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
85	0.009065	0.3575	b3155	yhbQ	-10.34	0.236900	54 -- 88	123 -- 160	GIY-YIG nuclease superfamily protein	_____________53______________________89\n_____________\|_______________________\|\n5'-UUU...GAUCC_____G__GACAAUAA_______ACCGG...GCG-3'\n______________GUACC_CC________GCUUUAU\n______________\|:\|\|\|_\|\|________\|\|\|\|:\|\|\n______________CGUGG_GG________CGAAGUA\n3'-UUU...UACCC_____G__AA_____________G-5'\n_____________\|_______________________\|\n_____________161_____________________122\n	245 -- 251	2 -- 8	-16.2438 kcal/mol	1.2562 kcal/mol	7.2187 kcal/mol	53 89@LB@ \| \|@LB@5'-UUU...GAUCC G GACAAUAA ACCGG...GCG-3'@LB@ GUACC CC GCUUUAU@LB@ \|:\|\|\| \|\| \|\|\|\|:\|\|@LB@ CGUGG GG CGAAGUA@LB@3'-UUU...UACCC G AA G-5'@LB@ \| \|@LB@ 161 122@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -16.2438 kcal/mol@LB@Unfolding Energy - mRNA 1.2562 kcal/mol@LB@Unfolding Energy - sRNA 7.2187 kcal/mol@LB@@LB@Position - mRNA 54 -- 88@LB@Position - sRNA 123 -- 160@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 2 -- 8@LB@
64	0.006252	0.3261	b3195	mlaF	-10.58	0.212925	52 -- 62	81 -- 91	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________51____________________________________63\n_____________\|_____________________________________\|\n5'-UUU...UUCAA___UAA___GA______________AAAA__A_____AGACG...GAG-3'\n______________GGU___AUU__GCGCC_AUGCUUAG____UC_ACGCA\n______________\|\|\|___\|\|\|__:\|:\|\|_\|\|:\|\|:\|\|____\|\|_\|\|:\|\|\n______________CCA___UAA__UGUGG_UAUGAGUC____AG_UGUGU\n3'-UUU...ACCGC___C_____AA_____U____________________ACUAC...UAG-5'\n_____________\|_____________________________________\|\n_____________92____________________________________80\n	166 -- 172	174 -- 180	-23.2269 kcal/mol	9.4943 kcal/mol	5.22711 kcal/mol	51 63@LB@ \| \|@LB@5'-UUU...UUCAA UAA GA AAAA A AGACG...GAG-3'@LB@ GGU AUU GCGCC AUGCUUAG UC ACGCA@LB@ \|\|\| \|\|\| :\|:\|\| \|\|:\|\|:\|\| \|\| \|\|:\|\|@LB@ CCA UAA UGUGG UAUGAGUC AG UGUGU@LB@3'-UUU...ACCGC C AA U ACUAC...UAG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -23.2269 kcal/mol@LB@Unfolding Energy - mRNA 9.4943 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 52 -- 62@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 174 -- 180@LB@
173	0.0197	0.3812	b3210	arcB	-10.66	0.206219	214 -- 224	197 -- 207	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________213_________________225\n_____________\|___________________\|\n5'-UGC...UAACG_____G_____________AUUAU...UUC-3'\n______________UAACU_UCAGAAUUG_GGU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|\n______________GUUGA_AGUCUUAAC_CCA\n3'-UUU...GUUCA_____A_________G___GUAGG...UAG-5'\n_____________\|___________________\|\n_____________208_________________196\n	156 -- 162	138 -- 144	-19.5528 kcal/mol	4.59493 kcal/mol	5.63708 kcal/mol	213 225@LB@ \| \|@LB@5'-UGC...UAACG G AUUAU...UUC-3'@LB@ UAACU UCAGAAUUG GGU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|@LB@ GUUGA AGUCUUAAC CCA@LB@3'-UUU...GUUCA A G GUAGG...UAG-5'@LB@ \| \|@LB@ 208 196@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.5528 kcal/mol@LB@Unfolding Energy - mRNA 4.59493 kcal/mol@LB@Unfolding Energy - sRNA 5.63708 kcal/mol@LB@@LB@Position - mRNA 214 -- 224@LB@Position - sRNA 197 -- 207@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 138 -- 144@LB@
