Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
111	0.005436	0.1728	stm2683	yfjB	-15.36	0.103307	255 -- 299	43 -- 90	NAD(+) kinase	_____________254___________________________________________________________________300\n_____________\|_____________________________________________________________________\|\n5'-CUC...UUCGC__________GAU____UU______UUCAA__________ACUCACAUU_____AUCAAUCU_______AAGGA...AGG-3'\n______________UUAUUAUGGG___CAGA__CAGGGU________GGGAAGU___________GUC________UCGCUAC\n______________\|:\|:\|\|\|\|\|:___\|\|\|\|__\|\|\|\|\|\|________:\|\|\|\|\|\|___________\|\|\|________\|\|\|\|\|\|\|\n______________AGUGAUACCU___GUCU__GUCCCA________UCCUUCA___________CAG________AGCGAUG\n3'-UUU...UAAUU_________________________UUUACAUG_______CUUUUUCCCAU__________________GCACC...UCA-5'\n_____________\|_____________________________________________________________________\|\n_____________91____________________________________________________________________42\n	179 -- 185	115 -- 121	-40.6869 kcal/mol	14.2494 kcal/mol	12.858 kcal/mol	254 300@LB@ \| \|@LB@5'-CUC...UUCGC GAU UU UUCAA ACUCACAUU AUCAAUCU AAGGA...AGG-3'@LB@ UUAUUAUGGG CAGA CAGGGU GGGAAGU GUC UCGCUAC@LB@ \|:\|:\|\|\|\|\|: \|\|\|\| \|\|\|\|\|\| :\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ AGUGAUACCU GUCU GUCCCA UCCUUCA CAG AGCGAUG@LB@3'-UUU...UAAUU UUUACAUG CUUUUUCCCAU GCACC...UCA-5'@LB@ \| \|@LB@ 91 42@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -40.6869 kcal/mol@LB@Unfolding Energy - mRNA 14.2494 kcal/mol@LB@Unfolding Energy - sRNA 12.858 kcal/mol@LB@@LB@Position - mRNA 255 -- 299@LB@Position - sRNA 43 -- 90@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 115 -- 121@LB@
112	0.005549	0.1728	stm0602	ybdH	-14.01	0.169356	159 -- 193	39 -- 79	oxidoreductase	_____________158_____________194\n_____________\|_______________\|\n5'-GCG...CCCUA_G_____________GAACC...AGC-3'\n______________A_GACAACACAACAU\n______________\|_:\|\|\|\|\|\|\|\|\|\|\|\|\n______________U_UUGUUGUGUUGUA\n3'-UUU...GUUUG_G_____________GUGUU...UCA-5'\n_____________\|_______________\|\n_____________80______________38\n	196 -- 202	70 -- 76	-18.8338 kcal/mol	1.20586 kcal/mol	3.77892 kcal/mol	158 194@LB@ \| \|@LB@5'-GCG...CCCUA G GAACC...AGC-3'@LB@ A GACAACACAACAU@LB@ \| :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ U UUGUUGUGUUGUA@LB@3'-UUU...GUUUG G GUGUU...UCA-5'@LB@ \| \|@LB@ 80 38@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -18.8338 kcal/mol@LB@Unfolding Energy - mRNA 1.20586 kcal/mol@LB@Unfolding Energy - sRNA 3.77892 kcal/mol@LB@@LB@Position - mRNA 159 -- 193@LB@Position - sRNA 39 -- 79@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 70 -- 76@LB@
