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
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@
127	0.01193	0.3024	b3625	waaY	-10.33	0.012897	24 -- 38	26 -- 41	lipopolysaccharide core biosynthesis protein	_____________23_______________39\n_____________\|________________\|\n5'-CCA...AAAAU________________CCCCU...UAA-3'\n______________AGC_UUUAGAAAAUUC\n______________\|\|\|_:\|\|\|:\|\|\|\|\|\|\|\n______________UCG_GAAUUUUUUAAG\n3'-UUU...GUUCU___U____________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	32 -- 38	26 -- 32	-12.5754 kcal/mol	0.594404 kcal/mol	1.64829 kcal/mol	23 39@LB@ \| \|@LB@5'-CCA...AAAAU CCCCU...UAA-3'@LB@ AGC UUUAGAAAAUUC@LB@ \|\|\| :\|\|\|:\|\|\|\|\|\|\|@LB@ UCG GAAUUUUUUAAG@LB@3'-UUU...GUUCU U CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -12.5754 kcal/mol@LB@Unfolding Energy - mRNA 0.594404 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 26 -- 32@LB@
131	0.01234	0.3033	b4139	aspA	-5.03	0.315570	237 -- 252	26 -- 41	aspartate ammonia-lyase	_____________236______________253\n_____________\|________________\|\n5'-GAU...UGUUG_____CA_________CAGCU...ACU-3'\n______________GGUAC__GGGAAGUUC\n______________:\|:\|\|__:::\|\|:\|\|\|\n______________UCGUG__UUUUUUAAG\n3'-UUU...GUUCU_____AA_________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	246 -- 252	26 -- 32	-10.8102 kcal/mol	4.127 kcal/mol	1.64829 kcal/mol	236 253@LB@ \| \|@LB@5'-GAU...UGUUG CA CAGCU...ACU-3'@LB@ GGUAC GGGAAGUUC@LB@ :\|:\|\| :::\|\|:\|\|\|@LB@ UCGUG UUUUUUAAG@LB@3'-UUU...GUUCU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -10.8102 kcal/mol@LB@Unfolding Energy - mRNA 4.127 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 237 -- 252@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 26 -- 32@LB@
139	0.01338	0.3093	b3765	yifB	-8.91	0.033732	103 -- 139	26 -- 57	magnesium chelatase family protein and putative transcriptional regulator	_____________102______________________________________140\n_____________\|________________________________________\|\n5'-AAA...ACUUC______ACAAA___A_____AUC__C______________ACGAA...CGA-3'\n______________ACUUGC_____UAA_CAGGA___AG_CACU___AAAAUUC\n______________\|\|\|\|\|\|_____\|\|\|_\|\|:\|\|___\|\|_\|\|\|\|___\|\|\|\|\|\|\|\n______________UGAACG_____AUU_GUUCU___UC_GUGA___UUUUAAG\n3'-UUU...UACUU______A_______C_______________AUU_______CAAUG...CAA-5'\n_____________\|________________________________________\|\n_____________58_______________________________________25\n	133 -- 139	26 -- 32	-18.0428 kcal/mol	2.85625 kcal/mol	6.27605 kcal/mol	102 140@LB@ \| \|@LB@5'-AAA...ACUUC ACAAA A AUC C ACGAA...CGA-3'@LB@ ACUUGC UAA CAGGA AG CACU AAAAUUC@LB@ \|\|\|\|\|\| \|\|\| \|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UGAACG AUU GUUCU UC GUGA UUUUAAG@LB@3'-UUU...UACUU A C AUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -18.0428 kcal/mol@LB@Unfolding Energy - mRNA 2.85625 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 103 -- 139@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 26 -- 32@LB@
