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
71	0.001416	0.07026	b0880	cspD	-7.58	0.355655	51 -- 57	1 -- 7	inhibitor of DNA replication cold shock protein homolog		_____________50______58\n_____________\|_______\|\n5'-AUC...AUUCA_______CCCUU...CCA-3'\n______________UACCUGC\n______________:\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	51 -- 57	1 -- 7	-10.3464 kcal/mol	0.429757 kcal/mol	2.34039 kcal/mol	50 58@LB@ \| \|@LB@5'-AUC...AUUCA CCCUU...CCA-3'@LB@ UACCUGC@LB@ :\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -10.3464 kcal/mol@LB@Unfolding Energy - mRNA 0.429757 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 51 -- 57@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 1 -- 7@LB@
147	0.005701	0.1366	b1622	malY	-7.52	0.364460	44 -- 91	35 -- 85	PLP-dependent beta-cystathionase and maltose regulon regulator		_____________43____________________________________________________92\n_____________\|_____________________________________________________\|\n5'-UCG...GAUAU____C____UAA_______GCACU__________CAAUC___________C__AGUAC...UCA-3'\n______________GUCG_UUGU___UGUGCAG_________GAAGGA_____GGGCAAU_UGG_GU\n______________:\|\|:_\|\|\|\|___\|:\|\|\|\|\|_________:\|\|\|\|\|_____:\|:\|\|\|\|_\|\|\|_\|:\n______________UAGU_AACA___AUACGUC_________UUUCCU_____UCUGUUA_ACC_CG\n3'-UUU...AUGCU____U____CG________AUUAAGUUU______UCAU________U___U__CGUUG...ACG-5'\n_____________\|_____________________________________________________\|\n_____________86____________________________________________________34\n	79 -- 85	42 -- 48	-29.3049 kcal/mol	13.5755 kcal/mol	8.20283 kcal/mol	43 92@LB@ \| \|@LB@5'-UCG...GAUAU C UAA GCACU CAAUC C AGUAC...UCA-3'@LB@ GUCG UUGU UGUGCAG GAAGGA GGGCAAU UGG GU@LB@ :\|\|: \|\|\|\| \|:\|\|\|\|\| :\|\|\|\|\| :\|:\|\|\|\| \|\|\| \|:@LB@ UAGU AACA AUACGUC UUUCCU UCUGUUA ACC CG@LB@3'-UUU...AUGCU U CG AUUAAGUUU UCAU U U CGUUG...ACG-5'@LB@ \| \|@LB@ 86 34@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -29.3049 kcal/mol@LB@Unfolding Energy - mRNA 13.5755 kcal/mol@LB@Unfolding Energy - sRNA 8.20283 kcal/mol@LB@@LB@Position - mRNA 44 -- 91@LB@Position - sRNA 35 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
146	0.005657	0.1365	b4322	uxuA	-7.47	0.371307	180 -- 195	52 -- 75	mannonate hydrolase		_____________179______________________196\n_____________\|________________________\|\n5'-CAU...ACCCA________________________AAAUC...AUA-3'\n______________CUAUGU________GAAAGAGGAA\n______________\|\|\|\|\|:________:\|\|\|:\|\|\|\|\|\n______________GAUACG________UUUUUUCCUU\n3'-UUU...AACAC______UCAUUAAG__________CAUUC...ACG-5'\n_____________\|________________________\|\n_____________76_______________________51\n	189 -- 195	52 -- 58	-13.8583 kcal/mol	2.68591 kcal/mol	3.70263 kcal/mol	179 196@LB@ \| \|@LB@5'-CAU...ACCCA AAAUC...AUA-3'@LB@ CUAUGU GAAAGAGGAA@LB@ \|\|\|\|\|: :\|\|\|:\|\|\|\|\|@LB@ GAUACG UUUUUUCCUU@LB@3'-UUU...AACAC UCAUUAAG CAUUC...ACG-5'@LB@ \| \|@LB@ 76 51@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -13.8583 kcal/mol@LB@Unfolding Energy - mRNA 2.68591 kcal/mol@LB@Unfolding Energy - sRNA 3.70263 kcal/mol@LB@@LB@Position - mRNA 180 -- 195@LB@Position - sRNA 52 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@LB@
