Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
60	0.003101	0.1789	b1849	purT	-10.92	0.194410	188 -- 196	17 -- 25	phosphoribosylglycinamide formyltransferase 2		_____________187_______197\n_____________\|_________\|\n5'-UUU...AAUCA_________CGUUA...GUC-3'\n______________GGGGAUAUU\n______________\|\|\|\|\|:\|\|:\n______________CCCCUGUAG\n3'-UUU...UUUUA_________UUUCU...CCG-5'\n_____________\|_________\|\n_____________26________16\n	190 -- 196	17 -- 23	-14.1846 kcal/mol	2.60139 kcal/mol	0.664736 kcal/mol	187 197@LB@ \| \|@LB@5'-UUU...AAUCA CGUUA...GUC-3'@LB@ GGGGAUAUU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCUGUAG@LB@3'-UUU...UUUUA UUUCU...CCG-5'@LB@ \| \|@LB@ 26 16@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -14.1846 kcal/mol@LB@Unfolding Energy - mRNA 2.60139 kcal/mol@LB@Unfolding Energy - sRNA 0.664736 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 17 -- 25@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
152	0.01123	0.2504	b1872	torZ	-17.40	0.006326	76 -- 107	1 -- 34	trimethylamine N-oxide reductase system III catalytic subunit	b0997 b3551	_____________75___________________________________108\n_____________\|____________________________________\|\n5'-ACG...CAUUG___AA_________________CC_________A__GAAAA...AGA-3'\n______________CCA__GGAAUGGGGGCA_CGAA____AGCA_UG_GC\n______________\|\|\|__::\|\|\|\|\|\|\|:\|\|_\|:\|\|____\|\|\|\|_\|\|_\|\|\n______________GGU__UUUUACCCCUGU_GUUU____UCGU_AC_CG\n3'-UUU...CCCGA___G_____________A____CUUU____C_____-5'\n_____________\|___________________________________\|\n_____________35__________________________________1\n	86 -- 92	19 -- 25	-29.6219 kcal/mol	7.95271 kcal/mol	4.26884 kcal/mol	75 108@LB@ \| \|@LB@5'-ACG...CAUUG AA CC A GAAAA...AGA-3'@LB@ CCA GGAAUGGGGGCA CGAA AGCA UG GC@LB@ \|\|\| ::\|\|\|\|\|\|\|:\|\| \|:\|\| \|\|\|\| \|\| \|\|@LB@ GGU UUUUACCCCUGU GUUU UCGU AC CG@LB@3'-UUU...CCCGA G A CUUU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -29.6219 kcal/mol@LB@Unfolding Energy - mRNA 7.95271 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 76 -- 107@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 19 -- 25@LB@
150	0.01097	0.2504	b1878	flhE	-16.24	0.013409	257 -- 279	3 -- 25	proton seal during flagellar secretion		_____________256_____________________280\n_____________\|_______________________\|\n5'-CGU...GGGGA________G_C___C________UAGGA...AUC-3'\n______________GGGGAUGU_G_AGG_AAGUAGUG\n______________\|\|\|\|\|::\|_:_\|\|:_\|\|\|:\|\|\|\|\n______________CCCCUGUA_U_UCU_UUCGUCAC\n3'-UUU...UUUUA________G_U___U________CG-5'\n_____________\|_______________________\|\n_____________26______________________2\n	273 -- 279	3 -- 9	-26.0465 kcal/mol	7.2914 kcal/mol	2.5166 kcal/mol	256 280@LB@ \| \|@LB@5'-CGU...GGGGA G C C UAGGA...AUC-3'@LB@ GGGGAUGU G AGG AAGUAGUG@LB@ \|\|\|\|\|::\| : \|\|: \|\|\|:\|\|\|\|@LB@ CCCCUGUA U UCU UUCGUCAC@LB@3'-UUU...UUUUA G U U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -26.0465 kcal/mol@LB@Unfolding Energy - mRNA 7.2914 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 3 -- 9@LB@
