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
31	0.0001757	0.01997	b4222	ytfP	-8.86	0.198985	202 -- 224	67 -- 90	GGCT-like protein	_____________201_______________________225\n_____________\|_________________________\|\n5'-ACC...AGCAA_______AU_________CG_____UUACG...ACC-3'\n______________UGCGAAU___UUGU_CUA__GCAGU\n______________\|:\|\|\|\|\|___\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________AUGCUUA___AACA_GAU__CGUCA\n3'-UUU...GCAGC_______GUU____C___A______UUAAG...ACG-5'\n_____________\|_________________________\|\n_____________91________________________66\n	202 -- 208	84 -- 90	-18.173 kcal/mol	4.78992 kcal/mol	4.5307 kcal/mol	201 225@LB@ \| \|@LB@5'-ACC...AGCAA AU CG UUACG...ACC-3'@LB@ UGCGAAU UUGU CUA GCAGU@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ AUGCUUA AACA GAU CGUCA@LB@3'-UUU...GCAGC GUU C A UUAAG...ACG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -18.173 kcal/mol@LB@Unfolding Energy - mRNA 4.78992 kcal/mol@LB@Unfolding Energy - sRNA 4.5307 kcal/mol@LB@@LB@Position - mRNA 202 -- 224@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 84 -- 90@LB@
22	6.552e-05	0.01049	b3829	metE	-13.68	0.011485	203 -- 246	1 -- 47	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase	_____________202_____________________________________________247\n_____________\|_______________________________________________\|\n5'-GAG...AAAAU________U__AUC____A_______G__UCCCUC_____G______GUCGC...GUG-3'\n______________GACAAUAU_GA_____AC_CCC_UCG_UU______GCGUU_GCCUGC\n______________\|\|\|\|\|\|\|\|_\|\|_____\|\|_\|\|\|_\|\|\|_\|\|______\|\|:\|\|_:\|\|\|\|\|\n______________CUGUUAUA_CU_____UG_GGG_AGC_AA______CGUAA_UGGACG\n3'-UUU...UCAUU________C__CGCGU__C___U___G__CUGCAA_____G______-5'\n_____________\|______________________________________________\|\n_____________48_____________________________________________1\n	204 -- 210	40 -- 46	-38.0501 kcal/mol	7.59426 kcal/mol	16.7767 kcal/mol	202 247@LB@ \| \|@LB@5'-GAG...AAAAU U AUC A G UCCCUC G GUCGC...GUG-3'@LB@ GACAAUAU GA AC CCC UCG UU GCGUU GCCUGC@LB@ \|\|\|\|\|\|\|\| \|\| \|\| \|\|\| \|\|\| \|\| \|\|:\|\| :\|\|\|\|\|@LB@ CUGUUAUA CU UG GGG AGC AA CGUAA UGGACG@LB@3'-UUU...UCAUU C CGCGU C U G CUGCAA G -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -38.0501 kcal/mol@LB@Unfolding Energy - mRNA 7.59426 kcal/mol@LB@Unfolding Energy - sRNA 16.7767 kcal/mol@LB@@LB@Position - mRNA 203 -- 246@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 40 -- 46@LB@
155	0.006038	0.137	b4374	yjjG	-10.88	0.067155	203 -- 266	1 -- 54	dUMP phosphatase	_____________202_____________________________________________________________________267\n_____________\|_______________________________________________________________________\|\n5'-CUG...AUAAU__________________UUUUCUUU______G__GAAA____GUUUACCUU____U___________G__CUGCA...CCU-3'\n______________GAAGUGGGAC____UGGA________GAUGCC_AU____CGCU_________UGAC____CAUUCACC_GC\n______________\|\|\|\|\|::\|\|\|____\|\|\|\|________:\|:\|\|\|_\|\|____\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|_\|\|\n______________CUUCAUUCUG____ACCU________UUGCGG_UA____GCGA_________ACUG____GUAAGUGG_CG\n3'-UUU...UUUUC__________UUAU____CGCG__________G_______________________CAAC________A__-5'\n_____________\|______________________________________________________________________\|\n_____________55_____________________________________________________________________1\n	