Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
21	0.0001799	0.02879	b0107	hofB	-20.93	0.000028	267 -- 289	25 -- 48	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________266______________________290\n_____________\|________________________\|\n5'-CCA...GCGAA__________A__U__________CGAUG...CUU-3'\n______________GAGGUGGUUC_UG_UGCGG_UAGU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|_\|:\|:\|_\|\|\|:\n______________CUCCACCAAG_AC_AUGUC_AUCG\n3'-UUU...GAUUC__________G__C_____G____UAAAA...UCG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	270 -- 276	39 -- 45	-28.7026 kcal/mol	3.21789 kcal/mol	4.55759 kcal/mol	266 290@LB@ \| \|@LB@5'-CCA...GCGAA A U CGAUG...CUU-3'@LB@ GAGGUGGUUC UG UGCGG UAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|:\|:\| \|\|\|:@LB@ CUCCACCAAG AC AUGUC AUCG@LB@3'-UUU...GAUUC G C G UAAAA...UCG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -20.93 kcal/mol@LB@Hybridization Energy -28.7026 kcal/mol@LB@Unfolding Energy - mRNA 3.21789 kcal/mol@LB@Unfolding Energy - sRNA 4.55759 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 39 -- 45@LB@
157	0.007972	0.1694	b4350	hsdR	-17.86	0.001148	15 -- 50	1 -- 35	endonuclease R Type I restriction enzyme	_____________14____________________________________51\n_____________\|_____________________________________\|\n5'-UAG...UCAUA_____UC__U___GAAUCA____AG____________UACUA...ACA-3'\n______________GUACA__CU_GCA_______GGU__AUGUUUUUCGGC\n______________\|\|\|\|\|__\|\|_\|\|\|_______\|\|\|__\|\|\|\|\|\|\|\|\|:\|\|\n______________CAUGU__GA_CGU_______CCA__UACAAAAAGUCG\n3'-UUU...AGGAC_____C___U___AAAAUAC___A_____________-5'\n_____________\|____________________________________\|\n_____________36___________________________________1\n	44 -- 50	1 -- 7	-27.1826 kcal/mol	7.83025 kcal/mol	1.49508 kcal/mol	14 51@LB@ \| \|@LB@5'-UAG...UCAUA UC U GAAUCA AG UACUA...ACA-3'@LB@ GUACA CU GCA GGU AUGUUUUUCGGC@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|:\|\|@LB@ CAUGU GA CGU CCA UACAAAAAGUCG@LB@3'-UUU...AGGAC C U AAAAUAC A -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -17.86 kcal/mol@LB@Hybridization Energy -27.1826 kcal/mol@LB@Unfolding Energy - mRNA 7.83025 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 15 -- 50@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 1 -- 7@LB@
176	0.009679	0.1848	b4348	hsdS	-12.85	0.041875	168 -- 192	15 -- 42	specificity determinant for hsdM and hsdR	_____________167__________________________193\n_____________\|____________________________\|\n5'-CUG...CGUCA___G____A____A________G_____GUGAA...UAA-3'\n______________GUU_CUGG___AG__AGCGUUU_GUGGG\n______________\|\|\|_\|\|\|\|___\|\|__\|\|\|:\|\|\|_:\|\|\|\|\n______________CAA_GACC___UC__UCGUAAA_UACCC\n3'-UUU...UCCAC___G____AUG__GA_______A_____AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________43___________________________14\n	180 -- 186	21 -- 27	-24.8178 kcal/mol	7.40251 kcal/mol	4.57031 kcal/mol	167 193@LB@ \| \|@LB@5'-CUG...CGUCA G A A G GUGAA...UAA-3'@LB@ GUU CUGG AG AGCGUUU GUGGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|:\|\|\| :\|\|\|\|@LB@ CAA GACC UC UCGUAAA UACCC@LB@3'-UUU...UCCAC G AUG GA A AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -12.85 kcal/mol@LB@Hybridization Energy -24.8178 kcal/mol@LB@Unfolding Energy - mRNA 7.40251 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 168 -- 192@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 21 -- 27@LB@
