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
155	0.03087	0.6177	b1003	yccJ	-9.03	0.064630	130 -- 145	43 -- 56	uncharacterized protein	_____________129______________146\n_____________\|________________\|\n5'-CCU...UUGCU_____UC_________AUGUC...GGU-3'\n______________CGUUA__AAGGGGAAU\n______________\|\|\|:\|__\|\|\|:\|\|\|\|\|\n______________GCAGU__UUCUCCUUA\n3'-UUU...ACCGG________________AAGUA...ACA-5'\n_____________\|________________\|\n_____________57_______________42\n	139 -- 145	43 -- 49	-13.8314 kcal/mol	3.84343 kcal/mol	0.953958 kcal/mol	129 146@LB@ \| \|@LB@5'-CCU...UUGCU UC AUGUC...GGU-3'@LB@ CGUUA AAGGGGAAU@LB@ \|\|\|:\| \|\|\|:\|\|\|\|\|@LB@ GCAGU UUCUCCUUA@LB@3'-UUU...ACCGG AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -13.8314 kcal/mol@LB@Unfolding Energy - mRNA 3.84343 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 130 -- 145@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 43 -- 49@LB@
79	0.01695	0.6177	b0435	bolA	-9.02	0.064980	184 -- 202	38 -- 55	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________183_________________203\n_____________\|___________________\|\n5'-UGA...GCGUU___G______AU_______GAUGA...CCG-3'\n______________GUC_GAGGAG__AUUUCAU\n______________\|\|\|_:\|:\|\|\|__\|\|\|\|\|\|\|\n______________CAG_UUUCUC__UAAAGUA\n3'-UUU...CCGGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	196 -- 202	38 -- 44	-15.2358 kcal/mol	5.04311 kcal/mol	1.17036 kcal/mol	183 203@LB@ \| \|@LB@5'-UGA...GCGUU G AU GAUGA...CCG-3'@LB@ GUC GAGGAG AUUUCAU@LB@ \|\|\| :\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAG UUUCUC UAAAGUA@LB@3'-UUU...CCGGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.2358 kcal/mol@LB@Unfolding Energy - mRNA 5.04311 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
157	0.03134	0.6177	b4086	alsC	-8.98	0.066369	183 -- 191	45 -- 53	D-allose ABC transporter permease	_____________182_______192\n_____________\|_________\|\n5'-CGC...AUGAG_________GAUUA...CGA-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	185 -- 191	45 -- 51	-13.528 kcal/mol	3.63363 kcal/mol	0.917553 kcal/mol	182 192@LB@ \| \|@LB@5'-CGC...AUGAG GAUUA...CGA-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.528 kcal/mol@LB@Unfolding Energy - mRNA 3.63363 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 45 -- 51@LB@
109	0.02227	0.6177	b4040	ubiA	-8.97	0.066674	182 -- 194	44 -- 55	p-hydroxybenzoate octaprenyltransferase	_____________181___________195\n_____________\|_____________\|\n5'-AGC...CCGUU__A_U________AAAAA...UAU-3'\n______________GU_C_AAGAGGAA\n______________\|\|_\|_\|\|\|\|\|\|\|\|\n______________CA_G_UUCUCCUU\n3'-UUU...CCGGG____U________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________56____________43\n	188 -- 194	44 -- 50	-10.7786 kcal/mol	0.870226 kcal/mol	0.941432 kcal/mol	181 195@LB@ \| \|@LB@5'-AGC...CCGUU A U AAAAA...UAU-3'@LB@ GU C AAGAGGAA@LB@ \|\| \| \|\|\|\|\|\|\|\|@LB@ CA G UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -10.7786 kcal/mol@LB@Unfolding Energy - mRNA 0.870226 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
95	0.01894	0.6177	b0407	yajC	-8.94	0.067585	73 -- 105	45 -- 79	SecYEG protein translocase auxillary subunit	_____________72___________________________________106\n_____________\|____________________________________\|\n5'-UCU...CGUUU______G___U_A___AA______A___________UAAAU...UUU-3'\n______________GAUGGC_GGU_U_CGC____GGCU__UUGAAGAGGG\n______________:\|\|\|\|\|_::\|_\|_\|\|\|____\|\|\|:__\|::\|\|\|\|\|\|:\n______________UUACCG_UUA_A_GCG____CCGG__AGUUUCUCCU\n______3'-UUUUU______G___U_____AUAA____GC__________UAAAG...ACA-5'\n_____________\|____________________________________\|\n_____________80___________________________________44\n	99 -- 105	45 -- 51	-30.8043 kcal/mol	8.31146 kcal/mol	13.5551 kcal/mol	72 106@LB@ \| \|@LB@5'-UCU...CGUUU G U A AA A UAAAU...UUU-3'@LB@ GAUGGC GGU U CGC GGCU UUGAAGAGGG@LB@ :\|\|\|\|\| ::\| \| \|\|\| \|\|\|: \|::\|\|\|\|\|\|:@LB@ UUACCG UUA A GCG CCGG AGUUUCUCCU@LB@ 3'-UUUUU G U AUAA GC UAAAG...ACA-5'@LB@ \| \|@LB@ 80 44@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -30.8043 kcal/mol@LB@Unfolding Energy - mRNA 8.31146 kcal/mol@LB@Unfolding Energy - sRNA 13.5551 kcal/mol@LB@@LB@Position - mRNA 73 -- 105@LB@Position - sRNA 45 -- 79@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 45 -- 51@LB@
