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
55	0.01149	0.6177	b3287	def	-9.61	0.049470	133 -- 146	41 -- 54	peptide deformylase	_____________132____________147\n_____________\|______________\|\n5'-AUA...GUCAA______________GUCUA...AUG-3'\n______________UCAGAGGGGGAUUU\n______________\|\|\|:\|\|:\|\|:\|\|\|\|\n______________AGUUUCUCCUUAAA\n3'-UUU...CGGGC______________GUAAA...ACA-5'\n_____________\|______________\|\n_____________55_____________40\n	140 -- 146	41 -- 47	-17.2173 kcal/mol	6.66439 kcal/mol	0.946064 kcal/mol	132 147@LB@ \| \|@LB@5'-AUA...GUCAA GUCUA...AUG-3'@LB@ UCAGAGGGGGAUUU@LB@ \|\|\|:\|\|:\|\|:\|\|\|\|@LB@ AGUUUCUCCUUAAA@LB@3'-UUU...CGGGC GUAAA...ACA-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -17.2173 kcal/mol@LB@Unfolding Energy - mRNA 6.66439 kcal/mol@LB@Unfolding Energy - sRNA 0.946064 kcal/mol@LB@@LB@Position - mRNA 133 -- 146@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 41 -- 47@LB@
162	0.03332	0.6177	b3304	rplR	-8.58	0.079933	170 -- 177	46 -- 53	50S ribosomal subunit protein L18	_____________169______178\n_____________\|________\|\n5'-AUC...CGUAC________CUAAG...GUC-3'\n______________CAAAGAGG\n______________\|\|\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	171 -- 177	46 -- 52	-11.2869 kcal/mol	1.80103 kcal/mol	0.910679 kcal/mol	169 178@LB@ \| \|@LB@5'-AUC...CGUAC CUAAG...GUC-3'@LB@ CAAAGAGG@LB@ \|\|\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.2869 kcal/mol@LB@Unfolding Energy - mRNA 1.80103 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 170 -- 177@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 46 -- 52@LB@
127	0.0247	0.6177	b3306	rpsH	-8.61	0.078593	53 -- 64	46 -- 57	30S ribosomal subunit protein S8	_____________52___________65\n_____________\|____________\|\n5'-AGC...CGCUG________C___UCGUC...AAG-3'\n______________CCGUCAAA_AGG\n______________\|\|\|\|\|\|\|\|_\|\|\|\n______________GGCAGUUU_UCC\n3'-UUU...AACCG________C___UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	54 -- 60	50 -- 56	-14.2597 kcal/mol	2.91134 kcal/mol	2.7365 kcal/mol	52 65@LB@ \| \|@LB@5'-AGC...CGCUG C UCGUC...AAG-3'@LB@ CCGUCAAA AGG@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ GGCAGUUU UCC@LB@3'-UUU...AACCG C UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -14.2597 kcal/mol@LB@Unfolding Energy - mRNA 2.91134 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 50 -- 56@LB@
44	0.008636	0.6129	b3317	rplB	-9.78	0.045660	184 -- 194	43 -- 55	50S ribosomal subunit protein L2	_____________183___________195\n_____________\|_____________\|\n5'-GCA...AGUAA_____________AAUAC...UGC-3'\n______________GUC__GGAGGAGU\n______________\|\|\|__:\|\|\|\|\|:\|\n______________CAG__UCUCCUUA\n3'-UUU...CCGGG___UU________AAGUA...ACA-5'\n_____________\|_____________\|\n_____________56____________42\n	188 -- 194	43 -- 49	-13.3143 kcal/mol	2.58995 kcal/mol	0.946481 kcal/mol	183 195@LB@ \| \|@LB@5'-GCA...AGUAA AAUAC...UGC-3'@LB@ GUC GGAGGAGU@LB@ \|\|\| :\|\|\|\|\|:\|@LB@ CAG UCUCCUUA@LB@3'-UUU...CCGGG UU AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.3143 kcal/mol@LB@Unfolding Energy - mRNA 2.58995 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 184 -- 194@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
118	0.0238	0.6177	b3321	rpsJ	-9.75	0.046314	151 -- 177	30 -- 55	30S ribosomal subunit protein S10	_____________150___________________________178\n_____________\|_____________________________\|\n5'-UUC...AAUGG___U_________AA_______CG_____AAAAU...GUG-3'\n______________GUC___GAGGAGU__UCAUUUU__UUUAU\n______________\|\|\|___\|\|\|\|\|:\|__\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CAG___CUCCUUA__AGUAAAA__AAAUA\n3'-UUU...CCGGG___UUU_______A_______________AUAAU...ACA-5'\n_____________\|_____________________________\|\n_____________56____________________________29\n	164 -- 170	35 -- 41	-16.2369 kcal/mol	5.30163 kcal/mol	1.18773 kcal/mol	150 178@LB@ \| \|@LB@5'-UUC...AAUGG U AA CG AAAAU...GUG-3'@LB@ GUC GAGGAGU UCAUUUU UUUAU@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ CAG CUCCUUA AGUAAAA AAAUA@LB@3'-UUU...CCGGG UUU A AUAAU...ACA-5'@LB@ \| \|@LB@ 56 29@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -16.2369 kcal/mol@LB@Unfolding Energy - mRNA 5.30163 kcal/mol@LB@Unfolding Energy - sRNA 1.18773 kcal/mol@LB@@LB@Position - mRNA 151 -- 177@LB@Position - sRNA 30 -- 55@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 35 -- 41@LB@
