Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
199	0.008811	0.1558	b4515	cydX	-11.13	0.020449	151 -- 184	5 -- 31	cytochrome d (bd-I) ubiquinol oxidase subunit X		_____________150________________________________185\n_____________\|__________________________________\|\n5'-ACC...CCAAA_______UU______AAC___CACUC________AAGUA...GUC-3'\n______________GAAGAUA__GAACGU___ACC_____UCUGUACU\n______________:\|\|\|\|\|\|__\|\|\|\|:\|___\|\|\|_____\|\|\|\|\|\|\|:\n______________UUUCUAU__CUUGUA___UGG_____AGACAUGG\n3'-AUU...CAGAC_______________GAA________________GAUG-5'\n_____________\|__________________________________\|\n_____________32_________________________________4\n	178 -- 184	5 -- 11	-22.8813 kcal/mol	3.72257 kcal/mol	8.05162 kcal/mol	150 185@LB@ \| \|@LB@5'-ACC...CCAAA UU AAC CACUC AAGUA...GUC-3'@LB@ GAAGAUA GAACGU ACC UCUGUACU@LB@ :\|\|\|\|\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\|:@LB@ UUUCUAU CUUGUA UGG AGACAUGG@LB@3'-AUU...CAGAC GAA GAUG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -22.8813 kcal/mol@LB@Unfolding Energy - mRNA 3.72257 kcal/mol@LB@Unfolding Energy - sRNA 8.05162 kcal/mol@LB@@LB@Position - mRNA 151 -- 184@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 5 -- 11@LB@
105	0.003348	0.1101	b2218	rcsC	-11.03	0.021992	174 -- 214	1 -- 37	hybrid sensory kinase in two-component regulatory system with RcsB and YojN		_____________173_______________________________________215\n_____________\|_________________________________________\|\n5'-AGC...CCAUC____ACCU____C_____U__GCC______AAA________UUCUU...CCG-3'\n______________GGUC____GAGG_GGAGC_UC___CCUUUG___UACCUUGC\n______________\|\|\|\|____:\|\|:_:\|\|:\|_\|\|___\|\|\|:\|\|___\|\|\|\|:\|:\|\n______________CCAG____UUCU_UCUUG_AG___GGAGAC___AUGGGAUG\n3'-AUU...AUUUU____ACU_____A_____U__AAU_________________-5'\n_____________\|________________________________________\|\n_____________38_______________________________________1\n	208 -- 214	1 -- 7	-33.3544 kcal/mol	10.9963 kcal/mol	11.3499 kcal/mol	173 215@LB@ \| \|@LB@5'-AGC...CCAUC ACCU C U GCC AAA UUCUU...CCG-3'@LB@ GGUC GAGG GGAGC UC CCUUUG UACCUUGC@LB@ \|\|\|\| :\|\|: :\|\|:\| \|\| \|\|\|:\|\| \|\|\|\|:\|:\|@LB@ CCAG UUCU UCUUG AG GGAGAC AUGGGAUG@LB@3'-AUU...AUUUU ACU A U AAU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -33.3544 kcal/mol@LB@Unfolding Energy - mRNA 10.9963 kcal/mol@LB@Unfolding Energy - sRNA 11.3499 kcal/mol@LB@@LB@Position - mRNA 174 -- 214@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@LB@
88	0.002339	0.09349	b3878	yihQ	-11.00	0.022508	260 -- 267	1 -- 8	putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase	b3656	_____________259______268\n_____________\|________\|\n5'-AAC...AGUUU________AUUUU...GCA-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	261 -- 267	1 -- 7	-13.427 kcal/mol	0.33456 kcal/mol	2.11603 kcal/mol	259 268@LB@ \| \|@LB@5'-AAC...AGUUU AUUUU...GCA-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -13.427 kcal/mol@LB@Unfolding Energy - mRNA 0.33456 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 260 -- 267@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.004686	0.1239	b3081	fadH	