91	0.002503	0.09689	b1062	pyrC	-7.37	0.386343	231 -- 263	1 -- 35	dihydro-orotase		_____________230_______________________________________264\n_____________\|_________________________________________\|\n5'-GCG...AGAUC_____________________ACUG___CC_______CC__GAUGG...CCA-3'\n______________CGC__CGCCCA______GACG____GCA__UUCACCU__GC\n______________\|\|\|__\|\|\|\|\|\|______\|\|\|\|____\|\|\|__\|\|\|\|\|\|\|__\|\|\n______________GCG__GCGGGU______CUGC____CGU__AAGUGGA__CG\n3'-UUU...ACCUC___UU______AGCGAA____AA__________________-5'\n_____________\|________________________________________\|\n_____________36_______________________________________1\n	253 -- 259	3 -- 9	-30.041 kcal/mol	7.38685 kcal/mol	15.286 kcal/mol	230 264@LB@ \| \|@LB@5'-GCG...AGAUC ACUG CC CC GAUGG...CCA-3'@LB@ CGC CGCCCA GACG GCA UUCACCU GC@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|@LB@ GCG GCGGGU CUGC CGU AAGUGGA CG@LB@3'-UUU...ACCUC UU AGCGAA AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -30.041 kcal/mol@LB@Unfolding Energy - mRNA 7.38685 kcal/mol@LB@Unfolding Energy - sRNA 15.286 kcal/mol@LB@@LB@Position - mRNA 231 -- 263@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 3 -- 9@LB@
161	0.006314	0.1377	b4099	phnI	-7.36	0.387929	194 -- 228	46 -- 79	ribophosphonate triphosphate synthase complex putative catalytic subunit		_____________193__________________________________229\n_____________\|____________________________________\|\n5'-AGC...GGAGG______G_____C__UGC___U_________C____AGGCG...GCG-3'\n______________UGUGCU_AUGUA_GU____CG_GAAAGGGGG_GAGA\n______________\|\|\|\|\|\|_\|\|\|:\|_\|\|____\|:_:\|\|\|\|\|::\|_:\|\|\|\n______________ACACGA_UACGU_CA____GU_UUUUCCUUC_UUCU\n3'-UUU...AGUUA_______________UUAA__U_________A____GUUAU...ACG-5'\n_____________\|____________________________________\|\n_____________80___________________________________45\n	217 -- 223	51 -- 57	-26.8268 kcal/mol	14.1464 kcal/mol	5.32077 kcal/mol	193 229@LB@ \| \|@LB@5'-AGC...GGAGG G C UGC U C AGGCG...GCG-3'@LB@ UGUGCU AUGUA GU CG GAAAGGGGG GAGA@LB@ \|\|\|\|\|\| \|\|\|:\| \|\| \|: :\|\|\|\|\|::\| :\|\|\|@LB@ ACACGA UACGU CA GU UUUUCCUUC UUCU@LB@3'-UUU...AGUUA UUAA U A GUUAU...ACG-5'@LB@ \| \|@LB@ 80 45@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -26.8268 kcal/mol@LB@Unfolding Energy - mRNA 14.1464 kcal/mol@LB@Unfolding Energy - sRNA 5.32077 kcal/mol@LB@@LB@Position - mRNA 194 -- 228@LB@Position - sRNA 46 -- 79@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 51 -- 57@LB@
86	0.002341	0.09591	b0144	gluQ	-7.21	0.411815	221 -- 264	26 -- 65	glutamyl-Q tRNA(Asp) synthetase		_____________220__________________________________________265\n_____________\|____________________________________________\|\n5'-AGA...UUUUU__________AU__C__ACAC_______AUU__C___UU_____CCUCU...UGA-3'\n______________GUUCAAAGAG__GA_AG____ACAGUAU___GG_CGC__CGCCC\n______________:\|\|\|\|\|\|:\|:__\|\|_\|\|____\|\|\|:\|\|\|___:\|_\|\|\|__\|\|\|\|\|\n______________UAAGUUUUUU__CU_UC____UGUUAUA___UC_GCG__GCGGG\n3'-UUU...GUCAU__________C______AUUC_______CC_______UU_____UAGCG...ACG-5'\n_____________\|____________________________________________\|\n_____________66___________________________________________25\n	242 -- 248	40 -- 46	-28.4973 kcal/mol	7.75098 kcal/mol	13.5387 kcal/mol	220 265@LB@ \| \|@LB@5'-AGA...UUUUU AU C ACAC AUU C UU CCUCU...UGA-3'@LB@ GUUCAAAGAG GA AG ACAGUAU GG CGC CGCCC@LB@ :\|\|\|\|\|\|:\|: \|\| \|\| \|\|\|:\|\|\| :\| \|\|\| \|\|\|\|\|@LB@ UAAGUUUUUU CU UC UGUUAUA UC GCG GCGGG@LB@3'-UUU...GUCAU C AUUC CC UU UAGCG...ACG-5'@LB@ \| \|@LB@ 66 25@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -28.4973 kcal/mol@LB@Unfolding Energy - mRNA 7.75098 kcal/mol@LB@Unfolding Energy - sRNA 13.5387 kcal/mol@LB@@LB@Position - mRNA 221 -- 264@LB@Position - sRNA 26 -- 65@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 40 -- 46@LB@
