Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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	Additional homologs
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding		_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
153	0.006198	0.1406	b3459	panM	-8.50	0.116540	144 -- 151	50 -- 57	PanD autocleavage accelerator panothenate synthesis		_____________143______152\n_____________\|________\|\n5'-AAA...AAGCC________AAUUA...UUG-3'\n______________UCCGAUUA\n______________\|\|\|\|\|\|\|\|\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	145 -- 151	50 -- 56	-10.246 kcal/mol	1.44461 kcal/mol	0.317388 kcal/mol	143 152@LB@ \| \|@LB@5'-AAA...AAGCC AAUUA...UUG-3'@LB@ UCCGAUUA@LB@ \|\|\|\|\|\|\|\|@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -10.246 kcal/mol@LB@Unfolding Energy - mRNA 1.44461 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 144 -- 151@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
76	0.001511	0.06993	b3465	rsmD	-10.43	0.033857	227 -- 244	49 -- 65	16S rRNA m(2)G966 methyltransferase SAM-dependent		_____________226________________245\n_____________\|__________________\|\n5'-UUG...GGCAG____________C_____UGGCG...GCC-3'\n______________CGGCCAAAUCCG_AUUAU\n______________\|:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________GUCGGUUUAGGC_UAAUG\n3'-AUU...UAUAA__________________CACUU...AUG-5'\n_____________\|__________________\|\n_____________66_________________48\n	232 -- 238	54 -- 60	-22.129 kcal/mol	5.5281 kcal/mol	6.19707 kcal/mol	226 245@LB@ \| \|@LB@5'-UUG...GGCAG C UGGCG...GCC-3'@LB@ CGGCCAAAUCCG AUUAU@LB@ \|:\|\|\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ GUCGGUUUAGGC UAAUG@LB@3'-AUU...UAUAA CACUU...AUG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -22.129 kcal/mol@LB@Unfolding Energy - mRNA 5.5281 kcal/mol@LB@Unfolding Energy - sRNA 6.19707 kcal/mol@LB@@LB@Position - mRNA 227 -- 244@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 54 -- 60@LB@
64	0.001083	0.05856	b3471	yhhQ	-11.41	0.016564	49 -- 60	44 -- 55	DUF165 family inner membrane protein		_____________48___________61\n_____________\|____________\|\n5'-AAA...GUUAA____________AAUUA...UUC-3'\n______________CGAUUGCGUGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________GCUAAUGCACUU\n3'-AUU...UUUAG____________CAUUU...AUG-5'\n_____________\|____________\|\n_____________56___________43\n	54 -- 60	44 -- 50	-16.5289 kcal/mol	2.50651 kcal/mol	2.62518 kcal/mol	48 61@LB@ \| \|@LB@5'-AAA...GUUAA AAUUA...UUC-3'@LB@ CGAUUGCGUGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ GCUAAUGCACUU@LB@3'-AUU...UUUAG CAUUU...AUG-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -16.5289 kcal/mol@LB@Unfolding Energy - mRNA 2.50651 kcal/mol@LB@Unfolding Energy - sRNA 2.62518 kcal/mol@LB@@LB@Position - mRNA 49 -- 60@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 44 -- 50@LB@
141	0.00519	0.1284	b3550	yiaC	-7.29	0.227336	55 -- 76	1 -- 22	GNAT family putative N-acetyltransferase		_____________54______________________77\n_____________\|_______________________\|\n5'-AAU...CAUCU_____C______CGAC_______CUAAG...GGC-3'\n______________ACGUC__GCCUC____GCCCUAU\n______________\|\|:\|\|__:\|\|\|\|____:\|\|\|\|\|:\n______________UGUAG__UGGAG____UGGGAUG\n3'-AUU...UAUCU_____AA_____ACA________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	70 -- 76	1 -- 7	-20.6815 kcal/mol	5.4259 kcal/mol	7.99236 kcal/mol	54 77@LB@ \| \|@LB@5'-AAU...CAUCU C CGAC CUAAG...GGC-3'@LB@ ACGUC GCCUC GCCCUAU@LB@ \|\|:\|\| :\|\|\|\| :\|\|\|\|\|:@LB@ UGUAG UGGAG UGGGAUG@LB@3'-AUU...UAUCU AA ACA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -20.6815 kcal/mol@LB@Unfolding Energy - mRNA 5.4259 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 55 -- 76@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 1 -- 7@LB@
