Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
139	0.01488	0.3575	b2167	fruA	-12.05	0.108648	223 -- 242	167 -- 187	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________222___________________243\n_____________\|_____________________\|\n5'-CGC...UAUUG_________________G___CGCGC...AAA-3'\n______________ACGCUAAU_CUCGGUCA_GCA\n______________\|\|:\|:\|\|\|_\|\|\|:\|\|\|\|_:\|\|\n______________UGUGGUUA_GAGUCAGU_UGU\n3'-UUU...UAAAA________U________G___ACUAC...UAG-5'\n_____________\|_____________________\|\n_____________188___________________166\n	232 -- 238	171 -- 177	-25.758 kcal/mol	6.7352 kcal/mol	5.05492 kcal/mol	222 243@LB@ \| \|@LB@5'-CGC...UAUUG G CGCGC...AAA-3'@LB@ ACGCUAAU CUCGGUCA GCA@LB@ \|\|:\|:\|\|\| \|\|\|:\|\|\|\| :\|\|@LB@ UGUGGUUA GAGUCAGU UGU@LB@3'-UUU...UAAAA U G ACUAC...UAG-5'@LB@ \| \|@LB@ 188 166@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -25.758 kcal/mol@LB@Unfolding Energy - mRNA 6.7352 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 223 -- 242@LB@Position - sRNA 167 -- 187@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 171 -- 177@LB@
12	0.0007005	0.1842	b1101	ptsG	-16.86	0.011310	173 -- 192	168 -- 187	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________172__________________193\n_____________\|____________________\|\n5'-CAU...AAAAA_____C________GA____UCUCA...GUU-3'\n______________GCACC_AUACUCAG__GCAC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|__:\|\|\|\n______________UGUGG_UAUGAGUC__UGUG\n3'-UUU...UAAAA_____U________AG____UACUA...UAG-5'\n_____________\|____________________\|\n_____________188__________________167\n	180 -- 186	174 -- 180	-27.3381 kcal/mol	3.90127 kcal/mol	4.88067 kcal/mol	172 193@LB@ \| \|@LB@5'-CAU...AAAAA C GA UCUCA...GUU-3'@LB@ GCACC AUACUCAG GCAC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGUGG UAUGAGUC UGUG@LB@3'-UUU...UAAAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -16.86 kcal/mol@LB@Hybridization Energy -27.3381 kcal/mol@LB@Unfolding Energy - mRNA 3.90127 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 174 -- 180@LB@
117	0.01283	0.3575	b3096	mzrA	-10.41	0.230387	15 -- 55	168 -- 208	modulator of EnvZ/OmpR regulon	_____________14________________________________________________________56\n_____________\|_________________________________________________________\|\n_____5'-UCAACU____G____________________________GAUCCUGA___CU__G________GCUCG...AGC-3'\n______________GGAU_AGCGG______UCUGCU_GUGGGU_AUU________CAA__CU_GGUUACAU\n______________::\|:_\|\|\|:\|______\|\|\|\|\|\|_\|:\|\|\|\|_\|\|\|________\|\|\|__\|\|_:\|\|:\|\|\|:\n______________UUUG_UCGUC______AGACGA_CGCCCA_UAA________GUU__GA_UCAGUGUG\n______3'-UUUUU____G_____CAUAUU______C______C___AAUGUG_____AU__G________UACUA...UAG-5'\n_____________\|_________________________________________________________\|\n_____________209_______________________________________________________167\n	49 -- 55	168 -- 174	-40.4023 kcal/mol	11.8856 kcal/mol	18.3074 kcal/mol	14 56@LB@ \| \|@LB@ 5'-UCAACU G GAUCCUGA CU G GCUCG...AGC-3'@LB@ GGAU AGCGG UCUGCU GUGGGU AUU CAA CU GGUUACAU@LB@ ::\|: \|\|\|:\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\| \|\|\| \|\| :\|\|:\|\|\|:@LB@ UUUG UCGUC AGACGA CGCCCA UAA GUU GA UCAGUGUG@LB@ 3'-UUUUU G CAUAUU C C AAUGUG AU G UACUA...UAG-5'@LB@ \| \|@LB@ 209 167@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -40.4023 kcal/mol@LB@Unfolding Energy - mRNA 11.8856 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 15 -- 55@LB@Position - sRNA 168 -- 208@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 168 -- 174@LB@
