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	Additional homologs
114	0.00366	0.1131	b0162	cdaR	-8.46	0.240590	33 -- 47	64 -- 77	carbohydrate diacid regulon transcriptional regulator; autoregulator		_____________32______________48\n_____________\|_______________\|\n5'-CAA...CUACC____A__________CUCCC...GGC-3'\n______________UGUU_AUGCAGUAAU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|\|\n______________ACGA_UACGUCAUUA\n3'-UUU...UUAAC_______________AGUUU...ACG-5'\n_____________\|_______________\|\n_____________78______________63\n	41 -- 47	64 -- 70	-14.8052 kcal/mol	3.39589 kcal/mol	2.94867 kcal/mol	32 48@LB@ \| \|@LB@5'-CAA...CUACC A CUCCC...GGC-3'@LB@ UGUU AUGCAGUAAU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|\|@LB@ ACGA UACGUCAUUA@LB@3'-UUU...UUAAC AGUUU...ACG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -14.8052 kcal/mol@LB@Unfolding Energy - mRNA 3.39589 kcal/mol@LB@Unfolding Energy - sRNA 2.94867 kcal/mol@LB@@LB@Position - mRNA 33 -- 47@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 64 -- 70@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@
73	0.001571	0.0758	b3746	ravA	-8.41	0.246327	240 -- 262	54 -- 75	hexameric AAA+ MoxR family ATPase putative molecular chaperone		_____________239_____________________263\n_____________\|_______________________\|\n5'-UGA...CCCGC___A_____UC___G________GCUUU...UAU-3'\n______________CUG_GCAGU__GUU_GAAAAGGG\n______________\|\|:_\|\|\|\|\|__:\|\|_:\|\|\|\|:\|\|\n______________GAU_CGUCA__UAA_UUUUUUCC\n3'-UUU...AACAC___A_____U____G________UUCAU...ACG-5'\n_____________\|_______________________\|\n_____________76______________________53\n	256 -- 262	54 -- 60	-19.2007 kcal/mol	7.09588 kcal/mol	3.69534 kcal/mol	239 263@LB@ \| \|@LB@5'-UGA...CCCGC A UC G GCUUU...UAU-3'@LB@ CUG GCAGU GUU GAAAAGGG@LB@ \|\|: \|\|\|\|\| :\|\| :\|\|\|\|:\|\|@LB@ GAU CGUCA UAA UUUUUUCC@LB@3'-UUU...AACAC A U G UUCAU...ACG-5'@LB@ \| \|@LB@ 76 53@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.2007 kcal/mol@LB@Unfolding Energy - mRNA 7.09588 kcal/mol@LB@Unfolding Energy - sRNA 3.69534 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 54 -- 75@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 54 -- 60@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@
179	0.007631	0.1495	b3229	sspA	-8.36	0.252415	276 -- 298	54 -- 83	stringent starvation protein A phage P1 late gene activator RNAP-associated acid-resistance protein inactive glutathione S-transferase homolog		_____________275_____________________________299\n_____________\|_______________________________\|\n5'-CCA...AGGUC__C____________________________UG-3'\n______________CG_AUUGUGCUG_GC_______UGAGAAAGG\n______________\|:_\|\|\|\|\|\|\|\|:_\|\|_______::\|:\|\|\|\|\|\n______________GU_UAACACGAU_CG_______GUUUUUUCC\n3'-UUU...GCUUA____________A__UCAUUAA_________UUCAU...ACG-5'\n_____________\|_______________________________\|\n_____________84______________________________53\n	292 -- 298	54 -- 60	-18.0489 kcal/mol	5.94535 kcal/mol	3.74667 kcal/mol	275 299@LB@ \| \|@LB@5'-CCA...AGGUC C UG-3'@LB@ CG AUUGUGCUG GC UGAGAAAGG@LB@ \|: \|\|\|\|\|\|\|\|: \|\| ::\|:\|\|\|\|\|@LB@ GU UAACACGAU CG GUUUUUUCC@LB@3'-UUU...GCUUA A UCAUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 84 53@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -18.0489 kcal/mol@LB@Unfolding Energy - mRNA 5.94535 kcal/mol@LB@Unfolding Energy - sRNA 3.74667 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 54 -- 60@LB@
