Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
158	0.00827	0.1845	stm1712	acnA	-14.47	0.143385	236 -- 294	48 -- 104	aconitate hydratase 1	_____________235_________________295\n_____________\|___________________\|\n5'-AUC...CAACC_______G_AU________CGCAA...GCG-3'\n______________CUGUGGA_A__CAGGGUAA\n______________\|\|:\|\|\|\|_\|__\|\|\|\|\|\|\|\|\n______________GAUACCU_U__GUCCCAUU\n3'-UUU...UUAGU_______G_CU________UACAU...UCA-5'\n_____________\|___________________\|\n_____________105_________________47\n	167 -- 173	149 -- 155	-24.0869 kcal/mol	10.3759 kcal/mol	4.11594 kcal/mol	235 295@LB@ \| \|@LB@5'-AUC...CAACC G AU CGCAA...GCG-3'@LB@ CUGUGGA A CAGGGUAA@LB@ \|\|:\|\|\|\| \| \|\|\|\|\|\|\|\|@LB@ GAUACCU U GUCCCAUU@LB@3'-UUU...UUAGU G CU UACAU...UCA-5'@LB@ \| \|@LB@ 105 47@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -24.0869 kcal/mol@LB@Unfolding Energy - mRNA 10.3759 kcal/mol@LB@Unfolding Energy - sRNA 4.11594 kcal/mol@LB@@LB@Position - mRNA 236 -- 294@LB@Position - sRNA 48 -- 104@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 149 -- 155@LB@
31	0.0007673	0.08814	stm0403	yajB	-17.88	0.039643	23 -- 70	41 -- 90	ACP phosphodiesterase	_____________22_____________71\n_____________\|______________\|\n5'-CCC...GGGUA_______AU_____AUUCG...AUU-3'\n______________GUGGGCA__CAGGG\n______________:\|\|\|:\|\|__\|\|\|\|\|\n______________UACCUGU__GUCCC\n3'-UUU...AGUGA_______CU_____AUUUA...UCA-5'\n_____________\|______________\|\n_____________91_____________40\n	57 -- 63	159 -- 165	-19.6891 kcal/mol	4.4153 kcal/mol	3.13232 kcal/mol	22 71@LB@ \| \|@LB@5'-CCC...GGGUA AU AUUCG...AUU-3'@LB@ GUGGGCA CAGGG@LB@ :\|\|\|:\|\| \|\|\|\|\|@LB@ UACCUGU GUCCC@LB@3'-UUU...AGUGA CU AUUUA...UCA-5'@LB@ \| \|@LB@ 91 40@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -19.6891 kcal/mol@LB@Unfolding Energy - mRNA 4.4153 kcal/mol@LB@Unfolding Energy - sRNA 3.13232 kcal/mol@LB@@LB@Position - mRNA 23 -- 70@LB@Position - sRNA 41 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 159 -- 165@LB@
137	0.006825	0.1774	stm1196	acpP	-14.14	0.161333	197 -- 223	36 -- 60	acyl carrier protein	_____________196___________________________________________224\n_____________\|_____________________________________________\|\n5'-ACU...AGAAC_______GAAA_____C____A____CU__GCGUUAA________AAGUA...UGG-3'\n______________GCGUUAA____AUUAU_GGCG_ACAG__GG_______GCAGGAAG\n______________:\|:\|\|\|\|____\|:\|\|\|_\|:\|:_\|\|\|\|__\|\|_______:\|\|\|\|\|\|\|\n______________UGUAAUU____UGAUA_CUGU_UGUC__CC_______UGUCCUUC\n3'-UUU...CACGA_______AG_______C____C________AUUUACA________ACUUU...UCA-5'\n_____________\|_____________________________________________\|\n_____________61____________________________________________35\n	258 -- 264	137 -- 143	-28.6095 kcal/mol	10.3633 kcal/mol	7.13805 kcal/mol	196 224@LB@ \| \|@LB@5'-ACU...AGAAC GAAA C A CU GCGUUAA AAGUA...UGG-3'@LB@ GCGUUAA AUUAU GGCG ACAG GG GCAGGAAG@LB@ :\|:\|\|\|\| \|:\|\|\| \|:\|: \|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ UGUAAUU UGAUA CUGU UGUC CC UGUCCUUC@LB@3'-UUU...CACGA AG C C AUUUACA ACUUU...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -28.6095 kcal/mol@LB@Unfolding Energy - mRNA 10.3633 kcal/mol@LB@Unfolding Energy - sRNA 7.13805 kcal/mol@LB@@LB@Position - mRNA 197 -- 223@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 137 -- 143@LB@
