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
56	0.0008344	0.05242	b3651	trmH	-7.19	0.238334	68 -- 84	17 -- 32	tRNA mG18-2'-O-methyltransferase SAM-dependent	_____________67________________85\n_____________\|_________________\|\n5'-CGC...GAAGA_________UC______ACAGC...UUU-3'\n______________GAAAGAUGG__GCGUCU\n______________\|\|\|\|\|\|\|:\|__:\|:\|\|\|\n______________CUUUCUAUC__UGUAGA\n3'-AUU...CCAGA_________U_______AUGGA...AUG-5'\n_____________\|_________________\|\n_____________33________________16\n	70 -- 76	24 -- 30	-18.3937 kcal/mol	6.9506 kcal/mol	4.26839 kcal/mol	67 85@LB@ \| \|@LB@5'-CGC...GAAGA UC ACAGC...UUU-3'@LB@ GAAAGAUGG GCGUCU@LB@ \|\|\|\|\|\|\|:\| :\|:\|\|\|@LB@ CUUUCUAUC UGUAGA@LB@3'-AUU...CCAGA U AUGGA...AUG-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -18.3937 kcal/mol@LB@Unfolding Energy - mRNA 6.9506 kcal/mol@LB@Unfolding Energy - sRNA 4.26839 kcal/mol@LB@@LB@Position - mRNA 68 -- 84@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 24 -- 30@LB@
159	0.006413	0.1413	b4242	mgtA	-7.15	0.243258	247 -- 262	45 -- 58	magnesium transporter	_____________246______________263\n_____________\|________________\|\n5'-GGU...UUCCC________CAU_____UCCAU...UGG-3'\n______________GUCUGGUU___CGUGA\n______________:\|\|:\|:\|\|___\|\|\|\|\|\n______________UAGGCUAA___GCACU\n3'-AUU...CGGUU________U_______UCAUU...AUG-5'\n_____________\|________________\|\n_____________59_______________44\n	248 -- 254	51 -- 57	-12.639 kcal/mol	3.2244 kcal/mol	2.28003 kcal/mol	246 263@LB@ \| \|@LB@5'-GGU...UUCCC CAU UCCAU...UGG-3'@LB@ GUCUGGUU CGUGA@LB@ :\|\|:\|:\|\| \|\|\|\|\|@LB@ UAGGCUAA GCACU@LB@3'-AUU...CGGUU U UCAUU...AUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -12.639 kcal/mol@LB@Unfolding Energy - mRNA 3.2244 kcal/mol@LB@Unfolding Energy - sRNA 2.28003 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 51 -- 57@LB@
196	0.008709	0.1558	b2498	upp	-7.14	0.244299	249 -- 259	45 -- 56	uracil phosphoribosyltransferase	_____________248__________260\n_____________\|____________\|\n5'-GGC...UGGGA____________GCAAG...CCG-3'\n______________CUGA_UGCGUGA\n______________\|:\|\|_\|:\|\|\|\|\|\n______________GGCU_AUGCACU\n3'-AUU...GUUUA____A_______UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	253 -- 259	45 -- 51	-12.6155 kcal/mol	3.20986 kcal/mol	2.27945 kcal/mol	248 260@LB@ \| \|@LB@5'-GGC...UGGGA GCAAG...CCG-3'@LB@ CUGA UGCGUGA@LB@ \|:\|\| \|:\|\|\|\|\|@LB@ GGCU AUGCACU@LB@3'-AUU...GUUUA A UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -12.6155 kcal/mol@LB@Unfolding Energy - mRNA 3.20986 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 249 -- 259@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
44	0.000471	0.03766	b3624	waaZ	-7.10	0.250129	289 -- 295	1 -- 7	lipopolysaccharide KdoIII transferase; lipopolysaccharide core biosynthesis protein	_____________288_____296\n_____________\|_______\|\n5'-AGA...UUCGG_______AUCGC-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	289 -- 295	1 -- 7	-11.6335 kcal/mol	2.52016 kcal/mol	2.03949 kcal/mol	288 296@LB@ \| \|@LB@5'-AGA...UUCGG AUCGC-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -11.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.52016 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
181	0.007802	0.1516	b1797	yeaR	-7.07	0.254063	142 -- 149	2 -- 9	DUF1971 family protein nitrate-inducible	_____________141______150\n_____________\|________\|\n5'-UGC...CAGGC________AAACG...AAG-3'\n______________GUACCCUG\n______________\|\|\|\|\|\|\|:\n______________CAUGGGAU\n3'-AUU...GGAGA________G-5'\n_____________\|________\|\n_____________10_______1\n	143 -- 149	2 -- 8	-12.2602 kcal/mol	3.09143 kcal/mol	2.12684 kcal/mol	141 150@LB@ \| \|@LB@5'-UGC...CAGGC AAACG...AAG-3'@LB@ GUACCCUG@LB@ \|\|\|\|\|\|\|:@LB@ CAUGGGAU@LB@3'-AUU...GGAGA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -12.2602 kcal/mol@LB@Unfolding Energy - mRNA 3.09143 kcal/mol@LB@Unfolding Energy - sRNA 2.12684 kcal/mol@LB@@LB@Position - mRNA 142 -- 149@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 2 -- 8@LB@