194	0.008684	0.1548	b1242	ychE	-7.20	0.413978	105 -- 113	48 -- 56	UPF0056 family inner membrane protein		_____________104_______114\n_____________\|_________\|\n5'-CAU...UAGUU_________AAAAU...GCA-3'\n______________AGGAGGUGA\n______________\|\|\|\|:\|\|:\|\n______________UCCUUCAUU\n3'-UUU...UUUUU_________CUGUU...ACG-5'\n_____________\|_________\|\n_____________57________47\n	107 -- 113	48 -- 54	-10.6218 kcal/mol	2.70901 kcal/mol	0.718267 kcal/mol	104 114@LB@ \| \|@LB@5'-CAU...UAGUU AAAAU...GCA-3'@LB@ AGGAGGUGA@LB@ \|\|\|\|:\|\|:\|@LB@ UCCUUCAUU@LB@3'-UUU...UUUUU CUGUU...ACG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -10.6218 kcal/mol@LB@Unfolding Energy - mRNA 2.70901 kcal/mol@LB@Unfolding Energy - sRNA 0.718267 kcal/mol@LB@@LB@Position - mRNA 105 -- 113@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 48 -- 54@LB@
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@
120	0.004053	0.119	b2441	eutB	-6.09	0.606518	293 -- 299	73 -- 79	ethanolamine ammonia-lyase large subunit heavy chain		_____________292_____300\n_____________\|_______\|\n5'-CUG...GGGGA_______G-3'\n______________UGUGCUG\n______________\|\|\|\|\|\|:\n______________ACACGAU\n3'-UUU...AGUUA_______ACGUC...ACG-5'\n_____________\|_______\|\n_____________80______72\n	293 -- 299	73 -- 79	-8.7652 kcal/mol	1.34517 kcal/mol	1.33434 kcal/mol	292 300@LB@ \| \|@LB@5'-CUG...GGGGA G-3'@LB@ UGUGCUG@LB@ \|\|\|\|\|\|:@LB@ ACACGAU@LB@3'-UUU...AGUUA ACGUC...ACG-5'@LB@ \| \|@LB@ 80 72@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.7652 kcal/mol@LB@Unfolding Energy - mRNA 1.34517 kcal/mol@LB@Unfolding Energy - sRNA 1.33434 kcal/mol@LB@@LB@Position - mRNA 293 -- 299@LB@Position - sRNA 73 -- 79@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 73 -- 79@LB@
197	0.008895	0.1548	b2844	yqeF	-5.48	0.714940	222 -- 246	20 -- 39	short chain acyltransferase		_____________221_______________________247\n_____________\|_________________________\|\n5'-CCA...UUGUC_______UACG___A_______G__GCUUU...UCG-3'\n______________GGGGCGU____GAC_CCUAUCG_CU\n______________\|\|:\|\|\|:____:\|\|_\|\|:\|\|\|\|_\|\|\n______________CCUCGCG____UUG_GGGUAGC_GA\n3'-UUU...UUAUA______________C__________ACUGC...ACG-5'\n_____________\|_________________________\|\n_____________40________________________19\n	237 -- 243	22 -- 28	-25.7666 kcal/mol	8.11246 kcal/mol	12.1811 kcal/mol	221 247@LB@ \| \|@LB@5'-CCA...UUGUC UACG A G GCUUU...UCG-3'@LB@ GGGGCGU GAC CCUAUCG CU@LB@ \|\|:\|\|\|: :\|\| \|\|:\|\|\|\| \|\|@LB@ CCUCGCG UUG GGGUAGC GA@LB@3'-UUU...UUAUA C ACUGC...ACG-5'@LB@ \| \|@LB@ 40 19@LB@@LB@@LB@Energy -5.48 kcal/mol@LB@Hybridization Energy -25.7666 kcal/mol@LB@Unfolding Energy - mRNA 8.11246 kcal/mol@LB@Unfolding Energy - sRNA 12.1811 kcal/mol@LB@@LB@Position - mRNA 222 -- 246@LB@Position - sRNA 20 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 22 -- 28@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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