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	Additional homologs
41	0.003653	0.2912	b2842	kduD	-13.01	0.069205	14 -- 50	128 -- 174	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; KDG oxidoreductase; 20-ketosteroid reductase	b4266 b2774	_____________13_______________________________________________51\n_____________\|________________________________________________\|\n5'-CCG...AACGC______U____________________GAG____________G_____CCCGA...CGG-3'\n______________GUCAUA_UGUGAUGCA_______UAAC___CAG____GCGGU_AUCUC\n______________\|\|\|\|:\|_::\|\|\|\|\|\|\|_______:\|\|\|___\|\|\|____\|\|\|\|\|_\|\|\|:\|\n______________CAGUGU_GUACUACGU_______GUUG___GUC____CGCCA_UAGGG\n3'-UUU...UGAGU________________CCGUUCA____AAA___UUAA_____G_____UGACG...UAG-5'\n_____________\|________________________________________________\|\n_____________175______________________________________________127\n	23 -- 29	160 -- 166	-35.8105 kcal/mol	9.71011 kcal/mol	15.5834 kcal/mol	13 51@LB@ \| \|@LB@5'-CCG...AACGC U GAG G CCCGA...CGG-3'@LB@ GUCAUA UGUGAUGCA UAAC CAG GCGGU AUCUC@LB@ \|\|\|\|:\| ::\|\|\|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|@LB@ CAGUGU GUACUACGU GUUG GUC CGCCA UAGGG@LB@3'-UUU...UGAGU CCGUUCA AAA UUAA G UGACG...UAG-5'@LB@ \| \|@LB@ 175 127@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -35.8105 kcal/mol@LB@Unfolding Energy - mRNA 9.71011 kcal/mol@LB@Unfolding Energy - sRNA 15.5834 kcal/mol@LB@@LB@Position - mRNA 14 -- 50@LB@Position - sRNA 128 -- 174@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 160 -- 166@LB@
42	0.003683	0.2912	b2221	atoD	-14.87	0.028783	141 -- 155	6 -- 19	acetyl-CoA:acetoacetyl-CoA transferase alpha subunit		_____________140_____________156\n_____________\|_______________\|\n5'-UAU...AUUCU_____U_________AUUGC...CCC-3'\n______________GGCAC_CCCCUUGCU\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________CCGUG_GGGGAACGA\n3'-UUU...GUACC_______________AGUAG-5'\n_____________\|_______________\|\n_____________20______________5\n	149 -- 155	6 -- 12	-27.0081 kcal/mol	4.79018 kcal/mol	8.30673 kcal/mol	140 156@LB@ \| \|@LB@5'-UAU...AUUCU U AUUGC...CCC-3'@LB@ GGCAC CCCCUUGCU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCGUG GGGGAACGA@LB@3'-UUU...GUACC AGUAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0081 kcal/mol@LB@Unfolding Energy - mRNA 4.79018 kcal/mol@LB@Unfolding Energy - sRNA 8.30673 kcal/mol@LB@@LB@Position - mRNA 141 -- 155@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 6 -- 12@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@
44	0.003817	0.292	b0967	rlmI	-10.41	0.230051	81 -- 118	128 -- 161	23S rRNA m(5)C1962 methyltransferase SAM-dependent		_____________80_________________________________119\n_____________\|__________________________________\|\n5'-CGU...UGAAC____C___AAACC_______UUAU_CA_______GACAU...AAG-3'\n______________UCGC_CGU_____CAGGCAA____G__GACUUUC\n______________\|\|:\|_\|:\|_____\|\|\|\|\|\|\|____\|__:\|\|\|\|\|\|\n______________AGUG_GUA_____GUCCGUU____C__UUGAAAG\n3'-UUU...GAGUC____U___CUAC_____________AG_______UCUUA...UAG-5'\n_____________\|__________________________________\|\n_____________162________________________________127\n	95 -- 101	145 -- 151	-21.0542 kcal/mol	5.99356 kcal/mol	