75	0.00423	0.1979	b1917	yecC	-10.99	0.188691	288 -- 298	1 -- 11	putative ABC transporter ATPase		_____________287_________299\n_____________\|___________\|\n5'-CUG...CUGGC___________AA-3'\n______________GAAGUGGUGGC\n______________:\|\|\|::\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	292 -- 298	1 -- 7	-16.6045 kcal/mol	4.33348 kcal/mol	1.27751 kcal/mol	287 299@LB@ \| \|@LB@5'-CUG...CUGGC AA-3'@LB@ GAAGUGGUGGC@LB@ :\|\|\|::\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.6045 kcal/mol@LB@Unfolding Energy - mRNA 4.33348 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.00768	0.2368	b1923	fliC	-14.29	0.040892	38 -- 54	4 -- 25	flagellar filament structural protein (flagellin)		_____________37_____________________55\n_____________\|______________________\|\n5'-GUU...AAUAA______________________AUUUC...CUU-3'\n______________GGGG____CAGAGAAAAG_AGU\n______________\|\|\|\|____\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CCCC____GUUUCUUUUC_UCA\n3'-UUU...UUUUA____UGUA__________G___CCG-5'\n_____________\|______________________\|\n_____________26_____________________3\n	45 -- 51	8 -- 14	-19.9416 kcal/mol	3.14092 kcal/mol	2.51306 kcal/mol	37 55@LB@ \| \|@LB@5'-GUU...AAUAA AUUUC...CUU-3'@LB@ GGGG CAGAGAAAAG AGU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CCCC GUUUCUUUUC UCA@LB@3'-UUU...UUUUA UGUA G CCG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -19.9416 kcal/mol@LB@Unfolding Energy - mRNA 3.14092 kcal/mol@LB@Unfolding Energy - sRNA 2.51306 kcal/mol@LB@@LB@Position - mRNA 38 -- 54@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 8 -- 14@LB@
174	0.0127	0.2504	b1960	vsr	-15.05	0.027057	161 -- 177	1 -- 19	DNA mismatch endonuclease of very short patch repair		_____________160_________________178\n_____________\|___________________\|\n5'-UCG...CAAAA______C____________GUUGC...CCG-3'\n______________AUCAAA___AGGCGGUGGC\n______________\|\|\|\|\|\|___\|:\|\|:\|\|\|\|\|\n______________UAGUUU___UUCGUCACCG\n3'-UUU...CCCUG______CUU__________-5'\n_____________\|__________________\|\n_____________20_________________1\n	171 -- 177	1 -- 7	-22.0844 kcal/mol	5.58177 kcal/mol	1.45734 kcal/mol	160 178@LB@ \| \|@LB@5'-UCG...CAAAA C GUUGC...CCG-3'@LB@ AUCAAA AGGCGGUGGC@LB@ \|\|\|\|\|\| \|:\|\|:\|\|\|\|\|@LB@ UAGUUU UUCGUCACCG@LB@3'-UUU...CCCUG CUU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -22.0844 kcal/mol@LB@Unfolding Energy - mRNA 5.58177 kcal/mol@LB@Unfolding Energy - sRNA 1.45734 kcal/mol@LB@@LB@Position - mRNA 161 -- 177@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 1 -- 7@LB@
185	0.0132	0.2504	b2009	sbmC	-15.75	0.018057	263 -- 294	1 -- 27	DNA gyrase inhibitor		_____________262______________________________295\n_____________\|________________________________\|\n5'-CUG...GGCCC_____AACA____G___________UU__A__AGUUGA-3'\n______________GUGGG____GACG_UAAAGAAAGGC__UG_GC\n______________:\|\|\|\|____\|\|\|:_:\|\|\|\|\|\|\|:\|\|__\|\|_\|\|\n______________UACCC____CUGU_GUUUCUUUUCG__AC_CG\n3'-UUU...UGUUU_____________A___________UC_____-5'\n_____________\|_______________________________\|\n_____________28______________________________1\n	281 -- 287	7 -- 13	-27.1244 kcal/mol	8.85955 kcal/mol	2.51867 kcal/mol	262 295@LB@ \| \|@LB@5'-CUG...GGCCC AACA G UU A AGUUGA-3'@LB@ GUGGG GACG UAAAGAAAGGC UG GC@LB@ :\|\|\|\| \|\|\|: :\|\|\|\|\|\|\|:\|\| \|\| \|\|@LB@ UACCC CUGU GUUUCUUUUCG AC CG@LB@3'-UUU...UGUUU A UC -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -27.1244 kcal/mol@LB@Unfolding Energy - mRNA 8.85955 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 263 -- 294@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@LB@
