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
99	0.003254	0.1114	b2839	lysR	-9.43	0.148712	276 -- 282	1 -- 7	transcriptional activator of lysA; autorepressor		_____________275_____283\n_____________\|_______\|\n5'-GGC...CGGCA_______UACAC...CAA-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	276 -- 282	1 -- 7	-13.2779 kcal/mol	1.51062 kcal/mol	2.34039 kcal/mol	275 283@LB@ \| \|@LB@5'-GGC...CGGCA UACAC...CAA-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2779 kcal/mol@LB@Unfolding Energy - mRNA 1.51062 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
130	0.00465	0.126	b2916	argP	-9.43	0.148863	238 -- 266	47 -- 73	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor		_____________237___________________________267\n_____________\|_____________________________\|\n5'-GGC...ACUGG__________ACG____C_____UU____CGCGC...CAG-3'\n______________AUGCGGUGAU___UGAA_GAGGA__UGAG\n______________\|\|\|\|:\|\|:\|\|___::\|\|_:\|\|\|\|__\|:\|\|\n______________UACGUCAUUA___GUUU_UUCCU__AUUC\n3'-UUU...CACGA__________A______U_____UC____UGUUA...ACG-5'\n_____________\|_____________________________\|\n_____________74____________________________46\n	240 -- 246	65 -- 71	-19.9139 kcal/mol	5.97985 kcal/mol	4.50495 kcal/mol	237 267@LB@ \| \|@LB@5'-GGC...ACUGG ACG C UU CGCGC...CAG-3'@LB@ AUGCGGUGAU UGAA GAGGA UGAG@LB@ \|\|\|\|:\|\|:\|\| ::\|\| :\|\|\|\| \|:\|\|@LB@ UACGUCAUUA GUUU UUCCU AUUC@LB@3'-UUU...CACGA A U UC UGUUA...ACG-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -19.9139 kcal/mol@LB@Unfolding Energy - mRNA 5.97985 kcal/mol@LB@Unfolding Energy - sRNA 4.50495 kcal/mol@LB@@LB@Position - mRNA 238 -- 266@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 65 -- 71@LB@
186	0.008102	0.1535	b1768	pncA	-9.42	0.149628	191 -- 212	21 -- 39	nicotinamidase/pyrazinamidase		_____________190____________________213\n_____________\|______________________\|\n5'-UAA...AUUAA____A_U_________CC____GCCCU...CUA-3'\n______________GGAG_C_GUAAUGCCC__UCGC\n______________\|\|\|\|_\|_\|:\|\|:\|\|\|\|__\|\|\|\|\n______________CCUC_G_CGUUGCGGG__AGCG\n3'-UUU...UUAUA________________U_____AACUG...ACG-5'\n_____________\|______________________\|\n_____________40_____________________20\n	200 -- 206	26 -- 32	-26.7187 kcal/mol	5.14291 kcal/mol	12.1569 kcal/mol	190 213@LB@ \| \|@LB@5'-UAA...AUUAA A U CC GCCCU...CUA-3'@LB@ GGAG C GUAAUGCCC UCGC@LB@ \|\|\|\| \| \|:\|\|:\|\|\|\| \|\|\|\|@LB@ CCUC G CGUUGCGGG AGCG@LB@3'-UUU...UUAUA U AACUG...ACG-5'@LB@ \| \|@LB@ 40 20@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -26.7187 kcal/mol@LB@Unfolding Energy - mRNA 5.14291 kcal/mol@LB@Unfolding Energy - sRNA 12.1569 kcal/mol@LB@@LB@Position - mRNA 191 -- 212@LB@Position - sRNA 21 -- 39@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 26 -- 32@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@
39	0.0003198	0.02889	b3960	argH	-9.38	0.152930	179 -- 221	28 -- 64	argininosuccinate lyase		_____________178__________________________________________222\n_____________\|____________________________________________\|\n5'-GCA...UGAAU_______U_____AACAG___UAU____CUU_____________UUUAC...AUA-3'\n______________UUCAAAA_AAGGA_____AGU___GGCA___UGGGGCG_GGCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|_____\|\|\|___\|:\|\|___\|\|\|:\|\|\|_::\|\|:\n______________AAGUUUU_UUCCU_____UCA___CUGU___ACCUCGC_UUGCG\n3'-UUU...UCAUU_____________________UU_____UAU_______G_____GGUAG...ACG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	