-11.00	0.022420	2 -- 21	1 -- 24	2 4-dienoyl-CoA reductase NADH and FMN-linked		_____________1________________________22\n_____________\|________________________\|\n__________5'-U_____C__________________AUGUG...ACC-3'\n______________GGACG_CUUAUC_C___GCCCUAC\n______________\|:\|\|:_\|\|\|\|:\|_\|___:\|\|\|\|\|\|\n______________CUUGU_GAAUGG_G___UGGGAUG\n3'-AUU...UCUAU_____A______A_ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	15 -- 21	1 -- 7	-21.5738 kcal/mol	2.57038 kcal/mol	8.02158 kcal/mol	1 22@LB@ \| \|@LB@ 5'-U C AUGUG...ACC-3'@LB@ GGACG CUUAUC C GCCCUAC@LB@ \|:\|\|: \|\|\|\|:\| \| :\|\|\|\|\|\|@LB@ CUUGU GAAUGG G UGGGAUG@LB@3'-AUU...UCUAU A A ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -21.5738 kcal/mol@LB@Unfolding Energy - mRNA 2.57038 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 1 -- 7@LB@
67	0.001147	0.05856	b2319	usg	-10.96	0.023185	203 -- 221	18 -- 36	putative semialdehyde dehydrogenase		_____________202_________________222\n_____________\|___________________\|\n5'-GAG...ACCAU_________C_________GCCGU...AAA-3'\n______________GUCUGAAGG_UGGAACAUU\n______________\|\|\|\|\|\|\|:\|_\|:\|\|\|\|\|\|:\n______________CAGACUUUC_AUCUUGUAG\n3'-AUU...UUUUC_________U_________AAUGG...AUG-5'\n_____________\|___________________\|\n_____________37__________________17\n	215 -- 221	18 -- 24	-22.956 kcal/mol	5.32254 kcal/mol	6.60045 kcal/mol	202 222@LB@ \| \|@LB@5'-GAG...ACCAU C GCCGU...AAA-3'@LB@ GUCUGAAGG UGGAACAUU@LB@ \|\|\|\|\|\|\|:\| \|:\|\|\|\|\|\|:@LB@ CAGACUUUC AUCUUGUAG@LB@3'-AUU...UUUUC U AAUGG...AUG-5'@LB@ \| \|@LB@ 37 17@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.956 kcal/mol@LB@Unfolding Energy - mRNA 5.32254 kcal/mol@LB@Unfolding Energy - sRNA 6.60045 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 18 -- 36@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 18 -- 24@LB@
145	0.005462	0.1325	b3239	yhcO	-10.93	0.023720	179 -- 225	2 -- 55	putative barnase inhibitor		_____________178______________________________________________________226\n_____________\|________________________________________________________\|\n5'-CUA...CGCCG___A_______C___________AAC______________A_______________AUGAG...GCG-3'\n______________CGA__ACGUGA_GGU____GG_C____AGAU_GAAUAUUU_UACCUUUG_AUUUUG\n______________\|\|\|__\|\|\|\|\|\|_:\|\|____\|\|_\|____\|\|\|\|_\|\|\|:\|\|:\|_\|\|\|\|\|:\|\|_\|:::\|:\n______________GCU__UGCACU_UCA____CC_G____UCUA_CUUGUAGA_AUGGAGAC_UGGGAU\n3'-AUU...UUUAG___AA__________UUUU__A_ACUU____U_________________A______G-5'\n_____________\|________________________________________________________\|\n_____________56_______________________________________________________1\n	213 -- 219	9 -- 15	-30.2735 kcal/mol	6.67064 kcal/mol	12.6986 kcal/mol	178 226@LB@ \| \|@LB@5'-CUA...CGCCG A C AAC A AUGAG...GCG-3'@LB@ CGA ACGUGA GGU GG C AGAU GAAUAUUU UACCUUUG AUUUUG@LB@ \|\|\| \|\|\|\|\|\| :\|\| \|\| \| \|\|\|\| \|\|\|:\|\|:\| \|\|\|\|\|:\|\| \|:::\|:@LB@ GCU UGCACU UCA CC G UCUA CUUGUAGA AUGGAGAC UGGGAU@LB@3'-AUU...UUUAG AA UUUU A ACUU U A G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -30.2735 kcal/mol@LB@Unfolding Energy - mRNA 6.67064 kcal/mol@LB@Unfolding Energy - sRNA 12.6986 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 9 -- 15@LB@
