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
136	0.01456	0.3575	b0369	hemB	-9.31	0.367566	203 -- 221	75 -- 90	5-aminolevulinate dehydratase (porphobilinogen synthase)	_____________202________________222\n_____________\|__________________\|\n5'-CCA...UAAAA_______ACCC_______GGUAU...UGC-3'\n______________CAUCCCU____UGCUUCA\n______________\|\|:\|\|\|:____\|\|\|\|\|\|\|\n______________GUGGGGG____ACGAAGU\n3'-UUU...ACCCC_______A__________AG-5'\n_____________\|__________________\|\n_____________91_________________74\n	153 -- 159	3 -- 9	-17.8942 kcal/mol	1.92924 kcal/mol	7.09151 kcal/mol	202 222@LB@ \| \|@LB@5'-CCA...UAAAA ACCC GGUAU...UGC-3'@LB@ CAUCCCU UGCUUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ GUGGGGG ACGAAGU@LB@3'-UUU...ACCCC A AG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -17.8942 kcal/mol@LB@Unfolding Energy - mRNA 1.92924 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 3 -- 9@LB@
167	0.01932	0.3812	b2912	fau	-13.57	0.053124	153 -- 189	109 -- 152	5-formyltetrahydrofolate cyclo-ligase family protein	_____________152__________190\n_____________\|____________\|\n5'-GAA...UGAGC____________GUCCG...UGG-3'\n______________AUGCUCGGUC_C\n______________\|\|:\|\|\|:\|\|\|_\|\n______________UAUGAGUCAG_G\n3'-UUU...GUGGU__________U_UGUAC...UAG-5'\n_____________\|____________\|\n_____________153__________108\n	31 -- 37	172 -- 178	-13.9133 kcal/mol	3.57919 kcal/mol	0.28482 kcal/mol	152 190@LB@ \| \|@LB@5'-GAA...UGAGC GUCCG...UGG-3'@LB@ AUGCUCGGUC C@LB@ \|\|:\|\|\|:\|\|\| \|@LB@ UAUGAGUCAG G@LB@3'-UUU...GUGGU U UGUAC...UAG-5'@LB@ \| \|@LB@ 153 108@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -13.9133 kcal/mol@LB@Unfolding Energy - mRNA 3.57919 kcal/mol@LB@Unfolding Energy - sRNA 0.28482 kcal/mol@LB@@LB@Position - mRNA 153 -- 189@LB@Position - sRNA 109 -- 152@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 172 -- 178@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@
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@
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@
30	0.002398	0.2633	b0494	tesA	-12.69	0.080698	14 -- 26	126 -- 138	acyl-CoA thioesterase 1 and protease I and lysophospholipase L1	_____________13____________27\n_____________\|_____________\|\n5'-UCC...AUGUA_____________CAGAC...UGG-3'\n______________GCGGUUGUCCCAC\n______________\|\|\|\|\|::\|\|\|\|\|\|\n______________CGCCAGUAGGGUG\n3'-UUU...CUUAA_____________ACGUA...UAG-5'\n_____________\|_____________\|\n_____________139___________125\n	20 -- 26	126 -- 132	-24.3083 kcal/mol	5.59054 kcal/mol	8.249 kcal/mol	13 27@LB@ \| \|@LB@5'-UCC...AUGUA CAGAC...UGG-3'@LB@ GCGGUUGUCCCAC@LB@ \|\|\|\|\|::\|\|\|\|\|\|@LB@ CGCCAGUAGGGUG@LB@3'-UUU...CUUAA ACGUA...UAG-5'@LB@ \| \|@LB@ 139 125@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.3083 kcal/mol@LB@Unfolding Energy - mRNA 5.59054 kcal/mol@LB@Unfolding Energy - sRNA 8.249 kcal/mol@LB@@LB@Position - mRNA 14 -- 26@LB@Position - sRNA 126 -- 138@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 126 -- 132@LB@
181	0.0209	0.3833	b2233	yfaL	-9.66	0.317681	275 -- 285	50 -- 60	adhesin	_____________274______________286\n_____________\|________________\|\n5'-UAU...UCUCU___AA__G________CGGUC...CAU-3'\n______________GCU__CG_UGUCGCGG\n______________:\|\|__\|\|_\|\|\|\|\|\|\|\|\n______________UGA__GC_ACAGCGCC\n3'-UUU...CGUGU___A___G________AUUUU...UAG-5'\n_____________\|________________\|\n_____________61_______________49\n	279 -- 285	50 -- 56	-20.2435 kcal/mol	4.65708 kcal/mol	6.1451 kcal/mol	274 286@LB@ \| \|@LB@5'-UAU...UCUCU AA G CGGUC...CAU-3'@LB@ GCU CG UGUCGCGG@LB@ :\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UGA GC ACAGCGCC@LB@3'-UUU...CGUGU A G AUUUU...UAG-5'@LB@ \| \|@LB@ 61 49@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -20.2435 kcal/mol@LB@Unfolding Energy - mRNA 4.65708 kcal/mol@LB@Unfolding Energy - sRNA 6.1451 kcal/mol@LB@@LB@Position - mRNA 275 -- 285@LB@Position - sRNA 50 -- 60@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 50 -- 56@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@
59	0.005693	0.3247	b1959	yedA	-9.74	0.306961	258 -- 278	1 -- 22	amino acid exporter for phenylalanine threonine	_____________257_______279\n_____________\|_________\|\n5'-UCA...UGAUA_________CAGGU...GCU-3'\n______________CUUGCUUCA\n______________\|\|\|\|\|\|\|\|\|\n______________GAACGAAGU\n3'-UUU...UGGGG_________AG-5'\n_____________\|_________\|\n_____________23________0\n	90 -- 96	3 -- 9	-13.1616 kcal/mol	3.16944 kcal/mol	1.03153 kcal/mol	257 279@LB@ \| \|@LB@5'-UCA...UGAUA CAGGU...GCU-3'@LB@ CUUGCUUCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GAACGAAGU@LB@3'-UUU...UGGGG AG-5'@LB@ \| \|@LB@ 23 0@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.1616 kcal/mol@LB@Unfolding Energy - mRNA 3.16944 kcal/mol@LB@Unfolding Energy - sRNA 1.03153 kcal/mol@LB@@LB@Position - mRNA 258 -- 278@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 3 -- 9@LB@
92	0.01029	0.3575	b3360	pabA	-10.28	0.244097	93 -- 100	16 -- 23	aminodeoxychorismate synthase subunit II	_____________92__________101\n_____________\|___________\|\n5'-GCG...ACCUC___________UUGUG...CGU-3'\n______________UACCAGUACUU\n______________:\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________24__________15\n	250 -- 256	176 -- 182	-13.2399 kcal/mol	3.06354 kcal/mol	3.38772 kcal/mol	92 101@LB@ \| \|@LB@5'-GCG...ACCUC UUGUG...CGU-3'@LB@ UACCAGUACUU@LB@ :\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 24 15@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -13.2399 kcal/mol@LB@Unfolding Energy - mRNA 3.06354 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 16 -- 23@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 176 -- 182@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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service.

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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