50	0.001812	0.1291	stm3207	ygiH	-15.41	0.101358	70 -- 101	63 -- 93	acyl-phosphate--glycerol-3-phosphate O-acyltransferase	_____________69___________________________________102\n_____________\|____________________________________\|\n5'-UAU...CGAAA_____UCUAU__________U_______________UGCCU...CGC-3'\n______________GUUGC_____AAAUACAAUA_C____CAUCACGACC\n______________:\|\|\|\|_____\|\|\|:\|\|\|\|:\|_\|____\|\|\|\|\|\|:\|\|\|\n______________UAACG_____UUUGUGUUGU_G____GUAGUGUUGG\n3'-UUU...CUGGU____________________U_UGUU__________CAUUC...UCA-5'\n_____________\|____________________________________\|\n_____________94___________________________________62\n	95 -- 101	63 -- 69	-25.69 kcal/mol	1.94006 kcal/mol	8.62086 kcal/mol	69 102@LB@ \| \|@LB@5'-UAU...CGAAA UCUAU U UGCCU...CGC-3'@LB@ GUUGC AAAUACAAUA C CAUCACGACC@LB@ :\|\|\|\| \|\|\|:\|\|\|\|:\| \| \|\|\|\|\|\|:\|\|\|@LB@ UAACG UUUGUGUUGU G GUAGUGUUGG@LB@3'-UUU...CUGGU U UGUU CAUUC...UCA-5'@LB@ \| \|@LB@ 94 62@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -25.69 kcal/mol@LB@Unfolding Energy - mRNA 1.94006 kcal/mol@LB@Unfolding Energy - sRNA 8.62086 kcal/mol@LB@@LB@Position - mRNA 70 -- 101@LB@Position - sRNA 63 -- 93@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 63 -- 69@LB@
122	0.00604	0.1758	stm2353	hisQ	-14.65	0.134227	190 -- 212	140 -- 163	amino acid ABC transporter permease	_____________189______________________213\n_____________\|________________________\|\n5'-GAU...CAACA________UGCAUGU_________UUUUC...UCG-3'\n______________GGACAGGC________UGUACGGG\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|:\|\|\n______________CCUGUCUG________ACAUGUCC\n3'-UUU...UGAUA________UCCCAUUU________UUCAC...UCA-5'\n_____________\|________________________\|\n_____________164______________________139\n	206 -- 212	140 -- 146	-25.7393 kcal/mol	6.65037 kcal/mol	3.70771 kcal/mol	189 213@LB@ \| \|@LB@5'-GAU...CAACA UGCAUGU UUUUC...UCG-3'@LB@ GGACAGGC UGUACGGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|:\|\|@LB@ CCUGUCUG ACAUGUCC@LB@3'-UUU...UGAUA UCCCAUUU UUCAC...UCA-5'@LB@ \| \|@LB@ 164 139@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -25.7393 kcal/mol@LB@Unfolding Energy - mRNA 6.65037 kcal/mol@LB@Unfolding Energy - sRNA 3.70771 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 140 -- 163@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 140 -- 146@LB@
68	0.003225	0.1596	stm3930	yifK	-15.10	0.113746	177 -- 247	44 -- 93	amino acid permease	_____________176____________________248\n_____________\|______________________\|\n5'-CUU...GAACC_______________UG_G___UUAUG...GCG-3'\n______________GUUGCAAACACGACA__A_GAU\n______________:\|\|\|\|\|\|\|\|\|\|:\|\|\|__\|_:\|:\n______________UAACGUUUGUGUUGU__U_UUG\n3'-UUU...CUGGU_______________UG_G___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________94_____________________43\n	185 -- 191	79 -- 85	-22.6062 kcal/mol	5.26496 kcal/mol	3.80917 kcal/mol	176 248@LB@ \| \|@LB@5'-CUU...GAACC UG G UUAUG...GCG-3'@LB@ GUUGCAAACACGACA A GAU@LB@ :\|\|\|\|\|\|\|\|\|\|:\|\|\| \| :\|:@LB@ UAACGUUUGUGUUGU U UUG@LB@3'-UUU...CUGGU UG G UAGUG...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -22.6062 kcal/mol@LB@Unfolding Energy - mRNA 5.26496 kcal/mol@LB@Unfolding Energy - sRNA 3.80917 kcal/mol@LB@@LB@Position - mRNA 177 -- 247@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 79 -- 85@LB@
126	0.006333	0.1774	stm1584	ansP	-14.21	0.157463	122 -- 184	36 -- 93	amino acid permease	_____________121_________________185\n_____________\|___________________\|\n5'-AUA...UGUCA________UAUAACA____ACGUA...GUC-3'\n______________GGACAGGC_______GGUA\n______________\|\|\|\|\|\|:\|_______\|\|\|\|\n______________CCUGUCUG_______CCAU\n3'-UUU...UGAUA________UC_________UUACA...UCA-5'\n_____________\|___________________\|\n_____________94__________________35\n	178 -- 184	156 -- 162	-15.5225 kcal/mol	4.18435 kcal/mol	3.12041 kcal/mol	121 185@LB@ \| \|@LB@5'-AUA...UGUCA UAUAACA ACGUA...GUC-3'@LB@ GGACAGGC GGUA@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ CCUGUCUG CCAU@LB@3'-UUU...UGAUA UC UUACA...UCA-5'@LB@ \| \|@LB@ 94 35@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -15.5225 kcal/mol@LB@Unfolding Energy - mRNA 4.18435 kcal/mol@LB@Unfolding Energy - sRNA 3.12041 kcal/mol@LB@@LB@Position - mRNA 122 -- 184@LB@Position - sRNA 36 -- 93@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 156 -- 162@LB@