59	0.0008996	0.0531	b1310	ycjN	-10.87	0.024752	113 -- 129	42 -- 59	putative ABC sugar transporter periplasmic binding protein		_____________112________________130\n_____________\|__________________\|\n5'-UUC...GUCGG__________________UGAUA...UUA-3'\n______________GAUCUGAUUA_GUGAAGU\n______________:\|\|\|:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAGGCUAAU_CACUUCA\n3'-AUU...UCGGU__________G_______UUUUC...AUG-5'\n_____________\|__________________\|\n_____________60_________________41\n	123 -- 129	42 -- 48	-20.0101 kcal/mol	5.87569 kcal/mol	3.27976 kcal/mol	112 130@LB@ \| \|@LB@5'-UUC...GUCGG UGAUA...UUA-3'@LB@ GAUCUGAUUA GUGAAGU@LB@ :\|\|\|:\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUAGGCUAAU CACUUCA@LB@3'-AUU...UCGGU G UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -20.0101 kcal/mol@LB@Unfolding Energy - mRNA 5.87569 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 113 -- 129@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 42 -- 48@LB@
18	6.719e-05	0.01313	b2935	tktA	-10.85	0.025018	263 -- 275	52 -- 64	transketolase 1 thiamine triphosphate-binding		_____________262___________276\n_____________\|_____________\|\n5'-AAG...CAGAA_____________CACCC...UGG-3'\n______________AGCCAAAUCCGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGGUUUAGGCUA\n3'-AUU...AUAAG_____________AUGCA...AUG-5'\n_____________\|_____________\|\n_____________65____________51\n	269 -- 275	52 -- 58	-21.1603 kcal/mol	4.16811 kcal/mol	6.16128 kcal/mol	262 276@LB@ \| \|@LB@5'-AAG...CAGAA CACCC...UGG-3'@LB@ AGCCAAAUCCGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGGUUUAGGCUA@LB@3'-AUU...AUAAG AUGCA...AUG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -21.1603 kcal/mol@LB@Unfolding Energy - mRNA 4.16811 kcal/mol@LB@Unfolding Energy - sRNA 6.16128 kcal/mol@LB@@LB@Position - mRNA 263 -- 275@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 52 -- 58@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor		_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
19	8.831e-05	0.01635	b3389	aroB	-10.54	0.031183	4 -- 17	42 -- 56	3-dehydroquinate synthase		_____________3_______________18\n_____________\|_______________\|\n________5'-ACA___CC__________UCUGG...CGG-3'\n______________CCG___GCGUGAAGU\n______________\|\|\|___:\|\|\|\|\|\|\|\|\n______________GGC___UGCACUUCA\n3'-AUU...GUUUA___UAA_________UUUUC...AUG-5'\n_____________\|_______________\|\n_____________57______________41\n	11 -- 17	42 -- 48	-15.9415 kcal/mol	2.13198 kcal/mol	3.27911 kcal/mol	3 18@LB@ \| \|@LB@ 5'-ACA CC UCUGG...CGG-3'@LB@ CCG GCGUGAAGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|@LB@ GGC UGCACUUCA@LB@3'-AUU...GUUUA UAA UUUUC...AUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.9415 kcal/mol@LB@Unfolding Energy - mRNA 2.13198 kcal/mol@LB@Unfolding Energy - sRNA 3.27911 kcal/mol@LB@@LB@Position - mRNA 4 -- 17@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 42 -- 48@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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