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
62	0.001027	0.05816	b0717	ybgP	-6.75	0.488398	48 -- 57	53 -- 62	putative periplasmic pilin chaperone	b3047	_____________47_________58\n_____________\|__________\|\n5'-GCG...GUUGG__________CAUGC...CCA-3'\n______________CGAGGAAGGA\n______________\|:\|::\|\|\|\|\|\n______________GUUUUUUCCU\n3'-UUU...AUUAA__________UCAUU...ACG-5'\n_____________\|__________\|\n_____________63_________52\n	51 -- 57	53 -- 59	-10.1576 kcal/mol	0.982686 kcal/mol	2.4254 kcal/mol	47 58@LB@ \| \|@LB@5'-GCG...GUUGG CAUGC...CCA-3'@LB@ CGAGGAAGGA@LB@ \|:\|::\|\|\|\|\|@LB@ GUUUUUUCCU@LB@3'-UUU...AUUAA UCAUU...ACG-5'@LB@ \| \|@LB@ 63 52@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -10.1576 kcal/mol@LB@Unfolding Energy - mRNA 0.982686 kcal/mol@LB@Unfolding Energy - sRNA 2.4254 kcal/mol@LB@@LB@Position - mRNA 48 -- 57@LB@Position - sRNA 53 -- 62@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 53 -- 59@LB@
70	0.001371	0.06901	b2989	yghU	-9.78	0.124117	251 -- 269	4 -- 23	putative S-transferase		_____________250__________________270\n_____________\|____________________\|\n5'-UUA...AAAUC_________GC_________AAUAU...CGC-3'\n______________CGC_UGGCG__GCGUUCGCC\n______________\|\|\|_\|\|:\|\|__\|\|:\|\|\|:\|\|\n______________GCG_ACUGC__CGUAAGUGG\n3'-UUU...GGGUA___A_____AA_________ACG-5'\n_____________\|____________________\|\n_____________24___________________3\n	263 -- 269	4 -- 10	-26.6155 kcal/mol	8.73321 kcal/mol	8.10973 kcal/mol	250 270@LB@ \| \|@LB@5'-UUA...AAAUC GC AAUAU...CGC-3'@LB@ CGC UGGCG GCGUUCGCC@LB@ \|\|\| \|\|:\|\| \|\|:\|\|\|:\|\|@LB@ GCG ACUGC CGUAAGUGG@LB@3'-UUU...GGGUA A AA ACG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.6155 kcal/mol@LB@Unfolding Energy - mRNA 8.73321 kcal/mol@LB@Unfolding Energy - sRNA 8.10973 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
109	0.003466	0.1114	b4485	ytfR	-10.51	0.083206	29 -- 56	35 -- 61	putative sugar ABC transporter ATPase		_____________28____________________________57\n_____________\|_____________________________\|\n5'-CCU...AAGAA___UU__A_________AA__________AUUGA...GCC-3'\n______________GAA__AG_GAAG_AAGA__AAUAUGGGGU\n______________:\|\|__\|\|_\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|:\|:\n______________UUU__UC_CUUC_UUCU__UUAUACCUCG\n3'-UUU...UUAAG___UU_______A____G___________CGUUG...ACG-5'\n_____________\|_____________________________\|\n_____________62____________________________34\n	50 -- 56	35 -- 41	-20.6661 kcal/mol	5.51365 kcal/mol	4.61294 kcal/mol	28 57@LB@ \| \|@LB@5'-CCU...AAGAA UU A AA AUUGA...GCC-3'@LB@ GAA AG GAAG AAGA AAUAUGGGGU@LB@ :\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ UUU UC CUUC UUCU UUAUACCUCG@LB@3'-UUU...UUAAG UU A G CGUUG...ACG-5'@LB@ \| \|@LB@ 62 34@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -20.6661 kcal/mol@LB@Unfolding Energy - mRNA 5.51365 kcal/mol@LB@Unfolding Energy - sRNA 4.61294 kcal/mol@LB@@LB@Position - mRNA 29 -- 56@LB@Position - sRNA 35 -- 61@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 35 -- 41@LB@
93	0.002751	0.1042	b3407	yhgF	-15.01	0.004479	248 -- 282	1 -- 31	putative transcriptional accessory protein		_____________247_________________________________283\n_____________\|___________________________________\|\n5'-CCC...CAGGC_______GAACA_G______C__C___________UUGAC...CCG-3'\n______________GCGCCCG_____G_UUGACG_UG_CGUUCGCCUGC\n______________:\|\|\|\|\|:_____\|_\|\|\|\|\|\|_\|\|_\|:\|\|\|:\|\|\|\|\|\n______________UGCGGGU_____C_AACUGC_AC_GUAAGUGGACG\n3'-UUU...CGCGU_______AG____G______A______________-5'\n_____________\|__________________________________\|\n_____________32_________________________________1\n	276 -- 282	1 -- 7	-43.3047 kcal/mol	13.2535 kcal/mol	15.0438 kcal/mol	247 283@LB@ \| \|@LB@5'-CCC...CAGGC GAACA G C C UUGAC...CCG-3'@LB@ GCGCCCG G UUGACG UG CGUUCGCCUGC@LB@ :\|\|\|\|\|: \| \|\|\|\|\|\| \|\| \|:\|\|\|:\|\|\|\|\|@LB@ UGCGGGU C AACUGC AC GUAAGUGGACG@LB@3'-UUU...CGCGU AG G A -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -43.3047 kcal/mol@LB@Unfolding Energy - mRNA 13.2535 kcal/mol@LB@Unfolding Energy - sRNA 15.0438 kcal/mol@LB@@LB@Position - mRNA 248 -- 282@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
