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
58	0.002968	0.1645	b0421	ispA	-9.70	0.019970	54 -- 76	25 -- 47	geranyltranstransferase	_____________53______________________77\n_____________\|_______________________\|\n5'-CUG...CCGCU_G__________GAAC_______AACGC...UCG-3'\n______________G_AAGAGGCGCU____GAGUUCG\n______________\|_\|\|\|\|:\|\|:\|\|____:\|:\|\|\|\|\n______________C_UUCUUCGUGA____UUUAAGC\n3'-UUU...GAAUU_G__________AUUU_______AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	70 -- 76	25 -- 31	-22.3845 kcal/mol	6.43631 kcal/mol	6.25056 kcal/mol	53 77@LB@ \| \|@LB@5'-CUG...CCGCU G GAAC AACGC...UCG-3'@LB@ G AAGAGGCGCU GAGUUCG@LB@ \| \|\|\|\|:\|\|:\|\| :\|:\|\|\|\|@LB@ C UUCUUCGUGA UUUAAGC@LB@3'-UUU...GAAUU G AUUU AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -22.3845 kcal/mol@LB@Unfolding Energy - mRNA 6.43631 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 54 -- 76@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 25 -- 31@LB@
140	0.01344	0.3093	b0426	yajQ	-3.92	0.510019	240 -- 246	37 -- 43	phage Phi6 host factor ATP/GTP binding protein	_____________239_____247\n_____________\|_______\|\n5'-UAA...UUCAG_______GUAAC...GUA-3'\n______________GAAGCAC\n______________\|\|\|\|\|\|\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	240 -- 246	37 -- 43	-10.1802 kcal/mol	2.59742 kcal/mol	3.6595 kcal/mol	239 247@LB@ \| \|@LB@5'-UAA...UUCAG GUAAC...GUA-3'@LB@ GAAGCAC@LB@ \|\|\|\|\|\|\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -3.92 kcal/mol@LB@Hybridization Energy -10.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.59742 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 37 -- 43@LB@
93	0.006966	0.2379	b0436	tig	-6.81	0.123164	173 -- 190	25 -- 42	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________172________________191\n_____________\|__________________\|\n5'-UAC...UGACC_______GU__UUU____AGGUA...UCA-3'\n______________GAGCACU__GA___UUUG\n______________:\|\|\|\|\|\|__:\|___\|\|:\|\n______________UUCGUGA__UU___AAGC\n3'-UUU...CGUUC_______AU__UUU____AAUGU...CAA-5'\n_____________\|__________________\|\n_____________43_________________24\n	173 -- 179	36 -- 42	-10.673 kcal/mol	2.21437 kcal/mol	1.64855 kcal/mol	172 191@LB@ \| \|@LB@5'-UAC...UGACC GU UUU AGGUA...UCA-3'@LB@ GAGCACU GA UUUG@LB@ :\|\|\|\|\|\| :\| \|\|:\|@LB@ UUCGUGA UU AAGC@LB@3'-UUU...CGUUC AU UUU AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -10.673 kcal/mol@LB@Unfolding Energy - mRNA 2.21437 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 173 -- 190@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 36 -- 42@LB@
121	0.01057	0.2813	b0452	tesB	-8.75	0.037433	210 -- 223	26 -- 40	acyl-CoA thioesterase 2	_____________209_____________224\n_____________\|_______________\|\n5'-CAA...GUCAG_______________ACUGA...AGG-3'\n______________GCGC_UAAAAAAUUU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|:\n______________CGUG_AUUUUUUAAG\n3'-UUU...UUCUU____A__________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	217 -- 223	26 -- 32	-10.9054 kcal/mol	0.50684 kcal/mol	1.64811 kcal/mol	209 224@LB@ \| \|@LB@5'-CAA...GUCAG ACUGA...AGG-3'@LB@ GCGC UAAAAAAUUU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:@LB@ CGUG AUUUUUUAAG@LB@3'-UUU...UUCUU A CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -10.9054 kcal/mol@LB@Unfolding Energy - mRNA 0.50684 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 210 -- 223@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 26 -- 32@LB@