45	0.009176	0.6129	b3389	aroB	-8.88	0.069424	203 -- 218	37 -- 52	3-dehydroquinate synthase	_____________202______________219\n_____________\|________________\|\n5'-ACA...GUUAU________UUG_____ACUCU...CGG-3'\n______________GGAGAGGA___UCGUU\n______________::\|\|\|\|\|\|___\|\|:\|\|\n______________UUUCUCCU___AGUAA\n3'-UUU...GGCAG________UAA_____AAAAA...ACA-5'\n_____________\|________________\|\n_____________53_______________36\n	204 -- 210	45 -- 51	-14.6346 kcal/mol	4.67835 kcal/mol	1.07641 kcal/mol	202 219@LB@ \| \|@LB@5'-ACA...GUUAU UUG ACUCU...CGG-3'@LB@ GGAGAGGA UCGUU@LB@ ::\|\|\|\|\|\| \|\|:\|\|@LB@ UUUCUCCU AGUAA@LB@3'-UUU...GGCAG UAA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.6346 kcal/mol@LB@Unfolding Energy - mRNA 4.67835 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 203 -- 218@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 45 -- 51@LB@
23	0.004411	0.5992	b3390	aroK	-10.22	0.037117	283 -- 298	39 -- 54	shikimate kinase I	_____________282______________299\n_____________\|________________\|\n5'-UGG...ACAAC____UAU_________CG-3'\n______________UCAA___GGAAUUUUA\n______________\|\|\|\|___\|\|\|\|\|\|\|:\|\n______________AGUU___CCUUAAAGU\n3'-UUU...CGGGC____UCU_________AAAAA...ACA-5'\n_____________\|________________\|\n_____________55_______________38\n	292 -- 298	39 -- 45	-11.8677 kcal/mol	0.499768 kcal/mol	1.1491 kcal/mol	282 299@LB@ \| \|@LB@5'-UGG...ACAAC UAU CG-3'@LB@ UCAA GGAAUUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|:\|@LB@ AGUU CCUUAAAGU@LB@3'-UUU...CGGGC UCU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -11.8677 kcal/mol@LB@Unfolding Energy - mRNA 0.499768 kcal/mol@LB@Unfolding Energy - sRNA 1.1491 kcal/mol@LB@@LB@Position - mRNA 283 -- 298@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@LB@
47	0.009275	0.6129	b3412	bioH	-9.55	0.050822	229 -- 245	38 -- 55	pimeloyl-ACP methyl ester carboxylesterase	_____________228_________________246\n_____________\|___________________\|\n5'-GGC...CAAAG_____________G_____CUUGU...ACG-3'\n______________GUC__AGGGGAAU_UUCAU\n______________\|\|\|__\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________CAG__UCUCCUUA_AAGUA\n3'-UUU...CCGGG___UU______________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	233 -- 239	43 -- 49	-15.7204 kcal/mol	5.00086 kcal/mol	1.17036 kcal/mol	228 246@LB@ \| \|@LB@5'-GGC...CAAAG G CUUGU...ACG-3'@LB@ GUC AGGGGAAU UUCAU@LB@ \|\|\| \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ CAG UCUCCUUA AAGUA@LB@3'-UUU...CCGGG UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -15.7204 kcal/mol@LB@Unfolding Energy - mRNA 5.00086 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 229 -- 245@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 43 -- 49@LB@
111	0.02245	0.6177	b3413	gntX	-10.38	0.034336	253 -- 267	41 -- 55	DNA catabolic protein	_____________252_____________268\n_____________\|_______________\|\n5'-CCC...GUUAG____UU_________GUUCG...AUA-3'\n______________GUCA__GGGGGAUUU\n______________\|\|\|\|__\|:\|\|:\|\|\|\|\n______________CAGU__CUCCUUAAA\n3'-UUU...CCGGG____UU_________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	261 -- 267	41 -- 47	-16.783 kcal/mol	5.45091 kcal/mol	0.947844 kcal/mol	252 268@LB@ \| \|@LB@5'-CCC...GUUAG UU GUUCG...AUA-3'@LB@ GUCA GGGGGAUUU@LB@ \|\|\|\| \|:\|\|:\|\|\|\|@LB@ CAGU CUCCUUAAA@LB@3'-UUU...CCGGG UU GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.783 kcal/mol@LB@Unfolding Energy - mRNA 5.45091 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 253 -- 267@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 41 -- 47@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase	_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@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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