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
68	0.00983	0.4523	b1321	ycjX	-10.80	0.066674	34 -- 41	55 -- 62	DUF463 family protein puatative P-loop NTPase	_____________33_______42\n_____________\|________\|\n5'-UGA...UAAAU________ACAUA...CAG-3'\n______________AGUAGGGG\n______________\|:\|\|\|\|\|\|\n______________UUAUCCCC\n3'-UUU...CAACU________AUUUG...UCG-5'\n_____________\|________\|\n_____________63_______54\n	35 -- 41	55 -- 61	-12.2037 kcal/mol	1.3787 kcal/mol	0.0270923 kcal/mol	33 42@LB@ \| \|@LB@5'-UGA...UAAAU ACAUA...CAG-3'@LB@ AGUAGGGG@LB@ \|:\|\|\|\|\|\|@LB@ UUAUCCCC@LB@3'-UUU...CAACU AUUUG...UCG-5'@LB@ \| \|@LB@ 63 54@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -12.2037 kcal/mol@LB@Unfolding Energy - mRNA 1.3787 kcal/mol@LB@Unfolding Energy - sRNA 0.0270923 kcal/mol@LB@@LB@Position - mRNA 34 -- 41@LB@Position - sRNA 55 -- 62@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 55 -- 61@LB@
135	0.02191	0.526	b1342	ydaN	-17.19	0.001818	129 -- 197	1 -- 58	putative Zn(II) transporter	_____________128______________________________________________________________________198\n_____________\|________________________________________________________________________\|\n5'-CGU...GUAAU_______UG_______GCGUAACAGGGC______GCUA____UACA________UGC___________A___ACUGU...AUG-3'\n______________GGGGUGA__AGAUGUU____________CAGAAG_____GAC______AAAUAA___GUUGAUGAUGG_GGC\n______________\|\|\|\|\|:\|__\|\|\|::\|\|____________\|\|\|\|\|:_____\|\|\|______\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|:_:\|\|\n______________CCCCAUU__UCUGUAA____________GUCUUU_____CUG______UUUAUU___CAAUUACUACU_UCG\n3'-UUU...UUUAU_______UG_________________________ACUUA___CCAUUA______U_____________A___-5'\n_____________\|_______________________________________________________________________\|\n_____________59______________________________________________________________________1\n	187 -- 193	5 -- 11	-40.4273 kcal/mol	16.9018 kcal/mol	6.33758 kcal/mol	128 198@LB@ \| \|@LB@5'-CGU...GUAAU UG GCGUAACAGGGC GCUA UACA UGC A ACUGU...AUG-3'@LB@ GGGGUGA AGAUGUU CAGAAG GAC AAAUAA GUUGAUGAUGG GGC@LB@ \|\|\|\|\|:\| \|\|\|::\|\| \|\|\|\|\|: \|\|\| \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|: :\|\|@LB@ CCCCAUU UCUGUAA GUCUUU CUG UUUAUU CAAUUACUACU UCG@LB@3'-UUU...UUUAU UG ACUUA CCAUUA U A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -17.19 kcal/mol@LB@Hybridization Energy -40.4273 kcal/mol@LB@Unfolding Energy - mRNA 16.9018 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 129 -- 197@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 5 -- 11@LB@
168	0.02737	0.531	b1385	feaB	-11.89	0.038862	180 -- 210	1 -- 28	phenylacetaldehyde dehydrogenase	_____________179_____________________________211\n_____________\|_______________________________\|\n5'-UUG...CACUG_____AU_______AAA________CAG___CGCAU...GUG-3'\n______________GGUAA__AAUAAGG___AGUGAUGA___AGC\n______________\|\|\|\|\|__\|\|\|\|\|:\|___\|:\|\|\|\|\|\|___\|\|\|\n______________CCAUU__UUAUUUC___UUACUACU___UCG\n3'-UUU...UACUG_____AU_______AA_________A_____-5'\n_____________\|______________________________\|\n_____________29_____________________________1\n	198 -- 204	5 -- 11	-19.4278 kcal/mol	6.77275 kcal/mol	0.766821 kcal/mol	179 211@LB@ \| \|@LB@5'-UUG...CACUG AU AAA CAG CGCAU...GUG-3'@LB@ GGUAA AAUAAGG AGUGAUGA AGC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\|\|\|\|\|\| \|\|\|@LB@ CCAUU UUAUUUC UUACUACU UCG@LB@3'-UUU...UACUG AU AA A -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -19.4278 kcal/mol@LB@Unfolding Energy - mRNA 6.77275 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 180 -- 210@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
