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
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@
162	0.006351	0.1377	b1869	yecN	-10.06	0.106335	266 -- 273	1 -- 8	MAPEG family inner membrane protein		_____________265______274\n_____________\|________\|\n5'-UCA...GUCGU________GAAUG...GCG-3'\n______________UCGCCUGC\n______________\|\|:\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	267 -- 273	1 -- 7	-14.5941 kcal/mol	2.17055 kcal/mol	2.36381 kcal/mol	265 274@LB@ \| \|@LB@5'-UCA...GUCGU GAAUG...GCG-3'@LB@ UCGCCUGC@LB@ \|\|:\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.06 kcal/mol@LB@Hybridization Energy -14.5941 kcal/mol@LB@Unfolding Energy - mRNA 2.17055 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 266 -- 273@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
163	0.006379	0.1377	b2210	mqo	-11.85	0.037664	161 -- 168	1 -- 8	malate dehydrogenase FAD/NAD(P)-binding domain		_____________160______169\n_____________\|________\|\n5'-GGC...AAAUC________AAUAA...AUG-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	162 -- 168	1 -- 7	-15.6271 kcal/mol	1.41654 kcal/mol	2.36381 kcal/mol	160 169@LB@ \| \|@LB@5'-GGC...AAAUC AAUAA...AUG-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -15.6271 kcal/mol@LB@Unfolding Energy - mRNA 1.41654 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 161 -- 168@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
164	0.006461	0.1377	b0864	artP	-11.21	0.055481	74 -- 84	70 -- 80	arginine ABC transporter ATPase		_____________73__________85\n_____________\|___________\|\n5'-AAA...UUAUU___________UUAUU...UAC-3'\n______________UUGUGCUAUGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AACACGAUACG\n3'-UUU...UAGUU___________UCAUU...ACG-5'\n_____________\|___________\|\n_____________81__________69\n	78 -- 84	70 -- 76	-15.8897 kcal/mol	2.86206 kcal/mol	1.81863 kcal/mol	73 85@LB@ \| \|@LB@5'-AAA...UUAUU UUAUU...UAC-3'@LB@ UUGUGCUAUGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AACACGAUACG@LB@3'-UUU...UAGUU UCAUU...ACG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -15.8897 kcal/mol@LB@Unfolding Energy - mRNA 2.86206 kcal/mol@LB@Unfolding Energy - sRNA 1.81863 kcal/mol@LB@@LB@Position - mRNA 74 -- 84@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 70 -- 76@LB@
165	0.006479	0.1377	b3132	kbaZ	-14.08	0.008730	160 -- 208	44 -- 89	tagatose 6-phosphate aldolase 1 kbaZ subunit	b2095	_____________159__________________________________________________209\n_____________\|____________________________________________________\|\n5'-CGC...ACAAA_____A_____AA_____C________CUGAACU_________A____A___UCUGA...CAA-3'\n______________ACGAA__GAUU____UAU_GCAGUAAU_______GGAGAGGAA_GUGA_ACA\n______________\|\|\|\|\|__:\|\|\|____\|\|\|_\|\|\|\|\|\|\|\|_______::\|:\|\|\|\|\|_\|\|:\|_\|\|\|\n______________UGCUU__UUAA____AUA_CGUCAUUA_______UUUUUCCUU_CAUU_UGU\n3'-UUU...CAGCA_____AG____CACG____________AGU__________________C___UAUAC...ACG-5'\n_____________\|____________________________________________________\|\n_____________90___________________________________________________43\n	193 -- 199	52 -- 58	-26.7556 kcal/mol	6.95106 kcal/mol	5.72676 kcal/mol	159 209@LB@ \| \|@LB@5'-CGC...ACAAA A AA C CUGAACU A A UCUGA...CAA-3'@LB@ ACGAA GAUU UAU GCAGUAAU GGAGAGGAA GUGA ACA@LB@ \|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|\| ::\|:\|\|\|\|\| \|\|:\| \|\|\|@LB@ UGCUU UUAA AUA CGUCAUUA UUUUUCCUU CAUU UGU@LB@3'-UUU...CAGCA AG CACG AGU C UAUAC...ACG-5'@LB@ \| \|@LB@ 90 43@LB@@LB@@LB@Energy -14.08 kcal/mol@LB@Hybridization Energy -26.7556 kcal/mol@LB@Unfolding Energy - mRNA 6.95106 kcal/mol@LB@Unfolding Energy - sRNA 5.72676 kcal/mol@LB@@LB@Position - mRNA 160 -- 208@LB@Position - sRNA 44 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 52 -- 58@LB@
