Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
33	0.002101	0.2088	b1300	puuC	-8.92	0.198515	81 -- 101	2 -- 20	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase	b0312	_____________80____________________102\n_____________\|_____________________\|\n5'-GGC...CGGCU___AG_______U________AGAAU...AAA-3'\n______________UGA__GAUGAAG_GUAUAUAA\n______________\|\|\|__:\|\|:\|\|\|_\|:\|\|\|\|\|\|\n______________ACU__UUAUUUC_CGUAUAUU\n3'-UUU...UAGAC___G_________________G-5'\n_____________\|_____________________\|\n_____________21____________________1\n	94 -- 100	3 -- 9	-14.4968 kcal/mol	1.34672 kcal/mol	4.22649 kcal/mol	80 102@LB@ \| \|@LB@5'-GGC...CGGCU AG U AGAAU...AAA-3'@LB@ UGA GAUGAAG GUAUAUAA@LB@ \|\|\| :\|\|:\|\|\| \|:\|\|\|\|\|\|@LB@ ACU UUAUUUC CGUAUAUU@LB@3'-UUU...UAGAC G G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.92 kcal/mol@LB@Hybridization Energy -14.4968 kcal/mol@LB@Unfolding Energy - mRNA 1.34672 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 3 -- 9@LB@
83	0.007014	0.2822	b0815	opgE	-11.11	0.070482	164 -- 204	2 -- 58	OPG biosynthetic transmembrane phosphoethanolamine transferase		_____________163________________________________________________________205\n_____________\|__________________________________________________________\|\n5'-UUU...GACGC_____________C__________________________U_______U_________AUUUA...GCU-3'\n______________CAG_GGUAA_GCA_AUGGC_______________GUUUGU_ACGAUAG_GGCAUAUGA\n______________\|\|\|_\|\|:\|\|_\|\|\|_\|\|\|\|\|_______________:\|:\|\|\|_\|\|:\|\|\|:_\|\|\|\|\|\|\|:\|\n______________GUC_CCGUU_CGU_UACCG_______________UAGACA_UGUUAUU_CCGUAUAUU\n3'-UUU...UUUUA___A_____A_________GGUUGUCUUUUAUUU______C_______U_________G-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	197 -- 203	3 -- 9	-40.5172 kcal/mol	17.2586 kcal/mol	12.1475 kcal/mol	163 205@LB@ \| \|@LB@5'-UUU...GACGC C U U AUUUA...GCU-3'@LB@ CAG GGUAA GCA AUGGC GUUUGU ACGAUAG GGCAUAUGA@LB@ \|\|\| \|\|:\|\| \|\|\| \|\|\|\|\| :\|:\|\|\| \|\|:\|\|\|: \|\|\|\|\|\|\|:\|@LB@ GUC CCGUU CGU UACCG UAGACA UGUUAUU CCGUAUAUU@LB@3'-UUU...UUUUA A A GGUUGUCUUUUAUUU C U G-5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -40.5172 kcal/mol@LB@Unfolding Energy - mRNA 17.2586 kcal/mol@LB@Unfolding Energy - sRNA 12.1475 kcal/mol@LB@@LB@Position - mRNA 164 -- 204@LB@Position - sRNA 2 -- 58@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
87	0.007653	0.2889	b1881	cheZ	-13.56	0.018568	164 -- 190	2 -- 28	chemotaxis regulator protein phosphatase for CheY		_____________163_________________________191\n_____________\|___________________________\|\n5'-AUU...UCAAC_______U___G__ACU__________GGAUG...GGG-3'\n______________AAAAUCU_UGA_AA___GGGCAUGUGA\n______________\|\|\|\|\|\|\|_\|\|\|_\|\|___:\|\|\|\|\|:\|:\|\n______________UUUUAGA_ACU_UU___UCCGUAUAUU\n3'-UUU...UUUUA_______C___G__AUU__________G-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	183 -- 189	3 -- 9	-22.696 kcal/mol	4.24203 kcal/mol	4.89261 kcal/mol	163 191@LB@ \| \|@LB@5'-AUU...UCAAC U G ACU GGAUG...GGG-3'@LB@ AAAAUCU UGA AA GGGCAUGUGA@LB@ \|\|\|\|\|\|\| \|\|\| \|\| :\|\|\|\|\|:\|:\|@LB@ UUUUAGA ACU UU UCCGUAUAUU@LB@3'-UUU...UUUUA C G AUU G-5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -22.696 kcal/mol@LB@Unfolding Energy - mRNA 4.24203 kcal/mol@LB@Unfolding Energy - sRNA 4.89261 kcal/mol@LB@@LB@Position - mRNA 164 -- 190@LB@Position - sRNA 2 -- 28@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 3 -- 9@LB@