43	0.004693	0.3568	b1395	paaH	-8.91	0.157263	246 -- 258	49 -- 61	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent	_____________245___________259\n_____________\|_____________\|\n5'-GGC...GCACC_______C_____UUGCU...UGU-3'\n______________AUGGGGG_AGGCA\n______________\|\|:\|\|\|\|_\|::\|\|\n______________UAUCCCC_UUUGU\n3'-UUU...AACUU_______A_____CUGUA...UCG-5'\n_____________\|_____________\|\n_____________62____________48\n	246 -- 252	55 -- 61	-14.1165 kcal/mol	4.46726 kcal/mol	0.738192 kcal/mol	245 259@LB@ \| \|@LB@5'-GGC...GCACC C UUGCU...UGU-3'@LB@ AUGGGGG AGGCA@LB@ \|\|:\|\|\|\| \|::\|\|@LB@ UAUCCCC UUUGU@LB@3'-UUU...AACUU A CUGUA...UCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -14.1165 kcal/mol@LB@Unfolding Energy - mRNA 4.46726 kcal/mol@LB@Unfolding Energy - sRNA 0.738192 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 55 -- 61@LB@
112	0.01793	0.5155	b1418	cybB	-10.08	0.093429	125 -- 145	33 -- 57	cytochrome b561	_____________124_______________________146\n_____________\|_________________________\|\n5'-AAC...AAAAC_________________________AUUUU...UCC-3'\n______________GGGUGAACA_AUAUUU___AAUGAA\n______________\|\|\|\|:\|\|\|\|_\|:\|\|\|:___\|\|\|\|\|\|\n______________CCCAUUUGU_UGUAAG___UUACUU\n3'-UUU...UUAUC_________C______UCU______ACUGC...UCG-5'\n_____________\|_________________________\|\n_____________58________________________32\n	127 -- 133	49 -- 55	-19.5073 kcal/mol	3.1607 kcal/mol	6.2643 kcal/mol	124 146@LB@ \| \|@LB@5'-AAC...AAAAC AUUUU...UCC-3'@LB@ GGGUGAACA AUAUUU AAUGAA@LB@ \|\|\|\|:\|\|\|\| \|:\|\|\|: \|\|\|\|\|\|@LB@ CCCAUUUGU UGUAAG UUACUU@LB@3'-UUU...UUAUC C UCU ACUGC...UCG-5'@LB@ \| \|@LB@ 58 32@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -19.5073 kcal/mol@LB@Unfolding Energy - mRNA 3.1607 kcal/mol@LB@Unfolding Energy - sRNA 6.2643 kcal/mol@LB@@LB@Position - mRNA 125 -- 145@LB@Position - sRNA 33 -- 57@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 49 -- 55@LB@
52	0.0063	0.3902	b1473	yddG	-8.84	0.162012	257 -- 264	2 -- 9	aromatic amino acid exporter	_____________256______265\n_____________\|________\|\n5'-GCG...AGCAC________GAUUG...CGG-3'\n______________GAUGGUAG\n______________\|\|\|\|:\|\|\|\n______________CUACUAUC\n3'-UUU...AAUUA________G-5'\n_____________\|________\|\n_____________10_______1\n	258 -- 264	2 -- 8	-10.1209 kcal/mol	1.26064 kcal/mol	0.0191352 kcal/mol	256 265@LB@ \| \|@LB@5'-GCG...AGCAC GAUUG...CGG-3'@LB@ GAUGGUAG@LB@ \|\|\|\|:\|\|\|@LB@ CUACUAUC@LB@3'-UUU...AAUUA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -10.1209 kcal/mol@LB@Unfolding Energy - mRNA 1.26064 kcal/mol@LB@Unfolding Energy - sRNA 0.0191352 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 2 -- 8@LB@
29	0.00201	0.2275	b1479	maeA	-13.16	0.019904	170 -- 200	29 -- 59	malate dehydrogenase decarboxylating NAD-requiring; malic enzyme	_____________169_________________________________201\n_____________\|___________________________________\|\n5'-UAG...CCCCC___________________AAAAA___________AUGGA...GCA-3'\n______________AGGG____AUGGAUAUUCA_____GAGUGAGUGAC\n______________\|\|\|\|____\|::\|\|:\|\|\|\|\|_____:\|:\|\|\|:\|\|\|\|\n______________UCCC____UGUCUGUAAGU_____UUUACUUACUG\n3'-UUU...CUUUA____CAUU___________C_______________CCAUU...UCG-5'\n_____________\|___________________________________\|\n_____________60__________________________________28\n	194 -- 200	29 -- 35	-27.1811 kcal/mol	7.73175 kcal/mol	6.28641 kcal/mol	169 201@LB@ \| \|@LB@5'-UAG...CCCCC AAAAA AUGGA...GCA-3'@LB@ AGGG AUGGAUAUUCA GAGUGAGUGAC@LB@ \|\|\|\| \|::\|\|:\|\|\|\|\| :\|:\|\|\|:\|\|\|\|@LB@ UCCC UGUCUGUAAGU UUUACUUACUG@LB@3'-UUU...CUUUA CAUU C CCAUU...UCG-5'@LB@ \| \|@LB@ 60 28@LB@@LB@@LB@Energy -13.16 kcal/mol@LB@Hybridization Energy -27.1811 kcal/mol@LB@Unfolding Energy - mRNA 7.73175 kcal/mol@LB@Unfolding Energy - sRNA 6.28641 kcal/mol@LB@@LB@Position - mRNA 170 -- 200@LB@Position - sRNA 29 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 29 -- 35@LB@