7.97203 kcal/mol	80 119@LB@ \| \|@LB@5'-CGU...UGAAC C AAACC UUAU CA GACAU...AAG-3'@LB@ UCGC CGU CAGGCAA G GACUUUC@LB@ \|\|:\| \|:\| \|\|\|\|\|\|\| \| :\|\|\|\|\|\|@LB@ AGUG GUA GUCCGUU C UUGAAAG@LB@3'-UUU...GAGUC U CUAC AG UCUUA...UAG-5'@LB@ \| \|@LB@ 162 127@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.99356 kcal/mol@LB@Unfolding Energy - sRNA 7.97203 kcal/mol@LB@@LB@Position - mRNA 81 -- 118@LB@Position - sRNA 128 -- 161@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 145 -- 151@LB@
45	0.003942	0.2948	b0686	ybfF	-11.97	0.113030	234 -- 245	63 -- 74	acyl-CoA esterase		_____________233__________246\n_____________\|____________\|\n5'-CUU...CACAA____________AAUUC...GCG-3'\n______________AACCAGCACAAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUGGUCGUGUUG\n3'-UUU...UUGCG____________AAGCG...UAG-5'\n_____________\|____________\|\n_____________75___________62\n	239 -- 245	63 -- 69	-18.9732 kcal/mol	1.15073 kcal/mol	9.24135 kcal/mol	233 246@LB@ \| \|@LB@5'-CUU...CACAA AAUUC...GCG-3'@LB@ AACCAGCACAAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUGGUCGUGUUG@LB@3'-UUU...UUGCG AAGCG...UAG-5'@LB@ \| \|@LB@ 75 62@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -18.9732 kcal/mol@LB@Unfolding Energy - mRNA 1.15073 kcal/mol@LB@Unfolding Energy - sRNA 9.24135 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 63 -- 74@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 63 -- 69@LB@
46	0.004081	0.2985	b2466	ypfG	-10.37	0.233995	256 -- 280	68 -- 95	DUF1176 family protein		_____________255_____281\n_____________\|_______\|\n5'-AAA...CAAAC_______UUAAU...UCA-3'\n______________GUCACAU\n______________\|\|\|\|\|\|:\n______________CAGUGUG\n3'-UUU...UGAGU_______UACUA...UAG-5'\n_____________\|_______\|\n_____________96______67\n	57 -- 63	168 -- 174	-9.42181 kcal/mol	2.13246 kcal/mol	0.260649 kcal/mol	255 281@LB@ \| \|@LB@5'-AAA...CAAAC UUAAU...UCA-3'@LB@ GUCACAU@LB@ \|\|\|\|\|\|:@LB@ CAGUGUG@LB@3'-UUU...UGAGU UACUA...UAG-5'@LB@ \| \|@LB@ 96 67@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -9.42181 kcal/mol@LB@Unfolding Energy - mRNA 2.13246 kcal/mol@LB@Unfolding Energy - sRNA 0.260649 kcal/mol@LB@@LB@Position - mRNA 256 -- 280@LB@Position - sRNA 68 -- 95@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 168 -- 174@LB@
47	0.004619	0.3205	b4142	groS	-15.85	0.018169	259 -- 271	196 -- 208	Cpn10 chaperonin GroES small subunit of GroESL		_____________258_______________________________272\n_____________\|_________________________________\|\n5'-UGA...AACUA_____________CAUCGUUCUG__________UGCAG...CUA-3'\n______________AAUCUGCUGGCGG__________ACCG__GCUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__________\|\|\|:__:\|\|\|\n______________UUAGACGACCGCC__________UGGU__UGAG\n3'-UUU...CCAUA_____________CACUAAAAUG____UA____UCAGU...UAG-5'\n_____________\|_________________________________\|\n_____________209_______________________________195\n	265 -- 271	196 -- 202	-33.1058 kcal/mol	10.148 kcal/mol	14.8106 kcal/mol	258 272@LB@ \| \|@LB@5'-UGA...AACUA CAUCGUUCUG UGCAG...CUA-3'@LB@ AAUCUGCUGGCGG ACCG GCUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|: :\|\|\|@LB@ UUAGACGACCGCC UGGU UGAG@LB@3'-UUU...CCAUA CACUAAAAUG UA UCAGU...UAG-5'@LB@ \| \|@LB@ 209 195@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -33.1058 kcal/mol@LB@Unfolding Energy - mRNA 10.148 kcal/mol@LB@Unfolding Energy - sRNA 14.8106 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 196 -- 208@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 196 -- 202@LB@
