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	Additional homologs
35	0.001151	0.1171	stm1336	rplT	-16.07	0.079235	51 -- 96	49 -- 98	50S ribosomal protein L20		_____________50_________________________________________97\n_____________\|__________________________________________\|\n5'-ACC...AAAAA______UA____UA__________CUG_______________AUGGU...GCG-3'\n______________GC_GAC__AACG____AACGUCAC___CGU___CCGAAAGCC\n______________\|\|_:\|\|__\|\|\|:____\|\|\|:\|\|\|\|___\|\|\|___\|\|:\|\|\|\|\|\|\n______________CG_UUG__UUGU____UUGUAGUG___GCA___GGUUUUCGG\n3'-UUU...GUUAA__U___UG____UGUG________UUG___UUC_________GUAGU...UCA-5'\n_____________\|__________________________________________\|\n_____________99_________________________________________48\n	75 -- 81	67 -- 73	-32.5949 kcal/mol	8.04744 kcal/mol	15.2217 kcal/mol	50 97@LB@ \| \|@LB@5'-ACC...AAAAA UA UA CUG AUGGU...GCG-3'@LB@ GC GAC AACG AACGUCAC CGU CCGAAAGCC@LB@ \|\| :\|\| \|\|\|: \|\|\|:\|\|\|\| \|\|\| \|\|:\|\|\|\|\|\|@LB@ CG UUG UUGU UUGUAGUG GCA GGUUUUCGG@LB@3'-UUU...GUUAA U UG UGUG UUG UUC GUAGU...UCA-5'@LB@ \| \|@LB@ 99 48@LB@@LB@@LB@Energy -16.07 kcal/mol@LB@Hybridization Energy -32.5949 kcal/mol@LB@Unfolding Energy - mRNA 8.04744 kcal/mol@LB@Unfolding Energy - sRNA 15.2217 kcal/mol@LB@@LB@Position - mRNA 51 -- 96@LB@Position - sRNA 49 -- 98@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 67 -- 73@LB@
157	0.008234	0.1845	stm0693	fur	-16.04	0.080078	199 -- 253	31 -- 90	ferric iron uptake transcriptional regulator		_____________198________________________254\n_____________\|__________________________\|\n5'-GCA...AUUCC___U___UG__________C______AAGAA...ACG-3'\n______________GCA_GAC__ACAACAAUAC_GCAUUA\n______________\|\|\|_:\|\|__\|\|\|\|\|\|\|:\|\|_:\|\|\|:\|\n______________CGU_UUG__UGUUGUUGUG_UGUAGU\n3'-UUU...GUUAA___________________U______GUUGG...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________30\n	211 -- 217	75 -- 81	-20.9388 kcal/mol	2.89423 kcal/mol	5.29697 kcal/mol	198 254@LB@ \| \|@LB@5'-GCA...AUUCC U UG C AAGAA...ACG-3'@LB@ GCA GAC ACAACAAUAC GCAUUA@LB@ \|\|\| :\|\| \|\|\|\|\|\|\|:\|\| :\|\|\|:\|@LB@ CGU UUG UGUUGUUGUG UGUAGU@LB@3'-UUU...GUUAA U GUUGG...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -16.04 kcal/mol@LB@Hybridization Energy -20.9388 kcal/mol@LB@Unfolding Energy - mRNA 2.89423 kcal/mol@LB@Unfolding Energy - sRNA 5.29697 kcal/mol@LB@@LB@Position - mRNA 199 -- 253@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