126	0.01383	0.3575	b1843	yobB	-8.48	0.503741	101 -- 118	168 -- 185	C-N hydrolase family protein	_____________100____________119\n_____________\|______________\|\n5'-CCU...AACUU____AG________UUUCU...CCA-3'\n______________AUAC__AGUUACAC\n______________\|\|\|\|__\|\|\|:\|\|\|\|\n______________UAUG__UCAGUGUG\n3'-UUU...GUGGU____AG________UACUA...UAG-5'\n_____________\|______________\|\n_____________186____________167\n	112 -- 118	168 -- 174	-13.9608 kcal/mol	3.09724 kcal/mol	0.286881 kcal/mol	100 119@LB@ \| \|@LB@5'-CCU...AACUU AG UUUCU...CCA-3'@LB@ AUAC AGUUACAC@LB@ \|\|\|\| \|\|\|:\|\|\|\|@LB@ UAUG UCAGUGUG@LB@3'-UUU...GUGGU AG UACUA...UAG-5'@LB@ \| \|@LB@ 186 167@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -13.9608 kcal/mol@LB@Unfolding Energy - mRNA 3.09724 kcal/mol@LB@Unfolding Energy - sRNA 0.286881 kcal/mol@LB@@LB@Position - mRNA 101 -- 118@LB@Position - sRNA 168 -- 185@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 168 -- 174@LB@
134	0.01437	0.3575	b1798	leuE	-11.20	0.161096	19 -- 44	168 -- 191	leucine efflux protein	_____________18_________________________45\n_____________\|__________________________\|\n5'-UGC...AGAAU________________UGCCGA____UACCC...AAA-3'\n______________UUUUACGCCAGUAUUU______GCAC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:\|:______:\|\|\|\n______________AAAAUGUGGUUAUGAG______UGUG\n3'-UUU...CCACU________________UCAG______UACUA...UAG-5'\n_____________\|__________________________\|\n_____________192________________________167\n	26 -- 32	178 -- 184	-22.4094 kcal/mol	4.02149 kcal/mol	4.92826 kcal/mol	18 45@LB@ \| \|@LB@5'-UGC...AGAAU UGCCGA UACCC...AAA-3'@LB@ UUUUACGCCAGUAUUU GCAC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|:\|: :\|\|\|@LB@ AAAAUGUGGUUAUGAG UGUG@LB@3'-UUU...CCACU UCAG UACUA...UAG-5'@LB@ \| \|@LB@ 192 167@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -22.4094 kcal/mol@LB@Unfolding Energy - mRNA 4.02149 kcal/mol@LB@Unfolding Energy - sRNA 4.92826 kcal/mol@LB@@LB@Position - mRNA 19 -- 44@LB@Position - sRNA 168 -- 191@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 178 -- 184@LB@
159	0.01779	0.3749	b2504	yfgG	-11.18	0.162405	230 -- 250	168 -- 187	uncharacterized protein	_____________229___________________251\n_____________\|_____________________\|\n5'-CCU...AAACG________UUAA_________GACCC...UUA-3'\n______________ACACCGAU____CAGUCGCAU\n______________\|\|\|\|\|:\|\|____\|\|\|\|\|:\|\|:\n______________UGUGGUUA____GUCAGUGUG\n3'-UUU...UAAAA________UGA__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	244 -- 250	168 -- 174	-22.7597 kcal/mol	5.28018 kcal/mol	4.88067 kcal/mol	229 251@LB@ \| \|@LB@5'-CCU...AAACG UUAA GACCC...UUA-3'@LB@ ACACCGAU CAGUCGCAU@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|:\|\|:@LB@ UGUGGUUA GUCAGUGUG@LB@3'-UUU...UAAAA UGA UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -11.18 kcal/mol@LB@Hybridization Energy -22.7597 kcal/mol@LB@Unfolding Energy - mRNA 5.28018 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 230 -- 250@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 168 -- 174@LB@
170	0.01941	0.3812	b3911	cpxA	-13.13	0.065341	265 -- 299	168 -- 204	sensory histidine kinase in two-component regulatory system with CpxR	_____________264______300\n_____________\|________\|\n5'-UAU...GUUUC________GAUAG...GCC-3'\n______________UGCUUCAU\n______________\|\|\|\|\|\|\|\|\n______________ACGAAGUA\n3'-UUU...GGGGA________G-5'\n_____________\|________\|\n_____________205______167\n	196 -- 202	2 -- 8	-10.3801 kcal/mol	3.0426 kcal/mol	0.709873 kcal/mol	264 300@LB@ \| \|@LB@5'-UAU...GUUUC GAUAG...GCC-3'@LB@ UGCUUCAU@LB@ \|\|\|\|\|\|\|\|@LB@ ACGAAGUA@LB@3'-UUU...GGGGA G-5'@LB@ \| \|@LB@ 205 167@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -10.3801 kcal/mol@LB@Unfolding Energy - mRNA 3.0426 kcal/mol@LB@Unfolding Energy - sRNA 0.709873 kcal/mol@LB@@LB@Position - mRNA 265 -- 299@LB@Position - sRNA 168 -- 204@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 2 -- 8@LB@
