Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
125	0.005266	0.1416	b0957	ompA	-12.88	0.041122	280 -- 293	25 -- 39	outer membrane protein A (3a;II*;G;d)	_____________279_____________294\n_____________\|_______________\|\n5'-CUU...UAACA_______________GCUAAAC-3'\n______________CCUGGUACA_CUGGU\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|:\n______________GGACCAUGU_GAUCG\n3'-UUU...ACCAA_________C_____UAAAA...UCG-5'\n_____________\|_______________\|\n_____________40______________24\n	282 -- 288	31 -- 37	-21.2564 kcal/mol	3.82713 kcal/mol	4.55153 kcal/mol	279 294@LB@ \| \|@LB@5'-CUU...UAACA GCUAAAC-3'@LB@ CCUGGUACA CUGGU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|:@LB@ GGACCAUGU GAUCG@LB@3'-UUU...ACCAA C UAAAA...UCG-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -21.2564 kcal/mol@LB@Unfolding Energy - mRNA 3.82713 kcal/mol@LB@Unfolding Energy - sRNA 4.55153 kcal/mol@LB@@LB@Position - mRNA 280 -- 293@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 31 -- 37@LB@
12	4.171e-05	0.01168	b0814	ompX	-14.35	0.017131	192 -- 226	1 -- 48	outer membrane protein X	_____________191______________________________________________227\n_____________\|________________________________________________\|\n5'-CUG...CAUUU_________A___AAAAAAAUU__________________C_______ACUGG...CAC-3'\n______________GAGGUGGUU__UG_________GCA____________UGU_UUUCAGC\n______________\|\|\|\|\|\|\|\|\|__\|\|_________\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________CUCCACCAA__AC_________CGU____________ACA_AAAGUCG\n3'-UUU...GAUUC_________GG__CAUGUCGAU___AAAAUACCCAAU___A_______-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	220 -- 226	1 -- 7	-27.166 kcal/mol	8.20777 kcal/mol	4.60955 kcal/mol	191 227@LB@ \| \|@LB@5'-CUG...CAUUU A AAAAAAAUU C ACUGG...CAC-3'@LB@ GAGGUGGUU UG GCA UGU UUUCAGC@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CUCCACCAA AC CGU ACA AAAGUCG@LB@3'-UUU...GAUUC GG CAUGUCGAU AAAAUACCCAAU A -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -27.166 kcal/mol@LB@Unfolding Energy - mRNA 8.20777 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 1 -- 7@LB@
103	0.00377	0.123	b2922	yggE	-10.91	0.111523	45 -- 69	24 -- 45	oxidative stress defense protein	_____________44________________________70\n_____________\|_________________________\|\n5'-GCA...GUUAU_______AU__CCU___________AGAGA...CCG-3'\n______________GUGGUUU__UG___UGCAGCUGGCG\n______________\|\|\|\|\|\|:__\|\|___\|:\|\|\|\|\|:\|\|:\n______________CACCAAG__AC___AUGUCGAUCGU\n3'-UUU...UCCUC_______G___C_____________AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________46________________________23\n	63 -- 69	24 -- 30	-26.0515 kcal/mol	10.579 kcal/mol	4.55794 kcal/mol	44 70@LB@ \| \|@LB@5'-GCA...GUUAU AU CCU AGAGA...CCG-3'@LB@ GUGGUUU UG UGCAGCUGGCG@LB@ \|\|\|\|\|\|: \|\| \|:\|\|\|\|\|:\|\|:@LB@ CACCAAG AC AUGUCGAUCGU@LB@3'-UUU...UCCUC G C AAAAU...UCG-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -26.0515 kcal/mol@LB@Unfolding Energy - mRNA 10.579 kcal/mol@LB@Unfolding Energy - sRNA 4.55794 kcal/mol@LB@@LB@Position - mRNA 45 -- 69@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 24 -- 30@LB@
177	0.009845	0.1869	b3241	aaeA	-6.34	0.565531	229 -- 235	29 -- 35	p-hydroxybenzoic acid efflux system component	_____________228_____236\n_____________\|_______\|\n5'-UCC...CUCCC_______CAUCA...CCG-3'\n______________GUACGGC\n______________\|\|\|\|:\|\|\n______________CAUGUCG\n3'-UUU...AGGAC_______AUCGU...UCG-5'\n_____________\|_______\|\n_____________36______28\n	229 -- 235	29 -- 35	-10.2139 kcal/mol	2.71034 kcal/mol	1.16584 kcal/mol	228 236@LB@ \| \|@LB@5'-UCC...CUCCC CAUCA...CCG-3'@LB@ GUACGGC@LB@ \|\|\|\|:\|\|@LB@ CAUGUCG@LB@3'-UUU...AGGAC AUCGU...UCG-5'@LB@ \| \|@LB@ 36 28@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.2139 kcal/mol@LB@Unfolding Energy - mRNA 2.71034 kcal/mol@LB@Unfolding Energy - sRNA 1.16584 kcal/mol@LB@@LB@Position - mRNA 229 -- 235@LB@Position - sRNA 29 -- 35@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 29 -- 35@LB@