257 -- 263	4 -- 10	-41.6423 kcal/mol	13.9643 kcal/mol	16.8 kcal/mol	202 267@LB@ \| \|@LB@5'-CUG...AUAAU UUUUCUUU G GAAA GUUUACCUU U G CUGCA...CCU-3'@LB@ GAAGUGGGAC UGGA GAUGCC AU CGCU UGAC CAUUCACC GC@LB@ \|\|\|\|\|::\|\|\| \|\|\|\| :\|:\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|@LB@ CUUCAUUCUG ACCU UUGCGG UA GCGA ACUG GUAAGUGG CG@LB@3'-UUU...UUUUC UUAU CGCG G CAAC A -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -41.6423 kcal/mol@LB@Unfolding Energy - mRNA 13.9643 kcal/mol@LB@Unfolding Energy - sRNA 16.8 kcal/mol@LB@@LB@Position - mRNA 203 -- 266@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 4 -- 10@LB@
95	0.002866	0.1063	b1338	abgA	-10.09	0.104797	206 -- 225	73 -- 94	p-aminobenzoyl-glutamate hydrolase A subunit	_____________205____________________226\n_____________\|______________________\|\n5'-GAU...AUGGA___UU_________________AUUCG...UCC-3'\n______________GUC___UGAAUCAAUU_UGUUA\n______________\|\|\|___:\|\|\|\|\|\|\|\|\|_\|\|:\|\|\n______________CAG___GCUUAGUUAA_ACGAU\n3'-UUU...AGCCG___CAU__________C_____ACGUC...ACG-5'\n_____________\|______________________\|\n_____________95_____________________72\n	214 -- 220	79 -- 85	-14.4971 kcal/mol	2.01447 kcal/mol	2.39569 kcal/mol	205 226@LB@ \| \|@LB@5'-GAU...AUGGA UU AUUCG...UCC-3'@LB@ GUC UGAAUCAAUU UGUUA@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| \|\|:\|\|@LB@ CAG GCUUAGUUAA ACGAU@LB@3'-UUU...AGCCG CAU C ACGUC...ACG-5'@LB@ \| \|@LB@ 95 72@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -14.4971 kcal/mol@LB@Unfolding Energy - mRNA 2.01447 kcal/mol@LB@Unfolding Energy - sRNA 2.39569 kcal/mol@LB@@LB@Position - mRNA 206 -- 225@LB@Position - sRNA 73 -- 94@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 79 -- 85@LB@
32	0.0001844	0.0203	b0006	yaaA	-10.88	0.067423	215 -- 223	1 -- 9	peroxide resistance protein lowers intracellular iron	_____________214_______224\n_____________\|_________\|\n5'-UUC...CUUAU_________GAAAA...AGU-3'\n______________UUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\n______________AAGUGGACG\n3'-UUU...AACGU_________-5'\n_____________\|________\|\n_____________10_______1\n	217 -- 223	1 -- 7	-15.2887 kcal/mol	2.04449 kcal/mol	2.37317 kcal/mol	214 224@LB@ \| \|@LB@5'-UUC...CUUAU GAAAA...AGU-3'@LB@ UUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ AAGUGGACG@LB@3'-UUU...AACGU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -15.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.04449 kcal/mol@LB@Unfolding Energy - sRNA 2.37317 kcal/mol@LB@@LB@Position - mRNA 215 -- 223@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@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@
115	0.003699	0.1133	b3343	tusB	-8.43	0.243717	216 -- 222	20 -- 26	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________215_____223\n_____________\|_______\|\n5'-GCU...CAUUA_______CACCC...GCG-3'\n______________CAUCGCU\n______________\|\|\|\|\|\|\|\n______________GUAGCGA\n3'-UUU...UGCGG_______ACUGC...ACG-5'\n_____________\|_______\|\n_____________27______19\n	216 -- 222	20 -- 26	-9.55221 kcal/mol	1.0434 kcal/mol	0.0768517 kcal/mol	215 223@LB@ \| \|@LB@5'-GCU...CAUUA CACCC...GCG-3'@LB@ CAUCGCU@LB@ \|\|\|\|\|\|\|@LB@ GUAGCGA@LB@3'-UUU...UGCGG ACUGC...ACG-5'@LB@ \| \|@LB@ 27 19@LB@@LB@@LB@Energy -8.43 kcal/mol@LB@Hybridization Energy -9.55221 kcal/mol@LB@Unfolding Energy - mRNA 1.0434 kcal/mol@LB@Unfolding Energy - sRNA 0.0768517 kcal/mol@LB@@LB@Position - mRNA 216 -- 222@LB@Position - sRNA 20 -- 26@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 20 -- 26@LB@
