Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
19	0.003501	0.593	b2019	hisG	-12.73	0.011332	183 -- 194	43 -- 54	ATP phosphoribosyltransferase	_____________182__________195\n_____________\|____________\|\n5'-UUU...CAGGU____________AACAA...AUC-3'\n______________UUAAAGAGGAAU\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUUUCUCCUUA\n3'-UUU...CGGGC____________AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	188 -- 194	43 -- 49	-14.9017 kcal/mol	1.23041 kcal/mol	0.944705 kcal/mol	182 195@LB@ \| \|@LB@5'-UUU...CAGGU AACAA...AUC-3'@LB@ UUAAAGAGGAAU@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUUUCUCCUUA@LB@3'-UUU...CGGGC AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -14.9017 kcal/mol@LB@Unfolding Energy - mRNA 1.23041 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
35	0.00713	0.6129	b2025	hisF	-8.66	0.076851	182 -- 193	46 -- 57	imidazole glycerol phosphate synthase catalytic subunit with HisH	_____________181__________194\n_____________\|____________\|\n5'-UCG...AUUCA____G_______CCAUC...UGC-3'\n______________CCGU_AAGGAGG\n______________\|\|\|\|_\|\|:\|\|\|\|\n______________GGCA_UUUCUCC\n3'-UUU...AACCG____G_______UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	187 -- 193	46 -- 52	-16.1254 kcal/mol	4.72855 kcal/mol	2.7365 kcal/mol	181 194@LB@ \| \|@LB@5'-UCG...AUUCA G CCAUC...UGC-3'@LB@ CCGU AAGGAGG@LB@ \|\|\|\| \|\|:\|\|\|\|@LB@ GGCA UUUCUCC@LB@3'-UUU...AACCG G UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -16.1254 kcal/mol@LB@Unfolding Energy - mRNA 4.72855 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 46 -- 52@LB@
175	0.03585	0.6177	b2028	ugd	-9.30	0.056993	217 -- 248	46 -- 74	UDP-glucose 6-dehydrogenase	_____________216______________________________249\n_____________\|________________________________\|\n5'-GCU...CAUUU______C_G_____GUA___________C___CUUCU...CAC-3'\n______________CCGGUA_U_GCUAU___GGCUUGUCAAA_GGG\n______________\|\|::\|\|_\|_\|\|\|\|\|___\|\|\|::\|\|\|\|\|\|_:\|\|\n______________GGUUAU_A_CGAUA___CCGGGCAGUUU_UCC\n3'-UUU...UUACC________G_____A_____________C___UUAAA...ACA-5'\n_____________\|________________________________\|\n_____________75_______________________________45\n	238 -- 244	50 -- 56	-30.8605 kcal/mol	10.2215 kcal/mol	11.335 kcal/mol	216 249@LB@ \| \|@LB@5'-GCU...CAUUU C G GUA C CUUCU...CAC-3'@LB@ CCGGUA U GCUAU GGCUUGUCAAA GGG@LB@ \|\|::\|\| \| \|\|\|\|\| \|\|\|::\|\|\|\|\|\| :\|\|@LB@ GGUUAU A CGAUA CCGGGCAGUUU UCC@LB@3'-UUU...UUACC G A C UUAAA...ACA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -30.8605 kcal/mol@LB@Unfolding Energy - mRNA 10.2215 kcal/mol@LB@Unfolding Energy - sRNA 11.335 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 50 -- 56@LB@
124	0.02431	0.6177	b2044	wcaL	-7.42	0.135034	145 -- 156	45 -- 56	putative glycosyl transferase	_____________144__________157\n_____________\|____________\|\n5'-GGG...GUGAG_______C____AUGCA...AGA-3'\n______________CGUCAGA_AGGA\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________GCAGUUU_UCCU\n3'-UUU...ACCGG_______C____UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	145 -- 151	50 -- 56	-12.5799 kcal/mol	4.21745 kcal/mol	0.938337 kcal/mol	144 157@LB@ \| \|@LB@5'-GGG...GUGAG C AUGCA...AGA-3'@LB@ CGUCAGA AGGA@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ GCAGUUU UCCU@LB@3'-UUU...ACCGG C UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -12.5799 kcal/mol@LB@Unfolding Energy - mRNA 4.21745 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 145 -- 156@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
94	0.01884	0.6177	b2048	cpsG	-10.80	0.028164	47 -- 56	45 -- 54	phosphomannomutase	_____________46_________57\n_____________\|__________\|\n5'-GGG...UUAUC__________UGAUG...GCG-3'\n______________UCGAAGAGGA\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	50 -- 56	45 -- 51	-14.144 kcal/mol	2.41054 kcal/mol	0.929144 kcal/mol	46 57@LB@ \| \|@LB@5'-GGG...UUAUC UGAUG...GCG-3'@LB@ UCGAAGAGGA@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -14.144 kcal/mol@LB@Unfolding Energy - mRNA 2.41054 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 47 -- 56@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 45 -- 51@LB@