95	0.007016	0.2379	b0464	acrR	-8.52	0.043413	219 -- 228	37 -- 46	transcriptional repressor	_____________218________229\n_____________\|__________\|\n5'-AAG...CCAAA__________AAGAA...CGC-3'\n______________CAAGAAGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	222 -- 228	37 -- 43	-15.2794 kcal/mol	1.54243 kcal/mol	5.21654 kcal/mol	218 229@LB@ \| \|@LB@5'-AAG...CCAAA AAGAA...CGC-3'@LB@ CAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -8.52 kcal/mol@LB@Hybridization Energy -15.2794 kcal/mol@LB@Unfolding Energy - mRNA 1.54243 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 37 -- 43@LB@
60	0.00317	0.1645	b0466	ybaM	-6.37	0.157728	143 -- 158	25 -- 40	DUF2496 family protein	_____________142_______________159\n_____________\|_________________\|\n5'-GCA...GCCAU_____GG__________AAAAC...CGC-3'\n______________GCGCU__AAAAAAU_CG\n______________\|\|:\|\|__\|\|\|\|\|\|\|_\|\|\n______________CGUGA__UUUUUUA_GC\n3'-UUU...UUCUU_____A________A__AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	150 -- 156	28 -- 34	-11.3444 kcal/mol	3.32327 kcal/mol	1.64821 kcal/mol	142 159@LB@ \| \|@LB@5'-GCA...GCCAU GG AAAAC...CGC-3'@LB@ GCGCU AAAAAAU CG@LB@ \|\|:\|\| \|\|\|\|\|\|\| \|\|@LB@ CGUGA UUUUUUA GC@LB@3'-UUU...UUCUU A A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -11.3444 kcal/mol@LB@Unfolding Energy - mRNA 3.32327 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 143 -- 158@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 28 -- 34@LB@
166	0.01873	0.3614	b0473	htpG	-6.61	0.137913	119 -- 133	26 -- 39	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase	_____________118_____________134\n_____________\|_______________\|\n5'-UCA...GCUCU_________UU____UCCCU...GUG-3'\n______________CGCUUGAAA__AUUC\n______________\|:\|\|\|:\|\|\|__\|\|\|\|\n______________GUGAAUUUU__UAAG\n3'-UUU...UCUUC_________U_____CAAUG...CAA-5'\n_____________\|_______________\|\n_____________40______________25\n	121 -- 127	31 -- 37	-10.0825 kcal/mol	1.82368 kcal/mol	1.64668 kcal/mol	118 134@LB@ \| \|@LB@5'-UCA...GCUCU UU UCCCU...GUG-3'@LB@ CGCUUGAAA AUUC@LB@ \|:\|\|\|:\|\|\| \|\|\|\|@LB@ GUGAAUUUU UAAG@LB@3'-UUU...UCUUC U CAAUG...CAA-5'@LB@ \| \|@LB@ 40 25@LB@@LB@@LB@Energy -6.61 kcal/mol@LB@Hybridization Energy -10.0825 kcal/mol@LB@Unfolding Energy - mRNA 1.82368 kcal/mol@LB@Unfolding Energy - sRNA 1.64668 kcal/mol@LB@@LB@Position - mRNA 119 -- 133@LB@Position - sRNA 26 -- 39@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 31 -- 37@LB@
