Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
184	0.02168	0.3768	b4380	yjjI	-6.70	0.131310	12 -- 49	9 -- 40	DUF3029 family protein putative glycine radical enzyme	_____________11________________________________________50\n_____________\|_________________________________________\|\n5'-ACA...ACUCC___ACACAC_______A_____AUCACAAUUA_________ACUUA...UGG-3'\n______________GCA_________UUCG_UACAC__________AGGAAAUCU\n______________\|\|\|_________\|\|\|\|_\|\|\|\|\|__________\|\|\|\|\|\|\|\|\|\n______________CGU_________AAGC_AUGUG__________UCCUUUAGA\n3'-UUU...UUCUU___GAAUUUUUU____A_____G__________________CUACACAA-5'\n_____________\|_________________________________________\|\n_____________41________________________________________8\n	43 -- 49	9 -- 15	-18.7623 kcal/mol	2.84333 kcal/mol	9.22063 kcal/mol	11 50@LB@ \| \|@LB@5'-ACA...ACUCC ACACAC A AUCACAAUUA ACUUA...UGG-3'@LB@ GCA UUCG UACAC AGGAAAUCU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CGU AAGC AUGUG UCCUUUAGA@LB@3'-UUU...UUCUU GAAUUUUUU A G CUACACAA-5'@LB@ \| \|@LB@ 41 8@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -18.7623 kcal/mol@LB@Unfolding Energy - mRNA 2.84333 kcal/mol@LB@Unfolding Energy - sRNA 9.22063 kcal/mol@LB@@LB@Position - mRNA 12 -- 49@LB@Position - sRNA 9 -- 40@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 9 -- 15@LB@
138	0.01322	0.3087	b1523	yneG	-4.22	0.452951	267 -- 281	24 -- 41	DUF4186 family protein	_____________266________________282\n_____________\|__________________\|\n5'-AUG...GUCUG_____________G____CAGUA...AAG-3'\n______________GGCA__UGAAAGA__CGU\n______________:\|\|\|__\|:\|\|\|:\|__\|\|\|\n______________UCGU__AUUUUUU__GCA\n3'-UUU...GUUCU____GA_______AA___AUGUG...CAA-5'\n_____________\|__________________\|\n_____________42_________________23\n	271 -- 277	29 -- 35	-8.58312 kcal/mol	2.71204 kcal/mol	1.64881 kcal/mol	266 282@LB@ \| \|@LB@5'-AUG...GUCUG G CAGUA...AAG-3'@LB@ GGCA UGAAAGA CGU@LB@ :\|\|\| \|:\|\|\|:\| \|\|\|@LB@ UCGU AUUUUUU GCA@LB@3'-UUU...GUUCU GA AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -4.22 kcal/mol@LB@Hybridization Energy -8.58312 kcal/mol@LB@Unfolding Energy - mRNA 2.71204 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 267 -- 281@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 29 -- 35@LB@
30	0.0008402	0.09021	b2792	yqcC	-12.92	0.001907	10 -- 25	38 -- 53	DUF446 family protein	_____________9________________26\n_____________\|________________\|\n5'-AUC...GGGUG__G_____________AUAGU...AAU-3'\n______________GU_UGAGCAGGAAGCA\n______________\|:_\|:\|\|\|\|:\|\|\|\|\|\|\n______________CG_AUUCGUUCUUCGU\n3'-UUU...UUGAA__A_____________GAAUU...CAA-5'\n_____________\|________________\|\n_____________54_______________37\n	19 -- 25	38 -- 44	-21.2799 kcal/mol	2.27149 kcal/mol	6.09301 kcal/mol	9 26@LB@ \| \|@LB@5'-AUC...GGGUG G AUAGU...AAU-3'@LB@ GU UGAGCAGGAAGCA@LB@ \|: \|:\|\|\|\|:\|\|\|\|\|\|@LB@ CG AUUCGUUCUUCGU@LB@3'-UUU...UUGAA A GAAUU...CAA-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 2.27149 kcal/mol@LB@Unfolding Energy - sRNA 6.09301 kcal/mol@LB@@LB@Position - mRNA 10 -- 25@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 38 -- 44@LB@