170	0.02048	0.4033	b3201	lptB	-9.27	0.170285	9 -- 55	2 -- 54	lipopolysaccharide export ABC transporter ATPase		_____________8______________________________________________________56\n_____________\|______________________________________________________\|\n___5'-UUCUGACG________UUAUC_G_______UC___________CA___U_____________GAUCA...GUC-3'\n______________GGUAAUGC_____U_CAGCAGG__GAUA______G__ACA_UAAGGGCG_AUAA\n______________\|\|:\|\|\|\|\|_____:_\|\|:\|\|\|:__:\|\|\|______\|__\|\|\|_\|\|\|:\|\|\|:_\|\|\|\|\n______________CCGUUACG_____G_GUUGUCU__UUAU______C__UGU_AUUUCCGU_UAUU\n3'-UUU...AGUCA________UUACC_G_______U_____UUUAGA_AC___U________A____G-5'\n_____________\|______________________________________________________\|\n_____________55_____________________________________________________1\n	45 -- 51	7 -- 13	-32.2484 kcal/mol	10.9323 kcal/mol	12.0447 kcal/mol	8 56@LB@ \| \|@LB@ 5'-UUCUGACG UUAUC G UC CA U GAUCA...GUC-3'@LB@ GGUAAUGC U CAGCAGG GAUA G ACA UAAGGGCG AUAA@LB@ \|\|:\|\|\|\|\| : \|\|:\|\|\|: :\|\|\| \| \|\|\| \|\|\|:\|\|\|: \|\|\|\|@LB@ CCGUUACG G GUUGUCU UUAU C UGU AUUUCCGU UAUU@LB@3'-UUU...AGUCA UUACC G U UUUAGA AC U A G-5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -32.2484 kcal/mol@LB@Unfolding Energy - mRNA 10.9323 kcal/mol@LB@Unfolding Energy - sRNA 12.0447 kcal/mol@LB@@LB@Position - mRNA 9 -- 55@LB@Position - sRNA 2 -- 54@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 7 -- 13@LB@
15	0.0005657	0.1268	b3715	yieH	-7.91	0.301098	195 -- 204	4 -- 13	phosphoenolpyruvate and 6-phosphogluconate phosphatase		_____________194________205\n_____________\|__________\|\n5'-CUG...AAAGG__________CCCGG...UUG-3'\n______________AAAGGCAUGU\n______________\|\|\|\|\|\|\|\|:\|\n______________UUUCCGUAUA\n3'-UUU...UGUUA__________UUG-5'\n_____________\|__________\|\n_____________14_________3\n	198 -- 204	4 -- 10	-12.382 kcal/mol	1.66065 kcal/mol	2.80714 kcal/mol	194 205@LB@ \| \|@LB@5'-CUG...AAAGG CCCGG...UUG-3'@LB@ AAAGGCAUGU@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UUUCCGUAUA@LB@3'-UUU...UGUUA UUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -7.91 kcal/mol@LB@Hybridization Energy -12.382 kcal/mol@LB@Unfolding Energy - mRNA 1.66065 kcal/mol@LB@Unfolding Energy - sRNA 2.80714 kcal/mol@LB@@LB@Position - mRNA 195 -- 204@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 4 -- 10@LB@