177	0.02028	0.3833	b1732	katE	-12.45	0.090323	227 -- 246	168 -- 187	catalase HPII heme d-containing	_____________226___________________247\n_____________\|_____________________\|\n5'-UGG...AACCC_______C__________C__UACAC...ACG-3'\n______________ACAUCAG_AC_CAGUCAC_AC\n______________\|\|\|:\|\|:_\|\|_\|\|\|\|\|\|\|_\|\|\n______________UGUGGUU_UG_GUCAGUG_UG\n3'-UUU...UAAAA_______A__A__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	237 -- 243	170 -- 176	-19.9766 kcal/mol	1.23864 kcal/mol	4.88067 kcal/mol	226 247@LB@ \| \|@LB@5'-UGG...AACCC C C UACAC...ACG-3'@LB@ ACAUCAG AC CAGUCAC AC@LB@ \|\|\|:\|\|: \|\| \|\|\|\|\|\|\| \|\|@LB@ UGUGGUU UG GUCAGUG UG@LB@3'-UUU...UAAAA A A UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.9766 kcal/mol@LB@Unfolding Energy - mRNA 1.23864 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 227 -- 246@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 170 -- 176@LB@
10	0.0006004	0.1842	b3656	yicI	-12.42	0.091283	58 -- 101	169 -- 207	putative alpha-glucosidase	_____________57_________102\n_____________\|__________\|\n5'-ACA...GAUAA__________G-3'\n______________UGAAAUGGUG\n______________\|:\|\|\|\|:\|\|\|\n______________AUUUUAUCAC\n3'-UUU...GCGCC__________GACUA...UAG-5'\n_____________\|__________\|\n_____________208________168\n	293 -- 299	40 -- 46	-9.13222 kcal/mol	0.486237 kcal/mol	4.51378 kcal/mol	57 102@LB@ \| \|@LB@5'-ACA...GAUAA G-3'@LB@ UGAAAUGGUG@LB@ \|:\|\|\|\|:\|\|\|@LB@ AUUUUAUCAC@LB@3'-UUU...GCGCC GACUA...UAG-5'@LB@ \| \|@LB@ 208 168@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -9.13222 kcal/mol@LB@Unfolding Energy - mRNA 0.486237 kcal/mol@LB@Unfolding Energy - sRNA 4.51378 kcal/mol@LB@@LB@Position - mRNA 58 -- 101@LB@Position - sRNA 169 -- 207@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 40 -- 46@LB@
18	0.001156	0.216	b3474	yhhT	-13.05	0.067927	149 -- 189	169 -- 204	UPF0118 family putative transporter	_____________148__________________________________________________________________190\n_____________\|____________________________________________________________________\|\n5'-GAC...GACGU____________UAAG____AGAAUAU________U_ACUCCCGC_____U______AAAA_______AGGAA...UCA-3'\n______________GAAAAUCAGCAG____AAUC_______UGCUGGCG_G________UACAC_UAAUAC____AGUCACA\n______________:\|\|\|\|:\|\|\|\|\|\|____\|\|\|\|_______\|\|\|\|\|\|\|\|_\|________\|\|\|\|\|_:\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUUUGGUCGUC____UUAG_______ACGACCGC_C________AUGUG_GUUAUG____UCAGUGU\n________3'-UUU____________CAUA_____________________CACUAAA_____________AG_________GUACU...UAG-5'\n_____________\|____________________________________________________________________\|\n_____________205__________________________________________________________________168\n	183 -- 189	169 -- 175	-48.4478 kcal/mol	16.2259 kcal/mol	18.3074 kcal/mol	148 190@LB@ \| \|@LB@5'-GAC...GACGU UAAG AGAAUAU U ACUCCCGC U AAAA AGGAA...UCA-3'@LB@ GAAAAUCAGCAG AAUC UGCUGGCG G UACAC UAAUAC AGUCACA@LB@ :\|\|\|\|:\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \| \|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUUUGGUCGUC UUAG ACGACCGC C AUGUG GUUAUG UCAGUGU@LB@ 3'-UUU CAUA CACUAAA AG GUACU...UAG-5'@LB@ \| \|@LB@ 205 168@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -48.4478 kcal/mol@LB@Unfolding Energy - mRNA 16.2259 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 149 -- 189@LB@Position - sRNA 169 -- 204@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 169 -- 175@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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