168	0.01885	0.3614	b1792	yeaO	-5.97	0.195997	133 -- 142	25 -- 34	DUF488 family protein	_____________132________143\n_____________\|__________\|\n5'-UGU...AGACA__________CUAAU...CCG-3'\n______________AAGAAAUUCG\n______________\|\|:\|\|\|\|\|\|\|\n______________UUUUUUAAGC\n3'-UUU...GUGAA__________AAUGU...CAA-5'\n_____________\|__________\|\n_____________35_________24\n	136 -- 142	25 -- 31	-8.43117 kcal/mol	1.28773 kcal/mol	1.16883 kcal/mol	132 143@LB@ \| \|@LB@5'-UGU...AGACA CUAAU...CCG-3'@LB@ AAGAAAUUCG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ UUUUUUAAGC@LB@3'-UUU...GUGAA AAUGU...CAA-5'@LB@ \| \|@LB@ 35 24@LB@@LB@@LB@Energy -5.97 kcal/mol@LB@Hybridization Energy -8.43117 kcal/mol@LB@Unfolding Energy - mRNA 1.28773 kcal/mol@LB@Unfolding Energy - sRNA 1.16883 kcal/mol@LB@@LB@Position - mRNA 133 -- 142@LB@Position - sRNA 25 -- 34@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 25 -- 31@LB@
109	0.009396	0.2693	b1958	yedI	-10.22	0.013950	83 -- 110	33 -- 54	DUF808 family inner membrane protein	_____________82_____________________________111\n_____________\|______________________________\|\n5'-AAA...CAUUC______________AUAUAAUU________UUGUU...CCG-3'\n______________UGCU__GGCGAGAG________GCACUUGA\n______________\|\|\|\|__:\|\|:\|\|\|:________\|\|\|\|\|\|:\|\n______________ACGA__UCGUUCUU________CGUGAAUU\n3'-UUU...UUUGA____AU________________________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________55_____________________________32\n	104 -- 110	33 -- 39	-21.3805 kcal/mol	4.98239 kcal/mol	6.17798 kcal/mol	82 111@LB@ \| \|@LB@5'-AAA...CAUUC AUAUAAUU UUGUU...CCG-3'@LB@ UGCU GGCGAGAG GCACUUGA@LB@ \|\|\|\| :\|\|:\|\|\|: \|\|\|\|\|\|:\|@LB@ ACGA UCGUUCUU CGUGAAUU@LB@3'-UUU...UUUGA AU UUUUA...CAA-5'@LB@ \| \|@LB@ 55 32@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 4.98239 kcal/mol@LB@Unfolding Energy - sRNA 6.17798 kcal/mol@LB@@LB@Position - mRNA 83 -- 110@LB@Position - sRNA 33 -- 54@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 33 -- 39@LB@
151	0.0157	0.3349	b0586	entF	-8.26	0.051334	189 -- 199	37 -- 47	enterobactin synthase multienzyme complex component ATP-dependent	_____________188_________200\n_____________\|___________\|\n5'-CCC...CAGUU___________AAUGA...UUG-3'\n______________GCAGGAGGCAC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	193 -- 199	37 -- 43	-17.6877 kcal/mol	4.1913 kcal/mol	5.23944 kcal/mol	188 200@LB@ \| \|@LB@5'-CCC...CAGUU AAUGA...UUG-3'@LB@ GCAGGAGGCAC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -17.6877 kcal/mol@LB@Unfolding Energy - mRNA 4.1913 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
135	0.01294	0.3087	b3785	wzzE	-4.46	0.409883	275 -- 291	39 -- 56	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein	_____________274_________________292\n_____________\|___________________\|\n5'-GCU...CGUAC___________U_______UAUGG...UUA-3'\n______________CUUGU__GGGC_GGGAAGC\n______________\|\|\|\|:__::\|\|_::\|\|\|\|\|\n______________GAACG__UUCG_UUCUUCG\n3'-UUU...ACUUU_____AA____________UGAAU...CAA-5'\n_____________\|___________________\|\n_____________57__________________38\n	285 -- 291	39 -- 45	-16.5835 kcal/mol	6.01236 kcal/mol	6.11167 kcal/mol	274 292@LB@ \| \|@LB@5'-GCU...CGUAC U UAUGG...UUA-3'@LB@ CUUGU GGGC GGGAAGC@LB@ \|\|\|\|: ::\|\| ::\|\|\|\|\|@LB@ GAACG UUCG UUCUUCG@LB@3'-UUU...ACUUU AA UGAAU...CAA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -4.46 kcal/mol@LB@Hybridization Energy -16.5835 kcal/mol@LB@Unfolding Energy - mRNA 6.01236 kcal/mol@LB@Unfolding Energy - sRNA 6.11167 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 39 -- 45@LB@