113	0.005549	0.1728	stm2948	cysJ	-13.61	0.194760	269 -- 298	56 -- 85	sulfite reductase [NADPH] flavoprotein subunit alpha	_____________268_______________________299\n_____________\|_________________________\|\n5'-GUU...CCGCU____UUACUG_______________UGACG...UUG-3'\n______________UUGC______GAACAUAACGACGCA\n______________\|\|\|\|______:\|\|\|\|:\|\|\|:\|\|:\|\|\n______________AACG______UUUGUGUUGUUGUGU\n3'-UUU...UGGUU_________________________UGUAG...UCA-5'\n_____________\|_________________________\|\n_____________86________________________55\n	195 -- 201	74 -- 80	-20.7575 kcal/mol	3.67756 kcal/mol	3.73922 kcal/mol	268 299@LB@ \| \|@LB@5'-GUU...CCGCU UUACUG UGACG...UUG-3'@LB@ UUGC GAACAUAACGACGCA@LB@ \|\|\|\| :\|\|\|\|:\|\|\|:\|\|:\|\|@LB@ AACG UUUGUGUUGUUGUGU@LB@3'-UUU...UGGUU UGUAG...UCA-5'@LB@ \| \|@LB@ 86 55@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -20.7575 kcal/mol@LB@Unfolding Energy - mRNA 3.67756 kcal/mol@LB@Unfolding Energy - sRNA 3.73922 kcal/mol@LB@@LB@Position - mRNA 269 -- 298@LB@Position - sRNA 56 -- 85@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 74 -- 80@LB@
114	0.005594	0.1728	stm4557	holD	-13.75	0.185681	35 -- 94	141 -- 186	DNA polymerase III subunit psi	_____________34_____________________________________________95\n_____________\|______________________________________________\|\n5'-AGG...AAAUC__________C____CAAGACUUCACUUGC_________A______ACAUG...UUC-3'\n______________AUCACUGUGG_GCAG_______________CGGGGUAAA___GCAG\n______________\|\|\|\|\|\|:\|\|\|_:\|\|\|_______________\|:\|\|\|\|\|\|\|___:\|\|\|\n______________UAGUGAUACC_UGUC_______________GUCCCAUUU___UGUC\n3'-UUU...GUAAU_______________U_______________________ACA____CUUCA...UCA-5'\n_____________\|______________________________________________\|\n_____________187____________________________________________140\n	83 -- 89	148 -- 154	-31.7183 kcal/mol	12.8981 kcal/mol	5.60568 kcal/mol	34 95@LB@ \| \|@LB@5'-AGG...AAAUC C CAAGACUUCACUUGC A ACAUG...UUC-3'@LB@ AUCACUGUGG GCAG CGGGGUAAA GCAG@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| :\|\|\|@LB@ UAGUGAUACC UGUC GUCCCAUUU UGUC@LB@3'-UUU...GUAAU U ACA CUUCA...UCA-5'@LB@ \| \|@LB@ 187 140@LB@@LB@@LB@Energy -13.75 kcal/mol@LB@Hybridization Energy -31.7183 kcal/mol@LB@Unfolding Energy - mRNA 12.8981 kcal/mol@LB@Unfolding Energy - sRNA 5.60568 kcal/mol@LB@@LB@Position - mRNA 35 -- 94@LB@Position - sRNA 141 -- 186@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 148 -- 154@LB@
115	0.005604	0.1728	stm0982	himD	-16.93	0.057154	154 -- 192	37 -- 75	integration host factor subunit beta	______________154________193\n______________\|__________\|\n___________5'-___________GGCUG...UGG-3'\n______________AACAACGCAAU\n______________\|\|\|\|\|\|:\|\|\|:\n______________UUGUUGUGUUG\n3'-UUU...UUGUG___________UAGUG...UCA-5'\n_____________\|___________\|\n_____________76__________36\n	5 -- 11	72 -- 78	-12.1177 kcal/mol	1.51678 kcal/mol	3.07616 kcal/mol	154 193@LB@ \| \|@LB@ 5'- GGCUG...UGG-3'@LB@ AACAACGCAAU@LB@ \|\|\|\|\|\|:\|\|\|:@LB@ UUGUUGUGUUG@LB@3'-UUU...UUGUG UAGUG...UCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -12.1177 kcal/mol@LB@Unfolding Energy - mRNA 1.51678 kcal/mol@LB@Unfolding Energy - sRNA 3.07616 kcal/mol@LB@@LB@Position - mRNA 154 -- 192@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 72 -- 78@LB@