5	2.271e-05	0.01463	b0476	aes	-9.47	0.023317	2 -- 45	10 -- 53	acetyl esterase	_____________1______________________________________________46\n_____________\|______________________________________________\|\n__________5'-C_____CG_________AUGUUU_____UA_________________UCAUG...CAA-3'\n______________GUUUA___GGGAAGUA______GGAUU__CGUU_UACCGGGAAAUU\n______________\|:\|\|\|___::\|\|\|\|:\|______::\|\|\|__\|\|\|\|_:\|\|\|:\|\|\|\|\|\|:\n______________CGAAU___UUCUUCGU______UUUAA__GCAA_GUGGUCCUUUAG\n3'-UUU...UUGAA_____UCG________GAAUUU___________U____________ACUAC...CAA-5'\n_____________\|______________________________________________\|\n_____________54_____________________________________________9\n	39 -- 45	10 -- 16	-31.5647 kcal/mol	8.26599 kcal/mol	13.8307 kcal/mol	1 46@LB@ \| \|@LB@ 5'-C CG AUGUUU UA UCAUG...CAA-3'@LB@ GUUUA GGGAAGUA GGAUU CGUU UACCGGGAAAUU@LB@ \|:\|\|\| ::\|\|\|\|:\| ::\|\|\| \|\|\|\| :\|\|\|:\|\|\|\|\|\|:@LB@ CGAAU UUCUUCGU UUUAA GCAA GUGGUCCUUUAG@LB@3'-UUU...UUGAA UCG GAAUUU U ACUAC...CAA-5'@LB@ \| \|@LB@ 54 9@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -31.5647 kcal/mol@LB@Unfolding Energy - mRNA 8.26599 kcal/mol@LB@Unfolding Energy - sRNA 13.8307 kcal/mol@LB@@LB@Position - mRNA 2 -- 45@LB@Position - sRNA 10 -- 53@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 10 -- 16@LB@
9	7.531e-05	0.02695	b0491	fetB	-11.86	0.004271	187 -- 209	25 -- 47	iron export ABC transporter permease; peroxide resistance protein	_____________186_____________________210\n_____________\|_______________________\|\n5'-GCC...GAAAU___________GCUAU___C___CAUAA...AGA-3'\n______________GCAGGAAGCAC_____GAA_UCG\n______________\|\|\|:\|\|\|\|\|\|\|_____:\|\|_\|\|\|\n______________CGUUCUUCGUG_____UUU_AGC\n3'-UUU...GAAUU___________AAUUU___A___AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	191 -- 197	37 -- 43	-22.8314 kcal/mol	4.71887 kcal/mol	6.25056 kcal/mol	186 210@LB@ \| \|@LB@5'-GCC...GAAAU GCUAU C CAUAA...AGA-3'@LB@ GCAGGAAGCAC GAA UCG@LB@ \|\|\|:\|\|\|\|\|\|\| :\|\| \|\|\|@LB@ CGUUCUUCGUG UUU AGC@LB@3'-UUU...GAAUU AAUUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -22.8314 kcal/mol@LB@Unfolding Energy - mRNA 4.71887 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
176	0.02022	0.37	b0495	ybbA	-5.55	0.244939	212 -- 247	24 -- 59	putative ABC transporter ATPase	_____________211___________________________________248\n_____________\|_____________________________________\|\n5'-GCC...GCGGA____A_____G____UCAUCAU___________C___CGGUC...UCA-3'\n______________AAAC_UUGUU_AAGU________CUUAAGAAGU_CGU\n______________\|\|\|\|_\|\|\|:\|_\|\|\|:________\|\|\|\|\|:\|\|:\|_\|\|\|\n______________UUUG_AACGA_UUCG________GAAUUUUUUA_GCA\n3'-UUU...CCUAC__________A____UUCUUCGU__________A___AUGUG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________23\n	235 -- 241	30 -- 36	-18.4731 kcal/mol	6.64875 kcal/mol	6.27609 kcal/mol	211 248@LB@ \| \|@LB@5'-GCC...GCGGA A G UCAUCAU C CGGUC...UCA-3'@LB@ AAAC UUGUU AAGU CUUAAGAAGU CGU@LB@ \|\|\|\| \|\|\|:\| \|\|\|: \|\|\|\|\|:\|\|:\| \|\|\|@LB@ UUUG AACGA UUCG GAAUUUUUUA GCA@LB@3'-UUU...CCUAC A UUCUUCGU A AUGUG...CAA-5'@LB@ \| \|@LB@ 60 23@LB@@LB@@LB@Energy -5.55 kcal/mol@LB@Hybridization Energy -18.4731 kcal/mol@LB@Unfolding Energy - mRNA 6.64875 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 212 -- 247@LB@Position - sRNA 24 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 30 -- 36@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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