Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
89	0.002455	0.09689	b0466	ybaM	-10.99	0.063193	248 -- 263	68 -- 82	DUF2496 family protein	_____________247______________264\n_____________\|________________\|\n5'-GCA...GAUUU__________C__G__GAAAA...CGC-3'\n______________GAUUGUGCUG_UG_AG\n______________:\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________UUAACACGAU_AC_UC\n3'-UUU...CUUAG_____________G__AUUAA...ACG-5'\n_____________\|________________\|\n_____________83_______________67\n	251 -- 257	73 -- 79	-16.1643 kcal/mol	2.45269 kcal/mol	2.72435 kcal/mol	247 264@LB@ \| \|@LB@5'-GCA...GAUUU C G GAAAA...CGC-3'@LB@ GAUUGUGCUG UG AG@LB@ :\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ UUAACACGAU AC UC@LB@3'-UUU...CUUAG G AUUAA...ACG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.1643 kcal/mol@LB@Unfolding Energy - mRNA 2.45269 kcal/mol@LB@Unfolding Energy - sRNA 2.72435 kcal/mol@LB@@LB@Position - mRNA 248 -- 263@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 73 -- 79@LB@
94	0.002802	0.105	b2905	gcvT	-11.27	0.053451	219 -- 244	68 -- 93	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________218_________________________245\n_____________\|___________________________\|\n5'-CUG...CUCCU_____________CACAC___U_____CGCUC...AAA-3'\n______________UUGUACGAA_CAA_____GCU_UGCGG\n______________\|:\|\|\|\|\|\|\|_\|\|\|_____\|\|\|_\|\|\|:\|\n______________AGCAUGCUU_GUU_____CGA_ACGUC\n3'-UUU...GCCGC_________A___AACA____U_____AUUAA...ACG-5'\n_____________\|___________________________\|\n_____________94__________________________67\n	221 -- 227	85 -- 91	-21.376 kcal/mol	5.42013 kcal/mol	4.68758 kcal/mol	218 245@LB@ \| \|@LB@5'-CUG...CUCCU CACAC U CGCUC...AAA-3'@LB@ UUGUACGAA CAA GCU UGCGG@LB@ \|:\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|:\|@LB@ AGCAUGCUU GUU CGA ACGUC@LB@3'-UUU...GCCGC A AACA U AUUAA...ACG-5'@LB@ \| \|@LB@ 94 67@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -21.376 kcal/mol@LB@Unfolding Energy - mRNA 5.42013 kcal/mol@LB@Unfolding Energy - sRNA 4.68758 kcal/mol@LB@@LB@Position - mRNA 219 -- 244@LB@Position - sRNA 68 -- 93@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 85 -- 91@LB@
145	0.00562	0.1365	b2532	trmJ	-9.44	0.148020	215 -- 233	68 -- 84	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent	_____________214_________________234\n_____________\|___________________\|\n5'-CGU...AAUAU__G__________G__G__ACGUC...UGU-3'\n______________UC_AAUUGUGCUG_UG_AG\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________AG_UUAACACGAU_AC_UC\n3'-UUU...UGCUU________________G__AUUAA...ACG-5'\n_____________\|___________________\|\n_____________85__________________67\n	221 -- 227	73 -- 79	-16.7979 kcal/mol	3.71432 kcal/mol	3.64047 kcal/mol	214 234@LB@ \| \|@LB@5'-CGU...AAUAU G G G ACGUC...UGU-3'@LB@ UC AAUUGUGCUG UG AG@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ AG UUAACACGAU AC UC@LB@3'-UUU...UGCUU G AUUAA...ACG-5'@LB@ \| \|@LB@ 85 67@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -16.7979 kcal/mol@LB@Unfolding Energy - mRNA 3.71432 kcal/mol@LB@Unfolding Energy - sRNA 3.64047 kcal/mol@LB@@LB@Position - mRNA 215 -- 233@LB@Position - sRNA 68 -- 84@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 73 -- 79@LB@