89	0.002865	0.1082	b2378	lpxP	-9.84	0.178666	41 -- 76	9 -- 35	palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase	_____________40____________________________________77\n_____________\|_____________________________________\|\n5'-AUU...AUAAA______AUACC_____C____CUCCUCGU________CCUGA...CUU-3'\n______________GUACAG_____GCAUU__AUG________GGUUAUGU\n______________\|\|\|\|\|\|_____\|\|\|\|\|__\|\|\|________\|\|\|\|\|\|\|\|\n______________CAUGUC_____CGUAA__UAC________CCAAUACA\n3'-UUU...AGGAC______GAU_______AA___________________AAAAGUCG-5'\n_____________\|_____________________________________\|\n_____________36____________________________________8\n	70 -- 76	9 -- 15	-19.6308 kcal/mol	8.30521 kcal/mol	1.48708 kcal/mol	40 77@LB@ \| \|@LB@5'-AUU...AUAAA AUACC C CUCCUCGU CCUGA...CUU-3'@LB@ GUACAG GCAUU AUG GGUUAUGU@LB@ \|\|\|\|\|\| \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CAUGUC CGUAA UAC CCAAUACA@LB@3'-UUU...AGGAC GAU AA AAAAGUCG-5'@LB@ \| \|@LB@ 36 8@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -19.6308 kcal/mol@LB@Unfolding Energy - mRNA 8.30521 kcal/mol@LB@Unfolding Energy - sRNA 1.48708 kcal/mol@LB@@LB@Position - mRNA 41 -- 76@LB@Position - sRNA 9 -- 35@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 9 -- 15@LB@
182	0.01043	0.1919	b1235	rssB	-12.59	0.048266	47 -- 57	25 -- 36	PcnB-degradosome interaction factor; response regulator	_____________46___________58\n_____________\|____________\|\n5'-AAU...CGGCC____________AGUGG...CAA-3'\n______________GG_ACAGCUGGC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________CC_UGUCGAUCG\n3'-UUU...AAGGA__A_________UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	51 -- 57	25 -- 31	-17.7308 kcal/mol	3.71782 kcal/mol	1.42738 kcal/mol	46 58@LB@ \| \|@LB@5'-AAU...CGGCC AGUGG...CAA-3'@LB@ GG ACAGCUGGC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ CC UGUCGAUCG@LB@3'-UUU...AAGGA A UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -17.7308 kcal/mol@LB@Unfolding Energy - mRNA 3.71782 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 47 -- 57@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 25 -- 31@LB@
48	0.001117	0.07744	b2829	ptsP	-13.12	0.035810	22 -- 37	14 -- 33	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________21___________________38\n_____________\|____________________\|\n5'-CCA...GUUUG____________________AAGUU...UGG-3'\n______________ACGGCUGGCG____AUGGGU\n______________\|\|:\|\|\|:\|\|:____\|\|\|\|\|\|\n______________UGUCGAUCGU____UACCCA\n3'-UUU...GACCA__________AAAA______AUACA...UCG-5'\n_____________\|____________________\|\n_____________34___________________13\n	25 -- 31	24 -- 30	-23.1334 kcal/mol	8.56068 kcal/mol	1.44884 kcal/mol	21 38@LB@ \| \|@LB@5'-CCA...GUUUG AAGUU...UGG-3'@LB@ ACGGCUGGCG AUGGGU@LB@ \|\|:\|\|\|:\|\|: \|\|\|\|\|\|@LB@ UGUCGAUCGU UACCCA@LB@3'-UUU...GACCA AAAA AUACA...UCG-5'@LB@ \| \|@LB@ 34 13@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -23.1334 kcal/mol@LB@Unfolding Energy - mRNA 8.56068 kcal/mol@LB@Unfolding Energy - sRNA 1.44884 kcal/mol@LB@@LB@Position - mRNA 22 -- 37@LB@Position - sRNA 14 -- 33@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 24 -- 30@LB@