116	0.005629	0.1728	stm2662	rluD	-17.46	0.046576	204 -- 257	36 -- 86	23S rRNA pseudouridine(1911/1915/1917) synthase	_____________203____________________258\n_____________\|______________________\|\n5'-UGA...UAUAU__________G___________CGCAA...GUU-3'\n______________GGCACAACGA_UACAAC_UCAC\n______________::\|\|\|\|\|\|:\|_:\|\|\|\|\|_\|\|\|\|\n______________UUGUGUUGUU_GUGUUG_AGUG\n3'-UUU...AACGU_________________U____UUGGC...UCA-5'\n_____________\|______________________\|\n_____________87_____________________35\n	206 -- 212	78 -- 84	-22.2469 kcal/mol	4.97176 kcal/mol	5.3513 kcal/mol	203 258@LB@ \| \|@LB@5'-UGA...UAUAU G CGCAA...GUU-3'@LB@ GGCACAACGA UACAAC UCAC@LB@ ::\|\|\|\|\|\|:\| :\|\|\|\|\| \|\|\|\|@LB@ UUGUGUUGUU GUGUUG AGUG@LB@3'-UUU...AACGU U UUGGC...UCA-5'@LB@ \| \|@LB@ 87 35@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -22.2469 kcal/mol@LB@Unfolding Energy - mRNA 4.97176 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 204 -- 257@LB@Position - sRNA 36 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 78 -- 84@LB@
117	0.005749	0.1738	stm2562	yfhA	-19.31	0.022783	16 -- 66	47 -- 100	two-component system response regulator GlrR	_____________15____________67\n_____________\|_____________\|\n5'-CUG...AGGCC_____________UCGAU...UCG-3'\n______________UUGCAAACGCAGC\n______________\|\|\|\|\|\|\|\|:\|\|:\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________101___________46\n	28 -- 34	80 -- 86	-18.759 kcal/mol	3.6583 kcal/mol	3.5889 kcal/mol	15 67@LB@ \| \|@LB@5'-CUG...AGGCC UCGAU...UCG-3'@LB@ UUGCAAACGCAGC@LB@ \|\|\|\|\|\|\|\|:\|\|:\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 101 46@LB@@LB@@LB@Energy -19.31 kcal/mol@LB@Hybridization Energy -18.759 kcal/mol@LB@Unfolding Energy - mRNA 3.6583 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 16 -- 66@LB@Position - sRNA 47 -- 100@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@LB@
118	0.005761	0.1738	stm1840	yobG	-17.14	0.052758	234 -- 267	153 -- 188	PhoP regulon feedback inhibition protein MgrB	_____________233____________________________________________________________________________________268\n_____________\|______________________________________________________________________________________\|\n5'-ACA...AGAGU___________AUUUCGAU____C_U_____GC________GGUA______U___U_____UGU________GUGUU_________GUGCG...AAU-3'\n______________GGAGUGAAAAA________GGGU_G_UCUCG__AUCGUGGU_______GUA_GCC_GUUGC___GGGCGCAG_____UAAUAUCAU\n______________\|:\|\|\|\|\|\|\|\|\|________\|\|\|\|_\|_\|\|\|\|\|__\|:\|\|\|\|\|\|_______\|:\|_:\|\|_:\|\|\|\|___:::\|:\|\|:_____:\|\|:\|\|\|\|:\n______________CUUCACUUUUU________CCCA_C_AGAGC__UGGCACCA_______CGU_UGG_UAACG___UUUGUGUU_____GUUGUAGUG\n3'-UUU...AUGUC_______________________U_______GA________GACUUAG___C___U________________GUUGU_________UUGGC...