169	0.009276	0.1945	stm0495	ybaK	-13.73	0.186840	16 -- 30	44 -- 58	aminoacyl-tRNA deacylase	_____________15_________________31\n_____________\|__________________\|\n5'-AAA...CAUUC____CU__G_________CGAAU...UGG-3'\n______________ACAC__AC_AUCACGAUC\n______________\|\|\|\|__\|\|_\|\|\|\|\|:\|:\|\n______________UGUG__UG_UAGUGUUGG\n3'-UUU...GUUGU____U_____________CAUUC...UCA-5'\n_____________\|__________________\|\n_____________59_________________43\n	264 -- 270	63 -- 69	-14.6876 kcal/mol	0.727125 kcal/mol	6.44907 kcal/mol	15 31@LB@ \| \|@LB@5'-AAA...CAUUC CU G CGAAU...UGG-3'@LB@ ACAC AC AUCACGAUC@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|:\|@LB@ UGUG UG UAGUGUUGG@LB@3'-UUU...GUUGU U CAUUC...UCA-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -14.6876 kcal/mol@LB@Unfolding Energy - mRNA 0.727125 kcal/mol@LB@Unfolding Energy - sRNA 6.44907 kcal/mol@LB@@LB@Position - mRNA 16 -- 30@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 63 -- 69@LB@
19	0.0004167	0.0781	stm0475	acrB	-19.12	0.024591	69 -- 114	139 -- 185	aminoglycoside/multidrug transporter permease	_____________68_______________________115\n_____________\|________________________\|\n5'-AAG...GUCCU____C_____U_____________AAUUA...CGC-3'\n______________GGCG_ACAGG_UAAA_GUACAGGA\n______________\|:\|:_\|\|\|\|\|_\|\|\|\|_\|\|\|\|\|\|\|\|\n______________CUGU_UGUCC_AUUU_CAUGUCCU\n3'-UUU...GAUAC____C_____C____A________UCACU...UCA-5'\n_____________\|________________________\|\n_____________186______________________138\n	108 -- 114	139 -- 145	-25.274 kcal/mol	6.90525 kcal/mol	3.69132 kcal/mol	68 115@LB@ \| \|@LB@5'-AAG...GUCCU C U AAUUA...CGC-3'@LB@ GGCG ACAGG UAAA GUACAGGA@LB@ \|:\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUGU UGUCC AUUU CAUGUCCU@LB@3'-UUU...GAUAC C C A UCACU...UCA-5'@LB@ \| \|@LB@ 186 138@LB@@LB@@LB@Energy -19.12 kcal/mol@LB@Hybridization Energy -25.274 kcal/mol@LB@Unfolding Energy - mRNA 6.90525 kcal/mol@LB@Unfolding Energy - sRNA 3.69132 kcal/mol@LB@@LB@Position - mRNA 69 -- 114@LB@Position - sRNA 139 -- 185@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 139 -- 145@LB@
21	0.000482	0.08173	stm1057	pepN	-18.92	0.026522	201 -- 244	36 -- 81	aminopeptidase N	_____________200______________245\n_____________\|________________\|\n5'-CUU...UUUAU___________C____GCCAA...AAA-3'\n______________GACACAACAGC_ACAA\n______________:\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUGUGUUGUUG_UGUU\n3'-UUU...AACGU________________GUAGU...UCA-5'\n_____________\|________________\|\n_____________82_______________35\n	207 -- 213	77 -- 83	-17.6161 kcal/mol	1.99149 kcal/mol	3.56182 kcal/mol	200 245@LB@ \| \|@LB@5'-CUU...UUUAU C GCCAA...AAA-3'@LB@ GACACAACAGC ACAA@LB@ :\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ UUGUGUUGUUG UGUU@LB@3'-UUU...AACGU GUAGU...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -18.92 kcal/mol@LB@Hybridization Energy -17.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.99149 kcal/mol@LB@Unfolding Energy - sRNA 3.56182 kcal/mol@LB@@LB@Position - mRNA 201 -- 244@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 77 -- 83@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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