15	0.0001004	0.02121	b2416	ptsI	-14.97	0.011388	179 -- 212	1 -- 32	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________178_________________________________213\n_____________\|___________________________________\|\n5'-GUG...AAAAU____CACA____AGG___________A___CA___AUUUU...CCG-3'\n______________CAGU____AGUA___UA_GGGUUAUG_UUU__GGC\n______________\|\|\|:____\|\|:\|___\|\|_\|\|\|\|\|\|\|\|_\|\|\|__:\|\|\n______________GUCG____UCGU___AU_CCCAAUAC_AAA__UCG\n3'-UUU...ACCAU____A_______AAA__A________A___AG___-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	197 -- 203	10 -- 16	-21.5882 kcal/mol	5.12711 kcal/mol	1.49075 kcal/mol	178 213@LB@ \| \|@LB@5'-GUG...AAAAU CACA AGG A CA AUUUU...CCG-3'@LB@ CAGU AGUA UA GGGUUAUG UUU GGC@LB@ \|\|\|: \|\|:\| \|\| \|\|\|\|\|\|\|\| \|\|\| :\|\|@LB@ GUCG UCGU AU CCCAAUAC AAA UCG@LB@3'-UUU...ACCAU A AAA A A AG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.97 kcal/mol@LB@Hybridization Energy -21.5882 kcal/mol@LB@Unfolding Energy - mRNA 5.12711 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 10 -- 16@LB@
155	0.007835	0.1694	b2239	glpQ	-10.90	0.112133	59 -- 106	1 -- 45	periplasmic glycerophosphodiester phosphodiesterase	_____________58________________________________________________107\n_____________\|_________________________________________________\|\n5'-CGG...ACACC____AC_____C__CUG__A_____GC_______UA____A__GG____AGCAU...UCA-3'\n______________GUGG__UUCUU_GG___GG_UGGCG__UUUAUGG___AUG_UU__CGGC\n______________\|\|\|\|__\|\|\|:\|_\|\|___:\|_\|:\|\|:__\|\|\|\|\|\|\|___\|\|\|_\|\|__\|:\|\|\n______________CACC__AAGGA_CC___UC_AUCGU__AAAUACC___UAC_AA__GUCG\n3'-UUU...UCCUC______________AUG__G_____A________CAA___A__AA____-5'\n_____________\|________________________________________________\|\n_____________46_______________________________________________1\n	86 -- 92	16 -- 22	-29.5358 kcal/mol	14.0238 kcal/mol	4.60935 kcal/mol	58 107@LB@ \| \|@LB@5'-CGG...ACACC AC C CUG A GC UA A GG AGCAU...UCA-3'@LB@ GUGG UUCUU GG GG UGGCG UUUAUGG AUG UU CGGC@LB@ \|\|\|\| \|\|\|:\| \|\| :\| \|:\|\|: \|\|\|\|\|\|\| \|\|\| \|\| \|:\|\|@LB@ CACC AAGGA CC UC AUCGU AAAUACC UAC AA GUCG@LB@3'-UUU...UCCUC AUG G A CAA A AA -5'@LB@ \| \|@LB@ 46 1@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -29.5358 kcal/mol@LB@Unfolding Energy - mRNA 14.0238 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 59 -- 106@LB@Position - sRNA 1 -- 45@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 16 -- 22@LB@
68	0.001845	0.09081	b2957	ansB	-14.03	0.020893	243 -- 268	22 -- 43	periplasmic L-asparaginase 2	_____________242________________________269\n_____________\|__________________________\|\n5'-AGC...UUAUG______AG_________AU_______ACCCA...GGA-3'\n______________GGUUUU__UGGUGCAGC__UGGCAUU\n______________\|\|\|\|::__\|\|\|\|:\|\|\|\|__\|:\|\|\|\|\|\n______________CCAAGG__ACCAUGUCG__AUCGUAA\n3'-UUU...CUCCA__________________________AAUAC...UCG-5'\n_____________\|__________________________\|\n_____________44_________________________21\n	262 -- 268	22 -- 28	-26.4763 kcal/mol	7.8858 kcal/mol	4.55803 kcal/mol	242 269@LB@ \| \|@LB@5'-AGC...UUAUG AG AU ACCCA...GGA-3'@LB@ GGUUUU UGGUGCAGC UGGCAUU@LB@ \|\|\|\|:: \|\|\|\|:\|\|\|\| \|:\|\|\|\|\|@LB@ CCAAGG ACCAUGUCG AUCGUAA@LB@3'-UUU...CUCCA AAUAC...UCG-5'@LB@ \| \|@LB@ 44 21@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -26.4763 kcal/mol@LB@Unfolding Energy - mRNA 7.8858 kcal/mol@LB@Unfolding Energy - sRNA 4.55803 kcal/mol@LB@@LB@Position - mRNA 243 -- 268@LB@Position - sRNA 22 -- 43@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 22 -- 28@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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