148	0.005829	0.1368	b2962	yggX	-8.12	0.280656	21 -- 35	68 -- 81	oxidative damage protective factor for iron-sulfur proteins	_____________20______________36\n_____________\|_______________\|\n5'-UCA...UAGAU______C________CUUCC...AGA-3'\n______________AUUGUG_CUAUGUGG\n______________\|\|\|\|\|\|_\|\|\|\|\|::\|\n______________UAACAC_GAUACGUC\n3'-UUU...UUAGU_______________AUUAA...ACG-5'\n_____________\|_______________\|\n_____________82______________67\n	28 -- 34	69 -- 75	-14.4611 kcal/mol	4.51468 kcal/mol	1.82249 kcal/mol	20 36@LB@ \| \|@LB@5'-UCA...UAGAU C CUUCC...AGA-3'@LB@ AUUGUG CUAUGUGG@LB@ \|\|\|\|\|\| \|\|\|\|\|::\|@LB@ UAACAC GAUACGUC@LB@3'-UUU...UUAGU AUUAA...ACG-5'@LB@ \| \|@LB@ 82 67@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -14.4611 kcal/mol@LB@Unfolding Energy - mRNA 4.51468 kcal/mol@LB@Unfolding Energy - sRNA 1.82249 kcal/mol@LB@@LB@Position - mRNA 21 -- 35@LB@Position - sRNA 68 -- 81@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 69 -- 75@LB@
170	0.006792	0.1407	b1884	cheR	-8.41	0.246459	6 -- 26	68 -- 89	chemotaxis regulator protein-glutamate methyltransferase	_____________5_______________________27\n_____________\|_______________________\|\n______5'-GCCAG______________A__CA____AACGC...UGA-3'\n______________AUGGAUCAG__GUG_CU__GCAG\n______________\|:\|:\|\|\|\|:__\|\|\|_\|\|__\|\|\|\|\n______________UGCUUAGUU__CAC_GA__CGUC\n3'-UUU...CAGCA_________AA______UA____AUUAA...ACG-5'\n_____________\|_______________________\|\n_____________90______________________67\n	8 -- 14	81 -- 87	-16.9281 kcal/mol	4.01768 kcal/mol	4.506 kcal/mol	5 27@LB@ \| \|@LB@ 5'-GCCAG A CA AACGC...UGA-3'@LB@ AUGGAUCAG GUG CU GCAG@LB@ \|:\|:\|\|\|\|: \|\|\| \|\| \|\|\|\|@LB@ UGCUUAGUU CAC GA CGUC@LB@3'-UUU...CAGCA AA UA AUUAA...ACG-5'@LB@ \| \|@LB@ 90 67@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -16.9281 kcal/mol@LB@Unfolding Energy - mRNA 4.01768 kcal/mol@LB@Unfolding Energy - sRNA 4.506 kcal/mol@LB@@LB@Position - mRNA 6 -- 26@LB@Position - sRNA 68 -- 89@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 81 -- 87@LB@
191	0.008524	0.1548	b3203	hpf	-8.75	0.209451	199 -- 206	68 -- 75	ribosome hibernation promoting factor HPF; stabilizes 100S dimers	_____________198______207\n_____________\|________\|\n5'-GAU...AGACA________CUCAA...GAA-3'\n______________CUAUGCAG\n______________\|\|\|\|\|\|\|\|\n______________GAUACGUC\n3'-UUU...AACAC________AUUAA...ACG-5'\n_____________\|________\|\n_____________76_______67\n	200 -- 206	68 -- 74	-11.4515 kcal/mol	0.966058 kcal/mol	1.73443 kcal/mol	198 207@LB@ \| \|@LB@5'-GAU...AGACA CUCAA...GAA-3'@LB@ CUAUGCAG@LB@ \|\|\|\|\|\|\|\|@LB@ GAUACGUC@LB@3'-UUU...AACAC AUUAA...ACG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.4515 kcal/mol@LB@Unfolding Energy - mRNA 0.966058 kcal/mol@LB@Unfolding Energy - sRNA 1.73443 kcal/mol@LB@@LB@Position - mRNA 199 -- 206@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 68 -- 74@LB@
200	0.008935	0.1548	b1427	rimL	-11.51	0.046463	223 -- 252	68 -- 89	ribosomal-protein-L7/L12-serine acetyltransferase	_____________222____________________________253\n_____________\|______________________________\|\n5'-GAU...AGUAA________C___AAUUACA_____U_____AAAAU...CCU-3'\n______________GCGAAUCA_UUG_______UGCUG_UGCAG\n______________:\|\|\|\|\|\|\|_\|\|\|_______\|\|\|\|:_\|\|\|\|\|\n______________UGCUUAGU_AAC_______ACGAU_ACGUC\n3'-UUU...CAGCA________U_____________________AUUAA...ACG-5'\n_____________\|______________________________\|\n_____________90_____________________________67\n	224 -- 230	82 -- 88	-23.0393 kcal/mol	7.0303 kcal/mol	4.506 kcal/mol	222 253@LB@ \| \|@LB@5'-GAU...AGUAA C AAUUACA U AAAAU...CCU-3'@LB@ GCGAAUCA UUG UGCUG UGCAG@LB@ :\|\|\|\|\|\|\| \|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UGCUUAGU AAC ACGAU ACGUC@LB@3'-UUU...CAGCA U AUUAA...ACG-5'@LB@ \| \|@LB@ 90 67@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -23.0393 kcal/mol@LB@Unfolding Energy - mRNA 7.0303 kcal/mol@LB@Unfolding Energy - sRNA 4.506 kcal/mol@LB@@LB@Position - mRNA 223 -- 252@LB@Position - sRNA 68 -- 89@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 82 -- 88@LB@