166	0.006486	0.1377	b0440	hupB	-11.63	0.043010	149 -- 200	46 -- 93	HU DNA-binding transcriptional regulator beta subunit		_____________148______________________________________________________201\n_____________\|________________________________________________________\|\n5'-CGC...CGCGU______CUUGAAG__U__________GAUAUA______AU__________AG____GUGAA...CUG-3'\n______________UCGUAC_______GA_UCAA__GUGC________AAUU__AAAGAGGAAG__AAGA\n______________\|\|\|\|\|\|_______\|\|_\|\|\|\|__\|\|\|\|________\|\|\|\|__\|\|\|:\|\|\|\|\|\|__\|\|\|\|\n______________AGCAUG_______CU_AGUU__CACG________UUAA__UUUUUCCUUC__UUCU\n3'-UUU...GCCGC_______________U____AA____AUACGUCA____GU__________A_____GUUAU...ACG-5'\n_____________\|________________________________________________________\|\n_____________94_______________________________________________________45\n	188 -- 194	51 -- 57	-29.0191 kcal/mol	11.8112 kcal/mol	5.57675 kcal/mol	148 201@LB@ \| \|@LB@5'-CGC...CGCGU CUUGAAG U GAUAUA AU AG GUGAA...CUG-3'@LB@ UCGUAC GA UCAA GUGC AAUU AAAGAGGAAG AAGA@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\| \|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ AGCAUG CU AGUU CACG UUAA UUUUUCCUUC UUCU@LB@3'-UUU...GCCGC U AA AUACGUCA GU A GUUAU...ACG-5'@LB@ \| \|@LB@ 94 45@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -29.0191 kcal/mol@LB@Unfolding Energy - mRNA 11.8112 kcal/mol@LB@Unfolding Energy - sRNA 5.57675 kcal/mol@LB@@LB@Position - mRNA 149 -- 200@LB@Position - sRNA 46 -- 93@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@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@
168	0.006702	0.1406	b2051	wcaH	-7.67	0.342256	86 -- 123	5 -- 40	GDP-mannose mannosyl hydrolase		_____________85_______________________________________124\n_____________\|________________________________________\|\n5'-GCG...ACUGC____U___AC_____UG____A_______UG_________GAAAU...UUG-3'\n______________UGGA_GUG__GCGCC__CAUC_GCUUGGC___GUA_UCAC\n______________\|\|\|\|_\|:\|__:\|\|\|\|__\|\|\|\|_\|\|\|\|\|:\|___\|:\|_\|\|\|\|\n______________ACCU_CGC__UGCGG__GUAG_CGAACUG___CGU_AGUG\n3'-UUU...GUUAU________GU___________________CAA___A____GACG-5'\n_____________\|________________________________________\|\n_____________41_______________________________________4\n	108 -- 114	16 -- 22	-36.6804 kcal/mol	13.756 kcal/mol	15.262 kcal/mol	85 124@LB@ \| \|@LB@5'-GCG...ACUGC U AC UG A UG GAAAU...UUG-3'@LB@ UGGA GUG GCGCC CAUC GCUUGGC GUA UCAC@LB@ \|\|\|\| \|:\| :\|\|\|\| \|\|\|\| \|\|\|\|\|:\| \|:\| \|\|\|\|@LB@ ACCU CGC UGCGG GUAG CGAACUG CGU AGUG@LB@3'-UUU...GUUAU GU CAA A GACG-5'@LB@ \| \|@LB@ 41 4@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -36.6804 kcal/mol@LB@Unfolding Energy - mRNA 13.756 kcal/mol@LB@Unfolding Energy - sRNA 15.262 kcal/mol@LB@@LB@Position - mRNA 86 -- 123@LB@Position - sRNA 5 -- 40@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 16 -- 22@LB@
169	0.006778	0.1407	b3300	secY	-11.17	0.056917	151 -- 190	56 -- 93	preprotein translocase membrane subunit		_____________150_______________________________________191\n_____________\|_________________________________________\|\n5'-CCU...GGCGC______UGCU_____AGC_____________AA________UAAGU...UCC-3'\n______________UCGUGC____AUCGA___UGCUG_GCGGUAA__UCGAGGAA\n______________\|\|\|\|:\|____\|\|\|:\|___\|\|\|\|:_\|\|:\|\|\|\|__\|\|:\|::\|\|\n______________AGCAUG____UAGUU___ACGAU_CGUCAUU__AGUUUUUU\n3'-UUU...GCCGC______CU_______AAC_____A_______A_________CCUUC...ACG-5'\n_____________\|_________________________________________\|\n_____________94________________________________________55\n	174 -- 180	65 -- 71	-28.5007 kcal/mol	12.5083 kcal/mol	4.83069 kcal/mol	150 191@LB@ \| \|@LB@5'-CCU...GGCGC UGCU AGC AA UAAGU...UCC-3'@LB@ UCGUGC AUCGA UGCUG GCGGUAA UCGAGGAA@LB@ \|\|\|\|:\| \|\|\|:\| \|\|\|\|: \|\|:\|\|\|\| \|\|:\|::\|\|@LB@ AGCAUG UAGUU ACGAU CGUCAUU AGUUUUUU@LB@3'-UUU...GCCGC CU AAC A A CCUUC...ACG-5'@LB@ \| \|@LB@ 94 55@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -28.5007 kcal/mol@LB@Unfolding Energy - mRNA 12.5083 kcal/mol@LB@Unfolding Energy - sRNA 4.83069 kcal/mol@LB@@LB@Position - mRNA 151 -- 190@LB@Position - sRNA 56 -- 93@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 65 -- 71@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@

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

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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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