1244	oppB	-5.52	0.247965	106 -- 113	36 -- 43	oligopeptide ABC transporter permease	_____________105______114\n_____________\|________\|\n5'-UCC...AUUGU________AAUGG...GCC-3'\n______________GAAGCACU\n______________\|\|\|\|\|\|\|\|\n______________CUUCGUGA\n3'-UUU...UCGUU________AUUUU...CAA-5'\n_____________\|________\|\n_____________44_______35\n	107 -- 113	36 -- 42	-11.7212 kcal/mol	2.50266 kcal/mol	3.69444 kcal/mol	105 114@LB@ \| \|@LB@5'-UCC...AUUGU AAUGG...GCC-3'@LB@ GAAGCACU@LB@ \|\|\|\|\|\|\|\|@LB@ CUUCGUGA@LB@3'-UUU...UCGUU AUUUU...CAA-5'@LB@ \| \|@LB@ 44 35@LB@@LB@@LB@Energy -5.52 kcal/mol@LB@Hybridization Energy -11.7212 kcal/mol@LB@Unfolding Energy - mRNA 2.50266 kcal/mol@LB@Unfolding Energy - sRNA 3.69444 kcal/mol@LB@@LB@Position - mRNA 106 -- 113@LB@Position - sRNA 36 -- 43@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 36 -- 42@LB@
96	0.007122	0.239	b2060	wzc	-5.51	0.249431	285 -- 291	37 -- 43	colanic acid production tyrosine-protein kinase; autokinase; Ugd phosphorylase	_____________284_____292\n_____________\|_______\|\n5'-GAA...UCAUU_______GCUGG...GGG-3'\n______________GAAGCGC\n______________\|\|\|\|\|:\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	285 -- 291	37 -- 43	-9.9751 kcal/mol	0.803081 kcal/mol	3.6595 kcal/mol	284 292@LB@ \| \|@LB@5'-GAA...UCAUU GCUGG...GGG-3'@LB@ GAAGCGC@LB@ \|\|\|\|\|:\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -5.51 kcal/mol@LB@Hybridization Energy -9.9751 kcal/mol@LB@Unfolding Energy - mRNA 0.803081 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 285 -- 291@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 37 -- 43@LB@
145	0.01456	0.3231	b1529	marC	-5.50	0.250589	206 -- 227	39 -- 59	UPF0056 family inner membrane protein	_____________205____________________228\n_____________\|______________________\|\n5'-UGG...AUGUU__________A______UU___CUGGG...GCA-3'\n______________AGAUUUGUUU_AAGCAA__GGC\n______________\|:\|:\|\|\|:\|\|_\|\|\|\|\|\|__:\|\|\n______________UUUGAACGAA_UUCGUU__UCG\n3'-UUU...CCUAC_________________CU___UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	207 -- 213	52 -- 58	-17.1508 kcal/mol	5.49588 kcal/mol	6.15149 kcal/mol	205 228@LB@ \| \|@LB@5'-UGG...AUGUU A UU CUGGG...GCA-3'@LB@ AGAUUUGUUU AAGCAA GGC@LB@ \|:\|:\|\|\|:\|\| \|\|\|\|\|\| :\|\|@LB@ UUUGAACGAA UUCGUU UCG@LB@3'-UUU...CCUAC CU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -5.50 kcal/mol@LB@Hybridization Energy -17.1508 kcal/mol@LB@Unfolding Energy - mRNA 5.49588 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 206 -- 227@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 52 -- 58@LB@
148	0.01496	0.3255	b2202	napC	-5.47	0.254772	189 -- 211	26 -- 46	quinol dehydrogenase electron source for NapAB	_____________188_____________________212\n_____________\|_______________________\|\n5'-ACG...GGAAA_______U____A__________UGACC...GUU-3'\n______________UAAGAGG_UAUU_UGGGAAAUUC\n______________:\|\|\|\|:\|_:\|:\|_\|:::\|\|\|\|\|\|\n______________GUUCUUC_GUGA_AUUUUUUAAG\n3'-UUU...AAUUC_______________________CAAUG...CAA-5'\n_____________\|_______________________\|\n_____________47______________________25\n	205 -- 211	26 -- 32	-14.2639 kcal/mol	2.66276 kcal/mol	6.13041 kcal/mol	188 212@LB@ \| \|@LB@5'-ACG...GGAAA U A UGACC...GUU-3'@LB@ UAAGAGG UAUU UGGGAAAUUC@LB@ :\|\|\|\|:\| :\|:\| \|:::\|\|\|\|\|\|@LB@ GUUCUUC GUGA AUUUUUUAAG@LB@3'-UUU...AAUUC CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -14.2639 kcal/mol@LB@Unfolding Energy - mRNA 2.66276 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 26 -- 32@LB@
97	0.007216	0.239	b2021	hisC	-5.42	0.261518	59 -- 66	37 -- 44	histidinol-phosphate aminotransferase	_____________58_______67\n_____________\|________\|\n5'-GUU...UUUCC________AUGAC...GGC-3'\n______________AGAAGCGC\n______________\|\|\|\|\|\|:\|\n______________UCUUCGUG\n3'-UUU...UUCGU________AAUUU...CAA-5'\n_____________\|________\|\n_____________45_______36\n	60 -- 66	37 -- 43	-11.6623 kcal/mol	1.85203 kcal/mol	4.39141 kcal/mol	58 67@LB@ \| \|@LB@5'-GUU...UUUCC AUGAC...GGC-3'@LB@ AGAAGCGC@LB@ \|\|\|\|\|\|:\|@LB@ UCUUCGUG@LB@3'-UUU...UUCGU AAUUU...CAA-5'@LB@ \| \|@LB@ 45 36@LB@@LB@@LB@Energy -5.42 kcal/mol@LB@Hybridization Energy -11.6623 kcal/mol@LB@Unfolding Energy - mRNA 1.85203 kcal/mol@LB@Unfolding Energy - sRNA 4.39141 kcal/mol@LB@@LB@Position - mRNA 59 -- 66@LB@Position - sRNA 37 -- 44@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 37 -- 43@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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