77	0.006658	0.2822	b3347	fkpA	-8.74	0.214444	80 -- 111	4 -- 28	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)		_____________79________________________________112\n_____________\|_________________________________\|\n5'-UGG...CAAAA________AAAAUAGA_________________CUGUA...CAG-3'\n______________AGAGUCUG________UGAUAAU_AGGGCGUGU\n______________\|:\|:\|\|\|\|________\|\|\|:\|\|\|_\|:\|\|\|:\|:\|\n______________UUUUAGAC________ACUGUUA_UUCCGUAUA\n3'-UUU...UUUUA_______________________U_________UUG-5'\n_____________\|_________________________________\|\n_____________29________________________________3\n	104 -- 110	5 -- 11	-22.6947 kcal/mol	9.05802 kcal/mol	4.89231 kcal/mol	79 112@LB@ \| \|@LB@5'-UGG...CAAAA AAAAUAGA CUGUA...CAG-3'@LB@ AGAGUCUG UGAUAAU AGGGCGUGU@LB@ \|:\|:\|\|\|\| \|\|\|:\|\|\| \|:\|\|\|:\|:\|@LB@ UUUUAGAC ACUGUUA UUCCGUAUA@LB@3'-UUU...UUUUA U UUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -22.6947 kcal/mol@LB@Unfolding Energy - mRNA 9.05802 kcal/mol@LB@Unfolding Energy - sRNA 4.89231 kcal/mol@LB@@LB@Position - mRNA 80 -- 111@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 5 -- 11@LB@
128	0.01375	0.3614	b1271	yciK	-9.18	0.177475	2 -- 35	4 -- 52	putative EmrKY-TolC system oxoacyl-(acyl carrier protein) reductase		_____________1_________________________________________________36\n_____________\|_________________________________________________\|\n__________5'-A___C__UU___________UUU________________C__________UAAGC...CAC-3'\n______________CAA_GC__UGGCUC_ACAG_______________ACAA___AGGCAUGU\n______________\|\|\|_\|\|__\|\|\|\|:\|_\|\|\|\|_______________\|\|\|\|___\|\|\|\|\|\|:\|\n______________GUU_CG__ACCGGG_UGUC_______________UGUU___UCCGUAUA\n3'-UUU...UCACC___A__UU______U____UUUUAUUUUAGACAC____AUU________UUG-5'\n_____________\|_________________________________________________\|\n_____________53________________________________________________3\n	29 -- 35	4 -- 10	-28.8633 kcal/mol	7.6461 kcal/mol	12.0385 kcal/mol	1 36@LB@ \| \|@LB@ 5'-A C UU UUU C UAAGC...CAC-3'@LB@ CAA GC UGGCUC ACAG ACAA AGGCAUGU@LB@ \|\|\| \|\| \|\|\|\|:\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ GUU CG ACCGGG UGUC UGUU UCCGUAUA@LB@3'-UUU...UCACC A UU U UUUUAUUUUAGACAC AUU UUG-5'@LB@ \| \|@LB@ 53 3@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -28.8633 kcal/mol@LB@Unfolding Energy - mRNA 7.6461 kcal/mol@LB@Unfolding Energy - sRNA 12.0385 kcal/mol@LB@@LB@Position - mRNA 2 -- 35@LB@Position - sRNA 4 -- 52@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 4 -- 10@LB@
80	0.006956	0.2822	b1914	uvrY	-9.02	0.189987	260 -- 281	5 -- 24	response regulator in two-component regulatory system with BarA		_____________259____________________282\n_____________\|______________________\|\n5'-UUC...CGCAU____GAA____UA_________AAAGU...CAU-3'\n______________UCUG___GAUA__AAGGGUAUA\n______________\|\|\|\|___\|\|:\|__\|\|:\|\|:\|\|\|\n______________AGAC___CUGU__UUUCCGUAU\n3'-UUU...AUUUU____A______UA_________AUUG-5'\n_____________\|______________________\|\n_____________25_____________________4\n	275 -- 281	5 -- 11	-15.9126 kcal/mol	2.27135 kcal/mol	4.61703 kcal/mol	259 282@LB@ \| \|@LB@5'-UUC...CGCAU GAA UA AAAGU...CAU-3'@LB@ UCUG GAUA AAGGGUAUA@LB@ \|\|\|\| \|\|:\| \|\|:\|\|:\|\|\|@LB@ AGAC CUGU UUUCCGUAU@LB@3'-UUU...AUUUU A UA AUUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.9126 kcal/mol@LB@Unfolding Energy - mRNA 2.27135 kcal/mol@LB@Unfolding Energy - sRNA 4.61703 kcal/mol@LB@@LB@Position - mRNA 260 -- 281@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 5 -- 11@LB@