50	0.002349	0.1648	b2040	rfbD	-20.63	0.000491	127 -- 157	3 -- 32	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit		_____________126______________________________158\n_____________\|________________________________\|\n5'-GAU...CCAAU__________UU____AUGU____________CCUAU...CUA-3'\n______________ACAAAAUGGG__GAUA_____GAAAAGUGGUG\n______________\|\|\|\|\|\|\|\|\|\|__\|\|:\|_____\|\|\|\|\|\|::\|\|\|\n______________UGUUUUACCC__CUGU_____CUUUUCGUCAC\n3'-UUU...CGAGG________________AGUUU___________CG-5'\n_____________\|________________________________\|\n_____________33_______________________________2\n	151 -- 157	3 -- 9	-27.2371 kcal/mol	4.0691 kcal/mol	2.53925 kcal/mol	126 158@LB@ \| \|@LB@5'-GAU...CCAAU UU AUGU CCUAU...CUA-3'@LB@ ACAAAAUGGG GAUA GAAAAGUGGUG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|::\|\|\|@LB@ UGUUUUACCC CUGU CUUUUCGUCAC@LB@3'-UUU...CGAGG AGUUU CG-5'@LB@ \| \|@LB@ 33 2@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -27.2371 kcal/mol@LB@Unfolding Energy - mRNA 4.0691 kcal/mol@LB@Unfolding Energy - sRNA 2.53925 kcal/mol@LB@@LB@Position - mRNA 127 -- 157@LB@Position - sRNA 3 -- 32@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 3 -- 9@LB@
162	0.012	0.2504	b2079	baeR	-15.58	0.019969	182 -- 201	6 -- 24	response regulator in two-component regulatory system with BaeS		_____________181__________________202\n_____________\|____________________\|\n5'-CAG...GGAAC_____UUA____________UGACC...CGA-3'\n______________GGGAU___CAGAGAGAAGUA\n______________\|\|\|\|:___\|\|:\|\|\|:\|\|\|:\|\n______________CCCUG___GUUUCUUUUCGU\n3'-UUU...UUUAC_____UA_____________CACCG-5'\n_____________\|____________________\|\n_____________25___________________5\n	195 -- 201	6 -- 12	-20.602 kcal/mol	4.32458 kcal/mol	0.702143 kcal/mol	181 202@LB@ \| \|@LB@5'-CAG...GGAAC UUA UGACC...CGA-3'@LB@ GGGAU CAGAGAGAAGUA@LB@ \|\|\|\|: \|\|:\|\|\|:\|\|\|:\|@LB@ CCCUG GUUUCUUUUCGU@LB@3'-UUU...UUUAC UA CACCG-5'@LB@ \| \|@LB@ 25 5@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -20.602 kcal/mol@LB@Unfolding Energy - mRNA 4.32458 kcal/mol@LB@Unfolding Energy - sRNA 0.702143 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 6 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
92	0.005693	0.2147	b2099	yegU	-12.49	0.099484	183 -- 197	7 -- 22	ADP-ribosylglycohydrolase family protein		_____________182______________198\n_____________\|________________\|\n5'-GUG...GCGUU________________UAAAU...CAC-3'\n______________GACA_CAAGGGGAAGU\n______________\|\|\|\|_\|\|\|:\|::\|\|\|:\n______________CUGU_GUUUCUUUUCG\n3'-UUU...UACCC____A___________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	191 -- 197	7 -- 13	-15.6094 kcal/mol	2.53245 kcal/mol	0.590875 kcal/mol	182 198@LB@ \| \|@LB@5'-GUG...GCGUU UAAAU...CAC-3'@LB@ GACA CAAGGGGAAGU@LB@ \|\|\|\| \|\|\|:\|::\|\|\|:@LB@ CUGU GUUUCUUUUCG@LB@3'-UUU...UACCC A UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -15.6094 kcal/mol@LB@Unfolding Energy - mRNA 2.53245 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 7 -- 13@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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