43	0.003721	0.2912	b3232	zapE	-10.85	0.189153	236 -- 256	70 -- 90	divisome ATPase	_____________235___________257\n_____________\|_____________\|\n5'-AGG...AACGG____UU_______AACCG...AAA-3'\n______________CCUU__UUUCGUC\n______________\|\|\|\|__:\|\|\|:\|\|\n______________GGAA__GAAGUAG\n3'-UUU...GUGGG____C________-5'\n_____________\|____________\|\n_____________91___________70\n	146 -- 152	1 -- 7	-9.27362 kcal/mol	0.691484 kcal/mol	1.04836 kcal/mol	235 257@LB@ \| \|@LB@5'-AGG...AACGG UU AACCG...AAA-3'@LB@ CCUU UUUCGUC@LB@ \|\|\|\| :\|\|\|:\|\|@LB@ GGAA GAAGUAG@LB@3'-UUU...GUGGG C -5'@LB@ \| \|@LB@ 91 70@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -9.27362 kcal/mol@LB@Unfolding Energy - mRNA 0.691484 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 236 -- 256@LB@Position - sRNA 70 -- 90@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
149	0.01599	0.3612	b3236	mdh	-10.77	0.195799	223 -- 232	196 -- 205	malate dehydrogenase NAD(P)-binding	_____________222_____233\n_____________\|_______\|\n5'-GUU...AUGAA_______GUCCU...AUG-3'\n______________AGUCGCA\n______________\|\|\|\|:\|\|\n______________UCAGUGU\n3'-UUU...AUGAG_______GUACU...UAG-5'\n_____________\|_______\|\n_____________206_____195\n	206 -- 212	169 -- 175	-8.87418 kcal/mol	1.40028 kcal/mol	0.26566 kcal/mol	222 233@LB@ \| \|@LB@5'-GUU...AUGAA GUCCU...AUG-3'@LB@ AGUCGCA@LB@ \|\|\|\|:\|\|@LB@ UCAGUGU@LB@3'-UUU...AUGAG GUACU...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -8.87418 kcal/mol@LB@Unfolding Energy - mRNA 1.40028 kcal/mol@LB@Unfolding Energy - sRNA 0.26566 kcal/mol@LB@@LB@Position - mRNA 223 -- 232@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 169 -- 175@LB@
72	0.007293	0.3408	b3240	aaeB	-15.57	0.020683	172 -- 248	45 -- 133	p-hydroxybenzoic acid efflux system component	_____________171________________249\n_____________\|__________________\|\n5'-ACU...ACAUA__________________CUGGC...UGG-3'\n______________UUCGCU_UUGCGGUAAAA\n______________\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\|\|\n______________AAGCGA_AGCGCCAUUUU\n3'-UUU...UGUUG______C___________AUCAC...UAG-5'\n_____________\|__________________\|\n_____________134________________44\n	240 -- 246	47 -- 53	-22.573 kcal/mol	5.7072 kcal/mol	6.14031 kcal/mol	171 249@LB@ \| \|@LB@5'-ACU...ACAUA CUGGC...UGG-3'@LB@ UUCGCU UUGCGGUAAAA@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|\|\|\|@LB@ AAGCGA AGCGCCAUUUU@LB@3'-UUU...UGUUG C AUCAC...UAG-5'@LB@ \| \|@LB@ 134 44@LB@@LB@@LB@Energy -15.57 kcal/mol@LB@Hybridization Energy -22.573 kcal/mol@LB@Unfolding Energy - mRNA 5.7072 kcal/mol@LB@Unfolding Energy - sRNA 6.14031 kcal/mol@LB@@LB@Position - mRNA 172 -- 248@LB@Position - sRNA 45 -- 133@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 47 -- 53@LB@
6	0.0003621	0.1842	b3242	aaeX	-9.38	0.356280	9 -- 19	125 -- 135	DUF1656 family putative inner membrane efflux pump associated protein	_____________8_________20\n_____________\|_________\|\n5'-GCG...CAUAA_________UAAUA...GGG-3'\n______________CAGUUACGC\n______________\|\|\|\|:\|\|:\|\n______________GUCAGUGUG\n3'-UUU...UAUGA_________UACUA...UAG-5'\n_____________\|_________\|\n_____________136_______124\n	75 -- 81	168 -- 174	-12.5845 kcal/mol	1.53643 kcal/mol	0.276974 kcal/mol	8 20@LB@ \| \|@LB@5'-GCG...CAUAA UAAUA...GGG-3'@LB@ CAGUUACGC@LB@ \|\|\|\|:\|\|:\|@LB@ GUCAGUGUG@LB@3'-UUU...UAUGA UACUA...UAG-5'@LB@ \| \|@LB@ 136 124@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -12.5845 kcal/mol@LB@Unfolding Energy - mRNA 1.53643 kcal/mol@LB@Unfolding Energy - sRNA 0.276974 kcal/mol@LB@@LB@Position - mRNA 9 -- 19@LB@Position - sRNA 125 -- 135@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 168 -- 174@LB@
