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
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@
113	0.01802	0.5155	b3910	yiiM	-13.90	0.013248	191 -- 239	40 -- 92	6-N-hydroxylaminopurine resistance protein		_____________190______________________________________________________240\n_____________\|________________________________________________________\|\n5'-UAA...GUGGA________A_____________________U_________C_______AGA_____GCUUA...UGC-3'\n______________GAGGGAAC__GAUGCGA__UAUCCGGUUGA_GUA____UA_ACAGGCA___UUCAG\n______________:\|:::\|\|\|__:\|\|\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_:\|\|____\|\|_\|\|\|\|:\|\|___\|\|\|\|\|\n______________UUUUUUUG__UUACGCU__GUAGGCCAACU_UAU____AU_UGUCUGU___AAGUC\n__________3'-U________GC_______CC___________U___CCCC__U_______________UUUAC...UCG-5'\n_____________\|________________________________________________________\|\n_____________93_______________________________________________________39\n	225 -- 231	45 -- 51	-43.4237 kcal/mol	10.1845 kcal/mol	19.3361 kcal/mol	190 240@LB@ \| \|@LB@5'-UAA...GUGGA A U C AGA GCUUA...UGC-3'@LB@ GAGGGAAC GAUGCGA UAUCCGGUUGA GUA UA ACAGGCA UUCAG@LB@ :\|:::\|\|\| :\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|\| :\|\| \|\| \|\|\|\|:\|\| \|\|\|\|\|@LB@ UUUUUUUG UUACGCU GUAGGCCAACU UAU AU UGUCUGU AAGUC@LB@ 3'-U GC CC U CCCC U UUUAC...UCG-5'@LB@ \| \|@LB@ 93 39@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -43.4237 kcal/mol@LB@Unfolding Energy - mRNA 10.1845 kcal/mol@LB@Unfolding Energy - sRNA 19.3361 kcal/mol@LB@@LB@Position - mRNA 191 -- 239@LB@Position - sRNA 40 -- 92@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 45 -- 51@LB@
37	0.00362	0.3212	b4479	dgoR	-15.45	0.005416	239 -- 256	41 -- 57	D-galactonate catabolism operon transcriptional repressor		_____________238________________257\n_____________\|__________________\|\n5'-UUU...ACGCU___________U______CGGCA...AAC-3'\n______________GGGUAAACAGA_CGUUCA\n______________\|\|\|\|\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________CCCAUUUGUCU_GUAAGU\n3'-UUU...UUAUC__________________CUUUA...UCG-5'\n_____________\|__________________\|\n_____________58_________________40\n	243 -- 249	47 -- 53	-24.0794 kcal/mol	2.38777 kcal/mol	6.24592 kcal/mol	238 257@LB@ \| \|@LB@5'-UUU...ACGCU U CGGCA...AAC-3'@LB@ GGGUAAACAGA CGUUCA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ CCCAUUUGUCU GUAAGU@LB@3'-UUU...UUAUC CUUUA...UCG-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -15.45 kcal/mol@LB@Hybridization Energy -24.0794 kcal/mol@LB@Unfolding Energy - mRNA 2.38777 kcal/mol@LB@Unfolding Energy - sRNA 6.24592 kcal/mol@LB@@LB@Position - mRNA 239 -- 256@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
186	0.03152	0.5492	b0922	mukF	-11.29	0.052395	27 -- 43	42 -- 57	chromosome condensin MukBEF kleisin-like subunit binds calcium		_____________26________________44\n_____________\|_________________\|\n5'-CUG...AUUAU____A____________GCGUG...UGG-3'\n______________GGGU_AGACAGGCGUUC\n______________\|\|\|\|_\|:\|\|\|\|:\|:\|\|\|\n______________CCCA_UUUGUCUGUAAG\n3'-UUU...UUAUC_________________UCUUU...UCG-5'\n_____________\|_________________\|\n_____________58________________41\n	33 -- 39	46 -- 52	-21.5353 kcal/mol	3.99758 kcal/mol	6.24533 kcal/mol	26 44@LB@ \| \|@LB@5'-CUG...AUUAU A GCGUG...UGG-3'@LB@ GGGU AGACAGGCGUUC@LB@ \|\|\|\| \|:\|\|\|\|:\|:\|\|\|@LB@ CCCA UUUGUCUGUAAG@LB@3'-UUU...UUAUC UCUUU...UCG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -11.29 kcal/mol@LB@Hybridization Energy -21.5353 kcal/mol@LB@Unfolding Energy - mRNA 3.99758 kcal/mol@LB@Unfolding Energy - sRNA 6.24533 kcal/mol@LB@@LB@Position - mRNA 27 -- 43@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 46 -- 52@LB@
