Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
191	0.03238	0.5507	b0445	ybaE	-8.08	0.221556	124 -- 136	4 -- 16	putative ABC transporter periplasmic binding protein		_____________123___________137\n_____________\|_____________\|\n5'-CGU...GACAC_____________UGAGU...GUU-3'\n______________GGUUAAUGGUGAU\n______________:\|\|\|\|\|\|\|:\|\|\|\|\n______________UCAAUUACUACUA\n3'-UUU...UUAUU_____________UCG-5'\n_____________\|_____________\|\n_____________17____________3\n	130 -- 136	4 -- 10	-14.6304 kcal/mol	6.50117 kcal/mol	0.0488422 kcal/mol	123 137@LB@ \| \|@LB@5'-CGU...GACAC UGAGU...GUU-3'@LB@ GGUUAAUGGUGAU@LB@ :\|\|\|\|\|\|\|:\|\|\|\|@LB@ UCAAUUACUACUA@LB@3'-UUU...UUAUU UCG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -14.6304 kcal/mol@LB@Unfolding Energy - mRNA 6.50117 kcal/mol@LB@Unfolding Energy - sRNA 0.0488422 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 4 -- 10@LB@
192	0.03268	0.5507	b3532	bcsB	-10.41	0.080313	186 -- 199	1 -- 12	regulator of cellulose synthase cyclic di-GMP binding		_____________185____________200\n_____________\|______________\|\n5'-AAG...UCAAC__________AC__GAUGA...UCA-3'\n______________AAUGAUGAUA__GC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________UUACUACUAU__CG\n3'-UUU...UUCAA______________-5'\n_____________\|_____________\|\n_____________13____________1\n	189 -- 195	3 -- 9	-11.9692 kcal/mol	1.52301 kcal/mol	0.0394463 kcal/mol	185 200@LB@ \| \|@LB@5'-AAG...UCAAC AC GAUGA...UCA-3'@LB@ AAUGAUGAUA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUACUACUAU CG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -11.9692 kcal/mol@LB@Unfolding Energy - mRNA 1.52301 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 3 -- 9@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor		_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
194	0.03269	0.5507	b2049	cpsB	-9.94	0.099932	179 -- 235	1 -- 54	mannose-1-phosphate guanyltransferase		_____________178________________________________________________________236\n_____________\|__________________________________________________________\|\n5'-ACA...AUUUA___________________AAUU______CA__CGAAACUCUAUCC___U________AGGUG...GCC-3'\n______________UAAAU_GAUAUUCGGGGAU____AUGGCG__GU_____________AGU_GUGAUGGC\n______________\|\|\|\|:_\|\|:\|\|\|\|:\|::\|\|____\|\|\|:\|\|__\|\|_____________\|:\|_:\|\|\|\|:\|\|\n______________AUUUG_CUGUAAGUCUUUA____UACUGC__CA_____________UUA_UACUAUCG\n3'-UUU...UCCCC_____U_____________CU____________UUAUUUAUUUCAA___C________-5'\n_____________\|_________________________________________________________\|\n_____________55________________________________________________________1\n	229 -- 235	1 -- 7	-30.0746 kcal/mol	13.8011 kcal/mol	6.33758 kcal/mol	178 236@LB@ \| \|@LB@5'-ACA...AUUUA AAUU CA CGAAACUCUAUCC U AGGUG...GCC-3'@LB@ UAAAU GAUAUUCGGGGAU AUGGCG GU AGU GUGAUGGC@LB@ \|\|\|\|: \|\|:\|\|\|\|:\|::\|\| \|\|\|:\|\| \|\| \|:\| :\|\|\|\|:\|\|@LB@ AUUUG CUGUAAGUCUUUA UACUGC CA UUA UACUAUCG@LB@3'-UUU...UCCCC U CU UUAUUUAUUUCAA C -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -30.0746 kcal/mol@LB@Unfolding Energy - mRNA 13.8011 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 179 -- 235@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
