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
5	0.0004437	0.2856	b0847	ybjL	-12.50	0.012601	224 -- 253	26 -- 55	putative transporter	_____________223____________________________254\n_____________\|______________________________\|\n5'-CUU...GAAUU______U_______A____CUG________UGUGG...GUU-3'\n______________GUUAAA_GGGAAUU_CAUU___UUAUUAUU\n______________\|\|:\|\|\|_:\|\|\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAGUUU_UCCUUAA_GUAA___AAUAAUAA\n3'-UUU...CCGGG______C_______A____AAA________UACGG...ACA-5'\n_____________\|______________________________\|\n_____________56_____________________________25\n	247 -- 253	26 -- 32	-19.6848 kcal/mol	5.99374 kcal/mol	1.18815 kcal/mol	223 254@LB@ \| \|@LB@5'-CUU...GAAUU U A CUG UGUGG...GUU-3'@LB@ GUUAAA GGGAAUU CAUU UUAUUAUU@LB@ \|\|:\|\|\| :\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAGUUU UCCUUAA GUAA AAUAAUAA@LB@3'-UUU...CCGGG C A AAA UACGG...ACA-5'@LB@ \| \|@LB@ 56 25@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -19.6848 kcal/mol@LB@Unfolding Energy - mRNA 5.99374 kcal/mol@LB@Unfolding Energy - sRNA 1.18815 kcal/mol@LB@@LB@Position - mRNA 224 -- 253@LB@Position - sRNA 26 -- 55@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 26 -- 32@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@
186	0.03879	0.6177	b2898	ygfZ	-4.98	0.377094	224 -- 230	51 -- 57	iron-sulfur cluster repair protein plumbagin resistance	_____________223_____231\n_____________\|_______\|\n5'-CGU...CCUCC_______CCUAC...CUG-3'\n______________CCGUCAG\n______________\|\|\|\|\|\|:\n______________GGCAGUU\n3'-UUU...AACCG_______UCUCC...ACA-5'\n_____________\|_______\|\n_____________58______50\n	224 -- 230	51 -- 57	-9.02345 kcal/mol	1.32881 kcal/mol	2.71582 kcal/mol	223 231@LB@ \| \|@LB@5'-CGU...CCUCC CCUAC...CUG-3'@LB@ CCGUCAG@LB@ \|\|\|\|\|\|:@LB@ GGCAGUU@LB@3'-UUU...AACCG UCUCC...ACA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -4.98 kcal/mol@LB@Hybridization Energy -9.02345 kcal/mol@LB@Unfolding Energy - mRNA 1.32881 kcal/mol@LB@Unfolding Energy - sRNA 2.71582 kcal/mol@LB@@LB@Position - mRNA 224 -- 230@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 51 -- 57@LB@
189	0.03933	0.6177	b2461	eutP	-9.78	0.045635	227 -- 240	44 -- 56	putative P-loop NTPase ethanolamine utilization protein	_____________226____________241\n_____________\|______________\|\n5'-AAA...GGUAG________C_____AAACA...CCG-3'\n______________CGUCGGGG_AGGAA\n______________\|\|\|\|:::\|_\|\|\|\|\|\n______________GCAGUUUC_UCCUU\n3'-UUU...ACCGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________57_____________43\n	228 -- 234	49 -- 55	-15.0697 kcal/mol	4.34178 kcal/mol	0.948902 kcal/mol	226 241@LB@ \| \|@LB@5'-AAA...GGUAG C AAACA...CCG-3'@LB@ CGUCGGGG AGGAA@LB@ \|\|\|\|:::\| \|\|\|\|\|@LB@ GCAGUUUC UCCUU@LB@3'-UUU...ACCGG AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -15.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.34178 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 227 -- 240@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 49 -- 55@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@
24	0.004602	0.5992	b0526	cysS	-10.20	0.037463	234 -- 245	41 -- 52	cysteinyl-tRNA synthetase	_____________233__________246\n_____________\|____________\|\n5'-GCC...GCCAA____________AAGCC...ACG-3'\n______________AAAGAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUUAAA\n3'-UUU...GGCAG____________GUAAA...ACA-5'\n_____________\|____________\|\n_____________53___________40\n	239 -- 245	41 -- 47	-14.6017 kcal/mol	3.53507 kcal/mol	0.867487 kcal/mol	233 246@LB@ \| \|@LB@5'-GCC...GCCAA AAGCC...ACG-3'@LB@ AAAGAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUUAAA@LB@3'-UUU...GGCAG GUAAA...ACA-5'@LB@ \| \|@LB@ 53 40@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6017 kcal/mol@LB@Unfolding Energy - mRNA 3.53507 kcal/mol@LB@Unfolding Energy - sRNA 0.867487 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 41 -- 52@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 41 -- 47@LB@