33	0.003163	0.3086	b4372	holD	-10.86	0.064637	82 -- 98	44 -- 58	DNA polymerase III psi subunit		_____________81________________99\n_____________\|_________________\|\n5'-AGG...UUGCC_______AU________GGAAU...UCC-3'\n______________GGGGUAA__GCAGACAU\n______________\|\|\|\|\|\|\|__:\|\|\|\|\|\|\|\n______________CCCCAUU__UGUCUGUA\n3'-UUU...UUUAU_________________AGUCU...UCG-5'\n_____________\|_________________\|\n_____________59________________43\n	92 -- 98	44 -- 50	-21.4924 kcal/mol	4.96784 kcal/mol	5.66232 kcal/mol	81 99@LB@ \| \|@LB@5'-AGG...UUGCC AU GGAAU...UCC-3'@LB@ GGGGUAA GCAGACAU@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|\|\|@LB@ CCCCAUU UGUCUGUA@LB@3'-UUU...UUUAU AGUCU...UCG-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -21.4924 kcal/mol@LB@Unfolding Energy - mRNA 4.96784 kcal/mol@LB@Unfolding Energy - sRNA 5.66232 kcal/mol@LB@@LB@Position - mRNA 82 -- 98@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 44 -- 50@LB@
54	0.006418	0.3902	b0946	zapC	-14.33	0.010402	184 -- 201	47 -- 63	FtsZ stabilizer		_____________183________________202\n_____________\|__________________\|\n5'-AUU...UUAUA_________AG_______UGCGA...GUU-3'\n______________GGGUAGGGG__AGGCAGA\n______________:::\|\|\|\|\|\|__\|::\|\|\|\|\n______________UUUAUCCCC__UUUGUCU\n3'-UUU...CCAAC_________A________GUAAG...UCG-5'\n_____________\|__________________\|\n_____________64_________________46\n	195 -- 201	47 -- 53	-19.5846 kcal/mol	3.17109 kcal/mol	2.08245 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...UUAUA AG UGCGA...GUU-3'@LB@ GGGUAGGGG AGGCAGA@LB@ :::\|\|\|\|\|\| \|::\|\|\|\|@LB@ UUUAUCCCC UUUGUCU@LB@3'-UUU...CCAAC A GUAAG...UCG-5'@LB@ \| \|@LB@ 64 46@LB@@LB@@LB@Energy -14.33 kcal/mol@LB@Hybridization Energy -19.5846 kcal/mol@LB@Unfolding Energy - mRNA 3.17109 kcal/mol@LB@Unfolding Energy - sRNA 2.08245 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 47 -- 63@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 47 -- 53@LB@
105	0.01645	0.5059	b0454	ybaZ	-8.45	0.190978	84 -- 93	47 -- 56	excision repair protein alkyltransferase-like protein ATL		_____________83_________94\n_____________\|__________\|\n5'-AGG...GACCU__________GUAGC...UUC-3'\n______________GGUAAACAGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUCU\n3'-UUU...UAUCC__________GUAAG...UCG-5'\n_____________\|__________\|\n_____________57_________46\n	87 -- 93	47 -- 53	-13.2019 kcal/mol	2.68818 kcal/mol	2.06629 kcal/mol	83 94@LB@ \| \|@LB@5'-AGG...GACCU GUAGC...UUC-3'@LB@ GGUAAACAGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUCU@LB@3'-UUU...UAUCC GUAAG...UCG-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -13.2019 kcal/mol@LB@Unfolding Energy - mRNA 2.68818 kcal/mol@LB@Unfolding Energy - sRNA 2.06629 kcal/mol@LB@@LB@Position - mRNA 84 -- 93@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 47 -- 53@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@
20	0.0009027	0.1482	b2696	csrA	-13.42	0.017327	268 -- 280	48 -- 60	pleiotropic regulatory protein for carbon source metabolism		_____________267___________281\n_____________\|_____________\|\n5'-CGG...AGUUU__________G__CAACC...GCG-3'\n______________UAGGGGUAAA_GG\n______________\|\|\|\|\|\|\|\|\|\|_:\|\n______________AUCCCCAUUU_UC\n3'-UUU...ACUUU__________G__UGUAA...UCG-5'\n_____________\|_____________\|\n_____________61____________47\n	271 -- 277	51 -- 57	-17.9026 kcal/mol	2.43021 kcal/mol	2.05446 kcal/mol	267 281@LB@ \| \|@LB@5'-CGG...AGUUU G CAACC...GCG-3'@LB@ UAGGGGUAAA GG@LB@ \|\|\|\|\|\|\|\|\|\| :\|@LB@ AUCCCCAUUU UC@LB@3'-UUU...ACUUU G UGUAA...UCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -17.9026 kcal/mol@LB@Unfolding Energy - mRNA 2.43021 kcal/mol@LB@Unfolding Energy - sRNA 2.05446 kcal/mol@LB@@LB@Position - mRNA 268 -- 280@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 51 -- 57@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@

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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