57	0.0009345	0.05776	b3755	yieP	-11.62	0.043293	183 -- 203	41 -- 61	putative transcriptional regulator		_____________182____________________204\n_____________\|______________________\|\n5'-UUC...AAAAA___________A__________CCUUU...CCG-3'\n______________GAAAAAGGAAG_UAAG_UAAUG\n______________:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|_:\|\|\|:\n______________UUUUUUCCUUC_AUUC_GUUAU\n3'-UUU...UUAAG________________U_____ACCUC...ACG-5'\n_____________\|______________________\|\n_____________62_____________________40\n	187 -- 193	51 -- 57	-16.3745 kcal/mol	2.38082 kcal/mol	2.36907 kcal/mol	182 204@LB@ \| \|@LB@5'-UUC...AAAAA A CCUUU...CCG-3'@LB@ GAAAAAGGAAG UAAG UAAUG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|:@LB@ UUUUUUCCUUC AUUC GUUAU@LB@3'-UUU...UUAAG U ACCUC...ACG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -16.3745 kcal/mol@LB@Unfolding Energy - mRNA 2.38082 kcal/mol@LB@Unfolding Energy - sRNA 2.36907 kcal/mol@LB@@LB@Position - mRNA 183 -- 203@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
67	0.00114	0.05992	b4141	yjeH	-12.53	0.024616	129 -- 146	73 -- 89	putative transporter		_____________128________________147\n_____________\|__________________\|\n5'-CAG...CAUAA_______U__________CCAUC...CUG-3'\n______________GCGAAUC_GAUUGUGCUA\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\|\|\|\n______________UGCUUAG_UUAACACGAU\n3'-UUU...CAGCA__________________ACGUC...ACG-5'\n_____________\|__________________\|\n_____________90_________________72\n	140 -- 146	73 -- 79	-22.1843 kcal/mol	7.4128 kcal/mol	2.24587 kcal/mol	128 147@LB@ \| \|@LB@5'-CAG...CAUAA U CCAUC...CUG-3'@LB@ GCGAAUC GAUUGUGCUA@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UGCUUAG UUAACACGAU@LB@3'-UUU...CAGCA ACGUC...ACG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -22.1843 kcal/mol@LB@Unfolding Energy - mRNA 7.4128 kcal/mol@LB@Unfolding Energy - sRNA 2.24587 kcal/mol@LB@@LB@Position - mRNA 129 -- 146@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 73 -- 79@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@
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@
118	0.004043	0.119	b1636	pdxY	-15.07	0.004282	119 -- 169	46 -- 90	pyridoxamine kinase		_____________118___________________________________________________170\n_____________\|_____________________________________________________\|\n5'-UAU...AGAAU___U____U_________GGAAAUA_____U___G_G________________AAUCA...UCU-3'\n______________UAC__GUC_GAUU_UGCU_______AUGCA_UAA_U_GAAAGGGGGAGUGAGA\n______________\|\|\|__:\|\|_:\|\|\|_\|\|\|\|_______\|\|\|\|\|_\|\|\|_\|_:\|\|\|::\|\|:\|\|\|:\|\|\|\n______________AUG__UAG_UUAA_ACGA_______UACGU_AUU_A_UUUUUUCCUUCAUUCU\n3'-UUU...GCAGC___CU________C________________C___A_G________________GUUAU...ACG-5'\n_____________\|_____________________________________________________\|\n_____________91____________________________________________________45\n	163 -- 169	46 -- 52	-32.4349 kcal/mol	11.9314 kcal/mol	5.43414 kcal/mol	118 170@LB@ \| \|@LB@5'-UAU...AGAAU U U GGAAAUA U G G AAUCA...UCU-3'@LB@ UAC GUC GAUU UGCU AUGCA UAA U GAAAGGGGGAGUGAGA@LB@ \|\|\| :\|\| :\|\|\| \|\|\|\| \|\|\|\|\| \|\|\| \| :\|\|\|::\|\|:\|\|\|:\|\|\|@LB@ AUG UAG UUAA ACGA UACGU AUU A UUUUUUCCUUCAUUCU@LB@3'-UUU...GCAGC CU C C A G GUUAU...ACG-5'@LB@ \| \|@LB@ 91 45@LB@@LB@@LB@Energy -15.07 kcal/mol@LB@Hybridization Energy -32.4349 kcal/mol@LB@Unfolding Energy - mRNA 11.9314 kcal/mol@LB@Unfolding Energy - sRNA 5.43414 kcal/mol@LB@@LB@Position - mRNA 119 -- 169@LB@Position - sRNA 46 -- 90@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 46 -- 52@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@

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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