40	0.0004513	0.03766	b3291	mscL	-6.99	0.263134	48 -- 58	55 -- 65	mechanosensitive channel protein high conductance	_____________47__________59\n_____________\|___________\|\n5'-UGU...UCUUC________C__UUUCU...UCU-3'\n______________CAGCCAAG_CC\n______________\|\|\|\|\|\|\|:_\|\|\n______________GUCGGUUU_GG\n3'-AUU...UAUAA________A__CUAAU...AUG-5'\n_____________\|___________\|\n_____________66__________54\n	49 -- 55	58 -- 64	-14.9389 kcal/mol	1.90813 kcal/mol	6.05961 kcal/mol	47 59@LB@ \| \|@LB@5'-UGU...UCUUC C UUUCU...UCU-3'@LB@ CAGCCAAG CC@LB@ \|\|\|\|\|\|\|: \|\|@LB@ GUCGGUUU GG@LB@3'-AUU...UAUAA A CUAAU...AUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -14.9389 kcal/mol@LB@Unfolding Energy - mRNA 1.90813 kcal/mol@LB@Unfolding Energy - sRNA 6.05961 kcal/mol@LB@@LB@Position - mRNA 48 -- 58@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 58 -- 64@LB@
137	0.004974	0.127	b0092	ddlB	-6.99	0.263821	283 -- 297	43 -- 56	D-alanine:D-alanine ligase	_____________282_____________298\n_____________\|_______________\|\n5'-UUC...GUUAG____AC_________GCG-3'\n______________CCGG__UGCGUGAAG\n______________\|\|\|:__\|:\|\|\|\|\|\|\|\n______________GGCU__AUGCACUUC\n3'-AUU...GUUUA____A__________AUUUU...AUG-5'\n_____________\|_______________\|\n_____________57______________42\n	291 -- 297	43 -- 49	-17.3937 kcal/mol	7.14584 kcal/mol	3.27327 kcal/mol	282 298@LB@ \| \|@LB@5'-UUC...GUUAG AC GCG-3'@LB@ CCGG UGCGUGAAG@LB@ \|\|\|: \|:\|\|\|\|\|\|\|@LB@ GGCU AUGCACUUC@LB@3'-AUU...GUUUA A AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -17.3937 kcal/mol@LB@Unfolding Energy - mRNA 7.14584 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
48	0.0005438	0.03933	b0811	glnH	-6.95	0.268265	70 -- 77	1 -- 8	glutamine transporter subunit	_____________69_______78\n_____________\|________\|\n5'-AUC...GGUAU________AAAUC...CCG-3'\n______________UGCCCUAU\n______________\|:\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	71 -- 77	1 -- 7	-10.5963 kcal/mol	1.549 kcal/mol	2.11603 kcal/mol	69 78@LB@ \| \|@LB@5'-AUC...GGUAU AAAUC...CCG-3'@LB@ UGCCCUAU@LB@ \|:\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -10.5963 kcal/mol@LB@Unfolding Energy - mRNA 1.549 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 70 -- 77@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 1 -- 7@LB@
142	0.005204	0.1284	b3931	hslU	-6.88	0.277791	3 -- 17	52 -- 65	molecular chaperone and ATPase component of HslUV protease	_____________2_______________18\n_____________\|_______________\|\n_________5'-UG________AAA____CUUAU...ACC-3'\n______________CAGCCAGA___CGAU\n______________\|\|\|\|\|\|:\|___\|\|\|\|\n______________GUCGGUUU___GCUA\n3'-AUU...UAUAA________AG_____AUGCA...AUG-5'\n_____________\|_______________\|\n_____________66______________51\n	4 -- 10	58 -- 64	-14.8174 kcal/mol	1.78514 kcal/mol	6.17277 kcal/mol	2 18@LB@ \| \|@LB@ 5'-UG AAA CUUAU...ACC-3'@LB@ CAGCCAGA CGAU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ GUCGGUUU GCUA@LB@3'-AUU...UAUAA AG AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -6.88 kcal/mol@LB@Hybridization Energy -14.8174 kcal/mol@LB@Unfolding Energy - mRNA 1.78514 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 3 -- 17@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 58 -- 64@LB@
162	0.006534	0.1413	b3771	ilvD	-6.87	0.280008	44 -- 51	49 -- 56	dihydroxyacid dehydratase	_____________43_______52\n_____________\|________\|\n5'-GCG...GUGGC________CAAAC...GUA-3'\n______________CCGGUUAC\n______________\|\|\|:\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	45 -- 51	49 -- 55	-9.72973 kcal/mol	2.55538 kcal/mol	0.317884 kcal/mol	43 52@LB@ \| \|@LB@5'-GCG...GUGGC CAAAC...GUA-3'@LB@ CCGGUUAC@LB@ \|\|\|:\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -6.87 kcal/mol@LB@Hybridization Energy -9.72973 kcal/mol@LB@Unfolding Energy - mRNA 2.55538 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 44 -- 51@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 49 -- 55@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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