175	0.02099	0.4033	b2913	serA	-5.57	0.642321	190 -- 257	5 -- 65	D-3-phosphoglycerate dehydrogenase		_____________189_____________________________________________________________________258\n_____________\|_______________________________________________________________________\|\n5'-UGU...AGACA___UU____AAA______AG___UCGC___AGAAA________U____UU____C________________CACCA...CCA-3'\n______________GGA__GGGU___UGGCAA__GUA____UGG_____GACA_AGA_UAAG__UCUG_UGGUA__GAAGGCGUG\n______________\|\|\|__:::\|___\|\|\|\|\|\|__\|:\|____\|\|\|_____:\|\|\|_\|:\|_\|\|\|:__\|\|\|\|_\|\|::\|__:\|\|\|\|\|:\|:\n______________CCU__UUUA___ACCGUU__CGU____ACC_____UUGU_UUU_AUUU__AGAC_ACUGU__UUUCCGUAU\n3'-UUU...UACAA_________GUC______A____U______GGG______C___U____U___________UA_________AUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________66______________________________________________________________________4\n	251 -- 257	5 -- 11	-32.5395 kcal/mol	14.8085 kcal/mol	12.157 kcal/mol	189 258@LB@ \| \|@LB@5'-UGU...AGACA UU AAA AG UCGC AGAAA U UU C CACCA...CCA-3'@LB@ GGA GGGU UGGCAA GUA UGG GACA AGA UAAG UCUG UGGUA GAAGGCGUG@LB@ \|\|\| :::\| \|\|\|\|\|\| \|:\| \|\|\| :\|\|\| \|:\| \|\|\|: \|\|\|\| \|\|::\| :\|\|\|\|\|:\|:@LB@ CCU UUUA ACCGUU CGU ACC UUGU UUU AUUU AGAC ACUGU UUUCCGUAU@LB@3'-UUU...UACAA GUC A U GGG C U U UA AUUG-5'@LB@ \| \|@LB@ 66 4@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -32.5395 kcal/mol@LB@Unfolding Energy - mRNA 14.8085 kcal/mol@LB@Unfolding Energy - sRNA 12.157 kcal/mol@LB@@LB@Position - mRNA 190 -- 257@LB@Position - sRNA 5 -- 65@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 5 -- 11@LB@
179	0.02223	0.4143	b2167	fruA	-7.15	0.399094	192 -- 200	5 -- 13	fused fructose-specific PTS enzymes: IIBcomponent/IIC components		_____________191_______201\n_____________\|_________\|\n5'-CGC...GCAGG_________AUGAA...AAA-3'\n______________AGAGGCAUA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCCGUAU\n3'-UUU...UGUUA_________AUUG-5'\n_____________\|_________\|\n_____________14________4\n	194 -- 200	5 -- 11	-11.8443 kcal/mol	1.8873 kcal/mol	2.80332 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...GCAGG AUGAA...AAA-3'@LB@ AGAGGCAUA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCCGUAU@LB@3'-UUU...UGUUA AUUG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -11.8443 kcal/mol@LB@Unfolding Energy - mRNA 1.8873 kcal/mol@LB@Unfolding Energy - sRNA 2.80332 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@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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service.

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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