74	0.00218	0.09621	b2722	hycD	-16.42	0.003958	87 -- 124	10 -- 46	hydrogenase 3 membrane subunit	_____________86_______________________________________125\n_____________\|________________________________________\|\n5'-UCA...AAUCC________U_______CG________GUGCGA___GA___CGUUG...ACC-3'\n______________GGUG__UC_CUGGUGC__GGCUGGCA______GGG__GUG\n______________\|\|\|\|__\|\|_\|\|\|\|\|:\|__:\|\|\|:\|\|\|______\|\|\|__:\|\|\n______________CCAC__AG_GACCAUG__UCGAUCGU______CCC__UAC\n3'-UUU...UUCCU____CA____________________AAAAUA___AA___AAAAA...UCG-5'\n_____________\|________________________________________\|\n_____________47_______________________________________9\n	104 -- 110	24 -- 30	-37.0223 kcal/mol	15.9993 kcal/mol	4.60552 kcal/mol	86 125@LB@ \| \|@LB@5'-UCA...AAUCC U CG GUGCGA GA CGUUG...ACC-3'@LB@ GGUG UC CUGGUGC GGCUGGCA GGG GUG@LB@ \|\|\|\| \|\| \|\|\|\|\|:\| :\|\|\|:\|\|\| \|\|\| :\|\|@LB@ CCAC AG GACCAUG UCGAUCGU CCC UAC@LB@3'-UUU...UUCCU CA AAAAUA AA AAAAA...UCG-5'@LB@ \| \|@LB@ 47 9@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -37.0223 kcal/mol@LB@Unfolding Energy - mRNA 15.9993 kcal/mol@LB@Unfolding Energy - sRNA 4.60552 kcal/mol@LB@@LB@Position - mRNA 87 -- 124@LB@Position - sRNA 10 -- 46@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 24 -- 30@LB@
127	0.005388	0.142	b2721	hycE	-10.66	0.125013	137 -- 158	1 -- 36	hydrogenase 3 large subunit	_____________136___________________________________159\n_____________\|_____________________________________\|\n5'-UUC...GGCUG___UU____UU__________________________GUUCG...UGA-3'\n______________GGU__GGCU__GCAU_______________UUUUAGC\n______________\|\|\|__:\|\|\|__\|\|\|\|_______________\|\|\|:\|\|\|\n______________CCA__UCGA__CGUA_______________AAAGUCG\n3'-UUU...AAGGA___UG____U_____AAAUACCCAAUACAA_______-5'\n_____________\|____________________________________\|\n_____________37___________________________________1\n	152 -- 158	1 -- 7	-16.3373 kcal/mol	4.17778 kcal/mol	1.49509 kcal/mol	136 159@LB@ \| \|@LB@5'-UUC...GGCUG UU UU GUUCG...UGA-3'@LB@ GGU GGCU GCAU UUUUAGC@LB@ \|\|\| :\|\|\| \|\|\|\| \|\|\|:\|\|\|@LB@ CCA UCGA CGUA AAAGUCG@LB@3'-UUU...AAGGA UG U AAAUACCCAAUACAA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -16.3373 kcal/mol@LB@Unfolding Energy - mRNA 4.17778 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 137 -- 158@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
198	0.01161	0.1971	b2712	hypF	-10.23	0.151482	281 -- 290	24 -- 33	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein	_____________280________291\n_____________\|__________\|\n5'-GAA...GUCUG__________CAGCA...UAA-3'\n______________GCAGCUGGCA\n______________:\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	284 -- 290	24 -- 30	-16.4359 kcal/mol	4.77953 kcal/mol	1.42716 kcal/mol	280 291@LB@ \| \|@LB@5'-GAA...GUCUG CAGCA...UAA-3'@LB@ GCAGCUGGCA@LB@ :\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -16.4359 kcal/mol@LB@Unfolding Energy - mRNA 4.77953 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 281 -- 290@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
3	2.088e-07	0.000234	b2077	iceT	-18.53	0.000593	226 -- 254	1 -- 30	putative citrate/iron-citrate/zinc-citrate efflux transporter	_____________225____________________________255\n_____________\|______________________________\|\n5'-CGG...CACCC_______A_______A_____GC_______UUCUU...UUC-3'\n______________GUUGGCA__UUGUGG_UUGUG__UUUCGGC\n______________\|:\|:\|\|\|__\|\|:\|\|\|_\|\|:\|\|__\|\|\|\|:\|\|\n______________CGAUCGU__AAUACC_AAUAC__AAAGUCG\n3'-UUU...CAUGU_______AA______C_____AA_______-5'\n_____________\|_____________________________\|\n_____________31____________________________1\n	248 -- 254	1 -- 7	-30.4381 kcal/mol	10.4245 kcal/mol	1.48556 kcal/mol	225 255@LB@ \| \|@LB@5'-CGG...CACCC A A GC UUCUU...UUC-3'@LB@ GUUGGCA UUGUGG UUGUG UUUCGGC@LB@ \|:\|:\|\|\| \|\|:\|\|\| \|\|:\|\| \|\|\|\|:\|\|@LB@ CGAUCGU AAUACC AAUAC AAAGUCG@LB@3'-UUU...CAUGU AA C AA -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -18.53 kcal/mol@LB@Hybridization Energy -30.4381 kcal/mol@LB@Unfolding Energy - mRNA 10.4245 kcal/mol@LB@Unfolding Energy - sRNA 1.48556 kcal/mol@LB@@LB@Position - mRNA 226 -- 254@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 1 -- 7@LB@