195	0.03271	0.5507	b3213	gltD	-10.79	0.067022	188 -- 211	38 -- 59	glutamate synthase 4Fe-4S protein small subunit		_____________187______________________212\n_____________\|________________________\|\n5'-AGC...CAGUA_______GC____AUGAG______UGUUU...AGC-3'\n______________AGGGGUA__AACA_____UCAGAA\n______________\|\|\|\|\|\|\|__\|\|\|\|_____\|\|\|\|\|\|\n______________UCCCCAU__UUGU_____AGUCUU\n3'-UUU...CUUUA_____________CUGUA______UACUU...UCG-5'\n_____________\|________________________\|\n_____________60_______________________37\n	188 -- 194	53 -- 59	-20.1632 kcal/mol	3.12506 kcal/mol	6.25108 kcal/mol	187 212@LB@ \| \|@LB@5'-AGC...CAGUA GC AUGAG UGUUU...AGC-3'@LB@ AGGGGUA AACA UCAGAA@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UCCCCAU UUGU AGUCUU@LB@3'-UUU...CUUUA CUGUA UACUU...UCG-5'@LB@ \| \|@LB@ 60 37@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -20.1632 kcal/mol@LB@Unfolding Energy - mRNA 3.12506 kcal/mol@LB@Unfolding Energy - sRNA 6.25108 kcal/mol@LB@@LB@Position - mRNA 188 -- 211@LB@Position - sRNA 38 -- 59@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 53 -- 59@LB@
196	0.0332	0.554	b0128	yadH	-11.13	0.056665	104 -- 121	39 -- 55	putative ABC transporter permease		_____________103________________122\n_____________\|__________________\|\n5'-UUA...GUUAA_______G__________UAUUA...UCA-3'\n______________GUGAGCA_GGCAUUCAGG\n______________\|\|:\|:\|\|_\|:\|\|\|\|\|\|\|:\n______________CAUUUGU_CUGUAAGUCU\n3'-UUU...AUCCC__________________UUACU...UCG-5'\n_____________\|__________________\|\n_____________56_________________38\n	114 -- 120	40 -- 46	-20.6932 kcal/mol	3.311 kcal/mol	6.24918 kcal/mol	103 122@LB@ \| \|@LB@5'-UUA...GUUAA G UAUUA...UCA-3'@LB@ GUGAGCA GGCAUUCAGG@LB@ \|\|:\|:\|\| \|:\|\|\|\|\|\|\|:@LB@ CAUUUGU CUGUAAGUCU@LB@3'-UUU...AUCCC UUACU...UCG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -20.6932 kcal/mol@LB@Unfolding Energy - mRNA 3.311 kcal/mol@LB@Unfolding Energy - sRNA 6.24918 kcal/mol@LB@@LB@Position - mRNA 104 -- 121@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 40 -- 46@LB@
197	0.03325	0.554	b4139	aspA	-12.92	0.022631	26 -- 66	25 -- 59	aspartate ammonia-lyase		_____________25_________________________________________67\n_____________\|__________________________________________\|\n5'-GAU...AAUUA________AA__C____C__________UCCAG__U______GAAAU...ACU-3'\n______________AGGGGUAA__AC_GACA_UUA_AAGUGA_____AU_ACGGUA\n______________\|\|\|\|\|\|\|\|__\|\|_\|\|\|\|_\|:\|_\|\|:\|\|\|_____\|\|_\|\|\|\|\|\|\n______________UCCCCAUU__UG_CUGU_AGU_UUUACU_____UA_UGCCAU\n3'-UUU...CUUUA____________U____A___C_____________C______UAUUU...UCG-5'\n_____________\|__________________________________________\|\n_____________60_________________________________________24\n	27 -- 33	52 -- 58	-28.0294 kcal/mol	8.80617 kcal/mol	6.29893 kcal/mol	25 67@LB@ \| \|@LB@5'-GAU...AAUUA AA C C UCCAG U GAAAU...ACU-3'@LB@ AGGGGUAA AC GACA UUA AAGUGA AU ACGGUA@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\| \|:\| \|\|:\|\|\| \|\| \|\|\|\|\|\|@LB@ UCCCCAUU UG CUGU AGU UUUACU UA UGCCAU@LB@3'-UUU...CUUUA U A C C UAUUU...UCG-5'@LB@ \| \|@LB@ 60 24@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -28.0294 kcal/mol@LB@Unfolding Energy - mRNA 8.80617 kcal/mol@LB@Unfolding Energy - sRNA 6.29893 kcal/mol@LB@@LB@Position - mRNA 26 -- 66@LB@Position - sRNA 25 -- 59@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 52 -- 58@LB@
