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
161	0.02632	0.526	b3670	ilvN	-9.27	0.134814	179 -- 196	49 -- 65	acetolactate synthase 1 small subunit	_____________178________________197\n_____________\|__________________\|\n5'-UCA...AAUAC________U___GG____AGCCA...CUU-3'\n______________UGAAAUGG_GGG__AAUA\n______________\|\|\|\|\|\|:\|_\|\|\|__\|\|:\|\n______________ACUUUAUC_CCC__UUGU\n3'-UUU...GGCCA____________AU____CUGUA...UCG-5'\n_____________\|__________________\|\n_____________66_________________48\n	180 -- 186	58 -- 64	-15.3061 kcal/mol	4.40463 kcal/mol	1.63404 kcal/mol	178 197@LB@ \| \|@LB@5'-UCA...AAUAC U GG AGCCA...CUU-3'@LB@ UGAAAUGG GGG AAUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ ACUUUAUC CCC UUGU@LB@3'-UUU...GGCCA AU CUGUA...UCG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3061 kcal/mol@LB@Unfolding Energy - mRNA 4.40463 kcal/mol@LB@Unfolding Energy - sRNA 1.63404 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 58 -- 64@LB@
162	0.02632	0.526	b1886	tar	-10.00	0.096892	244 -- 251	53 -- 60	methyl-accepting chemotaxis protein II	_____________243______252\n_____________\|________\|\n5'-UGC...GGUGC________UUCGC...UUC-3'\n______________UGGGGGUA\n______________\|:\|\|\|\|\|\|\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	245 -- 251	53 -- 59	-12.2006 kcal/mol	2.12623 kcal/mol	0.0710089 kcal/mol	243 252@LB@ \| \|@LB@5'-UGC...GGUGC UUCGC...UUC-3'@LB@ UGGGGGUA@LB@ \|:\|\|\|\|\|\|@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -12.2006 kcal/mol@LB@Unfolding Energy - mRNA 2.12623 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 244 -- 251@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 53 -- 59@LB@
163	0.02649	0.526	b3156	yhbS	-11.68	0.043230	178 -- 217	16 -- 53	GNAT family putative N-acetyltransferase	_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-CCG...AAACC______________U_______CC___C____UC_______AAUUC...AUC-3'\n______________AAACAGACA_UCGG_AGGUGAA__AUG_UAAU__GAGUAGA\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|_\|::\|\|\|\|__\|:\|_\|\|\|\|__:\|:\|\|:\|\n______________UUUGUCUGU_AGUC_UUUACUU__UGC_AUUA__UUUAUUU\n3'-UUU...CCCCA_________A____________AC___C_____________CAAUU...UCG-5'\n_____________\|_________________________________________\|\n_____________54________________________________________15\n	211 -- 217	16 -- 22	-26.1463 kcal/mol	8.14596 kcal/mol	6.32252 kcal/mol	177 218@LB@ \| \|@LB@5'-CCG...AAACC U CC C UC AAUUC...AUC-3'@LB@ AAACAGACA UCGG AGGUGAA AUG UAAU GAGUAGA@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| \|::\|\|\|\| \|:\| \|\|\|\| :\|:\|\|:\|@LB@ UUUGUCUGU AGUC UUUACUU UGC AUUA UUUAUUU@LB@3'-UUU...CCCCA A AC C CAAUU...UCG-5'@LB@ \| \|@LB@ 54 15@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -26.1463 kcal/mol@LB@Unfolding Energy - mRNA 8.14596 kcal/mol@LB@Unfolding Energy - sRNA 6.32252 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 16 -- 53@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 16 -- 22@LB@
164	0.02654	0.526	b3993	thiE	-11.45	0.048376	123 -- 151	37 -- 65	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)	_____________122____________________________152\n_____________\|______________________________\|\n5'-CAC...ACUAU_________AAU__________G_______ACUUC...UAC-3'\n______________UGAAAUGGG____GGCGGAUAU_UCGGAGA\n______________\|\|\|\|\|\|:\|\|____::\|:\|\|:\|\|_\|\|:\|\|:\|\n______________ACUUUAUCC____UUGUCUGUA_AGUCUUU\n3'-UUU...GGCCA_________CCAU_________________ACUUA...UCG-5'\n_____________\|______________________________\|\n_____________66_____________________________36\n	125 -- 131	57 -- 63	-26.5084 kcal/mol	7.89908 kcal/mol	7.1561 kcal/mol	122 152@LB@ \| \|@LB@5'-CAC...ACUAU AAU G ACUUC...UAC-3'@LB@ UGAAAUGGG GGCGGAUAU UCGGAGA@LB@ \|\|\|\|\|\|:\|\| ::\|:\|\|:\|\| \|\|:\|\|:\|@LB@ ACUUUAUCC UUGUCUGUA AGUCUUU@LB@3'-UUU...GGCCA CCAU ACUUA...UCG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -26.5084 kcal/mol@LB@Unfolding Energy - mRNA 7.89908 kcal/mol@LB@Unfolding Energy - sRNA 7.1561 kcal/mol@LB@@LB@Position - mRNA 123 -- 151@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 57 -- 63@LB@