21	0.004054	0.5992	b2076	mdtC	-11.67	0.018717	158 -- 193	45 -- 78	multidrug efflux system subunit C	_____________157____________________________________194\n_____________\|______________________________________\|\n5'-CUC...GCAUU____A____AAGC____UU__________UG_______GGCGU...CGG-3'\n______________GUGG_CCAA____CGCU____GCCCGUCA__AAGAGGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|____\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UACC_GGUU____GCGA____CGGGCAGU__UUCUCCU\n_____3'-UUUUUU_________AUA_____UAAC_________________UAAAG...ACA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________44\n	187 -- 193	45 -- 51	-37.8051 kcal/mol	12.6053 kcal/mol	13.5316 kcal/mol	157 194@LB@ \| \|@LB@5'-CUC...GCAUU A AAGC UU UG GGCGU...CGG-3'@LB@ GUGG CCAA CGCU GCCCGUCA AAGAGGA@LB@ :\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UACC GGUU GCGA CGGGCAGU UUCUCCU@LB@ 3'-UUUUUU AUA UAAC UAAAG...ACA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -37.8051 kcal/mol@LB@Unfolding Energy - mRNA 12.6053 kcal/mol@LB@Unfolding Energy - sRNA 13.5316 kcal/mol@LB@@LB@Position - mRNA 158 -- 193@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
82	0.01753	0.6177	b2204	napH	-9.88	0.043521	152 -- 162	42 -- 52	ferredoxin-type protein	_____________151_________163\n_____________\|___________\|\n5'-CAC...UGGCG___________AGGUC...UCU-3'\n______________AAAGGGGAGUU\n______________\|\|\|\|:\|\|\|:\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	156 -- 162	42 -- 48	-12.4472 kcal/mol	1.70007 kcal/mol	0.866923 kcal/mol	151 163@LB@ \| \|@LB@5'-CAC...UGGCG AGGUC...UCU-3'@LB@ AAAGGGGAGUU@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -12.4472 kcal/mol@LB@Unfolding Energy - mRNA 1.70007 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 42 -- 48@LB@
145	0.02855	0.6177	b2252	ais	-5.71	0.282709	182 -- 202	38 -- 55	putative LPS core heptose(II)-phosphate phosphatase	_____________181___________________203\n_____________\|_____________________\|\n5'-ACC...CGCUU___UAU___U_______A___GUUAG...GGA-3'\n______________GUC___AGG_GGAGUUU_CGU\n______________\|\|\|___\|:\|_\|\|\|:\|\|\|_\|:\|\n______________CAG___UUC_CCUUAAA_GUA\n3'-UUU...CCGGG___U_____U___________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	192 -- 198	41 -- 47	-12.7294 kcal/mol	5.84979 kcal/mol	1.17036 kcal/mol	181 203@LB@ \| \|@LB@5'-ACC...CGCUU UAU U A GUUAG...GGA-3'@LB@ GUC AGG GGAGUUU CGU@LB@ \|\|\| \|:\| \|\|\|:\|\|\| \|:\|@LB@ CAG UUC CCUUAAA GUA@LB@3'-UUU...CCGGG U U AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -5.71 kcal/mol@LB@Hybridization Energy -12.7294 kcal/mol@LB@Unfolding Energy - mRNA 5.84979 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 182 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 41 -- 47@LB@
92	0.01873	0.6177	b2297	pta	-7.94	0.106741	187 -- 219	22 -- 52	phosphate acetyltransferase	_____________186_______________________________220\n_____________\|_________________________________\|\n5'-CGC...UAACG________UAAAC___GUCCCG___________UGAUC...GUC-3'\n______________AAAGAGGA_____CGU______UAUUAUUAUGC\n______________\|\|\|\|\|\|\|\|_____\|:\|______\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCUCCU_____GUA______AUAAUAAUACG\n3'-UUU...GGCAG________UAAA____AAAAA____________GCAGU...ACA-5'\n_____________\|_________________________________\|\n_____________53________________________________21\n	213 -- 219	22 -- 28	-21.7034 kcal/mol	9.76868 kcal/mol	3.9903 kcal/mol	186 220@LB@ \| \|@LB@5'-CGC...UAACG UAAAC GUCCCG UGAUC...GUC-3'@LB@ AAAGAGGA CGU UAUUAUUAUGC@LB@ \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCU GUA AUAAUAAUACG@LB@3'-UUU...GGCAG UAAA AAAAA GCAGU...ACA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -21.7034 kcal/mol@LB@Unfolding Energy - mRNA 9.76868 kcal/mol@LB@Unfolding Energy - sRNA 3.9903 kcal/mol@LB@@LB@Position - mRNA 187 -- 219@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 22 -- 28@LB@
138	0.02658	0.6177	b2331	smrB	-9.17	0.060779	224 -- 232	45 -- 53	putative DNA endonuclease	_____________223_______233\n_____________\|_________\|\n5'-UCA...CUUAG_________CCAGG...GAC-3'\n______________CGAGGAGGA\n______________\|:\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	226 -- 232	45 -- 51	-12.8038 kcal/mol	2.72026 kcal/mol	0.917553 kcal/mol	223 233@LB@ \| \|@LB@5'-UCA...CUUAG CCAGG...GAC-3'@LB@ CGAGGAGGA@LB@ \|:\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.8038 kcal/mol@LB@Unfolding Energy - mRNA 2.72026 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 224 -- 232@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 45 -- 51@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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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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