162	0.008285	0.1719	b3671	ilvB	-15.19	0.009769	264 -- 284	22 -- 41	acetolactate synthase 2 large subunit	_____________263___________________285\n_____________\|_____________________\|\n5'-CUA...UUCAU_______A_____AG______AAGAU...GCA-3'\n______________UUCCUGG_ACAGC__GGCAUU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|__:\|\|\|\|\|\n______________AAGGACC_UGUCG__UCGUAA\n3'-UUU...CCACC_______A_____A_______AAUAC...UCG-5'\n_____________\|_____________________\|\n_____________42____________________21\n	264 -- 270	35 -- 41	-26.898 kcal/mol	7.14717 kcal/mol	4.5564 kcal/mol	263 285@LB@ \| \|@LB@5'-CUA...UUCAU A AG AAGAU...GCA-3'@LB@ UUCCUGG ACAGC GGCAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\| :\|\|\|\|\|@LB@ AAGGACC UGUCG UCGUAA@LB@3'-UUU...CCACC A A AAUAC...UCG-5'@LB@ \| \|@LB@ 42 21@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -26.898 kcal/mol@LB@Unfolding Energy - mRNA 7.14717 kcal/mol@LB@Unfolding Energy - sRNA 4.5564 kcal/mol@LB@@LB@Position - mRNA 264 -- 284@LB@Position - sRNA 22 -- 41@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 35 -- 41@LB@
199	0.0118	0.1975	b0077	ilvI	-11.98	0.066447	6 -- 27	1 -- 30	acetolactate synthase 3 large subunit	_____________5______________________________28\n_____________\|______________________________\|\n______5'-AAAUU_______AG_______A_____________CGAUU...UUU-3'\n______________GCU_GUA__UUGUGGG________UUCAGC\n______________\|\|\|_\|:\|__\|\|:\|\|\|\|________\|\|\|\|\|\|\n______________CGA_CGU__AAUACCC________AAGUCG\n3'-UUU...CAUGU___U___AA_______AAUACAAA______-5'\n_____________\|_____________________________\|\n_____________31____________________________1\n	14 -- 20	15 -- 21	-19.3299 kcal/mol	5.86615 kcal/mol	1.48556 kcal/mol	5 28@LB@ \| \|@LB@ 5'-AAAUU AG A CGAUU...UUU-3'@LB@ GCU GUA UUGUGGG UUCAGC@LB@ \|\|\| \|:\| \|\|:\|\|\|\| \|\|\|\|\|\|@LB@ CGA CGU AAUACCC AAGUCG@LB@3'-UUU...CAUGU U AA AAUACAAA -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.86615 kcal/mol@LB@Unfolding Energy - sRNA 1.48556 kcal/mol@LB@@LB@Position - mRNA 6 -- 27@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 15 -- 21@LB@
53	0.001234	0.07744	b0884	infA	-13.12	0.035785	57 -- 86	2 -- 40	translation initiation factor IF-1	_____________56_______________________________________87\n_____________\|________________________________________\|\n5'-UUU...UGCGC____________U____CG_____________________AGUAA...CUG-3'\n______________UUUUGGUGCGGC_UAGC___________UGUG_UUUUCGG\n______________\|::\|\|\|\|:\|:\|\|_\|\|\|\|___________\|:\|\|_\|\|\|\|\|:\|\n______________AGGACCAUGUCG_AUCG___________AUAC_AAAAGUC\n3'-UUU...CACCA_________________UAAAAUACCCA____A_______G-5'\n_____________\|________________________________________\|\n_____________41_______________________________________1\n	80 -- 86	2 -- 8	-28.8253 kcal/mol	11.0921 kcal/mol	4.60818 kcal/mol	56 87@LB@ \| \|@LB@5'-UUU...UGCGC U CG AGUAA...CUG-3'@LB@ UUUUGGUGCGGC UAGC UGUG UUUUCGG@LB@ \|::\|\|\|\|:\|:\|\| \|\|\|\| \|:\|\| \|\|\|\|\|:\|@LB@ AGGACCAUGUCG AUCG AUAC AAAAGUC@LB@3'-UUU...CACCA UAAAAUACCCA A G-5'@LB@ \| \|@LB@ 41 1@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -28.8253 kcal/mol@LB@Unfolding Energy - mRNA 11.0921 kcal/mol@LB@Unfolding Energy - sRNA 4.60818 kcal/mol@LB@@LB@Position - mRNA 57 -- 86@LB@Position - sRNA 2 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 2 -- 8@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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