46	0.0004731	0.03623	b2279	nuoK	-14.07	0.008802	136 -- 157	69 -- 92	NADH:ubiquinone oxidoreductase membrane subunit K	_____________135______________________158\n_____________\|________________________\|\n5'-GGU...AAGAG_________G__________A___AUCGU...UUG-3'\n______________CGUGCGGGU_AA__GUGCUG_GCA\n______________\|\|\|:\|\|::\|_\|\|__\|\|\|\|\|:_\|\|\|\n______________GCAUGCUUA_UU__CACGAU_CGU\n3'-UUU...CCGCA_________G__AA______A___CAUUA...ACG-5'\n_____________\|________________________\|\n_____________93_______________________68\n	138 -- 144	84 -- 90	-25.4547 kcal/mol	6.72556 kcal/mol	4.66371 kcal/mol	135 158@LB@ \| \|@LB@5'-GGU...AAGAG G A AUCGU...UUG-3'@LB@ CGUGCGGGU AA GUGCUG GCA@LB@ \|\|\|:\|\|::\| \|\| \|\|\|\|\|: \|\|\|@LB@ GCAUGCUUA UU CACGAU CGU@LB@3'-UUU...CCGCA G AA A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -25.4547 kcal/mol@LB@Unfolding Energy - mRNA 6.72556 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 136 -- 157@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 84 -- 90@LB@
61	0.001027	0.05816	b0443	fadM	-9.40	0.151451	193 -- 205	69 -- 81	long-chain acyl-CoA thioesterase III	_____________192___________206\n_____________\|_____________\|\n5'-GUU...AGGUU____C________AACAC...AUG-3'\n______________AUUG_GCUAUGCA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UAAC_CGAUACGU\n3'-UUU...UUAGU____A________CAUUA...ACG-5'\n_____________\|_____________\|\n_____________82____________68\n	199 -- 205	69 -- 75	-15.9471 kcal/mol	4.72824 kcal/mol	1.82028 kcal/mol	192 206@LB@ \| \|@LB@5'-GUU...AGGUU C AACAC...AUG-3'@LB@ AUUG GCUAUGCA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAAC CGAUACGU@LB@3'-UUU...UUAGU A CAUUA...ACG-5'@LB@ \| \|@LB@ 82 68@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -15.9471 kcal/mol@LB@Unfolding Energy - mRNA 4.72824 kcal/mol@LB@Unfolding Energy - sRNA 1.82028 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 69 -- 81@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
117	0.00395	0.1189	b3447	ggt	-7.92	0.307079	7 -- 34	69 -- 94	gamma-glutamyltranspeptidase	_____________6____________________________35\n_____________\|____________________________\|\n_____5'-GUUAGG_____UCA____AUUAA__G________AAGCC...CGU-3'\n______________GUUGU___GAGU_____UG_GCUGUGCA\n______________\|\|:\|\|___\|\|:\|_____\|\|_\|\|\|:\|\|\|\|\n______________CAGCA___CUUA_____AC_CGAUACGU\n3'-UUU...AGCCG_____UG_____GUUA___A________CAUUA...ACG-5'\n_____________\|____________________________\|\n_____________95___________________________68\n	28 -- 34	69 -- 75	-19.4914 kcal/mol	6.89072 kcal/mol	4.68367 kcal/mol	6 35@LB@ \| \|@LB@ 5'-GUUAGG UCA AUUAA G AAGCC...CGU-3'@LB@ GUUGU GAGU UG GCUGUGCA@LB@ \|\|:\|\| \|\|:\| \|\| \|\|\|:\|\|\|\|@LB@ CAGCA CUUA AC CGAUACGU@LB@3'-UUU...AGCCG UG GUUA A CAUUA...ACG-5'@LB@ \| \|@LB@ 95 68@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -19.4914 kcal/mol@LB@Unfolding Energy - mRNA 6.89072 kcal/mol@LB@Unfolding Energy - sRNA 4.68367 kcal/mol@LB@@LB@Position - mRNA 7 -- 34@LB@Position - sRNA 69 -- 94@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 69 -- 75@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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