189	0.03168	0.5492	b1533	eamA	-9.19	0.139150	178 -- 226	1 -- 49	cysteine and O-acetyl-L-serine efflux system	_____________177_______________________________________________________227\n_____________\|_________________________________________________________\|\n5'-GUU...ACAAA____GAA______________________AAU__CGCGA____A________U____GCUAC...UGA-3'\n______________AGAU___AUUCAGA_______GGCGGUAG___GU_____AAAG_UGG_GGUG_UGGC\n______________\|\|\|:___\|\|\|\|\|\|\|_______\|:\|\|\|\|\|:___:\|_____\|\|\|\|_\|::_\|:\|\|_\|:\|\|\n______________UCUG___UAAGUCU_______CUGCCAUU___UA_____UUUC_AUU_CUAC_AUCG\n3'-UUU...AUUUG______________UUACUUA________AUU___________A___A____U____-5'\n_____________\|________________________________________________________\|\n_____________50_______________________________________________________1\n	193 -- 199	24 -- 30	-25.3484 kcal/mol	9.82981 kcal/mol	6.32371 kcal/mol	177 227@LB@ \| \|@LB@5'-GUU...ACAAA GAA AAU CGCGA A U GCUAC...UGA-3'@LB@ AGAU AUUCAGA GGCGGUAG GU AAAG UGG GGUG UGGC@LB@ \|\|\|: \|\|\|\|\|\|\| \|:\|\|\|\|\|: :\| \|\|\|\| \|:: \|:\|\| \|:\|\|@LB@ UCUG UAAGUCU CUGCCAUU UA UUUC AUU CUAC AUCG@LB@3'-UUU...AUUUG UUACUUA AUU A A U -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -25.3484 kcal/mol@LB@Unfolding Energy - mRNA 9.82981 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 178 -- 226@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 24 -- 30@LB@
32	0.003146	0.3086	b1553	rzpQ	-12.95	0.022283	187 -- 223	23 -- 60	Rz-like protein Qin prophage	_____________186______________________________________224\n_____________\|________________________________________\|\n5'-UAU...CCUGC______AUA______UGAA_____UAUUC___________UUUUC...GUG-3'\n______________UGGGGG___GAACAG____UCAGA________AUGGUGAU\n______________\|:\|\|\|\|___:\|\|\|\|\|____\|\|\|\|\|________\|:\|\|\|:\|\|\n______________AUCCCC___UUUGUC____AGUCU________UGCCAUUA\n3'-UUU...ACUUU______A________UGUA_____UUACUUAC________UUUAU...UCG-5'\n_____________\|________________________________________\|\n_____________61_______________________________________22\n	217 -- 223	23 -- 29	-27.4351 kcal/mol	8.1631 kcal/mol	6.31885 kcal/mol	186 224@LB@ \| \|@LB@5'-UAU...CCUGC AUA UGAA UAUUC UUUUC...GUG-3'@LB@ UGGGGG GAACAG UCAGA AUGGUGAU@LB@ \|:\|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|:\|\|\|:\|\|@LB@ AUCCCC UUUGUC AGUCU UGCCAUUA@LB@3'-UUU...ACUUU A UGUA UUACUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 61 22@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -27.4351 kcal/mol@LB@Unfolding Energy - mRNA 8.1631 kcal/mol@LB@Unfolding Energy - sRNA 6.31885 kcal/mol@LB@@LB@Position - mRNA 187 -- 223@LB@Position - sRNA 23 -- 60@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 23 -- 29@LB@
166	0.02659	0.526	b1580	rspB	-9.76	0.108040	184 -- 209	1 -- 29	putative Zn-dependent NAD(P)-binding oxidoreductase	_____________183___________________________210\n_____________\|_____________________________\|\n5'-AUG...GGAAC______G_______A_______AA_____AUAUU...UUG-3'\n______________UGGUAA_GAGUAAG__UAAUGA____AGC\n______________:\|\|\|\|\|_:\|:\|\|\|:__\|\|\|\|\|\|____\|\|\|\n______________GCCAUU_UUUAUUU__AUUACU____UCG\n3'-UUU...UUACU______A_______CA______ACUA___-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	191 -- 197	16 -- 22	-16.0836 kcal/mol	4.192 kcal/mol	2.12711 kcal/mol	183 210@LB@ \| \|@LB@5'-AUG...GGAAC G A AA AUAUU...UUG-3'@LB@ UGGUAA GAGUAAG UAAUGA AGC@LB@ :\|\|\|\|\| :\|:\|\|\|: \|\|\|\|\|\| \|\|\|@LB@ GCCAUU UUUAUUU AUUACU UCG@LB@3'-UUU...UUACU A CA ACUA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -16.0836 kcal/mol@LB@Unfolding Energy - mRNA 4.192 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 16 -- 22@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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