70	0.01448	0.6177	b4012	yjaB	-8.12	0.098308	234 -- 242	44 -- 52	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233_______243\n_____________\|_________\|\n5'-AAG...AUGAG_________GAACU...CAG-3'\n______________GAAGGGGAG\n______________:\|\|\|:\|\|\|:\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	236 -- 242	44 -- 50	-9.78668 kcal/mol	0.80114 kcal/mol	0.860683 kcal/mol	233 243@LB@ \| \|@LB@5'-AAG...AUGAG GAACU...CAG-3'@LB@ GAAGGGGAG@LB@ :\|\|\|:\|\|\|:@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.78668 kcal/mol@LB@Unfolding Energy - mRNA 0.80114 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 44 -- 50@LB@
121	0.02422	0.6177	b0754	aroG	-7.67	0.121074	238 -- 245	47 -- 54	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase phenylalanine repressible	_____________237______246\n_____________\|________\|\n5'-CUU...AGAAA________UUACU...CGA-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	239 -- 245	47 -- 53	-9.80538 kcal/mol	1.24089 kcal/mol	0.897871 kcal/mol	237 246@LB@ \| \|@LB@5'-CUU...AGAAA UUACU...CGA-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -9.80538 kcal/mol@LB@Unfolding Energy - mRNA 1.24089 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 238 -- 245@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 47 -- 53@LB@
27	0.005027	0.5992	b3745	viaA	-10.46	0.033099	243 -- 253	42 -- 52	stimulator of RavA ATPase activity; von Willebrand factor domain protein	_____________242_________254\n_____________\|___________\|\n5'-ACG...UCAGC___________GAUCG...CGG-3'\n______________GAAGAGGGAUU\n______________:\|\|\|\|\|\|:\|\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	247 -- 253	42 -- 48	-12.7293 kcal/mol	1.40033 kcal/mol	0.866923 kcal/mol	242 254@LB@ \| \|@LB@5'-ACG...UCAGC GAUCG...CGG-3'@LB@ GAAGAGGGAUU@LB@ :\|\|\|\|\|\|:\|\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -12.7293 kcal/mol@LB@Unfolding Energy - mRNA 1.40033 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 243 -- 253@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 42 -- 48@LB@
125	0.02442	0.6177	b3181	greA	-6.11	0.239901	243 -- 260	40 -- 56	transcript cleavage factor	_____________242_________________261\n_____________\|___________________\|\n5'-CGC...AAUUA__________CU_______CUGAA...UCG-3'\n______________CG_CGAAGAG__GGAUUUU\n______________\|\|_\|:\|\|\|\|\|__\|:\|\|\|\|:\n______________GC_GUUUCUC__CUUAAAG\n3'-UUU...ACCGG__A________________UAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________39\n	245 -- 251	47 -- 53	-12.1125 kcal/mol	4.98158 kcal/mol	1.02557 kcal/mol	242 261@LB@ \| \|@LB@5'-CGC...AAUUA CU CUGAA...UCG-3'@LB@ CG CGAAGAG GGAUUUU@LB@ \|\| \|:\|\|\|\|\| \|:\|\|\|\|:@LB@ GC GUUUCUC CUUAAAG@LB@3'-UUU...ACCGG A UAAAA...ACA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -6.11 kcal/mol@LB@Hybridization Energy -12.1125 kcal/mol@LB@Unfolding Energy - mRNA 4.98158 kcal/mol@LB@Unfolding Energy - sRNA 1.02557 kcal/mol@LB@@LB@Position - mRNA 243 -- 260@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 47 -- 53@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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