84	0.001972	0.08273	b0968	yccX	-8.34	0.253881	183 -- 226	2 -- 49	weak acylphosphatase		_____________182_________________________________________________227\n_____________\|___________________________________________________\|\n5'-GGC...CAUUA_______GGA_____A________G_AA__C___________AA_______GGUUU...CCG-3'\n______________AGGAUAA____GAGC_GCAAUGUC_A__GU_______UGCAU__UUGCCUG\n______________\|:\|\|:\|\|____\|\|\|\|_\|\|\|\|:\|:\|_\|__\|:_______\|\|\|\|\|__\|::\|\|\|\|\n______________UUCUGUU____CUCG_CGUUGCGG_U__CG_______ACGUA__AGUGGAC\n3'-UUU...CUUCA_______AUAC_____________G_AG__AACUGCA______________G-5'\n_____________\|___________________________________________________\|\n_____________50__________________________________________________1\n	220 -- 226	2 -- 8	-35.2137 kcal/mol	10.0937 kcal/mol	16.7804 kcal/mol	182 227@LB@ \| \|@LB@5'-GGC...CAUUA GGA A G AA C AA GGUUU...CCG-3'@LB@ AGGAUAA GAGC GCAAUGUC A GU UGCAU UUGCCUG@LB@ \|:\|\|:\|\| \|\|\|\| \|\|\|\|:\|:\| \| \|: \|\|\|\|\| \|::\|\|\|\|@LB@ UUCUGUU CUCG CGUUGCGG U CG ACGUA AGUGGAC@LB@3'-UUU...CUUCA AUAC G AG AACUGCA G-5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -8.34 kcal/mol@LB@Hybridization Energy -35.2137 kcal/mol@LB@Unfolding Energy - mRNA 10.0937 kcal/mol@LB@Unfolding Energy - sRNA 16.7804 kcal/mol@LB@@LB@Position - mRNA 183 -- 226@LB@Position - sRNA 2 -- 49@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 2 -- 8@LB@
188	0.008258	0.1545	b3803	hemX	-8.31	0.258101	280 -- 297	46 -- 62	putative uroporphyrinogen III methyltransferase		_____________279________________298\n_____________\|__________________\|\n5'-AAA...CGCAA_______AAA________ACA-3'\n______________CAGAAAA___GAGUAAGA\n______________\|\|:\|\|\|\|___:\|\|\|\|\|\|\|\n______________GUUUUUU___UUCAUUCU\n3'-UUU...AUUAA_______CC_________GUUAU...ACG-5'\n_____________\|__________________\|\n_____________63_________________45\n	291 -- 297	46 -- 52	-11.8819 kcal/mol	0.215347 kcal/mol	3.36135 kcal/mol	279 298@LB@ \| \|@LB@5'-AAA...CGCAA AAA ACA-3'@LB@ CAGAAAA GAGUAAGA@LB@ \|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ GUUUUUU UUCAUUCU@LB@3'-UUU...AUUAA CC GUUAU...ACG-5'@LB@ \| \|@LB@ 63 45@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -11.8819 kcal/mol@LB@Unfolding Energy - mRNA 0.215347 kcal/mol@LB@Unfolding Energy - sRNA 3.36135 kcal/mol@LB@@LB@Position - mRNA 280 -- 297@LB@Position - sRNA 46 -- 62@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 46 -- 52@LB@
167	0.006646	0.1402	b0007	yaaJ	-8.17	0.274480	254 -- 261	1 -- 8	putative transporter		_____________253______262\n_____________\|________\|\n5'-CAA...AUGAU________UCUUC...GAU-3'\n______________UUACCUGC\n______________\|:\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	255 -- 261	1 -- 7	-12.8229 kcal/mol	2.29081 kcal/mol	2.36381 kcal/mol	253 262@LB@ \| \|@LB@5'-CAA...AUGAU UCUUC...GAU-3'@LB@ UUACCUGC@LB@ \|:\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -12.8229 kcal/mol@LB@Unfolding Energy - mRNA 2.29081 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 254 -- 261@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 1 -- 7@LB@
88	0.002437	0.09689	b0940	elfC	-8.14	0.278491	92 -- 131	23 -- 58	putative outer membrane fimbrial subunit export usher protein	b3144 b0532 b4317	_____________91_________________________________________132\n_____________\|__________________________________________\|\n5'-AUU...CUGCC________CCAAA_____GC___________AUCGAA_____AAUGA...CAC-3'\n______________AAAGGGGG______AAUA___AGCGUAACGU______CCAUC\n______________\|\|\|\|\|::\|______\|\|\|\|___\|\|\|\|:\|\|\|\|:______\|\|\|\|\|\n______________UUUCCUUC______UUAU___UCGCGUUGCG______GGUAG\n3'-UUU...AGUUU________AUUCUG____ACC_____________________CGAAC...ACG-5'\n_____________\|__________________________________________\|\n_____________59_________________________________________22\n	112 -- 118	30 -- 36	-29.3003 kcal/mol	7.72593 kcal/mol	13.4354 kcal/mol	91 132@LB@ \| \|@LB@5'-AUU...CUGCC CCAAA GC AUCGAA AAUGA...CAC-3'@LB@ AAAGGGGG AAUA AGCGUAACGU CCAUC@LB@ \|\|\|\|\|::\| \|\|\|\| \|\|\|\|:\|\|\|\|: \|\|\|\|\|@LB@ UUUCCUUC UUAU UCGCGUUGCG GGUAG@LB@3'-UUU...AGUUU AUUCUG ACC CGAAC...ACG-5'@LB@ \| \|@LB@ 59 22@LB@@LB@@LB@Energy -8.14 kcal/mol@LB@Hybridization Energy -29.3003 kcal/mol@LB@Unfolding Energy - mRNA 7.72593 kcal/mol@LB@Unfolding Energy - sRNA 13.4354 kcal/mol@LB@@LB@Position - mRNA 92 -- 131@LB@Position - sRNA 23 -- 58@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 30 -- 36@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@

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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