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
184	0.00812	0.1553	b4371	rsmC	-7.50	0.203534	191 -- 216	4 -- 25	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________190________________________217\n_____________\|__________________________\|\n5'-AUC...AUUGA________CC__G____CAUU_____CGGCA...UGC-3'\n______________GGAGCAUU__AU_UCUG____UACCC\n______________:\|\|:\|\|\|:__\|:_\|\|\|\|____\|\|\|\|\|\n______________UCUUGUAG__UG_AGAC____AUGGG\n3'-AUU...UUCUA________AA__G_____________AUG-5'\n_____________\|__________________________\|\n_____________26_________________________3\n	192 -- 198	18 -- 24	-20.5319 kcal/mol	5.03265 kcal/mol	8.0209 kcal/mol	190 217@LB@ \| \|@LB@5'-AUC...AUUGA CC G CAUU CGGCA...UGC-3'@LB@ GGAGCAUU AU UCUG UACCC@LB@ :\|\|:\|\|\|: \|: \|\|\|\| \|\|\|\|\|@LB@ UCUUGUAG UG AGAC AUGGG@LB@3'-AUU...UUCUA AA G AUG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -20.5319 kcal/mol@LB@Unfolding Energy - mRNA 5.03265 kcal/mol@LB@Unfolding Energy - sRNA 8.0209 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 18 -- 24@LB@
62	0.001059	0.05856	b3927	glpF	-11.40	0.016677	192 -- 203	48 -- 59	glycerol facilitator	_____________191__________204\n_____________\|____________\|\n5'-GAU...UUCAG____________AGUCA...AAG-3'\n______________GAUCCGAUUAUG\n______________:\|\|\|\|\|\|\|\|\|:\|\n______________UUAGGCUAAUGC\n3'-AUU...UCGGU____________ACUUC...AUG-5'\n_____________\|____________\|\n_____________60___________47\n	197 -- 203	48 -- 54	-15.6898 kcal/mol	2.7066 kcal/mol	1.55995 kcal/mol	191 204@LB@ \| \|@LB@5'-GAU...UUCAG AGUCA...AAG-3'@LB@ GAUCCGAUUAUG@LB@ :\|\|\|\|\|\|\|\|\|:\|@LB@ UUAGGCUAAUGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -15.6898 kcal/mol@LB@Unfolding Energy - mRNA 2.7066 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 192 -- 203@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@LB@
180	0.007734	0.1511	b3617	kbl	-7.53	0.200168	193 -- 210	43 -- 60	glycine C-acetyltransferase	_____________192________________211\n_____________\|__________________\|\n5'-UUU...CUGGA_____GCAA_________AAUUU...AAG-3'\n______________GAAUC____UGCGUGGAG\n______________:\|\|\|\|____\|:\|\|\|\|:\|\|\n______________UUUAG____AUGCACUUC\n3'-AUU...GUCGG_____GCUA_________AUUUU...AUG-5'\n_____________\|__________________\|\n_____________61_________________42\n	204 -- 210	43 -- 49	-15.3085 kcal/mol	4.51554 kcal/mol	3.27548 kcal/mol	192 211@LB@ \| \|@LB@5'-UUU...CUGGA GCAA AAUUU...AAG-3'@LB@ GAAUC UGCGUGGAG@LB@ :\|\|\|\| \|:\|\|\|\|:\|\|@LB@ UUUAG AUGCACUUC@LB@3'-AUU...GUCGG GCUA AUUUU...AUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -15.3085 kcal/mol@LB@Unfolding Energy - mRNA 4.51554 kcal/mol@LB@Unfolding Energy - sRNA 3.27548 kcal/mol@LB@@LB@Position - mRNA 193 -- 210@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 43 -- 49@LB@
192	0.008619	0.1558	b2561	yfhH	-12.96	0.004772	194 -- 222	4 -- 32	putative DNA-binding transcriptional regulator	_____________193____________________________223\n_____________\|______________________________\|\n5'-CCU...GCGAG________U_____G_______________GUCAG...GCC-3'\n______________GAAAGAUA_GAACG_CUUACUUC_GUAUCC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|:_\|\|\|\|\|:\|\|_\|\|\|:\|\|\n______________CUUUCUAU_CUUGU_GAAUGGAG_CAUGGG\n3'-AUU...CCAGA______________A________A______AUG-5'\n_____________\|______________________________\|\n_____________33_____________________________3\n	195 -- 201	25 -- 31	-31.2741 kcal/mol	9.51226 kcal/mol	8.82263 kcal/mol	193 223@LB@ \| \|@LB@5'-CCU...GCGAG U G GUCAG...GCC-3'@LB@ GAAAGAUA GAACG CUUACUUC GUAUCC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ CUUUCUAU CUUGU GAAUGGAG CAUGGG@LB@3'-AUU...CCAGA A A AUG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -31.2741 kcal/mol@LB@Unfolding Energy - mRNA 9.51226 kcal/mol@LB@Unfolding Energy - sRNA 8.82263 kcal/mol@LB@@LB@Position - mRNA 194 -- 222@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 25 -- 31@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter	_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@LB@
128	0.004347	0.1195	b3690	cbrA	-9.56	0.060736	197 -- 211	17 -- 31	colicin M resistance protein; FAD-binding protein putative oxidoreductase	_____________196_____________212\n_____________\|_______________\|\n5'-CAG...AGUGA_______________CGACG...AAA-3'\n______________AAAGAUGGAACAUUU\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\n______________UUUCUAUCUUGUAGA\n3'-AUU...CAGAC_______________AUGGA...AUG-5'\n_____________\|_______________\|\n_____________32______________16\n	204 -- 210	18 -- 24	-17.0326 kcal/mol	3.22818 kcal/mol	4.26586 kcal/mol	196 212@LB@ \| \|@LB@5'-CAG...AGUGA CGACG...AAA-3'@LB@ AAAGAUGGAACAUUU@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|@LB@ UUUCUAUCUUGUAGA@LB@3'-AUU...CAGAC AUGGA...AUG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -17.0326 kcal/mol@LB@Unfolding Energy - mRNA 3.22818 kcal/mol@LB@Unfolding Energy - sRNA 4.26586 kcal/mol@LB@@LB@Position - mRNA 197 -- 211@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