165	0.02655	0.526	b2388	glk	-7.68	0.259430	184 -- 233	1 -- 52	glucokinase	_____________183_____________________________________________________234\n_____________\|_______________________________________________________\|\n5'-CUA...ACUUU______G__GUU_____________AAA___UGCAUU_____C_______UG___GGCAC...AUU-3'\n______________AGCGGA_CA____GAA__GAAUGAC___GUA________AGU_GGUGAUG__GGC\n______________\|:\|:\|\|_\|\|____\|\|\|__\|\|\|\|\|\|\|___\|\|\|________\|\|\|_::\|\|\|\|\|__:\|\|\n______________UUGUCU_GU____CUU__CUUACUG___CAU________UCA_UUACUAC__UCG\n3'-UUU...CCCAU_________AAGU___UA_______C_____UAUUUAUU___A_______UA___-5'\n_____________\|______________________________________________________\|\n_____________53_____________________________________________________1\n	222 -- 228	6 -- 12	-28.455 kcal/mol	14.4434 kcal/mol	6.33555 kcal/mol	183 234@LB@ \| \|@LB@5'-CUA...ACUUU G GUU AAA UGCAUU C UG GGCAC...AUU-3'@LB@ AGCGGA CA GAA GAAUGAC GUA AGU GGUGAUG GGC@LB@ \|:\|:\|\| \|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| ::\|\|\|\|\| :\|\|@LB@ UUGUCU GU CUU CUUACUG CAU UCA UUACUAC UCG@LB@3'-UUU...CCCAU AAGU UA C UAUUUAUU A UA -5'@LB@ \| \|@LB@ 53 1@LB@@LB@@LB@Energy -7.68 kcal/mol@LB@Hybridization Energy -28.455 kcal/mol@LB@Unfolding Energy - mRNA 14.4434 kcal/mol@LB@Unfolding Energy - sRNA 6.33555 kcal/mol@LB@@LB@Position - mRNA 184 -- 233@LB@Position - sRNA 1 -- 52@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 6 -- 12@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@
167	0.02708	0.531	b3705	yidC	-10.20	0.088356	85 -- 115	24 -- 58	membrane protein insertase	_____________84____________________________________116\n_____________\|_____________________________________\|\n5'-CGC...GGUUU__A____UAAA_____GU_________U_________AACGC...CCC-3'\n______________GG_GUGA____AGGCA________UGG_UGACGGUGA\n______________\|\|_\|\|:\|____\|\|:\|\|________\|\|:_\|\|\|\|\|\|\|:\|\n______________CC_CAUU____UCUGU________ACU_ACUGCCAUU\n3'-UUU...UUUAU__C____UG_______AAGUCUUU___U_________AUUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________59____________________________________23\n	109 -- 115	24 -- 30	-23.9536 kcal/mol	7.45063 kcal/mol	6.30019 kcal/mol	84 116@LB@ \| \|@LB@5'-CGC...GGUUU A UAAA GU U AACGC...CCC-3'@LB@ GG GUGA AGGCA UGG UGACGGUGA@LB@ \|\| \|\|:\| \|\|:\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ CC CAUU UCUGU ACU ACUGCCAUU@LB@3'-UUU...UUUAU C UG AAGUCUUU U AUUUA...UCG-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -23.9536 kcal/mol@LB@Unfolding Energy - mRNA 7.45063 kcal/mol@LB@Unfolding Energy - sRNA 6.30019 kcal/mol@LB@@LB@Position - mRNA 85 -- 115@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 24 -- 30@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@
169	0.02775	0.531	b2110	yehC	-5.87	0.481945	191 -- 199	20 -- 28	putative periplasmic pilin chaperone	_____________190_______200\n_____________\|_________\|\n5'-CAG...CUCCA_________CAUGG...CCG-3'\n______________GGUAAUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUAUUU\n3'-UUU...UACUG_________AUUUC...UCG-5'\n_____________\|_________\|\n_____________29________19\n	193 -- 199	20 -- 26	-7.96952 kcal/mol	1.36589 kcal/mol	0.737257 kcal/mol	190 200@LB@ \| \|@LB@5'-CAG...CUCCA CAUGG...CCG-3'@LB@ GGUAAUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUAUUU@LB@3'-UUU...UACUG AUUUC...UCG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -7.96952 kcal/mol@LB@Unfolding Energy - mRNA 1.36589 kcal/mol@LB@Unfolding Energy - sRNA 0.737257 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 20 -- 26@LB@
170	0.02787	0.531	b3184	yhbE	-10.77	0.067448	1 -- 31	11 -- 53	EamA family inner membrane putative transporter	______________1__________________________________________32\n______________\|__________________________________________\|\n___________5'-_________GUA_________AUU___________________AGGCC...UGG-3'\n______________AAGCAGACG_____AAGUGAA___CG__________AAGUUAA\n______________\|\|:\|\|\|\|\|:_____\|\|:\|\|\|\|___\|\|__________\|\|\|\|\|\|\|\n______________UUUGUCUGU_____UUUACUU___GC__________UUCAAUU\n3'-UUU...CCCCA_________AAGUC_______ACU__CAUUAUUUAU_______ACUAC...UCG-5'\n_____________\|___________________________________________\|\n_____________54__________________________________________10\n	25 -- 31	11 -- 17	-18.1985 kcal/mol	1.09209 kcal/mol	6.3325 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GUA AUU AGGCC...UGG-3'@LB@ AAGCAGACG AAGUGAA CG AAGUUAA@LB@ \|\|:\|\|\|\|\|: \|\|:\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUGUCUGU UUUACUU GC UUCAAUU@LB@3'-UUU...CCCCA AAGUC ACU CAUUAUUUAU ACUAC...UCG-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -18.1985 kcal/mol@LB@Unfolding Energy - mRNA 1.09209 kcal/mol@LB@Unfolding Energy - sRNA 6.3325 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@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)

Job resubmission

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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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