142	0.01375	0.3119	b4166	queG	-9.76	0.019130	257 -- 284	36 -- 60	epoxyqueuosine reductase cobalamine-stimulated; queosine biosynthesis	_____________256__________________________285\n_____________\|____________________________\|\n5'-CGC...GGGCU______GG____UC______U_______ACCGA...UCA-3'\n______________GGAACU__GCUU__AGCAGG_AGGUAUU\n______________\|:\|\|\|\|__\|\|\|\|__\|\|\|\|:\|_\|:\|:\|:\|\n______________CUUUGA__CGAA__UCGUUC_UUCGUGA\n3'-UUU...CCCUA______A_____U_______________AUUUU...CAA-5'\n_____________\|____________________________\|\n_____________61___________________________35\n	278 -- 284	36 -- 42	-22.8123 kcal/mol	6.80174 kcal/mol	6.24973 kcal/mol	256 285@LB@ \| \|@LB@5'-CGC...GGGCU GG UC U ACCGA...UCA-3'@LB@ GGAACU GCUU AGCAGG AGGUAUU@LB@ \|:\|\|\|\| \|\|\|\| \|\|\|\|:\| \|:\|:\|:\|@LB@ CUUUGA CGAA UCGUUC UUCGUGA@LB@3'-UUU...CCCUA A U AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -22.8123 kcal/mol@LB@Unfolding Energy - mRNA 6.80174 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 257 -- 284@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 36 -- 42@LB@
133	0.0127	0.3077	b2452	eutH	-4.80	0.352106	186 -- 194	38 -- 46	ethanolamine transporter	_____________185_______195\n_____________\|_________\|\n5'-UUG...ACUAA_________AAGGC...UCC-3'\n______________CAGGGAGUA\n______________\|\|:\|:\|\|:\|\n______________GUUCUUCGU\n3'-UUU...AAUUC_________GAAUU...CAA-5'\n_____________\|_________\|\n_____________47________37\n	188 -- 194	38 -- 44	-8.62764 kcal/mol	1.2009 kcal/mol	2.62609 kcal/mol	185 195@LB@ \| \|@LB@5'-UUG...ACUAA AAGGC...UCC-3'@LB@ CAGGGAGUA@LB@ \|\|:\|:\|\|:\|@LB@ GUUCUUCGU@LB@3'-UUU...AAUUC GAAUU...CAA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.80 kcal/mol@LB@Hybridization Energy -8.62764 kcal/mol@LB@Unfolding Energy - mRNA 1.2009 kcal/mol@LB@Unfolding Energy - sRNA 2.62609 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 38 -- 44@LB@
163	0.0182	0.3566	b0397	sbcC	-8.10	0.056577	196 -- 210	26 -- 43	exonuclease dsDNA ATP-dependent	_____________195________________211\n_____________\|__________________\|\n5'-GAA...AACAC__________________UCAGC...UUG-3'\n______________GAAGCAU___GAAAAUUC\n______________\|\|\|\|\|\|:___:\|\|\|\|\|\|\|\n______________CUUCGUG___UUUUUAAG\n3'-UUU...UCGUU_______AAU________CAAUG...CAA-5'\n_____________\|__________________\|\n_____________44_________________25\n	204 -- 210	26 -- 32	-13.6528 kcal/mol	1.79109 kcal/mol	3.75931 kcal/mol	195 211@LB@ \| \|@LB@5'-GAA...AACAC UCAGC...UUG-3'@LB@ GAAGCAU GAAAAUUC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|\|@LB@ CUUCGUG UUUUUAAG@LB@3'-UUU...UCGUU AAU CAAUG...CAA-5'@LB@ \| \|@LB@ 44 25@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -13.6528 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 3.75931 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 26 -- 43@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 26 -- 32@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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