210 -- 216	34 -- 40	-30.4591 kcal/mol	8.02766 kcal/mol	13.054 kcal/mol	178 222@LB@ \| \|@LB@5'-GCA...UGAAU U AACAG UAU CUU UUUAC...AUA-3'@LB@ UUCAAAA AAGGA AGU GGCA UGGGGCG GGCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\| \|:\|\| \|\|\|:\|\|\| ::\|\|:@LB@ AAGUUUU UUCCU UCA CUGU ACCUCGC UUGCG@LB@3'-UUU...UCAUU UU UAU G GGUAG...ACG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -30.4591 kcal/mol@LB@Unfolding Energy - mRNA 8.02766 kcal/mol@LB@Unfolding Energy - sRNA 13.054 kcal/mol@LB@@LB@Position - mRNA 179 -- 221@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 34 -- 40@LB@
174	0.007207	0.145	b1034	ycdX	-9.36	0.154134	94 -- 120	35 -- 63	alkaline phosphatase		_____________93_____________________________121\n_____________\|______________________________\|\n5'-GGC...CCAGC__________________G___C__C____AAGUC...AAC-3'\n______________UCGAAAAAGGG___GAGA_GGU_UG_GGGC\n______________\|\|:\|\|\|\|\|\|\|:___:\|\|\|_::\|_\|\|_\|:\|\|\n______________AGUUUUUUCCU___UUCU_UUA_AC_CUCG\n3'-UUU...CAUUA___________UCA____G___U_______CGUUG...ACG-5'\n_____________\|______________________________\|\n_____________64_____________________________34\n	98 -- 104	53 -- 59	-21.9855 kcal/mol	6.52956 kcal/mol	6.08557 kcal/mol	93 121@LB@ \| \|@LB@5'-GGC...CCAGC G C C AAGUC...AAC-3'@LB@ UCGAAAAAGGG GAGA GGU UG GGGC@LB@ \|\|:\|\|\|\|\|\|\|: :\|\|\| ::\| \|\| \|:\|\|@LB@ AGUUUUUUCCU UUCU UUA AC CUCG@LB@3'-UUU...CAUUA UCA G U CGUUG...ACG-5'@LB@ \| \|@LB@ 64 34@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -21.9855 kcal/mol@LB@Unfolding Energy - mRNA 6.52956 kcal/mol@LB@Unfolding Energy - sRNA 6.08557 kcal/mol@LB@@LB@Position - mRNA 94 -- 120@LB@Position - sRNA 35 -- 63@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 53 -- 59@LB@
128	0.004569	0.1258	b3033	yqiB	-9.35	0.155553	90 -- 130	43 -- 87	DUF1249 protein YqiB		_____________89_____________________________________________131\n_____________\|______________________________________________\|\n5'-UGG...GCCGG_____________AUAC______GUA__________AAAUC_____CGCAG...GCG-3'\n______________GAA_CAG____GC____CAGUGG___GAAGAGGGGA_____GACAA\n______________\|\|\|_\|\|:____\|\|____\|\|\|\|::___:\|\|:\|:\|\|:\|_____\|\|\|\|\|\n______________CUU_GUU____CG____GUCAUU___UUUUUUCCUU_____CUGUU\n3'-UUU...GCAUG___A___AACA__AUAC______AAG__________CAUU______AUACC...ACG-5'\n_____________\|______________________________________________\|\n_____________88_____________________________________________42\n	114 -- 120	52 -- 58	-22.1335 kcal/mol	7.07839 kcal/mol	5.71172 kcal/mol	89 131@LB@ \| \|@LB@5'-UGG...GCCGG AUAC GUA AAAUC CGCAG...GCG-3'@LB@ GAA CAG GC CAGUGG GAAGAGGGGA GACAA@LB@ \|\|\| \|\|: \|\| \|\|\|\|:: :\|\|:\|:\|\|:\| \|\|\|\|\|@LB@ CUU GUU CG GUCAUU UUUUUUCCUU CUGUU@LB@3'-UUU...GCAUG A AACA AUAC AAG CAUU AUACC...ACG-5'@LB@ \| \|@LB@ 88 42@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -22.1335 kcal/mol@LB@Unfolding Energy - mRNA 7.07839 kcal/mol@LB@Unfolding Energy - sRNA 5.71172 kcal/mol@LB@@LB@Position - mRNA 90 -- 130@LB@Position - sRNA 43 -- 87@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@LB@