189	0.008373	0.1558	b1559	quuQ	-11.90	0.011421	197 -- 219	1 -- 24	Qin prophage; putative antitermination protein Q	_____________196______________________220\n_____________\|________________________\|\n5'-UCU...AGAAC______GA______GAA_______CAAAA...AUG-3'\n______________GAGCAU___ACCUU___GCCUUAC\n______________\|\|:\|\|\|___\|\|\|\|:___:\|\|:\|\|\|\n______________CUUGUA___UGGAG___UGGGAUG\n3'-AUU...UCUAU______GAA_____ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	213 -- 219	1 -- 7	-21.9861 kcal/mol	2.0909 kcal/mol	8.02158 kcal/mol	196 220@LB@ \| \|@LB@5'-UCU...AGAAC GA GAA CAAAA...AUG-3'@LB@ GAGCAU ACCUU GCCUUAC@LB@ \|\|:\|\|\| \|\|\|\|: :\|\|:\|\|\|@LB@ CUUGUA UGGAG UGGGAUG@LB@3'-AUU...UCUAU GAA ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -21.9861 kcal/mol@LB@Unfolding Energy - mRNA 2.0909 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 197 -- 219@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
176	0.007357	0.147	b2905	gcvT	-7.40	0.214118	198 -- 224	6 -- 30	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________197__________________________225\n_____________\|____________________________\|\n5'-CUG...AGGAC_______CAC____GACU__________GAACA...AAA-3'\n______________AAGAUGG___AACA_____CCUUUGUAC\n______________\|\|\|\|\|:\|___\|\|\|\|_____\|\|\|:\|\|\|\|\|\n______________UUCUAUC___UUGU_____GGAGACAUG\n3'-AUU...AGACU______________AGAAU_________GGAUG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	218 -- 224	6 -- 12	-21.3805 kcal/mol	5.97871 kcal/mol	8.02863 kcal/mol	197 225@LB@ \| \|@LB@5'-CUG...AGGAC CAC GACU GAACA...AAA-3'@LB@ AAGAUGG AACA CCUUUGUAC@LB@ \|\|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\|\|\|@LB@ UUCUAUC UUGU GGAGACAUG@LB@3'-AUU...AGACU AGAAU GGAUG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 5.97871 kcal/mol@LB@Unfolding Energy - sRNA 8.02863 kcal/mol@LB@@LB@Position - mRNA 198 -- 224@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 6 -- 12@LB@
156	0.006236	0.1406	b2922	yggE	-5.46	0.507768	199 -- 207	42 -- 50	oxidative stress defense protein	_____________198_______208\n_____________\|_________\|\n5'-GCA...GACUA_________UCAAA...CCG-3'\n______________ACGUGAAGU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCACUUCA\n3'-AUU...GCUAA_________UUUUC...AUG-5'\n_____________\|_________\|\n_____________51________41\n	201 -- 207	42 -- 48	-12.7727 kcal/mol	4.07491 kcal/mol	3.2504 kcal/mol	198 208@LB@ \| \|@LB@5'-GCA...GACUA UCAAA...CCG-3'@LB@ ACGUGAAGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCACUUCA@LB@3'-AUU...GCUAA UUUUC...AUG-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -5.46 kcal/mol@LB@Hybridization Energy -12.7727 kcal/mol@LB@Unfolding Energy - mRNA 4.07491 kcal/mol@LB@Unfolding Energy - sRNA 3.2504 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 42 -- 48@LB@
22	0.0001652	0.02641	b3566	xylF	-9.94	0.047349	202 -- 240	1 -- 33	D-xylose transporter subunit	_____________201_____________________________________241\n_____________\|_______________________________________\|\n5'-CGA...CACCA_____AUAA________C__CUCAC______C____C__UCCUG...AUG-3'\n______________UGAAA____AGAACAUU_UA_____CCUUUG_ACCU_AC\n______________\|\|\|\|\|____\|\|\|\|\|\|\|:_\|\|_____\|\|\|:\|\|_\|\|\|:_\|\|\n______________ACUUU____UCUUGUAG_AU_____GGAGAC_UGGG_UG\n3'-AUU...UCCAG_____CUA_________A_____________A____A__-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	212 -- 218	18 -- 24	-22.447 kcal/mol	3.48977 kcal/mol	9.04529 kcal/mol	201 241@LB@ \| \|@LB@5'-CGA...CACCA AUAA C CUCAC C C UCCUG...AUG-3'@LB@ UGAAA AGAACAUU UA CCUUUG ACCU AC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|: \|\| \|\|\|:\|\| \|\|\|: \|\|@LB@ ACUUU UCUUGUAG AU GGAGAC UGGG UG@LB@3'-AUU...UCCAG CUA A A A -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -22.447 kcal/mol@LB@Unfolding Energy - mRNA 3.48977 kcal/mol@LB@Unfolding Energy - sRNA 9.04529 kcal/mol@LB@@LB@Position - mRNA 202 -- 240@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 18 -- 24@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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