22	0.0001652	0.02641	b3566	xylF	-9.94	0.047349	202 -- 240	1 -- 33	D-xylose transporter subunit		_____________201_____________________________________241\n_____________\|_______________________________________\|\n5'-CGA...CACCA_____AUAA________C__CUCAC______C____C__UCCUG...AUG-3'\n______________UGAAA____AGAACAUU_UA_____CCUUUG_ACCU_AC\n______________\|\|\|\|\|____\|\|\|\|\|\|\|:_\|\|_____\|\|\|:\|\|_\|\|\|:_\|\|\n______________ACUUU____UCUUGUAG_AU_____GGAGAC_UGGG_UG\n3'-AUU...UCCAG_____CUA_________A_____________A____A__-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	212 -- 218	18 -- 24	-22.447 kcal/mol	3.48977 kcal/mol	9.04529 kcal/mol	201 241@LB@ \| \|@LB@5'-CGA...CACCA AUAA C CUCAC C C UCCUG...AUG-3'@LB@ UGAAA AGAACAUU UA CCUUUG ACCU AC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|: \|\| \|\|\|:\|\| \|\|\|: \|\|@LB@ ACUUU UCUUGUAG AU GGAGAC UGGG UG@LB@3'-AUU...UCCAG CUA A A A -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -22.447 kcal/mol@LB@Unfolding Energy - mRNA 3.48977 kcal/mol@LB@Unfolding Energy - sRNA 9.04529 kcal/mol@LB@@LB@Position - mRNA 202 -- 240@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 18 -- 24@LB@
31	0.0003178	0.03519	b3588	aldB	-11.98	0.010708	83 -- 100	1 -- 16	aldehyde dehydrogenase B		_____________82_________________101\n_____________\|__________________\|\n5'-GAA...UCAAC__________A___U___CCGUA...GGG-3'\n______________UAUCUCUGUA_CCC_UGC\n______________\|\|:\|\|\|\|\|\|\|_\|\|\|_\|:\|\n______________AUGGAGACAU_GGG_AUG\n3'-AUU...GUAGA__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	86 -- 92	7 -- 13	-19.6311 kcal/mol	1.07825 kcal/mol	6.59719 kcal/mol	82 101@LB@ \| \|@LB@5'-GAA...UCAAC A U CCGUA...GGG-3'@LB@ UAUCUCUGUA CCC UGC@LB@ \|\|:\|\|\|\|\|\|\| \|\|\| \|:\|@LB@ AUGGAGACAU GGG AUG@LB@3'-AUU...GUAGA -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.6311 kcal/mol@LB@Unfolding Energy - mRNA 1.07825 kcal/mol@LB@Unfolding Energy - sRNA 6.59719 kcal/mol@LB@@LB@Position - mRNA 83 -- 100@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 7 -- 13@LB@
158	0.00634	0.1412	b3598	yibI	-10.19	0.039756	289 -- 298	49 -- 58	DUF3302 family inner membrane protein	b3587	_____________288________299\n_____________\|__________\|\n5'-CGU...CCCUU__________CA-3'\n______________AUCUGAUUGC\n______________\|\|\|:\|\|\|\|:\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	292 -- 298	49 -- 55	-10.9433 kcal/mol	0.440755 kcal/mol	0.318367 kcal/mol	288 299@LB@ \| \|@LB@5'-CGU...CCCUU CA-3'@LB@ AUCUGAUUGC@LB@ \|\|\|:\|\|\|\|:\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -10.9433 kcal/mol@LB@Unfolding Energy - mRNA 0.440755 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
10	2.605e-05	0.009165	b3599	mtlA	-16.58	0.000118	1 -- 31	4 -- 28	mannitol-specific PTS enzyme: IIA IIB and IIC components		______________1_______________________________32\n______________\|_______________________________\|\n___________5'-___________ACGUCAA________C_____CCUAU...UCA-3'\n______________GAU_GAACGUC_______UUACCUCU_UACCC\n______________\|\|\|_\|\|\|\|:\|\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUA_CUUGUAG_______AAUGGAGA_AUGGG\n3'-AUU...ACUUU___U______________________C_____AUG-5'\n_____________\|________________________________\|\n_____________29_______________________________3\n	19 -- 25	10 -- 16	-27.7982 kcal/mol	3.19385 kcal/mol	8.04825 kcal/mol	1 32@LB@ \| \|@LB@ 5'- ACGUCAA C CCUAU...UCA-3'@LB@ GAU GAACGUC UUACCUCU UACCC@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUA CUUGUAG AAUGGAGA AUGGG@LB@3'-AUU...ACUUU U C AUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -16.58 kcal/mol@LB@Hybridization Energy -27.7982 kcal/mol@LB@Unfolding Energy - mRNA 3.19385 kcal/mol@LB@Unfolding Energy - sRNA 8.04825 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 10 -- 16@LB@
180	0.007734	0.1511	b3617	kbl	-7.53	0.200168	193 -- 210	43 -- 60	glycine C-acetyltransferase		_____________192________________211\n_____________\|__________________\|\n5'-UUU...CUGGA_____GCAA_________AAUUU...AAG-3'\n______________GAAUC____UGCGUGGAG\n______________:\|\|\|\|____\|:\|\|\|\|:\|\|\n______________UUUAG____AUGCACUUC\n3'-AUU...GUCGG_____GCUA_________AUUUU...AUG-5'\n_____________\|__________________\|\n_____________61_________________42\n	204 -- 210	43 -- 49	-15.3085 kcal/mol	4.51554 kcal/mol	3.27548 kcal/mol	192 211@LB@ \| \|@LB@5'-UUU...CUGGA GCAA AAUUU...AAG-3'@LB@ GAAUC UGCGUGGAG@LB@ :\|\|\|\| \|:\|\|\|\|:\|\|@LB@ UUUAG AUGCACUUC@LB@3'-AUU...GUCGG GCUA AUUUU...AUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -15.3085 kcal/mol@LB@Unfolding Energy - mRNA 4.51554 kcal/mol@LB@Unfolding Energy - sRNA 3.27548 kcal/mol@LB@@LB@Position - mRNA 193 -- 210@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 43 -- 49@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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