48	0.004626	0.3205	b3462	ftsX	-13.20	0.063258	14 -- 27	192 -- 205	putative ABC transporter permease		_____________13_____________28\n_____________\|______________\|\n5'-CAA...CGGUA__________AC__ACCGA...ACG-3'\n______________CUGCUGGCGG__GA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GACGACCGCC__CU\n3'-UUU...UAUUA__________CA__AAAAU...UAG-5'\n_____________\|______________\|\n_____________206____________191\n	17 -- 23	196 -- 202	-23.0043 kcal/mol	4.65554 kcal/mol	9.06563 kcal/mol	13 28@LB@ \| \|@LB@5'-CAA...CGGUA AC ACCGA...ACG-3'@LB@ CUGCUGGCGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GACGACCGCC CU@LB@3'-UUU...UAUUA CA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -23.0043 kcal/mol@LB@Unfolding Energy - mRNA 4.65554 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 196 -- 202@LB@
49	0.004667	0.3205	b1277	ribA	-9.86	0.291903	241 -- 249	16 -- 24	GTP cyclohydrolase II		_____________240________250\n_____________\|__________\|\n5'-CCA...AAUAC__________UUAUC...UCG-3'\n______________AGAACCAGCA\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUUGGUCGU\n_______3'-UUUU__________CCAUA...UAG-5'\n_____________\|__________\|\n_____________25_________15\n	178 -- 184	214 -- 220	-13.9783 kcal/mol	2.87719 kcal/mol	5.75438 kcal/mol	240 250@LB@ \| \|@LB@5'-CCA...AAUAC UUAUC...UCG-3'@LB@ AGAACCAGCA@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUUGGUCGU@LB@ 3'-UUUU CCAUA...UAG-5'@LB@ \| \|@LB@ 25 15@LB@@LB@@LB@Energy -9.86 kcal/mol@LB@Hybridization Energy -13.9783 kcal/mol@LB@Unfolding Energy - mRNA 2.87719 kcal/mol@LB@Unfolding Energy - sRNA 5.75438 kcal/mol@LB@@LB@Position - mRNA 241 -- 249@LB@Position - sRNA 16 -- 24@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 214 -- 220@LB@
50	0.004849	0.3217	b1079	flgH	-12.97	0.070541	130 -- 141	23 -- 34	flagellar protein of basal-body outer-membrane L ring		_____________129____________________142\n_____________\|______________________\|\n5'-ACU...CGAUC__A_____CA____________ACUCU...GGG-3'\n______________AG_UGCUG__AAAACUGACGCA\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________UC_ACGAC__UUUUGACUGCGU\n3'-UUU...UUUUA________UA____________ACCCC...UAG-5'\n_____________\|______________________\|\n_____________35_____________________22\n	135 -- 141	23 -- 29	-26.3449 kcal/mol	4.56982 kcal/mol	12.5314 kcal/mol	129 142@LB@ \| \|@LB@5'-ACU...CGAUC A CA ACUCU...GGG-3'@LB@ AG UGCUG AAAACUGACGCA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UC ACGAC UUUUGACUGCGU@LB@3'-UUU...UUUUA UA ACCCC...UAG-5'@LB@ \| \|@LB@ 35 22@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -26.3449 kcal/mol@LB@Unfolding Energy - mRNA 4.56982 kcal/mol@LB@Unfolding Energy - sRNA 12.5314 kcal/mol@LB@@LB@Position - mRNA 130 -- 141@LB@Position - sRNA 23 -- 34@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 23 -- 29@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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