165	0.01884	0.3812	b3291	mscL	-11.12	0.167422	252 -- 267	193 -- 208	mechanosensitive channel protein high conductance	_____________251_____268\n_____________\|_______\|\n5'-UGU...UGUCG_______AGGGA...UCU-3'\n______________GCUUCAU\n______________\|\|\|\|\|\|\|\n______________CGAAGUA\n3'-UUU...GGGAA_______G-5'\n_____________\|_______\|\n_____________209_____192\n	182 -- 188	2 -- 8	-9.41561 kcal/mol	2.23742 kcal/mol	0.70263 kcal/mol	251 268@LB@ \| \|@LB@5'-UGU...UGUCG AGGGA...UCU-3'@LB@ GCUUCAU@LB@ \|\|\|\|\|\|\|@LB@ CGAAGUA@LB@3'-UUU...GGGAA G-5'@LB@ \| \|@LB@ 209 192@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -9.41561 kcal/mol@LB@Unfolding Energy - mRNA 2.23742 kcal/mol@LB@Unfolding Energy - sRNA 0.70263 kcal/mol@LB@@LB@Position - mRNA 252 -- 267@LB@Position - sRNA 193 -- 208@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 2 -- 8@LB@
166	0.01886	0.3812	b3300	secY	-11.48	0.141920	168 -- 177	196 -- 205	preprotein translocase membrane subunit	_____________167_______________178\n_____________\|_________________\|\n5'-CCU...UCGAA____C_G__________CGAGG...UCC-3'\n______________GCUG_U_GCGGUAAAAU\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAC_A_CGCCAUUUUA\n3'-UUU...UGAAG______G__________UCACG...UAG-5'\n_____________\|_________________\|\n_____________206_______________195\n	177 -- 183	44 -- 50	-20.9884 kcal/mol	6.84834 kcal/mol	6.15722 kcal/mol	167 178@LB@ \| \|@LB@5'-CCU...UCGAA C G CGAGG...UCC-3'@LB@ GCUG U GCGGUAAAAU@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAC A CGCCAUUUUA@LB@3'-UUU...UGAAG G UCACG...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.9884 kcal/mol@LB@Unfolding Energy - mRNA 6.84834 kcal/mol@LB@Unfolding Energy - sRNA 6.15722 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 44 -- 50@LB@
83	0.008941	0.3575	b3343	tusB	-13.46	0.055944	1 -- 14	190 -- 203	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	______________1_____________15\n______________\|_____________\|\n___________5'-_______C______ACAUU...GCG-3'\n______________GCUGGCG_GUGAUU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________CGACCGC_CACUAA\n3'-UUU...UUAGA_______C______AAUGU...UAG-5'\n_____________\|______________\|\n_____________204____________189\n	1 -- 7	197 -- 203	-22.3351 kcal/mol	4.22102 kcal/mol	9.06745 kcal/mol	1 15@LB@ \| \|@LB@ 5'- C ACAUU...GCG-3'@LB@ GCUGGCG GUGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CGACCGC CACUAA@LB@3'-UUU...UUAGA C AAUGU...UAG-5'@LB@ \| \|@LB@ 204 189@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -22.3351 kcal/mol@LB@Unfolding Energy - mRNA 4.22102 kcal/mol@LB@Unfolding Energy - sRNA 9.06745 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 190 -- 203@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 197 -- 203@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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