198	0.03373	0.5555	b3915	fieF	-7.92	0.235762	278 -- 297	1 -- 19	ferrous iron and zinc transporter		_____________277__________________298\n_____________\|____________________\|\n5'-AAA...CUGAU____A__UU__C________AUA-3'\n______________UAAA_UU__UG_AUGGUGGU\n______________\|\|\|\|_\|\|__\|\|_\|\|\|:\|:\|:\n______________AUUU_AA__AC_UACUAUCG\n3'-UUU...UAUUU____C__UU___________-5'\n_____________\|___________________\|\n_____________20__________________1\n	291 -- 297	1 -- 7	-10.0103 kcal/mol	2.02347 kcal/mol	0.0638423 kcal/mol	277 298@LB@ \| \|@LB@5'-AAA...CUGAU A UU C AUA-3'@LB@ UAAA UU UG AUGGUGGU@LB@ \|\|\|\| \|\| \|\| \|\|\|:\|:\|:@LB@ AUUU AA AC UACUAUCG@LB@3'-UUU...UAUUU C UU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -10.0103 kcal/mol@LB@Unfolding Energy - mRNA 2.02347 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 278 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
199	0.03375	0.5555	b3860	dsbA	-9.14	0.142422	273 -- 281	48 -- 56	periplasmic protein disulfide isomerase I		_____________272_______282\n_____________\|_________\|\n5'-UUU...AAGAU_________UACAC...AAC-3'\n______________GGUAAACAG\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUC\n3'-UUU...UAUCC_________UGUAA...UCG-5'\n_____________\|_________\|\n_____________57________47\n	275 -- 281	48 -- 54	-12.2563 kcal/mol	1.07557 kcal/mol	2.03935 kcal/mol	272 282@LB@ \| \|@LB@5'-UUU...AAGAU UACAC...AAC-3'@LB@ GGUAAACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUC@LB@3'-UUU...UAUCC UGUAA...UCG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.2563 kcal/mol@LB@Unfolding Energy - mRNA 1.07557 kcal/mol@LB@Unfolding Energy - sRNA 2.03935 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
200	0.03384	0.5555	b0316	yahB	-11.86	0.039401	41 -- 57	47 -- 61	putative DNA-bindng transcriptional regulator	b0504	_____________40________________58\n_____________\|_________________\|\n5'-CUG...ACUGC__________UUU____AUAUG...CUU-3'\n______________GUGGGGGUAA___CAGA\n______________:\|:\|\|\|\|\|\|\|___\|\|\|\|\n______________UAUCCCCAUU___GUCU\n3'-UUU...AACUU__________U______GUAAG...UCG-5'\n_____________\|_________________\|\n_____________62________________46\n	44 -- 50	52 -- 58	-17.391 kcal/mol	3.44789 kcal/mol	2.08204 kcal/mol	40 58@LB@ \| \|@LB@5'-CUG...ACUGC UUU AUAUG...CUU-3'@LB@ GUGGGGGUAA CAGA@LB@ :\|:\|\|\|\|\|\|\| \|\|\|\|@LB@ UAUCCCCAUU GUCU@LB@3'-UUU...AACUU U GUAAG...UCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -17.391 kcal/mol@LB@Unfolding Energy - mRNA 3.44789 kcal/mol@LB@Unfolding Energy - sRNA 2.08204 kcal/mol@LB@@LB@Position - mRNA 41 -- 57@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 52 -- 58@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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