157	0.006139	0.1377	b2347	yfdC	-9.29	0.160067	171 -- 205	37 -- 76	putative inner membrane protein		_____________170________________________________________206\n_____________\|__________________________________________\|\n5'-GCA...CUUUA_____AC___C_______________________C_______CAACG...UCC-3'\n______________GCUAU__GUG_UAAUUCAAGA___GAAG__AGAC___AUGGA\n______________\|\|\|\|\|__\|::_\|\|\|\|\|\|\|\|:\|___\|\|\|\|__\|\|\|\|___\|\|\|\|\|\n______________CGAUA__CGU_AUUAAGUUUU___CUUC__UCUG___UACCU\n3'-UUU...UAACA__________C__________UUC____AU____UUA_____CGCGU...ACG-5'\n_____________\|__________________________________________\|\n_____________77_________________________________________36\n	185 -- 191	58 -- 64	-24.5838 kcal/mol	7.63937 kcal/mol	7.64142 kcal/mol	170 206@LB@ \| \|@LB@5'-GCA...CUUUA AC C C CAACG...UCC-3'@LB@ GCUAU GUG UAAUUCAAGA GAAG AGAC AUGGA@LB@ \|\|\|\|\| \|:: \|\|\|\|\|\|\|\|:\| \|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ CGAUA CGU AUUAAGUUUU CUUC UCUG UACCU@LB@3'-UUU...UAACA C UUC AU UUA CGCGU...ACG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -24.5838 kcal/mol@LB@Unfolding Energy - mRNA 7.63937 kcal/mol@LB@Unfolding Energy - sRNA 7.64142 kcal/mol@LB@@LB@Position - mRNA 171 -- 205@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 58 -- 64@LB@
98	0.003129	0.1114	b0357	frmR	-9.19	0.168108	184 -- 207	25 -- 48	regulator protein that represses frmRAB operon		_____________183______________________208\n_____________\|________________________\|\n5'-CUG...CAUGC________A__U___AA_______GUACU...CCG-3'\n______________AGAUGAUG_GG_GCG__AUGCCCA\n______________\|\|\|::\|\|:_\|\|_\|\|\|__\|:\|\|\|\|\|\n______________UCUGUUAU_CC_CGC__UGCGGGU\n3'-UUU...UUCAU________A__U___GU_______AGCGA...ACG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	201 -- 207	25 -- 31	-27.7971 kcal/mol	6.33291 kcal/mol	12.271 kcal/mol	183 208@LB@ \| \|@LB@5'-CUG...CAUGC A U AA GUACU...CCG-3'@LB@ AGAUGAUG GG GCG AUGCCCA@LB@ \|\|\|::\|\|: \|\| \|\|\| \|:\|\|\|\|\|@LB@ UCUGUUAU CC CGC UGCGGGU@LB@3'-UUU...UUCAU A U GU AGCGA...ACG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -27.7971 kcal/mol@LB@Unfolding Energy - mRNA 6.33291 kcal/mol@LB@Unfolding Energy - sRNA 12.271 kcal/mol@LB@@LB@Position - mRNA 184 -- 207@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 25 -- 31@LB@
156	0.006066	0.137	b0005	yaaX	-9.16	0.170742	96 -- 118	53 -- 73	DUF2502 family putative periplasmic protein	b2390	_____________95______________________119\n_____________\|_______________________\|\n5'-UCU...AAUAA_________C_______UU____UUGCG...AAU-3'\n______________AUGCGGUAA_UUAGAGA__AGGA\n______________\|\|\|\|:\|\|\|\|_\|:\|:\|:\|__\|\|\|\|\n______________UACGUCAUU_AGUUUUU__UCCU\n3'-UUU...CACGA_________A_____________UCAUU...ACG-5'\n_____________\|_______________________\|\n_____________74______________________52\n	98 -- 104	65 -- 71	-18.9701 kcal/mol	6.27714 kcal/mol	3.52907 kcal/mol	95 119@LB@ \| \|@LB@5'-UCU...AAUAA C UU UUGCG...AAU-3'@LB@ AUGCGGUAA UUAGAGA AGGA@LB@ \|\|\|\|:\|\|\|\| \|:\|:\|:\| \|\|\|\|@LB@ UACGUCAUU AGUUUUU UCCU@LB@3'-UUU...CACGA A UCAUU...ACG-5'@LB@ \| \|@LB@ 74 52@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -18.9701 kcal/mol@LB@Unfolding Energy - mRNA 6.27714 kcal/mol@LB@Unfolding Energy - sRNA 3.52907 kcal/mol@LB@@LB@Position - mRNA 96 -- 118@LB@Position - sRNA 53 -- 73@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 65 -- 71@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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