76	0.001842	0.08273	b1717	rpmI	-9.61	0.135308	218 -- 256	48 -- 92	50S ribosomal subunit protein L35	_____________217___________________________________________257\n_____________\|_____________________________________________\|\n5'-GCG...AAGAC_____________GC_____A___C____________ACC_____AGGUG...UGA-3'\n______________CGUACG___CGGU__UGCUA_GCG____UUCAAAAAA___GGUAA\n______________\|\|\|\|\|\|___\|::\|__\|\|\|\|\|_\|\|:____\|\|\|\|\|\|\|\|\|___:\|\|\|\|\n______________GCAUGC___GUUA__ACGAU_CGU____AAGUUUUUU___UCAUU\n3'-UUU...CCGCA______UUA____AC_____A___CAUU_________CCU_____CUGUU...ACG-5'\n_____________\|_____________________________________________\|\n_____________93____________________________________________47\n	242 -- 248	56 -- 62	-26.2826 kcal/mol	11.8203 kcal/mol	4.85131 kcal/mol	217 257@LB@ \| \|@LB@5'-GCG...AAGAC GC A C ACC AGGUG...UGA-3'@LB@ CGUACG CGGU UGCUA GCG UUCAAAAAA GGUAA@LB@ \|\|\|\|\|\| \|::\| \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ GCAUGC GUUA ACGAU CGU AAGUUUUUU UCAUU@LB@3'-UUU...CCGCA UUA AC A CAUU CCU CUGUU...ACG-5'@LB@ \| \|@LB@ 93 47@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -26.2826 kcal/mol@LB@Unfolding Energy - mRNA 11.8203 kcal/mol@LB@Unfolding Energy - sRNA 4.85131 kcal/mol@LB@@LB@Position - mRNA 218 -- 256@LB@Position - sRNA 48 -- 92@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 56 -- 62@LB@
59	0.0009764	0.05816	b0593	entC	-14.06	0.008887	219 -- 262	19 -- 57	isochorismate synthase 1	_____________218____________________________________________263\n_____________\|______________________________________________\|\n5'-GGC...UGGCU_________CAGC____C______CAACACUU______A_______UUUCU...CAG-3'\n______________GAGGAAGUA____AGAC___AUGG________GCGCCC_AUCGCUU\n______________:\|\|\|\|\|\|\|\|____\|\|\|\|___\|\|\|\|________:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUCCUUCAU____UCUG___UACC________UGCGGG_UAGCGAA\n3'-UUU...GUUUU_________________UUA____UCGCGU________________CUGCA...ACG-5'\n_____________\|______________________________________________\|\n_____________58_____________________________________________18\n	256 -- 262	19 -- 25	-38.3486 kcal/mol	10.4998 kcal/mol	13.7965 kcal/mol	218 263@LB@ \| \|@LB@5'-GGC...UGGCU CAGC C CAACACUU A UUUCU...CAG-3'@LB@ GAGGAAGUA AGAC AUGG GCGCCC AUCGCUU@LB@ :\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCCUUCAU UCUG UACC UGCGGG UAGCGAA@LB@3'-UUU...GUUUU UUA UCGCGU CUGCA...ACG-5'@LB@ \| \|@LB@ 58 18@LB@@LB@@LB@Energy -14.06 kcal/mol@LB@Hybridization Energy -38.3486 kcal/mol@LB@Unfolding Energy - mRNA 10.4998 kcal/mol@LB@Unfolding Energy - sRNA 13.7965 kcal/mol@LB@@LB@Position - mRNA 219 -- 262@LB@Position - sRNA 19 -- 57@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 19 -- 25@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@

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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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