88	0.00402	0.1596	stm2651	yfiQ	-16.02	0.080775	116 -- 159	50 -- 88	protein acetyltransferase		_____________115__________________________160\n_____________\|____________________________\|\n5'-CAA...AGGAA__________UCCGGGA___________AUAAA...GUA-3'\n______________AAACGCAACA_______AACGUCACAGC\n______________\|\|\|\|:\|\|\|\|\|_______\|\|\|:\|\|\|\|\|:\|\n______________UUUGUGUUGU_______UUGUAGUGUUG\n3'-UUU...UAACG__________UGUG______________GCAUU...UCA-5'\n_____________\|____________________________\|\n_____________89___________________________49\n	137 -- 143	64 -- 70	-25.6269 kcal/mol	4.45838 kcal/mol	7.90699 kcal/mol	115 160@LB@ \| \|@LB@5'-CAA...AGGAA UCCGGGA AUAAA...GUA-3'@LB@ AAACGCAACA AACGUCACAGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|\|:\|\|\|\|\|:\|@LB@ UUUGUGUUGU UUGUAGUGUUG@LB@3'-UUU...UAACG UGUG GCAUU...UCA-5'@LB@ \| \|@LB@ 89 49@LB@@LB@@LB@Energy -16.02 kcal/mol@LB@Hybridization Energy -25.6269 kcal/mol@LB@Unfolding Energy - mRNA 4.45838 kcal/mol@LB@Unfolding Energy - sRNA 7.90699 kcal/mol@LB@@LB@Position - mRNA 116 -- 159@LB@Position - sRNA 50 -- 88@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 64 -- 70@LB@
40	0.001409	0.1215	stm4578	serB	-16.00	0.081343	27 -- 78	37 -- 87	phosphoserine phosphatase SerB		_____________26___________________79\n_____________\|____________________\|\n5'-CUG...CAGUG________G___________GACUG...ACC-3'\n______________UG_AGACA_AACAAUACAAU\n______________\|\|_\|:\|\|\|_\|\|\|\|\|:\|\|\|\|:\n______________AC_UUUGU_UUGUUGUGUUG\n3'-UUU...GGUUA__G_____G___________UAGUG...UCA-5'\n_____________\|____________________\|\n_____________88___________________36\n	36 -- 42	72 -- 78	-19.1859 kcal/mol	2.1479 kcal/mol	3.80548 kcal/mol	26 79@LB@ \| \|@LB@5'-CUG...CAGUG G GACUG...ACC-3'@LB@ UG AGACA AACAAUACAAU@LB@ \|\| \|:\|\|\| \|\|\|\|\|:\|\|\|\|:@LB@ AC UUUGU UUGUUGUGUUG@LB@3'-UUU...GGUUA G G UAGUG...UCA-5'@LB@ \| \|@LB@ 88 36@LB@@LB@@LB@Energy -16.00 kcal/mol@LB@Hybridization Energy -19.1859 kcal/mol@LB@Unfolding Energy - mRNA 2.1479 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 27 -- 78@LB@Position - sRNA 37 -- 87@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 72 -- 78@LB@
138	0.007086	0.182	stm0624	citC	-16.00	0.081371	136 -- 192	38 -- 93	[citrate (pro-3S)-lyase] ligase	stm0058	_____________135___________________________193\n_____________\|_____________________________\|\n5'-AAA...AUCAA________________________A____GAAAA...AUA-3'\n______________GUUGC_AACACA___GCGCAACAU_UACA\n______________:\|\|\|\|_\|\|\|\|\|\|___:\|:\|\|\|\|\|\|_:\|\|\|\n______________UAACG_UUGUGU___UGUGUUGUA_GUGU\n3'-UUU...CUGGU_____U______UGU______________UGGCA...UCA-5'\n_____________\|_____________________________\|\n_____________94____________________________37\n	149 -- 155	70 -- 76	-24.6588 kcal/mol	7.05918 kcal/mol	6.32558 kcal/mol	135 193@LB@ \| \|@LB@5'-AAA...AUCAA A GAAAA...AUA-3'@LB@ GUUGC AACACA GCGCAACAU UACA@LB@ :\|\|\|\| \|\|\|\|\|\| :\|:\|\|\|\|\|\| :\|\|\|@LB@ UAACG UUGUGU UGUGUUGUA GUGU@LB@3'-UUU...CUGGU U UGU UGGCA...UCA-5'@LB@ \| \|@LB@ 94 37@LB@@LB@@LB@Energy -16.00 kcal/mol@LB@Hybridization Energy -24.6588 kcal/mol@LB@Unfolding Energy - mRNA 7.05918 kcal/mol@LB@Unfolding Energy - sRNA 6.32558 kcal/mol@LB@@LB@Position - mRNA 136 -- 192@LB@Position - sRNA 38 -- 93@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@