117	0.02321	0.6177	b1712	ihfA	-8.91	0.068436	115 -- 126	45 -- 56	integration host factor (IHF) DNA-binding protein alpha subunit	_____________114__________127\n_____________\|____________\|\n5'-CGU...ACACU__AA________GAUUG...AGA-3'\n______________CG__GAAGAGGA\n______________\|\|__:\|\|\|\|\|\|\|\n______________GC__UUUCUCCU\n3'-UUU...ACCGG__AG________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	120 -- 126	45 -- 51	-12.2887 kcal/mol	2.43966 kcal/mol	0.938337 kcal/mol	114 127@LB@ \| \|@LB@5'-CGU...ACACU AA GAUUG...AGA-3'@LB@ CG GAAGAGGA@LB@ \|\| :\|\|\|\|\|\|\|@LB@ GC UUUCUCCU@LB@3'-UUU...ACCGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -12.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.43966 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 115 -- 126@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 45 -- 51@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@
29	0.005664	0.6127	b3831	udp	-8.88	0.069383	184 -- 196	42 -- 54	uridine phosphorylase	_____________183___________197\n_____________\|_____________\|\n5'-AUC...CCGAU___C_________GUAUA...AGA-3'\n______________UCA_AGAGGAGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________AGU_UCUCCUUAA\n3'-UUU...CGGGC___U_________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________55____________41\n	190 -- 196	42 -- 48	-14.4874 kcal/mol	4.66075 kcal/mol	0.945538 kcal/mol	183 197@LB@ \| \|@LB@5'-AUC...CCGAU C GUAUA...AGA-3'@LB@ UCA AGAGGAGUU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ AGU UCUCCUUAA@LB@3'-UUU...CGGGC U AGUAA...ACA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.4874 kcal/mol@LB@Unfolding Energy - mRNA 4.66075 kcal/mol@LB@Unfolding Energy - sRNA 0.945538 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 42 -- 48@LB@
45	0.009176	0.6129	b3389	aroB	-8.88	0.069424	203 -- 218	37 -- 52	3-dehydroquinate synthase	_____________202______________219\n_____________\|________________\|\n5'-ACA...GUUAU________UUG_____ACUCU...CGG-3'\n______________GGAGAGGA___UCGUU\n______________::\|\|\|\|\|\|___\|\|:\|\|\n______________UUUCUCCU___AGUAA\n3'-UUU...GGCAG________UAA_____AAAAA...ACA-5'\n_____________\|________________\|\n_____________53_______________36\n	204 -- 210	45 -- 51	-14.6346 kcal/mol	4.67835 kcal/mol	1.07641 kcal/mol	202 219@LB@ \| \|@LB@5'-ACA...GUUAU UUG ACUCU...CGG-3'@LB@ GGAGAGGA UCGUU@LB@ ::\|\|\|\|\|\| \|\|:\|\|@LB@ UUUCUCCU AGUAA@LB@3'-UUU...GGCAG UAA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.6346 kcal/mol@LB@Unfolding Energy - mRNA 4.67835 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 203 -- 218@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 45 -- 51@LB@
165	0.0337	0.6177	b3983	rplK	-8.80	0.071896	189 -- 197	41 -- 49	50S ribosomal subunit protein L11	_____________188_______198\n_____________\|_________\|\n5'-ACC...AACUU_________AUAAU...UAA-3'\n______________GAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\n______________CUCCUUAAA\n3'-UUU...AGUUU_________GUAAA...ACA-5'\n_____________\|_________\|\n_____________50________40\n	191 -- 197	41 -- 47	-11.4231 kcal/mol	1.76644 kcal/mol	0.852225 kcal/mol	188 198@LB@ \| \|@LB@5'-ACC...AACUU AUAAU...UAA-3'@LB@ GAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUCCUUAAA@LB@3'-UUU...AGUUU GUAAA...ACA-5'@LB@ \| \|@LB@ 50 40@LB@@LB@@LB@Energy -8.80 kcal/mol@LB@Hybridization Energy -11.4231 kcal/mol@LB@Unfolding Energy - mRNA 1.76644 kcal/mol@LB@Unfolding Energy - sRNA 0.852225 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 41 -- 49@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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