148	0.01496	0.3255	b2202	napC	-5.47	0.254772	189 -- 211	26 -- 46	quinol dehydrogenase electron source for NapAB	_____________188_____________________212\n_____________\|_______________________\|\n5'-ACG...GGAAA_______U____A__________UGACC...GUU-3'\n______________UAAGAGG_UAUU_UGGGAAAUUC\n______________:\|\|\|\|:\|_:\|:\|_\|:::\|\|\|\|\|\|\n______________GUUCUUC_GUGA_AUUUUUUAAG\n3'-UUU...AAUUC_______________________CAAUG...CAA-5'\n_____________\|_______________________\|\n_____________47______________________25\n	205 -- 211	26 -- 32	-14.2639 kcal/mol	2.66276 kcal/mol	6.13041 kcal/mol	188 212@LB@ \| \|@LB@5'-ACG...GGAAA U A UGACC...GUU-3'@LB@ UAAGAGG UAUU UGGGAAAUUC@LB@ :\|\|\|\|:\| :\|:\| \|:::\|\|\|\|\|\|@LB@ GUUCUUC GUGA AUUUUUUAAG@LB@3'-UUU...AAUUC CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -14.2639 kcal/mol@LB@Unfolding Energy - mRNA 2.66276 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 26 -- 32@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@
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@
179	0.02107	0.3768	b3226	nanR	-7.22	0.096643	281 -- 296	26 -- 41	sialic acid-inducible nan operon repressor	_____________280______________297\n_____________\|________________\|\n5'-AUU...CCGCU_____G_______C__UCCG-3'\n______________GGCGC_UAAAAAA_UC\n______________:\|\|:\|_\|\|\|\|\|\|\|_\|\|\n______________UCGUG_AUUUUUU_AG\n3'-UUU...GUUCU_____A_______A__CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	287 -- 293	29 -- 35	-11.6683 kcal/mol	2.7952 kcal/mol	1.64829 kcal/mol	280 297@LB@ \| \|@LB@5'-AUU...CCGCU G C UCCG-3'@LB@ GGCGC UAAAAAA UC@LB@ :\|\|:\| \|\|\|\|\|\|\| \|\|@LB@ UCGUG AUUUUUU AG@LB@3'-UUU...GUUCU A A CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -11.6683 kcal/mol@LB@Unfolding Energy - mRNA 2.7952 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 29 -- 35@LB@
198	0.02375	0.3864	b3946	fsaB	-8.18	0.053967	105 -- 117	26 -- 40	fructose-6-phosphate aldolase 2	_____________104_____________118\n_____________\|_______________\|\n5'-UGG...AUCAU_______________CGUAA...CUG-3'\n______________GCAC__GAAGAAUUC\n______________\|\|\|\|__:\|\|:\|\|\|\|\|\n______________CGUG__UUUUUUAAG\n3'-UUU...UUCUU____AA_________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	111 -- 117	26 -- 32	-11.851 kcal/mol	2.02524 kcal/mol	1.64811 kcal/mol	104 118@LB@ \| \|@LB@5'-UGG...AUCAU CGUAA...CUG-3'@LB@ GCAC GAAGAAUUC@LB@ \|\|\|\| :\|\|:\|\|\|\|\|@LB@ CGUG UUUUUUAAG@LB@3'-UUU...UUCUU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.18 kcal/mol@LB@Hybridization Energy -11.851 kcal/mol@LB@Unfolding Energy - mRNA 2.02524 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 105 -- 117@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 26 -- 32@LB@
24	0.000694	0.09021	b2531	iscR	-7.21	0.097486	53 -- 65	27 -- 41	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________52______________66\n_____________\|_______________\|\n5'-AUG...AAAAU_______________AAAUA...AAC-3'\n______________GGCACU__GAAGGUU\n______________:\|\|\|\|\|__:\|\|::\|\|\n______________UCGUGA__UUUUUAA\n3'-UUU...GUUCU______AU_______GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	59 -- 65	27 -- 33	-10.1429 kcal/mol	1.29 kcal/mol	1.6427 kcal/mol	52 66@LB@ \| \|@LB@5'-AUG...AAAAU AAAUA...AAC-3'@LB@ GGCACU GAAGGUU@LB@ :\|\|\|\|\| :\|\|::\|\|@LB@ UCGUGA UUUUUAA@LB@3'-UUU...GUUCU AU GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -10.1429 kcal/mol@LB@Unfolding Energy - mRNA 1.29 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 53 -- 65@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 27 -- 33@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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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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