172	0.009395	0.1945	stm3373	mreC	-15.91	0.084075	179 -- 229	45 -- 87	rod shape-determining protein MreC		_____________178____________230\n_____________\|______________\|\n5'-UGA...UGUUA_____AG_______CAUUC...GGA-3'\n______________AUGGA__AGACGGG\n______________\|\|\|\|\|__\|\|\|\|:\|\|\n______________UACCU__UCUGUCC\n3'-UUU...AGUGA_____G________CAUUU...UCA-5'\n_____________\|______________\|\n_____________88_____________44\n	21 -- 27	153 -- 159	-16.2478 kcal/mol	4.60826 kcal/mol	2.82582 kcal/mol	178 230@LB@ \| \|@LB@5'-UGA...UGUUA AG CAUUC...GGA-3'@LB@ AUGGA AGACGGG@LB@ \|\|\|\|\| \|\|\|\|:\|\|@LB@ UACCU UCUGUCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 88 44@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -16.2478 kcal/mol@LB@Unfolding Energy - mRNA 4.60826 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 179 -- 229@LB@Position - sRNA 45 -- 87@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 153 -- 159@LB@
106	0.005253	0.1728	stm1172	flgM	-15.84	0.086212	196 -- 254	36 -- 82	anti-sigma-28 factor FlgM		_____________195________________255\n_____________\|__________________\|\n5'-GGC...GACGC__G_______________CCGGU...CGU-3'\n______________GC_AAAC_CAGCGACACG\n______________\|\|_\|\|\|\|_\|\|:\|:\|\|\|\|:\n______________CG_UUUG_GUUGUUGUGU\n3'-UUU...GUUAA_______U__________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________83_________________35\n	263 -- 269	74 -- 80	-18.0556 kcal/mol	5.48392 kcal/mol	3.73436 kcal/mol	195 255@LB@ \| \|@LB@5'-GGC...GACGC G CCGGU...CGU-3'@LB@ GC AAAC CAGCGACACG@LB@ \|\| \|\|\|\| \|\|:\|:\|\|\|\|:@LB@ CG UUUG GUUGUUGUGU@LB@3'-UUU...GUUAA U UGUAG...UCA-5'@LB@ \| \|@LB@ 83 35@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -18.0556 kcal/mol@LB@Unfolding Energy - mRNA 5.48392 kcal/mol@LB@Unfolding Energy - sRNA 3.73436 kcal/mol@LB@@LB@Position - mRNA 196 -- 254@LB@Position - sRNA 36 -- 82@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 74 -- 80@LB@
200	0.01112	0.198	stm2809	proV	-15.77	0.088450	57 -- 94	50 -- 85	glycine betaine/L-proline ABC transporter ATP-binding protein		_____________56______________________________________95\n_____________\|_______________________________________\|\n5'-UUC...AUCAC_____________C__________AUUCAU_________AAAUU...AAA-3'\n______________AGC_CGAUAGCAC____UCGCAAU______GCCAGAAGC\n______________\|:\|_\|:\|:\|:\|\|\|____\|\|:\|\|\|:______\|\|\|\|:\|\|\|\|\n______________UUG_GUUGUUGUG____AGUGUUG______CGGUUUUCG\n3'-UUU...AACGU___U_________UUGU_______GCAUU__________GGUAG...UCA-5'\n_____________\|_______________________________________\|\n_____________86______________________________________49\n	65 -- 71	75 -- 81	-32.303 kcal/mol	6.98444 kcal/mol	14.5427 kcal/mol	56 95@LB@ \| \|@LB@5'-UUC...AUCAC C AUUCAU AAAUU...AAA-3'@LB@ AGC CGAUAGCAC UCGCAAU GCCAGAAGC@LB@ \|:\| \|:\|:\|:\|\|\| \|\|:\|\|\|: \|\|\|\|:\|\|\|\|@LB@ UUG GUUGUUGUG AGUGUUG CGGUUUUCG@LB@3'-UUU...AACGU U UUGU GCAUU GGUAG...UCA-5'@LB@ \| \|@LB@ 86 49@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -32.303 kcal/mol@LB@Unfolding Energy - mRNA 6.98444 kcal/mol@LB@Unfolding Energy - sRNA 14.5427 kcal/mol@LB@@LB@Position - mRNA 57 -- 94@LB@Position - sRNA 50 -- 85@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 75 -- 81@LB@
149	0.007892	0.1845	stm2071	hisG	-15.61	0.094042	166 -- 245	36 -- 100	ATP phosphoribosyltransferase		_____________165________________________246\n_____________\|__________________________\|\n5'-UUU...AGACC__UU________A________G____ACGCA...AUU-3'\n______________GG__CAGACAGG_UAA____A_AGGA\n______________\|\|__\|\|\|\|\|\|\|\|_\|\|\|____\|_\|\|\|\|\n______________CC__GUCUGUCC_AUU____U_UCCU\n3'-UUU...UGAUA__U_________C___UACA_G____UCACU...UCA-5'\n_____________\|__________________________\|\n_____________101________________________35\n	177 -- 183	153 -- 159	-19.7047 kcal/mol	3.01127 kcal/mol	3.70983 kcal/mol	165 246@LB@ \| \|@LB@5'-UUU...AGACC UU A G ACGCA...AUU-3'@LB@ GG CAGACAGG UAA A AGGA@LB@ \|\| \|\|\|\|\|\|\|\| \|\|\| \| \|\|\|\|@LB@ CC GUCUGUCC AUU U UCCU@LB@3'-UUU...UGAUA U C UACA G UCACU...UCA-5'@LB@ \| \|@LB@ 101 35@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -19.7047 kcal/mol@LB@Unfolding Energy - mRNA 3.01127 kcal/mol@LB@Unfolding Energy - sRNA 3.70983 kcal/mol@LB@@LB@Position - mRNA 166 -- 245@LB@Position - sRNA 36 -- 100@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 153 -- 159@LB@
98	0.004857	0.1728	stm2811	proX	-15.53	0.097032	195 -- 224	56 -- 84	glycine betaine ABC transporter substrate-binding protein		_____________194________________________225\n_____________\|__________________________\|\n5'-GCA...AAGGA__________________________UAUUU...CUA-3'\n______________ACAACGAUGCGACAU____ACCGUGA\n______________\|\|\|\|\|:\|::\|:\|\|\|\|____\|\|\|\|\|:\|\n______________UGUUGUUGUGUUGUA____UGGCAUU\n3'-UUU...GUUUG_______________GUGU_______CGGUU...UCA-5'\n_____________\|__________________________\|\n_____________85_________________________55\n	210 -- 216	59 -- 65	-26.0076 kcal/mol	3.5169 kcal/mol	9.80321 kcal/mol	194 225@LB@ \| \|@LB@5'-GCA...AAGGA UAUUU...CUA-3'@LB@ ACAACGAUGCGACAU ACCGUGA@LB@ \|\|\|\|\|:\|::\|:\|\|\|\| \|\|\|\|\|:\|@LB@ UGUUGUUGUGUUGUA UGGCAUU@LB@3'-UUU...GUUUG GUGU CGGUU...UCA-5'@LB@ \| \|@LB@ 85 55@LB@@LB@@LB@Energy -15.53 kcal/mol@LB@Hybridization Energy -26.0076 kcal/mol@LB@Unfolding Energy - mRNA 3.5169 kcal/mol@LB@Unfolding Energy - sRNA 9.80321 kcal/mol@LB@@LB@Position - mRNA 195 -- 224@LB@Position - sRNA 56 -- 84@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 59 -- 65@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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