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________189____________________________________________________________________________________152\n	274 -- 280	67 -- 73	-62.0847 kcal/mol	28.922 kcal/mol	22.0106 kcal/mol	233 268@LB@ \| \|@LB@5'-ACA...AGAGU AUUUCGAU C U GC GGUA U U UGU GUGUU GUGCG...AAU-3'@LB@ GGAGUGAAAAA GGGU G UCUCG AUCGUGGU GUA GCC GUUGC GGGCGCAG UAAUAUCAU@LB@ \|:\|\|\|\|\|\|\|\|\| \|\|\|\| \| \|\|\|\|\| \|:\|\|\|\|\|\| \|:\| :\|\| :\|\|\|\| :::\|:\|\|: :\|\|:\|\|\|\|:@LB@ CUUCACUUUUU CCCA C AGAGC UGGCACCA CGU UGG UAACG UUUGUGUU GUUGUAGUG@LB@3'-UUU...AUGUC U GA GACUUAG C U GUUGU UUGGC...UCA-5'@LB@ \| \|@LB@ 189 152@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -62.0847 kcal/mol@LB@Unfolding Energy - mRNA 28.922 kcal/mol@LB@Unfolding Energy - sRNA 22.0106 kcal/mol@LB@@LB@Position - mRNA 234 -- 267@LB@Position - sRNA 153 -- 188@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 67 -- 73@LB@
119	0.005831	0.1745	stm1998	umuD	-19.31	0.022806	33 -- 72	46 -- 81	DNA polymerase V subunit UmuD	_____________32___________________73\n_____________\|____________________\|\n5'-AGA...AAAUA____C_______________CGGAA...ACA-3'\n______________UGCG_ACAUGACAAUACAAC\n______________\|\|\|:_\|\|\|::\|\|\|\|:\|\|\|\|\|\n______________ACGU_UGUGUUGUUGUGUUG\n3'-UUU...GGUUA____U_______________UAGUG...UCA-5'\n_____________\|____________________\|\n_____________82___________________45\n	45 -- 51	72 -- 78	-23.5929 kcal/mol	1.21213 kcal/mol	3.80548 kcal/mol	32 73@LB@ \| \|@LB@5'-AGA...AAAUA C CGGAA...ACA-3'@LB@ UGCG ACAUGACAAUACAAC@LB@ \|\|\|: \|\|\|::\|\|\|\|:\|\|\|\|\|@LB@ ACGU UGUGUUGUUGUGUUG@LB@3'-UUU...GGUUA U UAGUG...UCA-5'@LB@ \| \|@LB@ 82 45@LB@@LB@@LB@Energy -19.31 kcal/mol@LB@Hybridization Energy -23.5929 kcal/mol@LB@Unfolding Energy - mRNA 1.21213 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 33 -- 72@LB@Position - sRNA 46 -- 81@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 72 -- 78@LB@
120	0.006002	0.1758	stm2925	nlpD	-17.26	0.050371	258 -- 274	153 -- 170	lipoprotein NlpD	_____________257________________275\n_____________\|__________________\|\n5'-GUU...UGGUU___________U______UUGUA...CGG-3'\n______________UCACUAUGG_C_GGCAGG\n______________\|\|\|\|\|\|\|\|\|_\|_\|:\|\|\|\|\n______________AGUGAUACC_G_CUGUCC\n3'-UUU...UAAUU_________U_U______CAUUU...UCA-5'\n_____________\|__________________\|\n_____________171________________152\n	260 -- 266	162 -- 168	-24.411 kcal/mol	4.59255 kcal/mol	3.4766 kcal/mol	257 275@LB@ \| \|@LB@5'-GUU...UGGUU U UUGUA...CGG-3'@LB@ UCACUAUGG C GGCAGG@LB@ \|\|\|\|\|\|\|\|\| \| \|:\|\|\|\|@LB@ AGUGAUACC G CUGUCC@LB@3'-UUU...UAAUU U U CAUUU...UCA-5'@LB@ \| \|@LB@ 171 152@LB@@LB@@LB@Energy -17.26 kcal/mol@LB@Hybridization Energy -24.411 kcal/mol@LB@Unfolding Energy - mRNA 4.59255 kcal/mol@LB@Unfolding Energy - sRNA 3.4766 kcal/mol@LB@@LB@Position - mRNA 258 -- 274@LB@Position - sRNA 153 -- 170@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 162 -- 168@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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